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Merge pull request #1301 from mvdbeek/0.75.0
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mvdbeek committed Oct 29, 2022
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100 changes: 100 additions & 0 deletions HISTORY.rst
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.. to_doc
---------------------
0.75.0 (2022-10-28)
---------------------

* Update outdated cuffmerge url (thanks to `@martenson`_). `Pull Request
1247`_
* Set upstream branch when pushing workflows to GitHub (thanks to
`@simonbray`_). `Pull Request 1249`_
* restore --no_cleanup to set cleanup_job to never (thanks to `@bernt-matthias`_). `Pull Request 1255`_
* Drop support for Python 3.6 (thanks to `@simonbray`_). `Pull Request 1257`_
* Replace CoC with link to GalaxyProject's one (thanks to `@nsoranzo`_). `Pull
Request 1259`_
* Mains resource selector must be skipped (thanks to `@hexylena`_). `Pull
Request 1260`_
* Ignore cloudflare 503 status when checking links (thanks to `@bernt-matthias`_). `Pull Request 1262`_
* Document the use of mandatory macro parameters and add named macro tokens
(thanks to `@bernt-matthias`_). `Pull Request 1212`_
* Bump galaxy package requirements to 22.01 (thanks to `@bernt-matthias`_).
`Pull Request 1264`_
* Run local galaxy via gravity (thanks to `@mvdbeek`_). `Pull Request 1232`_
* Lint randomlines.xml file (thanks to `@simonbray`_). `Pull Request 1270`_
* Check if main requirement is `None` (thanks to `@bernt-matthias`_). `Pull
Request 1274`_
* Planemo type annotation: module planemo.commands.cmd_autoupdate (thanks to
`@gallardoalba`_). `Pull Request 1278`_
* Planemo type annotation: module planemo.cli (thanks to `@gallardoalba`_).
`Pull Request 1277`_
* Planemo type annotation: module cmd_clone (thanks to `@gallardoalba`_).
`Pull Request 1279`_
* Planemo type annotation: module cmd_tool_init (thanks to `@gallardoalba`_).
`Pull Request 1281`_
* Add type annotations to ``planemo.autoupdate`` module (thanks to
`@nsoranzo`_). `Pull Request 1283`_
* Planemo type annotation: module cmd_normalize (thanks to `@gallardoalba`_).
`Pull Request 1280`_
* Planemo type annotation: module planemo.conda (thanks to `@gallardoalba`_).
`Pull Request 1284`_
* Add type annotations to ``planemo.glob`` and ``planemo.virtualenv`` (thanks
to `@nsoranzo`_). `Pull Request 1287`_
* Drop ``conda_lint`` command (thanks to `@nsoranzo`_). `Pull Request 1288`_
* Type annotations for planemo.bioblend, planemo.git, and planemo.cwl.run
(thanks to `@adRn-s`_). `Pull Request 1285`_
* Add FAQ page to docs (thanks to `@simonbray`_). `Pull Request 1271`_
* Add type annotations to ``planemo.runnable`` and ``planemo.workflow_lint``
(thanks to `@nsoranzo`_). `Pull Request 1291`_
* Make `--channels` also affect mulled channels and update/extend howto use
bioconda artifacts (thanks to `@bernt-matthias`_). `Pull Request 1227`_
* Planemo type annotation: config, context and factory (thanks to
`@gallardoalba`_). `Pull Request 1292`_
* [Training] update templates to use new, more accessible box style (thanks to
`@shiltemann`_). `Pull Request 1293`_
* Pre-create expected output file on disk (thanks to `@mvdbeek`_). `Pull
Request 1276`_
* Control publish setting in .dockstore.yml, fix first release not appearing
on dockstore (thanks to `@mvdbeek`_). `Pull Request 1295`_
* Fix disclosure css for summary elements (thanks to `@mvdbeek`_). `Pull
Request 1294`_
* Enable providing multiple `--tool_data_table` options (thanks to
`@mvdbeek`_). `Pull Request 1296`_
* Make startup timeout configurable (thanks to `@mvdbeek`_). `Pull Request
1298`_
* Fix printing planemo test logs (thanks to `@mvdbeek`_). `Pull Request 1299`_
* Fix workflow test when input is optional but also workflow output (thanks to
`@mvdbeek`_). `Pull Request 1297`_

---------------------
0.74.11 (2022-06-08)
---------------------
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tools - and more experimental features involving Docker and Homebrew. 7d07782_

