{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":610290102,"defaultBranch":"main","name":"softpack-builder","ownerLogin":"wtsi-hgi","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2023-03-06T13:32:53.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/2567468?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1718747840.0","currentOid":""},"activityList":{"items":[{"before":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","after":"4ec9de77820978c3d37266121d83c65b95a7313d","ref":"refs/heads/snyk-fix-a6a94c52845835a31ba567de1628f45e","pushedAt":"2024-06-18T21:57:21.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sb10","name":"Sendu Bala","path":"/sb10","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/507951?s=80&v=4"},"commit":{"message":"fix: requirements.txt to reduce vulnerabilities\n\n\nThe following vulnerabilities are fixed by pinning transitive dependencies:\n- https://snyk.io/vuln/SNYK-PYTHON-URLLIB3-7267250","shortMessageHtmlLink":"fix: requirements.txt to reduce vulnerabilities"}},{"before":null,"after":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","ref":"refs/heads/snyk-fix-a6a94c52845835a31ba567de1628f45e","pushedAt":"2024-06-18T21:57:20.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"sb10","name":"Sendu Bala","path":"/sb10","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/507951?s=80&v=4"},"commit":{"message":"๐ merge from develop (#14)\n\n* :sparkles: add simulated build\r\n\r\n* add logging to simulated build\r\n\r\n* :sparkles: add environment REST API\r\n\r\n* :memo: updating inline docs\r\n\r\n* :wrench: update spack runtime config\r\n\r\n* ๐ง chore(pyproject.toml): fix formatting and add missing dependencies\r\nโจ feat(pyproject.toml): add fastapi dependency\r\n\r\n๐ fix(pyproject.toml): add disallow_untyped_calls and disallow_untyped_defs to mypy configuration\r\n\r\n๐ fix(cli.py): add return type hints to service() and main() functions\r\nโจ feat(config.yml): change server port from 8000 to 7080\r\nโจ feat(config.py): add manifest field to SpackConfig model and change config file path to ~/.softpack/builder/\r\n\r\n๐ง chore(environment.py): add type hints to methods and arguments\r\nโจ feat(environment.py): add support for Spack environment commands\r\n๐ perf(environment.py): improve build method to fail fast\r\n๐ fix(environment.py): fix environment_instantiate argument type\r\n\r\n๐ง chore(environment.py): add type hints to function arguments and return types\r\n\r\n๐ fix(utils.py): add type hints to async_exec function arguments and return value\r\n๐๏ธ chore(test_softpack_builder.py): delete unused test file and fixture\r\n\r\n* ๐ fix(app.py): add missing import for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. Add steps to get version from tag, checkout repo, and get changelog entry.\r\n\r\n* ๐ฅ chore(debug.yml): remove debug workflow file\r\n๐จ refactor(dev.yml): remove CODECOV_TOKEN secret from codecov-action\r\n๐ chore(release.yml): update changelog builder action to mikepenz/release-changelog-builder-action@v3.2.0 and remove changelog-reader-action. Update github_token input for peaceiris/actions-gh-pages@v3.","shortMessageHtmlLink":"๐ merge from develop (#14)"}},{"before":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","after":"e2454460d46413ce1609d319cef799756f2c8bdc","ref":"refs/heads/snyk-fix-99b4494404d20457558afce1b80aa88c","pushedAt":"2024-05-21T09:52:53.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sb10","name":"Sendu Bala","path":"/sb10","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/507951?s=80&v=4"},"commit":{"message":"fix: requirements.txt to reduce vulnerabilities\n\n\nThe following vulnerabilities are fixed by pinning transitive dependencies:\n- https://snyk.io/vuln/SNYK-PYTHON-REQUESTS-6928867","shortMessageHtmlLink":"fix: requirements.txt to reduce vulnerabilities"}},{"before":null,"after":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","ref":"refs/heads/snyk-fix-99b4494404d20457558afce1b80aa88c","pushedAt":"2024-05-21T09:52:52.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"sb10","name":"Sendu Bala","path":"/sb10","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/507951?s=80&v=4"},"commit":{"message":"๐ merge from develop (#14)\n\n* :sparkles: add simulated build\r\n\r\n* add logging to simulated build\r\n\r\n* :sparkles: add environment REST API\r\n\r\n* :memo: updating inline docs\r\n\r\n* :wrench: update spack runtime config\r\n\r\n* ๐ง chore(pyproject.toml): fix formatting and add missing dependencies\r\nโจ feat(pyproject.toml): add fastapi dependency\r\n\r\n๐ fix(pyproject.toml): add disallow_untyped_calls and disallow_untyped_defs to mypy configuration\r\n\r\n๐ fix(cli.py): add return type hints to service() and