galaxyproject/planemo issues and pull requests

#1380 - Expose some history related option to test

Issue - State: open - Opened by bernt-matthias over 1 year ago

#1379 - Fix for change of base_url in BioBlend 1.2.0

Pull Request - State: closed - Opened by nsoranzo over 1 year ago - 1 comment

#1378 - Optimize disk space usage for `planemo test`

Pull Request - State: closed - Opened by bernt-matthias over 1 year ago - 2 comments

#1377 - Update collection operation tool list

Pull Request - State: closed - Opened by mvdbeek over 1 year ago

#1376 - planemo autoupdate only considers main public toolshed when updating workflows

Issue - State: closed - Opened by jancrichter over 1 year ago - 1 comment

#1375 - Officially support Python 3.10 and 3.11

Pull Request - State: closed - Opened by nsoranzo over 1 year ago - 1 comment

#1374 - Fix links

Pull Request - State: closed - Opened by nsoranzo over 1 year ago - 8 comments

#1373 - Fix ``test_run_gxtool_randomlines`` test on Galaxy dev branch

Pull Request - State: closed - Opened by nsoranzo over 1 year ago

#1372 - Bump galaxy package requirements to allow for 23.0

Pull Request - State: closed - Opened by bernt-matthias over 1 year ago - 4 comments

#1371 - Sanitize and make output names unique

Pull Request - State: closed - Opened by mvdbeek over 1 year ago - 1 comment

#1370 - Add ``--biocontainers`` option to shed_lint

Pull Request - State: closed - Opened by mvdbeek over 1 year ago - 2 comments

#1369 - Increase bioblend retries for bad networks

Pull Request - State: closed - Opened by hexylena over 1 year ago - 2 comments

#1368 - [feature request] "start" and "check" modes for workflow testing

Issue - State: closed - Opened by hexylena over 1 year ago - 1 comment

#1367 - planemo test is not recursive anymore

Issue - State: open - Opened by lcottret over 1 year ago - 3 comments

#1366 - Symbolic links for tests data are not taken into account

Issue - State: open - Opened by lcottret over 1 year ago - 1 comment

#1365 - Error with workflow testing: Would be good to 'sanitize' destination

Issue - State: closed - Opened by lldelisle over 1 year ago - 3 comments

#1364 - fix regex of orcid + add test

Pull Request - State: closed - Opened by lldelisle over 1 year ago - 1 comment

#1363 - Extended container support

Pull Request - State: open - Opened by bernt-matthias over 1 year ago - 10 comments

#1362 - Is it possible to test data managers with planemo ?

Issue - State: closed - Opened by paulzierep over 1 year ago - 2 comments

#1361 - Support galaxy `galaxy_user` and `galaxy_group` from planemo commands

Issue - State: open - Opened by selten over 1 year ago

#1360 - [feature request] workflow_lint could use a structured data output

Issue - State: open - Opened by hexylena over 1 year ago - 1 comment
Labels: enhancement

#1359 - Planemo test denies having updated test data

Issue - State: open - Opened by tuncK over 1 year ago

#1358 - Drop `allow_none` for finding repository

Pull Request - State: closed - Opened by mvdbeek over 1 year ago - 4 comments

#1357 - Drop call to ``escape_non_unicode_symbols``

Pull Request - State: closed - Opened by nsoranzo over 1 year ago - 7 comments

#1356 - Pin allure-python-commons version

Pull Request - State: closed - Opened by tuncK over 1 year ago - 2 comments

#1355 - Added a note that docker is required for docker and biocontainers option

Pull Request - State: closed - Opened by paulzierep over 1 year ago

#1354 - Add docker install requirement in the docs

Issue - State: open - Opened by paulzierep over 1 year ago - 3 comments

#1353 - shed_create with testtoolshed fails

Issue - State: closed - Opened by paulzierep over 1 year ago - 8 comments

#1352 - `planemo test` parameter `--job_output_files` seems unused

Issue - State: open - Opened by bernt-matthias over 1 year ago - 1 comment

#1351 - Improve shed install for workflows

Pull Request - State: open - Opened by mvdbeek over 1 year ago

#1350 - Fix extraction of orcid identifiers for .dockstore.yml

Pull Request - State: closed - Opened by lldelisle over 1 year ago - 7 comments

#1349 - planemo serve does not display images in help section

Issue - State: open - Opened by lldelisle almost 2 years ago

#1348 - Fix orcid regex for dockstore_init

Pull Request - State: closed - Opened by lldelisle almost 2 years ago - 2 comments

#1347 - Store datasets by UUID

Pull Request - State: closed - Opened by bernt-matthias almost 2 years ago - 1 comment

#1346 - Fix virtualenv dir bookkeeping

Pull Request - State: closed - Opened by wm75 almost 2 years ago - 1 comment

#1345 - Bug in planemo test workflow with subworkflows

Issue - State: open - Opened by lldelisle almost 2 years ago - 1 comment

#1344 - Deprecate introduction slides folder

Pull Request - State: closed - Opened by hexylena almost 2 years ago - 2 comments

#1343 - planemo uses internal gx_venv even if galaxy_root brings its own .venv

Issue - State: closed - Opened by wm75 almost 2 years ago - 5 comments

#1342 - Rename the default branch to `main`

Issue - State: open - Opened by nsoranzo almost 2 years ago

#1341 - Unfold failed / errored tests automatically in report

Issue - State: open - Opened by bernt-matthias almost 2 years ago

#1340 - change conda by mamba ?

