Planemo

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* Bump galaxy packages to 22.05 (thanks to `bernt-matthias`_). `Pull Request
1275`_

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* Store datasets by UUID (thanks to `bernt-matthias`_). `Pull Request 1347`_
* Fix orcid regex for dockstore_init (thanks to `lldelisle`_). `Pull Request
1348`_
* Fix virtualenv dir bookkeeping (thanks to `wm75`_). `Pull Request 1346`_
* Deprecate introduction slides folder (thanks to `hexylena`_). `Pull Request
1344`_
* Remove note recommending installing dev versions from `planemo run` tutorial
(thanks to `simonbray`_). `Pull Request 1338`_
* Rename configuration option removed in tox 4.0 (thanks to `nsoranzo`_).
`Pull Request 1337`_
* Remove travis-ci.org badge from README.rst (thanks to `SimonWaldherr`_).
`Pull Request 1334`_

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* 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`_

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* Compare versions, not tool ids to find latest tool ids (thanks to
`mvdbeek`_). `Pull Request 1313`_
* Fix ``for_paths`` when path is directory of tools (thanks to `mvdbeek`_).
`Pull Request 1312`_
* Fix workflow_lint with list + check elements in collection (thanks to
`lldelisle`_). `Pull Request 1310`_
* Drop copy_tree workaround for tool sources (thanks to `mvdbeek`_). `Pull
Request 1308`_

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* Use `pytest.raises()` instead of ad-hoc `assert_raises_regexp()` context
manager (thanks to `nsoranzo`_). `Pull Request 1302`_
* Add planemo_ci_setup command (thanks to `mvdbeek`_). `Pull Request 1304`_
* Don't fail planemo autoupdate if tool version not found in tool shed (thanks
to `lldelisle`_). `Pull Request 1305`_
* workflow_lint: ensure that tool shed tool ids are valid (thanks to
`lldelisle`_). `Pull Request 1306`_
* Fix recording of virtual_env_dir (thanks to `mvdbeek`_). `Pull Request
1307`_

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* Restore running tool tests against directory (thanks to `mvdbeek`_). `Pull
Request 1303`_
* 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`_

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