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Bump version, rebuild docs, add changelog
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@mvdbeek
mvdbeek committed Nov 30, 2022
1 parent 50d88e4 commit e0a8f0d
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29 changes: 29 additions & 0 deletions HISTORY.rst
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.. to_doc
---------------------
0.75.3 (2022-11-30)
---------------------

* Mount test data dir read-only in docker (thanks to `@mvdbeek`_). `Pull
Request 1327`_
* Add traceback to report template (thanks to `@bernt-matthias`_). `Pull
Request 1332`_
* Add indent and sort_keys to tool_test_json (thanks to `@simonbray`_). `Pull
Request 1330`_
* Fix ``planemo shed_test`` (thanks to `@mvdbeek`_). `Pull Request 1329`_
* Add h5py dependency, required for comparing h5 files (thanks to
`@mvdbeek`_). `Pull Request 1326`_
* Update GitHub action versions (thanks to `@nsoranzo`_). `Pull Request 1322`_
* Fix "glone" typo in error message (thanks to `@bernt-matthias`_). `Pull
Request 1325`_
* Type annotation for input staging-related code (thanks to `@nsoranzo`_).
`Pull Request 1320`_
* Add creator dockstore (thanks to `@lldelisle`_). `Pull Request 1314`_

---------------------
0.75.2 (2022-11-02)
---------------------
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tools - and more experimental features involving Docker and Homebrew. 7d07782_

.. github_links
.. _Pull Request 1327: https://github.com/galaxyproject/planemo/pull/1327
.. _Pull Request 1332: https://github.com/galaxyproject/planemo/pull/1332
.. _Pull Request 1330: https://github.com/galaxyproject/planemo/pull/1330
.. _Pull Request 1329: https://github.com/galaxyproject/planemo/pull/1329
.. _Pull Request 1326: https://github.com/galaxyproject/planemo/pull/1326
.. _Pull Request 1322: https://github.com/galaxyproject/planemo/pull/1322
.. _Pull Request 1325: https://github.com/galaxyproject/planemo/pull/1325
.. _Pull Request 1320: https://github.com/galaxyproject/planemo/pull/1320
.. _Pull Request 1314: https://github.com/galaxyproject/planemo/pull/1314
.. _Pull Request 1313: https://github.com/galaxyproject/planemo/pull/1313
.. _Pull Request 1312: https://github.com/galaxyproject/planemo/pull/1312
.. _Pull Request 1310: https://github.com/galaxyproject/planemo/pull/1310
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2 changes: 1 addition & 1 deletion docs/commands/autoupdate.rst
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Expand Up @@ -57,7 +57,7 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
--test_timeout INTEGER Maximum runtime of a single test in seconds.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
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2 changes: 1 addition & 1 deletion docs/commands/ci_setup.rst
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Expand Up @@ -22,7 +22,7 @@ Useful for populating a CI cache.

--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
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5 changes: 3 additions & 2 deletions docs/commands/run.rst
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Expand Up @@ -23,7 +23,7 @@ Planemo command for running tools and jobs.

--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -183,7 +183,8 @@ Planemo command for running tools and jobs.
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
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5 changes: 3 additions & 2 deletions docs/commands/serve.rst
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Expand Up @@ -39,7 +39,7 @@ Galaxy instance.

--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -104,7 +104,8 @@ Galaxy instance.
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
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5 changes: 3 additions & 2 deletions docs/commands/shed_serve.rst
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Expand Up @@ -47,7 +47,7 @@ logged into and explored interactively.
mappings defined ~/.planemo.yml.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -112,7 +112,8 @@ logged into and explored interactively.
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
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77 changes: 74 additions & 3 deletions docs/commands/shed_test.rst
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Expand Up @@ -19,8 +19,6 @@ specified shed, find published artifacts (tools and dependencies)
corresponding to command-line arguments and ``.shed.yml`` file(s),
install these artifacts, and run the tool tests for these commands.

This command requires the target to be version 15.07 or newer.