main() functions\r\nโจ feat(config.yml): change server port from 8000 to 7080\r\nโจ feat(config.py): add manifest field to SpackConfig model and change config file path to ~/.softpack/builder/\r\n\r\n๐ง chore(environment.py): add type hints to methods and arguments\r\nโจ feat(environment.py): add support for Spack environment commands\r\n๐ perf(environment.py): improve build method to fail fast\r\n๐ fix(environment.py): fix environment_instantiate argument type\r\n\r\n๐ง chore(environment.py): add type hints to function arguments and return types\r\n\r\n๐ fix(utils.py): add type hints to async_exec function arguments and return value\r\n๐๏ธ chore(test_softpack_builder.py): delete unused test file and fixture\r\n\r\n* ๐ fix(app.py): add missing import for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. Add steps to get version from tag, checkout repo, and get changelog entry.\r\n\r\n* ๐ฅ chore(debug.yml): remove debug workflow file\r\n๐จ refactor(dev.yml): remove CODECOV_TOKEN secret from codecov-action\r\n๐ chore(release.yml): update changelog builder action to mikepenz/release-changelog-builder-action@v3.2.0 and remove changelog-reader-action. Update github_token input for peaceiris/actions-gh-pages@v3.","shortMessageHtmlLink":"๐ merge from develop (#14)"}},{"before":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","after":"e15720793c02d2496431fbfa2cdb0ded3310694e","ref":"refs/heads/snyk-fix-d05c62b830d0918dd29a2f261f6f2974","pushedAt":"2024-05-07T20:50:33.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sb10","name":"Sendu Bala","path":"/sb10","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/507951?s=80&v=4"},"commit":{"message":"fix: requirements.txt to reduce vulnerabilities\n\n\nThe following vulnerabilities are fixed by pinning transitive dependencies:\n- https://snyk.io/vuln/SNYK-PYTHON-JINJA2-6809379","shortMessageHtmlLink":"fix: requirements.txt to reduce vulnerabilities"}},{"before":null,"after":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","ref":"refs/heads/snyk-fix-d05c62b830d0918dd29a2f261f6f2974","pushedAt":"2024-05-07T20:50:32.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"sb10","name":"Sendu Bala","path":"/sb10","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/507951?s=80&v=4"},"commit":{"message":"๐ merge from develop (#14)\n\n* :sparkles: add simulated build\r\n\r\n* add logging to simulated build\r\n\r\n* :sparkles: add environment REST API\r\n\r\n* :memo: updating inline docs\r\n\r\n* :wrench: update spack runtime config\r\n\r\n* ๐ง chore(pyproject.toml): fix formatting and add missing dependencies\r\nโจ feat(pyproject.toml): add fastapi dependency\r\n\r\n๐ fix(pyproject.toml): add disallow_untyped_calls and disallow_untyped_defs to mypy configuration\r\n\r\n๐ fix(cli.py): add return type hints to service() and main() functions\r\nโจ feat(config.yml): change server port from 8000 to 7080\r\nโจ feat(config.py): add manifest field to SpackConfig model and change config file path to ~/.softpack/builder/\r\n\r\n๐ง chore(environment.py): add type hints to methods and arguments\r\nโจ feat(environment.py): add support for Spack environment commands\r\n๐ perf(environment.py): improve build method to fail fast\r\n๐ fix(environment.py): fix environment_instantiate argument type\r\n\r\n๐ง chore(environment.py): add type hints to function arguments and return types\r\n\r\n๐ fix(utils.py): add type hints to async_exec function arguments and return value\r\n๐๏ธ chore(test_softpack_builder.py): delete unused test file and fixture\r\n\r\n* ๐ fix(app.py): add missing import for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. Add steps to get version from tag, checkout repo, and get changelog entry.\r\n\r\n* ๐ฅ chore(debug.yml): remove debug workflow file\r\n๐จ refactor(dev.yml): remove CODECOV_TOKEN secret from codecov-action\r\n๐ chore(release.yml): update changelog builder action to mikepenz/release-changelog-builder-action@v3.2.0 and remove changelog-reader-action. Update github_token input for peaceiris/actions-gh-pages@v3.","shortMessageHtmlLink":"๐ merge from develop (#14)"}},{"before":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","after":"0023a268533fbee605af14ff8d5d2775e4d17f45","ref":"refs/heads/snyk-fix-9d7b6496165c75e423c51ac50cfc683a","pushedAt":"2024-04-14T20:13:10.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"sersorrel","name":"ash","path":"/sersorrel","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9433472?s=80&v=4"},"commit":{"message":"fix: requirements.txt to reduce vulnerabilities\n\n\nThe following vulnerabilities are fixed by pinning transitive dependencies:\n- https://snyk.io/vuln/SNYK-PYTHON-IDNA-6597975","shortMessageHtmlLink":"fix: requirements.txt to reduce vulnerabilities"}},{"before":null,"after":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","ref":"refs/heads/snyk-fix-9d7b6496165c75e423c51ac50cfc683a","pushedAt":"2024-04-14T20:13:10.