.. github_links
.. _Pull Request 1247: https://github.com/galaxyproject/planemo/pull/1247
.. _Pull Request 1249: https://github.com/galaxyproject/planemo/pull/1249
.. _Pull Request 1255: https://github.com/galaxyproject/planemo/pull/1255
.. _Pull Request 1257: https://github.com/galaxyproject/planemo/pull/1257
.. _Pull Request 1259: https://github.com/galaxyproject/planemo/pull/1259
.. _Pull Request 1260: https://github.com/galaxyproject/planemo/pull/1260
.. _Pull Request 1262: https://github.com/galaxyproject/planemo/pull/1262
.. _Pull Request 1212: https://github.com/galaxyproject/planemo/pull/1212
.. _Pull Request 1264: https://github.com/galaxyproject/planemo/pull/1264
.. _Pull Request 1232: https://github.com/galaxyproject/planemo/pull/1232
.. _Pull Request 1270: https://github.com/galaxyproject/planemo/pull/1270
.. _Pull Request 1274: https://github.com/galaxyproject/planemo/pull/1274
.. _Pull Request 1278: https://github.com/galaxyproject/planemo/pull/1278
.. _Pull Request 1277: https://github.com/galaxyproject/planemo/pull/1277
.. _Pull Request 1279: https://github.com/galaxyproject/planemo/pull/1279
.. _Pull Request 1281: https://github.com/galaxyproject/planemo/pull/1281
.. _Pull Request 1283: https://github.com/galaxyproject/planemo/pull/1283
.. _Pull Request 1280: https://github.com/galaxyproject/planemo/pull/1280
.. _Pull Request 1284: https://github.com/galaxyproject/planemo/pull/1284
.. _Pull Request 1287: https://github.com/galaxyproject/planemo/pull/1287
.. _Pull Request 1288: https://github.com/galaxyproject/planemo/pull/1288
.. _Pull Request 1285: https://github.com/galaxyproject/planemo/pull/1285
.. _Pull Request 1271: https://github.com/galaxyproject/planemo/pull/1271
.. _Pull Request 1291: https://github.com/galaxyproject/planemo/pull/1291
.. _Pull Request 1227: https://github.com/galaxyproject/planemo/pull/1227
.. _Pull Request 1292: https://github.com/galaxyproject/planemo/pull/1292
.. _Pull Request 1293: https://github.com/galaxyproject/planemo/pull/1293
.. _Pull Request 1276: https://github.com/galaxyproject/planemo/pull/1276
.. _Pull Request 1295: https://github.com/galaxyproject/planemo/pull/1295
.. _Pull Request 1294: https://github.com/galaxyproject/planemo/pull/1294
.. _Pull Request 1296: https://github.com/galaxyproject/planemo/pull/1296
.. _Pull Request 1298: https://github.com/galaxyproject/planemo/pull/1298
.. _Pull Request 1299: https://github.com/galaxyproject/planemo/pull/1299
.. _Pull Request 1297: https://github.com/galaxyproject/planemo/pull/1297
.. _Pull Request 1244: https://github.com/galaxyproject/planemo/pull/1244
.. _Pull Request 1242: https://github.com/galaxyproject/planemo/pull/1242
.. _Pull Request 1241: https://github.com/galaxyproject/planemo/pull/1241
Expand Down Expand Up @@ -2618,3 +2717,4 @@ History
.. _@gallardoalba: https://github.com/gallardoalba
.. _@stain: https://github.com/stain
.. _@profgiuseppe: https://github.com/profgiuseppe
.. _@adRn-s: https://github.com/adRn-s
3 changes: 2 additions & 1 deletion docs/commands.rst
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Expand Up @@ -41,6 +41,7 @@ documentation describes these commands.
.. include:: commands/profile_list.rst
.. include:: commands/project_init.rst
.. include:: commands/pull_request.rst
.. include:: commands/rerun.rst
.. include:: commands/run.rst
.. include:: commands/serve.rst
.. include:: commands/share_test.rst
Expand All @@ -66,4 +67,4 @@ documentation describes these commands.
.. include:: commands/workflow_job_init.rst
.. include:: commands/workflow_lint.rst
.. include:: commands/workflow_test_init.rst
.. include:: commands/workflow_upload.rst
.. include:: commands/workflow_upload.rst
63 changes: 14 additions & 49 deletions docs/commands/autoupdate.rst
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Expand Up @@ -18,167 +18,136 @@ Auto-update tool requirements by checking against Conda and updating if newer ve

