Update planemo to 0.75.25

[pyup-bot]

This PR updates planemo from 0.62.1 to 0.75.25.

Changelog

0.75.24

---------------------
* Workflow best practices: check that creator identifiers are URIs (thanks to
`elichad`_). `Pull Request 1458`_
* Update pinning for Galaxy 24.1 (thanks to `bernt-matthias`_). `Pull Request
1460`_
* Add option to create a minimal markdown test report (thanks to
`bernt-matthias`_). `Pull Request 1462`_
* Increase worflow linting (thanks to `lldelisle`_). `Pull Request 1463`_
* Run CI tests against newer Galaxy versions (thanks to `bernt-matthias`_).
`Pull Request 1466`_
* Add the option to provide a history id to run the workflow in (thanks to
`Delphine-L`_). `Pull Request 1461`_
* Make sure that skip list does not get `['']` (if no skip is given) (thanks
to `bernt-matthias`_). `Pull Request 1453`_
* Tool linting add `--skip_file` and remove lxml schema validation (thanks to
`bernt-matthias`_). `Pull Request 1420`_

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

0.75.23

---------------------
* Implement run/test/workflow_edit/autoupdate from non default tool sheds
(thanks to `mvdbeek`_). `Pull Request 1445`_
* Install prebuilt client by default (thanks to `mvdbeek`_). `Pull Request
1450`_
* Bump galaxy packages to allow for 24.0 (thanks to `bernt-matthias`_). `Pull
Request 1441`_
* replace dead link in conclusions (thanks to `martenson`_). `Pull Request
1447`_
* Add text to autopygen exceptions (thanks to `bernt-matthias`_). `Pull
Request 1444`_
* Drop circleci config (thanks to `mvdbeek`_). `Pull Request 1443`_
* Fix linting of asserts with children (thanks to `bernt-matthias`_). `Pull
Request 1442`_

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

0.75.22

---------------------
* Fix parsing of training ``metadata.yaml`` files (thanks to `nsoranzo`_).
`Pull Request 1439`_
* Fix markdown template: add missing closing details tag (thanks to `bernt-matthias`_). `Pull Request 1440`_
* Misc workflow linting improvements (thanks to `bernt-matthias`_). `Pull
Request 1437`_
* Don't skip requirements with an environment marker (thanks to `nsoranzo`_).
`Pull Request 1433`_
* Add `--host` parameter to allow listening on non-default hosts (thanks to
`selten`_). `Pull Request 1430`_

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

0.75.21

---------------------
* Add option to pass extra arguments to `docker run` (thanks to `bernt-matthias`_). `Pull Request 1428`_
* Fix workflow_edit (thanks to `mvdbeek`_). `Pull Request 1427`_
* Update to black 2024 stable style (thanks to `nsoranzo`_). `Pull Request
1425`_

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

0.75.20

---------------------
* Fix use of `package_name` attribute on `CondaTarget` objects (thanks to
`nsoranzo`_). `Pull Request 1424`_
* Don't crash autoupdate on non-PEP440-compliant tool versions (thanks to
`nsoranzo`_). `Pull Request 1422`_
* Add now mandatory readthedocs config files (thanks to `nsoranzo`_). `Pull
Request 1419`_
* Update action versions (thanks to `nsoranzo`_). `Pull Request 1416`_

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

0.75.19

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

* Update upper bound for galaxy packages to < 23.2 (thanks to `bernt-matthias`_). `Pull Request 1388`_
* Fix workflow download when using instance id (thanks to `mvdbeek`_). `Pull
Request 1412`_
* Remove introduction header from training init (thanks to `hexylena`_).
`Pull Request 1410`_

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

0.75.18

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

* Pretty-print workflow and use correct version of linked workflow in
``workflow_test_init`` (thanks to `mvdbeek`_). `Pull Request 1408`_
* Fix running workflow tests when there are multiple tests (thanks to
`mvdbeek`_). `Pull Request 1407`_
* Fix matching of tool ids to autoupdate (thanks to `nsoranzo`_). `Pull
Request 1406`_

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

0.75.17

---------------------
* Implement running tests against existing invocation (thanks to `mvdbeek`_).
`Pull Request 1401`_
* Fix test result download (thanks to `mvdbeek`_). `Pull Request 1402`_

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

0.75.16

---------------------
* No changes

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

0.75.15

---------------------
* Change info message for markdown readme in repo
(thanks to `bernt-matthias`_). `Pull Request 1398`_
* Make test reports more resilient to failing invocations (thanks to
`mvdbeek`_). `Pull Request 1400`_
* Fix zenodo test, drop explicit datatype mapping (thanks to `mvdbeek`_).
`Pull Request 1399`_
* Fix linting rule selection (thanks to `bernt-matthias`_). `Pull Request
1396`_
* Add missing ``Astronomy``, ``CLIP-seq`` and ``Materials science`` TS
categories (thanks to `bernt-matthias`_). `Pull Request 1397`_