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"sersorrel","name":"ash","path":"/sersorrel","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/9433472?s=80&v=4"},"commit":{"message":"๐ merge from develop (#14)\n\n* :sparkles: add simulated build\r\n\r\n* add logging to simulated build\r\n\r\n* :sparkles: add environment REST API\r\n\r\n* :memo: updating inline docs\r\n\r\n* :wrench: update spack runtime config\r\n\r\n* ๐ง chore(pyproject.toml): fix formatting and add missing dependencies\r\nโจ feat(pyproject.toml): add fastapi dependency\r\n\r\n๐ fix(pyproject.toml): add disallow_untyped_calls and disallow_untyped_defs to mypy configuration\r\n\r\n๐ fix(cli.py): add return type hints to service() and main() functions\r\nโจ feat(config.yml): change server port from 8000 to 7080\r\nโจ feat(config.py): add manifest field to SpackConfig model and change config file path to ~/.softpack/builder/\r\n\r\n๐ง chore(environment.py): add type hints to methods and arguments\r\nโจ feat(environment.py): add support for Spack environment commands\r\n๐ perf(environment.py): improve build method to fail fast\r\n๐ fix(environment.py): fix environment_instantiate argument type\r\n\r\n๐ง chore(environment.py): add type hints to function arguments and return types\r\n\r\n๐ fix(utils.py): add type hints to async_exec function arguments and return value\r\n๐๏ธ chore(test_softpack_builder.py): delete unused test file and fixture\r\n\r\n* ๐ fix(app.py): add missing import for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. Add steps to get version from tag, checkout repo, and get changelog entry.\r\n\r\n* ๐ฅ chore(debug.yml): remove debug workflow file\r\n๐จ refactor(dev.yml): remove CODECOV_TOKEN secret from codecov-action\r\n๐ chore(release.yml): update changelog builder action to mikepenz/release-changelog-builder-action@v3.2.0 and remove changelog-reader-action. Update github_token input for peaceiris/actions-gh-pages@v3.","shortMessageHtmlLink":"๐ merge from develop (#14)"}},{"before":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","after":"46b9b8db1f631f285ea6399a5a58a146bb38e295","ref":"refs/heads/snyk-fix-bdcb2f88f0164b18ef5772d5a01840e5","pushedAt":"2024-01-11T14:44:36.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"altaf-ali","name":"Altaf Ali","path":"/altaf-ali","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7231912?s=80&v=4"},"commit":{"message":"fix: requirements.txt to reduce vulnerabilities\n\n\nThe following vulnerabilities are fixed by pinning transitive dependencies:\n- https://snyk.io/vuln/SNYK-PYTHON-JINJA2-6150717","shortMessageHtmlLink":"fix: requirements.txt to reduce vulnerabilities"}},{"before":null,"after":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","ref":"refs/heads/snyk-fix-bdcb2f88f0164b18ef5772d5a01840e5","pushedAt":"2024-01-11T14:44:35.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"altaf-ali","name":"Altaf Ali","path":"/altaf-ali","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7231912?s=80&v=4"},"commit":{"message":"๐ merge from develop (#14)\n\n* :sparkles: add simulated build\r\n\r\n* add logging to simulated build\r\n\r\n* :sparkles: add environment REST API\r\n\r\n* :memo: updating inline docs\r\n\r\n* :wrench: update spack runtime config\r\n\r\n* ๐ง chore(pyproject.toml): fix formatting and add missing dependencies\r\nโจ feat(pyproject.toml): add fastapi dependency\r\n\r\n๐ fix(pyproject.toml): add disallow_untyped_calls and disallow_untyped_defs to mypy configuration\r\n\r\n๐ fix(cli.py): add return type hints to service() and main() functions\r\nโจ feat(config.yml): change server port from 8000 to 7080\r\nโจ feat(config.py): add manifest field to SpackConfig model and change config file path to ~/.softpack/builder/\r\n\r\n๐ง chore(environment.py): add type hints to methods and arguments\r\nโจ feat(environment.py): add support for Spack environment commands\r\n๐ perf(environment.py): improve build method to fail fast\r\n๐ fix(environment.py): fix environment_instantiate argument type\r\n\r\n๐ง chore(environment.py): add type hints to function arguments and return types\r\n\r\n๐ fix(utils.py): add type hints to async_exec function arguments and return value\r\n๐๏ธ chore(test_softpack_builder.py): delete unused test file and fixture\r\n\r\n* ๐ fix(app.py): add missing import for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. Add steps to get version from tag, checkout repo, and get changelog entry.