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refactor(docs): move from reST to Markdown (#703)
Convert docs from reStructuredText to Markdown so that the changelog file is compatible with Release Please.
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| # Authors | ||
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| The list of contributors in alphabetical order: | ||
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| - [Adelina Lintuluoto](https://orcid.org/0000-0002-0726-1452) | ||
| - [Audrius Mecionis](https://orcid.org/0000-0002-3759-1663) | ||
| - [Anton Khodak](https://orcid.org/0000-0003-3263-4553) | ||
| - [Camila Diaz](https://orcid.org/0000-0001-5543-797X) | ||
| - [Daniel Prelipcean](https://orcid.org/0000-0002-4855-194X) | ||
| - [Diego Rodriguez](https://orcid.org/0000-0003-0649-2002) | ||
| - [Dinos Kousidis](https://orcid.org/0000-0002-4914-4289) | ||
| - [Giuseppe Steduto](https://orcid.org/0009-0002-1258-8553) | ||
| - [Harri Hirvonsalo](https://orcid.org/0000-0002-5503-510X) | ||
| - [Jan Okraska](https://orcid.org/0000-0002-1416-3244) | ||
| - [Leticia Wanderley](https://orcid.org/0000-0003-4649-6630) | ||
| - [Marco Donadoni](https://orcid.org/0000-0003-2922-5505) | ||
| - [Marco Vidal](https://orcid.org/0000-0002-9363-4971) | ||
| - [Matthew Feickert](https://orcid.org/0000-0003-4124-7862) | ||
| - [Rokas Maciulaitis](https://orcid.org/0000-0003-1064-6967) | ||
| - [Sinclert Perez](https://www.linkedin.com/in/sinclert) | ||
| - [Tibor Simko](https://orcid.org/0000-0001-7202-5803) | ||
| - [Vladyslav Moisieienkov](https://orcid.org/0000-0001-9717-0775) |
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| # Changelog | ||
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| ## 0.9.2 (2023-12-19) | ||
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| - Changes `validate` command to show detailed errors when the specification file is not a valid YAML file. | ||
| - Changes the validation of specification files to show improved validation warnings, which also indicate where unexpected properties are located in the file. | ||
| - Fixes `create_workflow_from_json` API function to always load and send the workflow specification to the server. | ||
| - Fixes `list` command to accept case-insensitive column names when sorting the returned workflow runs via the `--sort` option. | ||
| - Fixes `run` wrapper command for workflows that do not contain `inputs` clause in their specification. | ||
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| ## 0.9.1 (2023-09-27) | ||
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| - Adds support for Python 3.12. | ||
| - Adds `prune` command to delete all intermediate files of a given workflow. Use with care. | ||
| - Changes `open` command to inform user about the auto-closure of interactive sessions after a certain inactivity timeout. | ||
| - Changes `validate` command to display non-critical validation warnings when checking the REANA specification file. | ||
| - Fixes `list` command to correctly list workflows when sorting them by their run number or by the size of their workspace. | ||
| - Fixes `du` command help message typo. | ||
| - Fixes `validation --environments` command to correctly handle fully-qualified image names. | ||
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| ## 0.9.0 (2023-01-26) | ||
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| - Adds support for Python 3.11. | ||
| - Adds support for `.gitignore` and `.reanaignore` to specify files that should not be uploaded to REANA. | ||
| - Adds `retention-rules-list` command to list the retention rules of a workflow. | ||
| - Changes REANA specification loading and validation functionalities by porting some of the logic to `reana-commons`. | ||
| - Changes `create` and `restart` commands to always upload the REANA specification file. | ||
| - Changes `delete` command to always delete the workflow's workspace. | ||
| - Changes `delete_workflow` Python API function to always delete the workflow's workspace. | ||
| - Changes `download` command to add the possibility to write files to the standard output via `-o -` option. | ||
| - Changes `list` command to hide deleted workflows by default. | ||
| - Changes `list` command to allow displaying deleted workflows via `--all` and `--show-deleted-runs` options. | ||
| - Changes `list` and `status` commands to allow displaying the duration of workflows with the `--include-duration` option. | ||
| - Changes `mv` command to allow moving files while a workflow is running. | ||
| - Changes `upload` command to prevent uploading symlinks. | ||
| - Changes `validation --environment` command to use Docker registry v2 APIs to check that a Docker image exists in DockerHub. | ||
| - Fixes `list` command to highlight the workflow specified in `REANA_WORKON` correctly. | ||
| - Fixes `secrets-delete` command error message when deleting non existing secrets. | ||
| - Fixes `start` command to report failed workflows as errors. | ||
| - Fixes `start` and `run` commands to correctly follow the execution of the workflow until termination. | ||
| - Fixes `status` command to respect output format provided by the `--format` option. | ||
| - Fixes `upload` command to report when input directories are listed under the `files` section in the REANA specification file and vice versa. | ||
| - Fixes `validate --environment` command to detect illegal whitespace characters in Docker image names. | ||
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| ## 0.8.1 (2022-02-15) | ||
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| - Adds support for creating reana-client standalone AppImage executables. | ||