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

0.75.14

---------------------
* Fix workflow_lint for json output values (thanks to `mvdbeek`_). `Pull
Request 1395`_

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

0.75.13

---------------------
* Add --skip to shed_lint (thanks to `bernt-matthias`_). `Pull Request 1394`_
* Remove API key requirement from training_init (thanks to `hexylena`_).
`Pull Request 1393`_
* Try to fix planemo test workflow when output is collection with identical
name (thanks to `lldelisle`_). `Pull Request 1391`_

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

0.75.12

---------------------
* Track subworkflow invocations after main invocation is scheduled (thanks to
`mvdbeek`_). `Pull Request 1389`_

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

0.75.11

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

* Implement automatic tool generation based on the source code of the tool
(thanks to `Kulivox`_). `Pull Request 1263`_
* Support for testing workflows with conditional steps (thanks to
`mvdbeek`_). `Pull Request 1387`_

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

0.75.10

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

* Add pick_value to distro_tools (thanks to `mvdbeek`_). `Pull Request 1385`_
* Allow missing conda_exec (thanks to `mstabrin`_). `Pull Request 1384`_
* Fix profile version test (thanks to `bernt-matthias`_). `Pull Request
1383`_
* Fix type comparisons (thanks to `bernt-matthias`_). `Pull Request 1382`_
* Added a note that docker is required for docker and biocontainers option
(thanks to `paulzierep`_). `Pull Request 1355`_
* Optimize disk space usage for `planemo test` (thanks to `bernt-matthias`_).
`Pull Request 1378`_
* Fix for change of base_url in BioBlend 1.2.0 (thanks to `nsoranzo`_). `Pull
Request 1379`_

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

0.75.9

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

* Update collection operation tool list (thanks to `mvdbeek`_). `Pull Request
1377`_
* Officially support Python 3.10 and 3.11 (thanks to `nsoranzo`_). `Pull
Request 1375`_
* Fix links (thanks to `nsoranzo`_). `Pull Request 1374`_
* Fix ``test_run_gxtool_randomlines`` test on Galaxy dev branch (thanks to
`nsoranzo`_). `Pull Request 1373`_

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

0.75.8

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

* Bump galaxy package requirements to allow for 23.0 (thanks to `bernt-matthias`_). `Pull Request 1372`_
* Sanitize and make output names unique (thanks to `mvdbeek`_). `Pull Request 1371`_
* Increase bioblend retries for bad networks (thanks to `hexylena`_). `Pull Request 1369`_
* Add ``--biocontainers`` option to shed_lint (thanks to `mvdbeek`_). `Pull Request 1370`_
* fix regex of orcid + add test (thanks to `lldelisle`_). `Pull Request 1364`_
* Drop `allow_none` for finding repository (thanks to `mvdbeek`_). `Pull Request 1358`_

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

0.75.7

---------------------
* Drop call to ``escape_non_unicode_symbols`` (thanks to `nsoranzo`_). `Pull
Request 1357`_

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

0.75.6

---------------------
* Allow running autoupdate against external server (thanks to `mvdbeek`_).
`Pull Request 1265`_
* Fix extraction of orcid identifiers for .dockstore.yml (thanks to
`lldelisle`_). `Pull Request 1350`_

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

0.75.5

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

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

0.75.4

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

* 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`_

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

0.75.3

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

* 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

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

* 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`_

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

0.75.1

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

* 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`_

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

0.75.0

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

* 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`_

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

0.74.11

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

* Removing broken link, update it to current doc (thanks to `profgiuseppe`_).
`Pull Request 1244`_
* Implement nested collection inputs and outputs in workflow_test_init `Pull
Request 1242`_
* More fixes for auto-generating workflow tests `Pull Request 1241`_
* Fix workflow_test_init for collection outputs `Pull Request 1239`_

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

0.74.10

---------------------
* Allow specifying URL and API key with workflow autoupdate and docs
improvements (thanks to `simonbray`_). `Pull Request 1237`_
* Pin planemo to last known working major galaxy version `Pull Request 1230`_
* Drop unused Python dependencies and upgrade syntax to Python 3.6 `Pull Request 1228`_
* Update `best_practice_search()` for changes in galaxy-tool-util `Pull Request 1224`_
* Make galaxy config `cleanup_job` depend on `--no_cleanup`
(thanks to `bernt-matthias`_). `Pull Request 1226`_
* Tool builder: add profile and suffix version
(thanks to `gallardoalba`_). `Pull Request 1222`_
* training-init: add the FAQ index page to tutorial folder
(thanks to `shiltemann`_). `Pull Request 1217`_
* Adding best practices and assertion checks to workflow_lint
(thanks to `simonbray`_). `Pull Request 1213`_
* Updates to workflow autoupdate required for IWC bot
(thanks to `simonbray`_). `Pull Request 1214`_
* Add test and fix for failing docker_galaxy engine
(thanks to `simonbray`_). `Pull Request 1215`_
* Generate workflow test from invocation id
(thanks to `simonbray`_). `Pull Request 1209`_
* Fixed minor typo in documentation
(thanks to `stain`_). `Pull Request 1206`_
* Add missing ToolShed categories `Pull Request 1207`_
* Use WorkflowId rather than StoredWorkflowId when autoupdating subworkflows
(thanks to `simonbray`_). `Pull Request 1205`_
* Always use random id_secret for testing (thanks to `bernt-matthias`_). `Pull Request 1198`_
* Add rerun subcommand for rerunning jobs (thanks to `simonbray`_). `Pull Request 1140`_