\r\n\r\n* ๐ฅ chore(debug.yml): remove debug workflow file\r\n๐จ refactor(dev.yml): remove CODECOV_TOKEN secret from codecov-action\r\n๐ chore(release.yml): update changelog builder action to mikepenz/release-changelog-builder-action@v3.2.0 and remove changelog-reader-action. Update github_token input for peaceiris/actions-gh-pages@v3.","shortMessageHtmlLink":"๐ merge from develop (#14)"}},{"before":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","after":"f993f0c377dc9d5030c0e2d8c9e0d536b131590f","ref":"refs/heads/snyk-fix-0c8947ae06d28f066542b4ae56de7acb","pushedAt":"2023-10-19T04:45:52.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"altaf-ali","name":"Altaf Ali","path":"/altaf-ali","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7231912?s=80&v=4"},"commit":{"message":"fix: requirements.txt to reduce vulnerabilities\n\n\nThe following vulnerabilities are fixed by pinning transitive dependencies:\n- https://snyk.io/vuln/SNYK-PYTHON-URLLIB3-6002459","shortMessageHtmlLink":"fix: requirements.txt to reduce vulnerabilities"}},{"before":null,"after":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","ref":"refs/heads/snyk-fix-0c8947ae06d28f066542b4ae56de7acb","pushedAt":"2023-10-19T04:45:51.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"altaf-ali","name":"Altaf Ali","path":"/altaf-ali","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7231912?s=80&v=4"},"commit":{"message":"๐ merge from develop (#14)\n\n* :sparkles: add simulated build\r\n\r\n* add logging to simulated build\r\n\r\n* :sparkles: add environment REST API\r\n\r\n* :memo: updating inline docs\r\n\r\n* :wrench: update spack runtime config\r\n\r\n* ๐ง chore(pyproject.toml): fix formatting and add missing dependencies\r\nโจ feat(pyproject.toml): add fastapi dependency\r\n\r\n๐ fix(pyproject.toml): add disallow_untyped_calls and disallow_untyped_defs to mypy configuration\r\n\r\n๐ fix(cli.py): add return type hints to service() and main() functions\r\nโจ feat(config.yml): change server port from 8000 to 7080\r\nโจ feat(config.py): add manifest field to SpackConfig model and change config file path to ~/.softpack/builder/\r\n\r\n๐ง chore(environment.py): add type hints to methods and arguments\r\nโจ feat(environment.py): add support for Spack environment commands\r\n๐ perf(environment.py): improve build method to fail fast\r\n๐ fix(environment.py): fix environment_instantiate argument type\r\n\r\n๐ง chore(environment.py): add type hints to function arguments and return types\r\n\r\n๐ fix(utils.py): add type hints to async_exec function arguments and return value\r\n๐๏ธ chore(test_softpack_builder.py): delete unused test file and fixture\r\n\r\n* ๐ fix(app.py): add missing import for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. Add steps to get version from tag, checkout repo, and get changelog entry.\r\n\r\n* ๐ฅ chore(debug.yml): remove debug workflow file\r\n๐จ refactor(dev.yml): remove CODECOV_TOKEN secret from codecov-action\r\n๐ chore(release.yml): update changelog builder action to mikepenz/release-changelog-builder-action@v3.2.0 and remove changelog-reader-action. Update github_token input for peaceiris/actions-gh-pages@v3.","shortMessageHtmlLink":"๐ merge from develop (#14)"}},{"before":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","after":"bb35193437f7cae59541342e7878183e40dd51c4","ref":"refs/heads/snyk-fix-5029dbdaec83dc3d6ab1b059c1e64d97","pushedAt":"2023-10-04T04:57:03.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"altaf-ali","name":"Altaf Ali","path":"/altaf-ali","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7231912?s=80&v=4"},"commit":{"message":"fix: requirements.txt to reduce vulnerabilities\n\n\nThe following vulnerabilities are fixed by pinning transitive dependencies:\n- https://snyk.io/vuln/SNYK-PYTHON-URLLIB3-5926907","shortMessageHtmlLink":"fix: requirements.txt to reduce vulnerabilities"}},{"before":null,"after":"2c321a9bed2c4f0b79bc4099c44511fa901c83f5","ref":"refs/heads/snyk-fix-5029dbdaec83dc3d6ab1b059c1e64d97","pushedAt":"2023-10-04T04:57:02.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"altaf-ali","name":"Altaf Ali","path":"/altaf-ali","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/7231912?s=80&v=4"},"commit":{"message":"๐ merge from develop (#14)\n\n* :sparkles: add simulated build\r\n\r\n* add logging to simulated build\r\n\r\n* :sparkles: add environment REST API\r\n\r\n* :memo: updating inline docs\r\n\r\n* :wrench: update spack runtime config\r\n\r\n* ๐ง chore(pyproject.toml): fix formatting and add missing dependencies\r\nโจ feat(pyproject.toml): add fastapi dependency\r\n\r\n๐ fix(pyproject.toml): add disallow_untyped_calls and disallow_untyped_defs to mypy configuration\r\n\r\n๐ fix(cli.py): add return type hints to service() and main() functions\r\nโจ feat(config.yml): change server port from 8000 to 7080\r\nโจ feat(config.py): add manifest field to SpackConfig model and change config file path to ~/.softpack/builder/\r\n\r\n๐ง chore(environment.py): add type hints to methods and arguments\r\nโจ feat(environment.py): add support for Spack environment commands\r\n๐ perf(environment.py): improve build method to fail fast\r\n๐ fix(environment.py): fix environment_instantiate argument type\r\n\r\n๐ง chore(environment.py): add type hints to function arguments and return types\r\n\r\n๐ fix(utils.py): add type hints to async_exec function arguments and return value\r\n๐๏ธ chore(test_softpack_builder.py): delete unused test file and fixture\r\n\r\n* ๐ fix(app.py): add missing import for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. 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for __version__ and add ServiceStatus class and root endpoint\r\nโจ feat(environment.py): add type ignore comments to env variable and async_exec function call\r\n\r\nโ
test(test_app.py): add test for HTTP GET request to root route\r\n\r\n* ๐ง chore(config): update ORAS model to allow optional username, token, and uri fields\r\n๐ง chore(config): update SpackConfig model to allow optional manifest field\r\n\r\n* ๐ feat(pyproject.toml): add essential-generators package\r\n๐ฅ chore(utils.py): remove async_exec function\r\nโป๏ธ refactor(environment.py): use a wrapper function for environment_create_flow in background task\r\n๐ง chore(tox.ini): add tests directory to autoflake and isort commands\r\n\r\n* ๐ fix(config.py): assign path variable before returning in classmethod\r\nโจ feat(environment.py): make flow_wrapper async function\r\n\r\n* โ
test(test_environment.py): add test for environment flow and env model creation\r\n\r\n* ๐ chore(dev.yml): rename workflow from 'dev workflow' to 'tests'\r\n๐ docs(README.md): add badges for issue resolution time and percentage of open issues\r\n\r\n๐ง chore(pyproject.toml): reformat dependencies section for better readability\r\n\r\n๐ฆ chore(pyproject.toml): add sqlalchemy and singleton-decorator dependencies\r\n๐ง chore(pyproject.toml): update softpack-builder script path\r\n๐ง chore(pyproject.toml): add pytest-asyncio, pytest-cases, and pytest-httpx to test extras\r\n๐ง chore(pyproject.toml): add filterwarnings option to pytest.ini_options section\r\n\r\n๐ feat(app.py): add Application class as a singleton to manage FastAPI application and Typer commands\r\n๐ง chore(app.py): refactor ServiceStatus to a dictionary\r\n๐ง chore(app.py): refactor root() to return a dictionary instead of ServiceStatus object\r\n๐ feat(app.py): add register_module() method to register a module with the application\r\n๐ feat(app.py): add url() method to get absolute URL path\r\n๐ feat(app.py): add main() method as the main command line entrypoint\r\n\r\n๐ฅ chore(cli.py): remove unused code\r\n๐ง chore(config.py): remove unused settings variable and method\r\n\r\n๐ feat(deployments.py): add Deployments class for building and running deployments\r\n\r\n๐ feat(environment.py): add delay_task function for testing purposes\r\n๐ง chore(environment.py): refactor Environment.Model to include from_yaml and asdict methods\r\n\r\n๐ feat(environment.py): add stage, create_manifest, and build methods to Environment class\r\n\r\n๐ง chore(environment.py): refactor create_environment_flow to use Prefect tasks and add delay_task to each task\r\n\r\n๐ feat(main.py): add SoftPack Builder main entrypoint\r\n๐ feat(service.py): add Service module with run command to start the SoftPack Builder REST API service\r\n\r\n๐ feat(conftest.py): add fixtures for TestClient, CLI, and service factory and service runners.\r\n\r\n๐จ test(test_app.py): fix test_root, test_openapi_docs, and test_openapi_redoc tests to use httpx instead of requests\r\nโจ feat(test_app.py): add test_register_module test to check if module is registered correctly in the application\r\n\r\n๐ test(test_deployments.py): add tests for Deployments class and its methods\r\n\r\n๐ง chore(test_environment.py): refactor test_environment_create_api to use a parameterized test\r\n๐ feat(test_environment.py): add test_environment_create_command to test environment creation via CLI\r\n\r\n๐จ fix(tests): fix flake8 errors in test_main.py\r\nโ
test(service.py): add test for service run\r\n๐จ fix(tox.ini): ignore D101, D102, D103, D107 in flake8 tests for tests directory\r\n\r\n* :sparkles: implement flow deployments\r\n\r\n* :package: update poetry lock file\r\n\r\n* ๐ fix(test_main.py): use pytest.raises context manager instead of try-except block in test_main function\r\n\r\n* ๐ chore(dev.yml): add Spack installation and create config file step to dev workflow\r\nโ