Issue - State: closed - Opened by pimarin almost 2 years ago - 2 comments

#1339 - Error in planemo testing

Issue - State: closed - Opened by domenico-simone almost 2 years ago - 3 comments

#1338 - Remove note recommending installing dev versions from `planemo run` tutorial

Pull Request - State: closed - Opened by simonbray almost 2 years ago - 1 comment

#1337 - Rename configuration option removed in tox 4.0

Pull Request - State: closed - Opened by nsoranzo almost 2 years ago - 1 comment
Labels: bug

#1336 - Add a ro mount of the tool path's LCA

Pull Request - State: closed - Opened by bernt-matthias almost 2 years ago - 6 comments

#1335 - planemo lint errors when value and deltra attrs in <has_size> contain suffixes

Issue - State: closed - Opened by maximskorik almost 2 years ago - 3 comments

#1334 - Remove travis-ci.org badge from README.rst

Pull Request - State: closed - Opened by SimonWaldherr almost 2 years ago

#1333 - Test failure for tool: Assertion for h5 fails claiming that h5py is not installed (but it is if you go to the venv for galaxy)

Issue - State: closed - Opened by pcm32 almost 2 years ago - 4 comments

#1332 - Add traceback to report template

Pull Request - State: closed - Opened by bernt-matthias almost 2 years ago

#1331 - planemo test ignoring `--test_timeout`?

Issue - State: open - Opened by bernt-matthias almost 2 years ago

#1330 - Add indent and sort_keys to tool_test_json

Pull Request - State: closed - Opened by simonbray almost 2 years ago

#1329 - Fix ``planemo shed_test``

Pull Request - State: closed - Opened by mvdbeek almost 2 years ago
Labels: bug

#1328 - Cannot locate xUnit report ... for tests (planemo 0.74.11)

Issue - State: open - Opened by eschen42 almost 2 years ago

#1327 - Mount test data dir read-only in docker

Pull Request - State: closed - Opened by mvdbeek almost 2 years ago - 2 comments

#1326 - Add h5py dependency, required for comparing h5 files

Pull Request - State: closed - Opened by mvdbeek almost 2 years ago

#1325 - Fix "glone" typo in error message

Pull Request - State: closed - Opened by bernt-matthias almost 2 years ago

#1324 - Planemo lint -- Select parameter has multiple options with the same text content

Issue - State: closed - Opened by qiagu almost 2 years ago - 2 comments

#1323 - Possibility to fail `test` if anything goes wrong.

Issue - State: open - Opened by bernt-matthias almost 2 years ago

#1322 - Update GitHub action versions

Pull Request - State: closed - Opened by nsoranzo almost 2 years ago

#1321 - Wrong linting of metadata_in_range

Issue - State: open - Opened by wm75 almost 2 years ago - 1 comment

#1320 - Type annotation for input staging-related code

Pull Request - State: closed - Opened by nsoranzo almost 2 years ago - 1 comment

#1319 - planemo test fails even when expect_failure set

Issue - State: closed - Opened by patrick-austin almost 2 years ago - 3 comments

#1318 - planemo workflow_edit currently not working?

Issue - State: closed - Opened by jancrichter almost 2 years ago - 1 comment

#1317 - Test log output misses information which test is currently executed

Issue - State: open - Opened by bernt-matthias almost 2 years ago

#1316 - Planemo test is ignoring `--failed`

Issue - State: open - Opened by bernt-matthias almost 2 years ago - 4 comments

#1315 - fix lint_tool_id for tools that are in toolshed but not found by tools_id

Pull Request - State: closed - Opened by lldelisle about 2 years ago - 1 comment

#1314 - Add creator dockstore

Pull Request - State: closed - Opened by lldelisle about 2 years ago - 6 comments

#1313 - Compare versions, not tool ids to find latest tool ids

Pull Request - State: closed - Opened by mvdbeek about 2 years ago - 1 comment

#1312 - Fix ``for_paths`` when path is directory of tools

Pull Request - State: closed - Opened by mvdbeek about 2 years ago - 2 comments

#1311 - [BUG] between version 0.75.0 and 0.75.1 on autoupdate

Issue - State: closed - Opened by lldelisle about 2 years ago - 2 comments

#1310 - Fix workflow_lint with list + check elements in collection

Pull Request - State: closed - Opened by lldelisle about 2 years ago - 4 comments

#1309 - [BUG] The new handling of the asserts section forgot a possible syntax

Issue - State: closed - Opened by lldelisle about 2 years ago - 3 comments

#1308 - Drop copy_tree workaround for tool sources

Pull Request - State: closed - Opened by mvdbeek about 2 years ago - 1 comment

#1307 - Fix recording of virtual_env_dir

Pull Request - State: closed - Opened by mvdbeek about 2 years ago - 1 comment

#1306 - workflow_lint: ensure that tool shed tool ids are valid

Pull Request - State: closed - Opened by lldelisle about 2 years ago - 3 comments