| - Adds support for Python 3.10. | ||
| - Adds workflow name validation for `create_workflow_from_json()` Python API function. | ||
| - Fixes formatting of error messages and sets appropriate exit status codes. | ||
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| ## 0.8.0 (2021-11-24) | ||
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| - Adds support for running and validating Snakemake workflows. | ||
| - Adds support for `outputs.directories` in `reana.yaml` allowing to easily download output directories. | ||
| - Adds new command `quota-show` to retrieve information about total CPU and Disk usage and quota limits. | ||
| - Adds new command `info` that retrieves general information about the cluster, such as available workspace path settings. | ||
| - Changes `validate` command to add the possibility to check the workflow against server capabilities such as desired workspace path via `--server-capabilities` option. | ||
| - Changes `list` command to add the possibility to filter by workflow status and search by workflow name via `--filter` option. | ||
| - Changes `list` command to add the possibility to filter and display all the runs of a given workflow via `-w` option. | ||
| - Changes `list` command to stop including workflow progress and workspace size by default. Please use new options `--include-progress` and `--include-workspace-size` to show this information. | ||
| - Changes `list --sessions` command to display the status of interactive sessions. | ||
| - Changes `logs` command to display also the start and finish times of individual jobs. | ||
| - Changes `ls` command to add the possibility to filter by file name, size and last-modified values via `--filter` option. | ||
| - Changes `du` command to add the possibility filter by file name and size via `--filter` option. | ||
| - Changes `delete` command to prevent hard-deletion of workflows. | ||
| - Changes Yadage workflow specification loading to be done in `reana-commons`. | ||
| - Changes CWL workflow engine to `cwltool` version `3.1.20210628163208`. | ||
| - Removes support for Python 2.7. Please use Python 3.6 or higher from now on. | ||
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| ## 0.7.5 (2021-07-05) | ||
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| - Changes workflow validation to display more granular output. | ||
| - Changes workflow parameters validation to warn about misused parameters for each step. | ||
| - Changes dependencies to unpin six so that client may be installed in more contexts. | ||
| - Fixes environment image validation not to test repetitively the same image. | ||
| - Fixes `upload_to_server()` Python API function to silently skip uploading in case of none-like inputs. | ||
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| ## 0.7.4 (2021-04-28) | ||
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| - Adds support of wildcard patterns to `ls` command. | ||
| - Adds support of directory download and wildcard patterns to `download` command. | ||
| - Changes `list` command to include deleted workflows by default. | ||
| - Fixes environment image validation info message where UIDs were switched. | ||
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| ## 0.7.3 (2021-03-24) | ||
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| - Adds validation of workflow input parameters to the `validate` command. | ||
| - Adds optional validation of workflow environment images (`--environments`) to the `validate` command. | ||
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| ## 0.7.2 (2021-01-15) | ||
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| - Adds support for Python 3.9. | ||
| - Fixes exception handling when uploading files. | ||
| - Fixes minor code warnings. | ||
| - Fixes traling slash issue from user exported REANA_SERVER_URL. | ||
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| ## 0.7.1 (2020-11-10) | ||
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| - Changes `ping` command output to include REANA client and server version information. | ||
| - Fixes `upload` command to properly display errors. | ||
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| ## 0.7.0 (2020-10-20) | ||
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| - Adds option to `logs` command to filter job logs according to compute backend, docker image, status and step name. | ||
| - Adds new `restart` command to restart previously run or failed workflows. | ||
| - Adds possibility to specify operational options in the `reana.yaml` of the workflow. | ||
| - Fixes user experience by preventing dots as part of the workflow name to avoid confusion with restart runs. | ||
| - Changes `du` command output format. | ||
| - Changes file loading to optimise CLI performance. | ||
| - Changes `logs` command to enhance formatting using marks and colours. | ||
| - Changes from Bravado to requests to improve download performance. | ||
| - Changes `ping` command to perform user access token validation. | ||
| - Changes defaults to accept both `reana.yaml` and `reana.yml` filenames. | ||
| - Changes `diff` command to improve output formatting. | ||
| - Changes code formatting to respect `black` coding style. | ||
| - Changes documentation to single-page layout. | ||
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| ## 0.6.1 (2020-06-09) | ||
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| - Fixes installation troubles for REANA 0.6.x release series by pinning several | ||
| dependencies. | ||
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| ## 0.6.0 (2019-12-27) | ||