test(conftest.py): add fixture for running Prefect agent and add specs for Argon and Zirconium projects\r\n\r\n๐ fix(test_environment.py): add create_environment import\r\nโจ feat(test_environment.py): add test_environment_create_flow test\r\n๐ง chore(tox.ini): add concurrency option to coverage run section\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job (#6)\r\n\r\n* ๐ fix(dev.yml): change 'repo' to 'repository' in 'Install Spack' job configuration\r\n\r\n* ๐ง chore(dev.yml): update branch names in workflow trigger to only use 'main' and 'develop' branches\r\n\r\n* ๐ง chore(dev.yml): refactor Create config file step to use environment variables for better readability and maintainability\r\n\r\n* ๐ fix(dev.yml): use env variable in CONFIG_FILE instead of hardcoding it\r\n\r\n* ๐ fix(dev.yml): change env variable from env.CONFIG_PATH to vars.CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): fix typo in CONFIG_FILE variable assignment\r\n๐ง chore(dev.yml): change CONFIG_FILE path to be relative to CONFIG_PATH\r\n\r\n* ๐ fix(dev.yml): update SPACK_COMMAND to use $GITHUB_WORKSPACE to locate spack binary\r\n๐ chore(dev.yml): add debugging information to the job\r\n\r\n* ๐ fix(dev.yml): remove SPACK_COMMAND environment variable and use direct path to spack command instead\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to relative path\r\nโจ feat(dev.yml): add debug information to script\r\n\r\n* ๐ fix(dev.yml): change path to config file to use HOME environment variable\r\n\r\n* ๐ fix(dev.yml): change CONFIG_PATH to $HOME/.softpack/builder\r\n๐ง chore(dev.yml): remove unnecessary echo, pwd, ls, and cat commands\r\n\r\n* merge feature/singularity (#7)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* merge from feature/singularity (#8)\r\n\r\n* ๐ง chore(config): add SingularityConfig model to Settings\r\n๐ง chore(deployments): change default deployment name to include flow name\r\n\r\n๐ feat(environment.py): add Manifest class to handle Spack manifest files\r\n๐ง chore(environment.py): add owner field to Environment data model\r\n๐ง chore(environment.py): change typing import to include Callable and cast\r\n๐ง chore(environment.py): change task import to Task and add FlowRunContext import\r\n๐ง chore(environment.py): change DaskTaskRunner import to use prefect_dask.task_runners\r\n๐ง chore(environment.py): change ShellOperation import to use prefect_shell\r\n๐ง chore(environment.py): change BaseModel import to use pydantic\r\n๐ง chore(environment.py): change list[str] to List[str] in Environment data model\r\n๐ง chore(environment.py): change dataclasses import to use dataclass decorator\r\n๐ง chore(environment.py): change Path import to use pathlib.Path\r\n๐ fix(environment.py): fix from_yaml method to use self.filename instead of filename argument\r\n๐\r\n\r\n๐จ refactor(environment.py): refactor Environment class to use Box for filenames and add task method\r\n๐ chore(environment.py): add task_run_name to Prefect task for better logging\r\n๐ fix(environment.py): pass kwargs to ShellOperation and spack_command methods\r\n\r\n๐จ refactor(environment.py): extract singularity_command method from Environment class\r\nโจ feat(environment.py): add create_container_definition method to create Spack manifest and Singularity definition\r\n\r\n๐ feat(environment.py): add create_container_definition task to create container definition\r\n๐ท chore(environment.py): use Environment.task decorator instead of @task() decorator\r\n๐ท chore(environment.py): use cast() to cast the return value of the task functions\r\n๐ท chore(environment.py): return FlowRunContext dictionary from create_environment function\r\n\r\n๐ chore(tests, tox): merge changes from branch 'guest' to 'main'\r\n๐ฅ chore(specs): add owner field to argon and zirconium projects\r\n๐ง chore(tox): update envlist to include python 3.9 and remove python 3.8 from gh-actions configuration\r\n\r\n* ๐ chore(config.yml): update spack version to v0.19.1\r\n๐ fix(environment.py): add --fakeroot flag to build command and convert filenames to strings\r\n\r\n* ๐ง chore(config.yml): add os_packages to container config\r\nโจ feat(config.yml): add strip option to container config\r\nโจ feat(config.yml): add concretizer.unify option to config view\r\n\r\n๐ fix(environment.py): replace dictionary with Box object to allow attribute access\r\n๐ฅ chore(environment.py): remove unused from_yaml method\r\nโจ feat(environment.py): use Box object to patch manifest and dump to file\r\n\r\n๐จ refactor(environment.py): change return type of create_manifest, concretize and build methods to Environment\r\nโจ feat(environment.py): add concretize method to Environment class\r\n๐ณ chore(environment.py): rename create_container_definition method to containerize in Environment class\r\n\r\n๐ chore(environment.py): refactor