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

0.74.9

---------------------
* Fix rendering of subworkflow steps for workflow testing report (thanks to
`simonbray`_). `Pull Request 1200`_
* Replace Galaxy interactor galaxy_requests_post with make_post_request from
BioBlend (thanks to `simonbray`_). `Pull Request 1201`_

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

0.74.8

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

* Exclude click 8.0.2. `Pull Request 1196`_
* Add tool version numbers to autoupdate logging (thanks to `simonbray`_).
`Pull Request 1188`_
* Allow tool autoupdate without conda installation (thanks to `simonbray`_).
`Pull Request 1193`_
* use correct key execution_problem in template (thanks to `bernt-matthias`_).
`Pull Request 1195`_

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

0.74.7

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

* Fix documentation to include ``--download_outputs`` flag (thanks to
`simonbray`_). `Pull Request 1184`_
* Select refgenie config based on Galaxy version `Pull Request 1187`_
* Extend autoupdate subcommand to workflows (thanks to `simonbray`_). `Pull
Request 1151`_

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

0.74.6

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

* Add JSON report for planemo run invocations (thanks to `simonbray`_). `Pull
Request 1153`_
* Ignore failure to download output datasets `Pull Request 1179`_
* Allow location to point to url for outputs `Pull Request 1180`_
* Fix --shed_install for gxformat2 workflows `Pull Request 1182`_
 
---------------------

0.74.5

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

* Remove iuc from default channels `Pull Request 1170`_
* Fix parsing of changelog for git release `Pull Request 1171`_
* Remove legacy commands, egg handling `Pull Request 1172`_
* Use bioblend's invoke_workflow `Pull Request 1173`_
* Create more useful output for failed invocations `Pull Request 1174`_
* Improve dockstore_init `Pull Request 1177`_

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

0.74.4

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

* Relicense under the MIT license `Pull Request 1169`_
* Revise log levels (thanks to `bernt-matthias`_). `Pull Request 1165`_
* Create upload_data subcommand (thanks to `simonbray`_). `Pull Request
1164`_
* Create ``--download_outputs`` flag for the ``run`` command
(thanks to `simonbray`_).
`Pull Request 1157`_
* Make simultaneous file upload configurable for the run and test commands
(thanks to `simonbray`_).
`Pull Request 1156`_
* Add option to add tags to a history with the ``run`` command
(thanks to `simonbray`_). `Pull Request 1154`_
* Revise Allure_ reporting experience for workflows. `Pull Request 1152`_

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

0.74.3

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

* Load both cat1 versions when testing workflows `Pull Request 1146`_
* Fix isolated virtualenv not getting activated `Pull Request 1145`_
* Use bioblend's make_get_request for authenticated request `Pull Request 1144`_
* Display live logs when Galaxy is run in background `Pull Request 1142`_

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

0.74.2

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

* Allow testing dir of workflows `Pull Request 1095`_
* Fix container register for gh workflow `Pull Request 1135`_, `Pull Request 1133`_
* Don't fail URL linting if blocked by CloudFlare `Pull Request 1134`_
1133`_
* Allow planemo run to stage exisiting datasets and relative paths (thanks to `simonbray`_).
`Pull Request 1128`_

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

0.74.1

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

* Fix ``ci_find_tools`` and ``ci_find_repos`` commands. `Pull Request 1127`_

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

0.74.0

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

* Allow running Galaxy workflow tests against externally defined workflows.
`Pull Request 1126`_, `Pull Request 1125`_,
`Pull Request 1123`_
* Require Python ``tabulate`` package for the ``list_invocations`` command.
`Pull Request 1124`_

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

0.73.0

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

* 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`_

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

0.72.0

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

* 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`_

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

0.71.0

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

* 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`_

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

0.70.0

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

* 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`_

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Links

• PyPI: https://pypi.org/project/planemo
• Changelog: https://data.safetycli.com/changelogs/planemo/
• Repo: https://github.com/galaxyproject/planemo

[pyup-bot]

Closing this in favor of #713