**Options**::


Expand Down Expand Up @@ -48,7 +46,7 @@ This command requires the target to be version 15.07 or newer.
mappings defined ~/.planemo.yml.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -97,6 +95,79 @@ This command requires the target to be version 15.07 or newer.
--tool_data_path DIRECTORY Directory where data used by tools is located.
Required if tests are run in docker and should
make use of external reference data.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
--dependency_resolvers_config_file FILE
Dependency resolver configuration for Galaxy
to target.
--brew_dependency_resolution Configure Galaxy to use plain brew dependency
resolution.
--shed_dependency_resolution Configure Galaxy to use brewed Tool Shed
dependency resolution.
--no_dependency_resolution Configure Galaxy with no dependency resolvers.
--conda_prefix DIRECTORY Conda prefix to use for conda dependency
commands.
--conda_exec FILE Location of conda executable.
--conda_channels, --conda_ensure_channels TEXT
Ensure conda is configured with specified
comma separated list of channels.
--conda_use_local Use locally built packages while building
Conda environments.
--conda_dependency_resolution Configure Galaxy to use only conda for
dependency resolution.
--conda_auto_install / --no_conda_auto_install
Conda dependency resolution for Galaxy will
attempt to install requested but missing
packages.
--conda_auto_init / --no_conda_auto_init
Conda dependency resolution for Galaxy will
auto install conda itself using miniconda if
not availabe on conda_prefix.
--simultaneous_uploads / --no_simultaneous_uploads
When uploading files to Galaxy for tool or
workflow tests or runs, upload multiple files
simultaneously without waiting for the
previous file upload to complete.
--check_uploads_ok / --no_check_uploads_ok
When uploading files to Galaxy for tool or
workflow tests or runs, check that the history
is in an 'ok' state before beginning tool or
workflow execution.
--profile TEXT Name of profile (created with the
profile_create command) to use with this
command.
--postgres Use postgres database type.
--database_type [postgres|postgres_docker|sqlite|auto]
Type of database to use for profile - 'auto',
'sqlite', 'postgres', and 'postgres_docker'
are available options. Use postgres to use an
existing postgres server you user can access
without a password via the psql command. Use
postgres_docker to have Planemo manage a
docker container running postgres. Data with
postgres_docker is not yet persisted past when
you restart the docker container launched by
Planemo so be careful with this option.
--postgres_psql_path TEXT Name or or path to postgres client binary
(psql).
--postgres_database_user TEXT Postgres username for managed development
databases.
--postgres_database_host TEXT Postgres host name for managed development
databases.
--postgres_database_port TEXT Postgres port for managed development
databases.
--file_path DIRECTORY Location for files created by Galaxy (e.g.
database/files).
--database_connection TEXT Database connection string to use for Galaxy.
--shed_tool_conf TEXT Location of shed tools conf file for Galaxy.
--shed_tool_path TEXT Location of shed tools directory for Galaxy.
--galaxy_single_user / --no_galaxy_single_user
By default Planemo will configure Galaxy to
run in single-user mode where there is just
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
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5 changes: 3 additions & 2 deletions docs/commands/test.rst
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Expand Up @@ -53,7 +53,7 @@ please careful and do not try this against production Galaxy instances.
generated traffic.
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -216,7 +216,8 @@ please careful and do not try this against production Galaxy instances.
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--ignore_dependency_problems When installing shed repositories for
workflows, ignore dependency issues. These
likely indicate a problem but in some cases
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5 changes: 3 additions & 2 deletions docs/commands/training_generate_from_wf.rst
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Expand Up @@ -28,7 +28,7 @@ Create tutorial skeleton from workflow.
--workflow_id TEXT ID of the workflow on the Galaxy instance
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -93,7 +93,8 @@ Create tutorial skeleton from workflow.
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
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5 changes: 3 additions & 2 deletions docs/commands/training_init.rst
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Expand Up @@ -38,7 +38,7 @@ Build training template from workflow.
Zenodo extension and Galaxy datatypes
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -103,7 +103,8 @@ Build training template from workflow.
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
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2 changes: 1 addition & 1 deletion docs/commands/upload_data.rst
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Expand Up @@ -33,7 +33,7 @@ the already completed data upload.

--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
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5 changes: 3 additions & 2 deletions docs/commands/workflow_convert.rst
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Expand Up @@ -20,7 +20,7 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa.
-o, --output FILE
--galaxy_root DIRECTORY Root of development galaxy directory to
execute command with.
--galaxy_python_version [3|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9|3.10|3.11]
Python version to start Galaxy under
--extra_tools PATH Extra tool sources to include in Galaxy's tool
panel (file or directory). These will not be
Expand Down Expand Up @@ -85,7 +85,8 @@ Convert Format 2 workflows to native Galaxy workflows, and vice-versa.
flavor used if engine type is specified as
``docker-galaxy``. Defaults to
quay.io/bgruening/galaxy.
--docker_extra_volume PATH Extra path to mount if --engine docker.
--docker_extra_volume PATH Extra path to mount if --engine docker or
`--biocontainers` or `--docker`.
--test_data DIRECTORY test-data directory to for specified tool(s).
--tool_data_table PATH tool_data_table_conf.xml file to for specified
tool(s).
Expand Down

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