Planemo

---------------------

* Integrate important features from gxwf_ for running workflows - including
building up profile commands for creating aliases, allowing referencing workflows
by external IDs, and listing invocations (thanks to `simonbray`_).
`Pull Request 1076`_
* Documentation for using ``planemo run`` to execute workflows (thanks to `simonbray`_).
`Pull Request 1102`_
* Add ``workflow_upload`` command for publishing each workflow of a repository with many
workflows to their own standalone repository.
`Pull Request 1091`_
* Update github commands to authenticate with a token rather than
username/password (thanks to `simonbray`_).
`Pull Request 1083`_
* Document "advanced" tool test debugging (thanks to `bernt-matthias`_).
`Pull Request 1108`_
* Various fixes for workflow commands - including ``workflow_convert``,
``workflow_lint``, ``workflow_job_init``, and ``workflow_test_init``
(thanks to `simonbray`_).
`Pull Request 1101`_, `Pull Request 1118`_, `Pull Request 1121`_,
`Pull Request 1116`_, `Pull Request 1064`_
* Allow outputting test results as Allure_ framework results.
`Pull Request 1115`_
* Fix ``run_tests.sh`` invocation `Pull Request 1099`_
* Tiny typo in debugging output (thanks to `abretaud`_). `Pull Request 1066`_
* Fix typo in 'planemo test' help text for --skip_venv (thanks to
`peterjc`_).
`Pull Request 1068`_
* Fixes for CLI when ``external_galaxy`` is used as the engine (thanks to
`simonbray`_).
`Pull Request 1072`_
* Updating base image to 20.05 for training topics
(thanks to `bedroesb`_).
`Pull Request 1074`_
* Changes to update_test_data testing mode (thanks to `simonbray`_).
`Pull Request 1079`_
* Fix docker options when filling ``job_conf.xml`` template.
`Pull Request 1086`_
* Explicit tests for Galaxy 20.09. `Pull Request 1093`_
* Minor fix for ``ci_find_repos`` command. `Pull Request 1094`_
* Fix a couple of Cheetah_ urls in Galaxy tool documentation (thanks to `martenson`_).
`Pull Request 1096`_
* Fix doc link from a redirect loop to a section (thanks to `martenson`_).
`Pull Request 1110`_
* Clarify ``tutorial.md`` usage of citations (thanks to `blankenberg`_).
`Pull Request 1114`_
* Fix ``ZeroDivisionError`` when no tests are executed (thanks to `simonbray`_).
`Pull Request 1120`_

---------------------

---------------------

* More documentation/support around running workflows including new command
to initialize workflow jobs ``workflow_init_job``.
`Pull Request 1052`_
* Workflow tests and documentation for tagging inputs. `Pull Request 1058`_
* Various documentation improvements.
`Pull Request 1061`_, `Pull Request 1062`_
* Add mypy type checking. `Pull Request 1060`_
* Progress decoupling Planemo's core from click & CLI interactions.
`Pull Request 1059`_
* Tests for workflow testing script. `Pull Request 821`_