create_environment function to use a list of tasks instead of individual tasks\r\n๐ fix(environment.py): rename create_container_definition task to containerize_environment\r\nโจ feat(environment.py): add concretize_environment task to concretize an environment before containerizing it\r\nโจ feat(environment.py): add containerize_environment task to containerize an environment\r\nโจ feat(environment.py): add build_environment task to build an environment\r\n\r\n* ๐ง chore(dev.yml): add steps to install Singularity and run code coverage with codecov-action\r\n\r\n* ๐ revert(dev.yml): downgrade Singularity version to 3.8.7\r\n\r\n* :wrench: updated spack config\r\n\r\n* ๐ chore(dev.yml): update spack reference to commit 6aa4c29119\r\n๐ fix(config.yml): add missing dependencies for spack build\r\n๐ fix(environment.py): fix logger initialization and spack command path\r\n\r\n* ๐ chore(dev.yml): update spack repository reference to commit 0707ffd4e466402bf19dff1add59eaf2b6d9154e\r\nโ
test(dev.yml): run tests using poetry run tox instead of tox directly\r\n\r\n* โจ feat(config.yml): add support for environment path and spack config\r\n๐ fix(environment.py): fix ImageSpec constructor arguments\r\nโจ feat(environment.py): add ImageSpec abstract class and BuildSpec and FinalSpec subclasses\r\nโจ feat(environment.py): add patch_manifest method to Environment class\r\nโจ feat(environment.py): add containerize method to Environment class\r\nโจ feat(environment.py): add build method to Environment class\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add EnvironmentConfig class to SpackConfig\r\nโจ feat(environment.py): add Environment classmethod to create Environment from model\r\nโจ feat(environment.py): add environment path to Environment constructor\r\nโจ feat(environment.py): add path attribute to Environment class\r\nโจ feat(environment.py): add patch method to BuildSpec\r\nโจ feat(environment.py): add patch method to FinalSpec\r\nโจ feat(environment.py): add args method to Build\r\n\r\n* ๐ง chore(makefile): remove tests directory from mypy command\r\n๐ง chore(config.yml): rename spack.environment to spack.environments\r\n๐ง chore(environment.py): change --directory to --bind and remove --allow-root and --force options\r\n๐ง chore(environment.py): change logger type to LoggerAdapter\r\n๐ง chore(test_environment.py): add settings fixture and change create_environment call to use Box\r\n\r\n* ๐ fix(conftest.py): use Path instead of str for environments path\r\n๐ fix(conftest.py): use tempfile.mkdtemp instead of TemporaryDirectory\r\n๐ fix(test_environment.py): reduce PREFECT_AGENT_TIMEOUT to 5 seconds\r\nโจ feat(test_environment.py): add prefect_agent fixture to join threads\r\nโจ feat(test_environment.py): add capsys fixture to capture stdout and stderr\r\n\r\n* ๐จ fix(test_environment.py): remove unused fixture 'prefect_agent' and commented out code\r\nโจ feat(test_environment.py): remove unused fixture 'prefect_agent' from test signature\r\n\r\n* ๐ feat(dev.yml): add step to install Spack templates\r\n๐ fix(conftest.py): use tmpdir fixture instead of tempfile to create temporary directory\r\n๐ fix(conftest.py): set path attribute of Environment.settings.spack.environments to Path object\r\n๐ feat(conftest.py): add Spack templates directory to Environment.settings.spack.manifest.spack.config.template_dirs\r\n๐ fix(test_environment.py): remove unused settings fixture from test_environment_create_flow() function signature\r\n\r\n* ๐ chore(dev.yml): add temporary files debug step to show workspace and spack-templates directory contents\r\n\r\n* ๐ง chore(dev.yml): create Spack config file and show its content\r\n๐ง chore(environment.py): remove settings attribute from Environment class and pass it as an argument to Manifest.patch() method\r\n๐ง chore(conftest.py): refactor fixture to patch app settings instead of Environment settings\r\n\r\n* ๐ chore(dev.yml): update spack-templates repository to wtsi-hgi/spack-templates\r\n๐ chore(dev.yml): create GPG key for softpack\r\n๐ง chore(config.yml): remove unused spack config options\r\n๐ง chore(config.yml): change spack cache and environments paths to /tmp\r\n๐ง chore(config.yml): add bind mount for spack cache and GPG key in Singularity build\r\n๐ง chore(environment.py): change spack environments path to /tmp\r\n๐ง chore(tests/conftest.py): change spack environments and cache paths to /tmp\r\n๐ง chore(tests/data/specs): remove argon.yml and zirconium.yml, add test-env.yml\r\n๐ง chore(tests/test_environment.py): increase Prefect agent timeout to 300 seconds\r\n\r\n* ๐ chore(dev.yml): add debug logs to check .gpg directory\r\nโจ feat(tox.ini): add verbose flag to pytest command\r\n\r\n* ๐ chore(dev.yml): add test for GPG