--dry-run Perform a dry run autoupdate without modifying
the XML files.
-r, --recursive Recursively perform command for
subdirectories.
--test Test updated XML files.
--skiplist TEXT Skiplist file, containing a list of tools for
which autoupdate should be skipped.
--skiplist TEXT Skiplist file, containing a list of tools or
workflows for which autoupdate should be
skipped.
--skip_requirements TEXT Comma-separated list of requirements which
should be not be updated. Default is
python,r-base,perl.
--update_test_data Update test-data directory with job outputs
(normally written to directory
--job_output_files if specified.)
--paste_test_data_paths / --no_paste_test_data_paths
By default Planemo will use or not use
Galaxy's path paste option to load test data
into a history based on the engine type it is
targeting. This can override the logic to
explicitly enable or disable path pasting.
--test_output PATH Output test report (HTML - for humans)
defaults to tool_test_output.html.
--test_output_text PATH Output test report (Basic text - for display
in CI)
--test_output_markdown PATH Output test report (Markdown style - for
humans & computers)
--test_output_xunit PATH Output test report (xunit style - for CI
systems
--test_output_junit PATH Output test report (jUnit style - for CI
systems
--test_output_allure DIRECTORY Output test allure2 framework resutls
--test_output_json PATH Output test report (planemo json) defaults to
tool_test_output.json.
--job_output_files DIRECTORY Write job outputs to specified directory.
--summary [none|minimal|compact]
Summary style printed to planemo's standard
output (see output reports for more complete
summary). Set to 'none' to disable completely.
--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|3.6|3.7|3.8|3.9]
--galaxy_python_version [3|3.7|3.8|3.9]
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
linted/tested/etc... but they will be
available to workflows and for interactive
use.
--install_galaxy Download and configure a disposable copy of
Galaxy from github.
--galaxy_branch TEXT Branch of Galaxy to target (defaults to
master) if a Galaxy root isn't specified.
--galaxy_source TEXT Git source of Galaxy to target (defaults to
the official galaxyproject github source if a
Galaxy root isn't specified.
--skip_venv Do not create or source a virtualenv
environment for Galaxy, this should be used to
preserve an externally configured virtual
environment or conda environment.
--no_cache_galaxy Skip caching of Galaxy source and dependencies
obtained with --install_galaxy. Not caching
this results in faster downloads (no git) - so
is better on throw away instances such with
TravisCI.
--no_cleanup Do not cleanup temp files created for and by
Galaxy.
--galaxy_email TEXT E-mail address to use when launching single-
user Galaxy server.
--docker / --no_docker Run Galaxy tools in Docker if enabled.
--docker_cmd TEXT Command used to launch docker (defaults to
docker).
--docker_sudo / --no_docker_sudo
Flag to use sudo when running docker.
--docker_host TEXT Docker host to target when executing docker
commands (defaults to localhost).
--docker_sudo_cmd TEXT sudo command to use when --docker_sudo is
enabled (defaults to sudo).
--mulled_containers, --biocontainers
Test tools against mulled containers (forces
--docker). Disables conda resolution unless
any conda option has been set explicitly.
--galaxy_startup_timeout INTEGER RANGE
Wait for galaxy to start before assuming
Galaxy did not start. [x>=1]
--job_config_file FILE Job configuration file for Galaxy to target.
--tool_dependency_dir DIRECTORY
Tool dependency dir for Galaxy to target.
--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',
Expand All @@ -191,22 +160,16 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
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.
Expand All @@ -216,9 +179,11 @@ Auto-update tool requirements by checking against Conda and updating if newer ve
one user and this user is automatically logged
it. Use --no_galaxy_single_user to prevent
Galaxy from running this way.
--report_level [all|warn|error]
--report_xunit PATH Output an XUnit report, useful for CI testing
--fail_level [warn|error]
--galaxy_url TEXT Remote Galaxy URL to use with external Galaxy
engine.
--galaxy_user_key TEXT User key to use with external Galaxy engine.
--help Show this message and exit.
2 changes: 0 additions & 2 deletions docs/commands/ci_find_repos.rst
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Expand Up @@ -25,11 +25,9 @@ or .dockstore.yml file.
--changed_in_commit_range TEXT Exclude paths unchanged in git commit range.
--chunk_count INTEGER Split output into chunks of this many item and
print --chunk such group.
--chunk INTEGER When output is split into --chunk_count
groups, output the group 0-indexedby this
option.
--output TEXT File to output to, or - for standard output.
--help Show this message and exit.

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