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| - Introduces user secrets management commands `secrets-add`, | ||
| `secrets-list` and `secrets-delete`. | ||
| - Enhances `run` and `create` commands to allow specifying | ||
| workfow via the `--workflow` flag. | ||
| - Introduces new command `version` to report client version. | ||
| - Fixes `upload` command behaviour for uploading very large files. | ||
| - Simplifies `run` command by removing free upload parameters. | ||
| - Upgrades `cwltool` to 1.0.20191022103248. | ||
| - Disables SSL verification warnings when talking to self-signed server | ||
| certificates. | ||
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| ## 0.5.0 (2019-04-24) | ||
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| - Introduces new `resources` field in `reana.yaml` specification file | ||
| allowing to declare computing resources needed for workflow runs, such as the | ||
| CVMFS repositories via `cvmfs` subfield. | ||
| - Improves `reana-client` embedded command-line documentation (`-help`) by | ||
| grouping commands and providing concrete usage examples for all commands. | ||
| - Enhances workflow `start` command allowing to override input parameters | ||
| (`--parameter`) and to specify additional operational options | ||
| (`--option`). | ||
| - Introduces new workflow `run` wrapper command that creates workflow, uploads | ||
| its input data and code and starts its execution. | ||
| - Introduces new workflow `stop` command for stopping a running workflow. | ||
| - Enhances workflow `logs` command output capabilities via new `--json` | ||
| option. | ||
| - Introduces new workflow `diff` command for comparing two workflow runs. | ||
| - Introduces new workflow `delete` command for deleting one or more workflow | ||
| runs. | ||
| - Introduces new session `open` command allowing to run interactive sessions | ||
| such as Jupyter notebook upon workflow workspace. | ||
| - Introduces new session `close` command for closing interactive sessions. | ||
| - Renames past `workflows` command to `list` allowing to list both workflow | ||
| runs and interactive sessions. | ||
| - Introduces new workspace `du` command for checking workspace disk usage. | ||
| - Introduces new workspace `mv` command for moving files within workspace. | ||
| - Introduces new workspace `rm` command for removing files within workspace. | ||
| - Renames past workspace `list` command to `ls` allowing to list workspace | ||
| files. Enhances its output capabilities via new `--format` option. | ||
| - Introduces new API function `create_workflow_from_json()` which allows | ||
| developers and third-party systems to create workflows directly from JSON | ||
| specification. | ||
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| ## 0.4.0 (2018-11-07) | ||
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| - Enhances test suite and increases code coverage. | ||
| - Changes license to MIT. | ||
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| ## 0.3.1 (2018-09-25) | ||
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| - Amends upload and download commands that will now upload/download all the | ||
| files specified in `reana.yaml` in case no arguments are provided. | ||
| - Fixes `status` command's JSON output mode. | ||
| - Upgrades CWL reference implementation to version `1.0.20180912090223`. | ||
| - Renames Serial workflow operational parameter from ``` CACHING``to ``CACHE ```. | ||
| - Adds support for Python 3.7. | ||
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| ## 0.3.0 (2018-08-10) | ||
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| - Adds support for | ||
| [Serial workflows](http://reana-workflow-engine-serial.readthedocs.io/en/latest/). | ||
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| - CLI refactored to a flat design: | ||
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| - `inputs`/`outputs`/`code` removed, everything is a file managed | ||
| : with upload/download/list commands. | ||
| - Removes `workflow` command, workflows are managed with | ||
| : `create`/`start`/`status`. | ||
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| - Removes `analyes` command, now `validate` is first level command. | ||
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| - `status` now shows the selected workflow progress and current command on | ||
| verbose mode. | ||
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| - Requires the usage of an access token to talk to REANA Server. | ||
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| - Fixes bug when uploading binary files. | ||
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| - Supports addition of workflow engine parameters when using `start` for | ||
| serial workflows. | ||
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| - Improves error messages. | ||
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| ## 0.2.0 (2018-04-20) | ||
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| - Adds support for Common Workflow Language workflows. | ||
| - Adds support for persistent user-selected workflow names. | ||
| - Enables file and directory input uploading using absolute paths. | ||
| - Adds new `status` command to display the current status of the client. | ||
| - Reduces verbosity level for commands and improves error messages. | ||
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| ## 0.1.0 (2018-01-30) | ||
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| - Initial public release. | ||
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