---------------------

---------------------

* Drop Python 2 support. `Pull Request 1026`_
* Rev Galaxy dependencies - including bumping bioblend to 0.14.0, galaxy-tool-util,
and unpinning cwltool (last of these thanks to thanks to `TMiguelT`_).
`Pull Request 1038`_, `Pull Request 1034`_
* Workflow linting, best practices, and tooling to assist in following them.
`Pull Request 1028`_, `Pull Request 1049`_, `Pull Request 1051`_
`Pull Request 1044`_
* Substantial rewrites to Galaxy workflow input staging - including allow nested
collection and composite inputs to Galaxy for ``run`` and ``test``.
`Pull Request 900`_, `Pull Request 1029`_
* Remove assorted older, likely unused commands. `Pull Request 1043`_
* Update installation.rst (thanks to `mblue9`_). `Pull Request 1032`_
* Automatic PyPI upload on tag using GitHub Actions.
`Pull Request 994`_
* Fix quay repository presence check for single target builds.
`Pull Request 993`_
* More fine grained options for ``--shed_install`` (thanks to `AndreasSko`_).
`Pull Request 1001`_
* Change default Python version for Galaxy (thanks to `bernt-matthias`_).
`Pull Request 1021`_
* Sort tests by id when merging (thanks to `bernt-matthias`_).
`Pull Request 1022`_
* Add ``--group_tools`` option to ``ci_find_tools``
(thanks to `bernt-matthias`_).
`Pull Request 1008`_
* Add shared data library path to the data upload box for training material
(thanks to `shiltemann`_).
`Pull Request 1013`_
* Add support for tool versions to tutorial template generator (thanks to
`shiltemann`_). `Pull Request 1041`_
* Only copy test files if they don't exist. `Pull Request 1037`_
* Improvements to loading stock tools for workflow testing and serving (
add new stock tools to list and check subworkflows).
`Pull Request 1031`_
* Fix link for composite data type docs (thanks to `bernt-matthias`_).
`Pull Request 1020`_
* Do not use ``gi._make_url()`` internal BioBlend method.
* Switch CWL examples to use https://schema.org/version/latest/schema.rdf
(thanks to `mr-c`_).
`Pull Request 1015`_
* Fix docs not to claim Galaxy can't run on Python 3.
`Pull Request 1023`_
* Improved abstractions around target Galaxy instance. `Pull Request 1046`_
* Add empty refgenie config for tests (thanks to `blankenberg`_).
`Pull Request 1025`_
* Substantial reworking of testing infrastructure.
`Pull Request 1024`_, `Pull Request 1003`_,
`Pull Request 1011`_, `Pull Request 1006`_,
`Pull Request 1040`_, `Pull Request 1036`_,
`Pull Request 1042`_

---------------------

---------------------

* Temporarily add galaxy-util requirement `Pull Request 991`_
* Make symlinks in tool tree work for planemo test `Pull Request 988`_
* Reduce use of ``shell=True`` in subprocesses `Pull Request 989`_
* Drop planemo database seed option `Pull Request 985`_
* Don't execute ``untar_to()`` subprocesses through the shell `Pull Request 984`_
* Allow setting database_connection for planemo test runs `Pull Request 986`_
* Fix copy-paste mistakes `Pull Request 983`_
* Add planemo list_repos command `Pull Request 982`_
* Make container_register build files with headers and include base_image `Pull Request 980`_
* Replace deprecated galaxy-lib requirement with galaxy-tool-util `Pull Request 978`_
* Close all opened files (thanks to `bernt-matthias`_). `Pull Request 979`_
* Build single requirement container, log if requirement not in best-practice channels `Pull Request 977`_
* Use tojson jinja2 filter instead of json.dumps `Pull Request 975`_
* Add merge_test_reports command `Pull Request 974`_
* Implement github workflow and fix profile commands if psql unavailable `Pull Request 976`_
* Fix planemo lint --biocontainers if no build number in container `Pull Request 972`_
* Update a training command (thanks to `hexylena`_). `Pull Request 973`_
* Allow passing through GALAXY_VIRTUAL_ENV variable to venv setup `Pull Request 971`_
* Correct help text (thanks to `hexylena`_). `Pull Request 970`_
* Remove unneeded html5lib requirement `Pull Request 968`_

---------------------

---------------------

* Init & update submodules when installing and creating packages. Stop
distributing eggs (thanks to `nsoranzo`_). 1ab8530_

---------------------

---------------------

* Use ``unicodify()`` on exceptions and subprocess outputs (thanks to
`nsoranzo`_) `Pull Request 944`_
* Do not override ``None`` with empty string (thanks to `ic4f`_). `Pull Request
950`_
* Update Docker template for training material generation (thanks to
`bedroesb`_). `Pull Request 958`_
* Add support for suite of repos with different owners (thanks to `nsoranzo`_).
`Pull Request 959`_
* Link for collection details updated in the docs (thanks to `martin-raden`_).
`Pull Request 963`_
* Move most tests to Python 3.7, drop Python 3.4 (thanks to `nsoranzo`_).
`Pull Request 964`_
* Remove confusing warning `Pull Request 966`_

---------------------