directory configuration\r\n\r\n* ๐ฅ chore(dev.yml): remove TEST GPG DIR step\r\n๐ chore(dev.yml): set SPACK_GNUPGHOME environment variable in Create GPG key step\r\n\r\n* ๐ chore(dev.yml): add optional input to enable tmate debugging in manually-triggered workflows\r\n\r\n* ๐ฅ chore(dev.yml): remove tmate debugging step from dev workflow\r\n๐ fix(dev.yml): add which command to show singularity location in Spack config step\r\nโจ feat(dev.yml): add tmate debugging step to dev workflow when manually triggered with debug_enabled input\r\n\r\n* ๐ fix(config.yml): use $HOME instead of tilde (~) to reference user's home directory in bind option\r\n\r\n* ๐ฅ chore(dev.yml): remove Spack config display step\r\nโจ feat(dev.yml): add code coverage step using codecov-action\r\n\r\n* ๐ฅ chore(tox.ini): remove verbose flag from pytest command\r\n\r\n* ๐ฅ refactor(environment.py): move settings attribute to the top of the class\r\n๐ fix(environment.py): remove redundant settings attribute assignment in __init__ method\r\n\r\n* ๐ fix(environment.py): fix logger initialization in init_logger method\r\n๐ fix(test_environment.py): fix test_environment_logger test case to properly test logger initialization\r\n\r\n* ๐ fix(environment.py): add exist_ok=True to mkdir method\r\n๐งช test(environment.py): add cleanup of created directory after test\r\n\r\n* ๐ง chore(pyproject.toml): update python version to >=3.9,<4.0\r\n๐ง chore(pyproject.toml): remove python version 3.8 from classifiers\r\n๐ง chore(pyproject.toml): remove target-version py38 from black configuration\r\n๐ง chore(environment.py): update docstring for from_model method\r\n๐ง chore(test_environment.py): update create_environment call to use Box\r\n๐ง chore(test_environment.py): remove unused PREFECT_AGENT_TIMEOUT variable\r\n๐ง chore(test_environment.py): update logger test to trigger exception\r\n\r\n* :sparkles: add artifacts support (#9)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* merge from feature/artifacts (#10)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* merge from feature/artifacts (#11)\r\n\r\n* :sparkles: add artifacts support\r\n\r\ninitial support for adding adding artifacts and pushing images to container registries\r\n\r\n* ๐ฆ chore(deps): add mergedeep to pyproject.toml\r\n๐ฆ chore(deps): add semver to pyproject.toml\r\n๐ฆ chore(tox): use poetry to manage dependencies\r\n๐ฆ chore(tox): add commands_pre to install dependencies before running commands in tox.ini\r\n\r\n* ๐ fix(models.py): make VaultConfig fields optional\r\n๐ fix(settings.py): catch KeyError when trying to read vault config from file and print to stderr\r\n\r\n* ๐ง chore(README.md): use --with instead of -E to install poetry environments\r\n๐ง chore(softpack_builder): rename register_module to register_serializer in all files\r\n\r\n* ๐ fix(app.py): change datetime format to string to avoid serialization issues\r\n๐ fix(artifacts.py): fix typo in variable name from registry to registry\r\n๐จ refactor(models.py): capitalize first letter of class docstring\r\n๐จ refactor(settings.py): rename config_dir to default_config_dir and add user_config_dir to improve semantics. Also remove unused imports.\r\n\r\n* ๐ฅ refactor(spack.py): remove unused buildcache create command and directory argument\r\n๐ feat(spack.py): add push command to buildcache to upload package to remote cache server using the hostname of the current machine\r\n\r\n* ๐ docs(spack.py): update docstring of env_buildcache method to reflect its functionality\r\n๐ feat(spack.py): add support for pushing build cache for a package using the command method\r\n\r\n* ๐ chore(requirements.txt): add new dependencies to the project to improve functionality and security\r\n\r\n* ๐ chore(api.py, app.py, artifacts.py, models.py, settings.py, container.py, deployments.py, environment.py, logger.py, main.py, modulefile.py, serializable.py, service.py, shell.py, singularity.py, spack.py, url.py): update license year and organization name in all files\r\n\r\n* ๐ chore(preview.yml): remove redundant 'workflow' from name and description\r\n๐ chore(release.yml): remove redundant 'workflow' from name and description\r\n\r\n* merge from feature/debug (#13)\r\n\r\n* ๐ feat(debug.yml): add debug workflow to run build with tmate debugging enabled on feature/debug branch and workflow_dispatch event. Add steps to get version from tag, checkout repo, and get changelog entry.\r\n\r\n* ๐ฅ chore(debug.yml): remove debug workflow file\r\n๐จ refactor(dev.yml): remove CODECOV_TOKEN secret from codecov-action\r\n๐ chore(release.yml): update changelog builder action to mikepenz/release-changelog-builder-action@v3.2.0 and remove changelog-reader-action. 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