Ecosyste.ms: Issues

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GitHub / galaxyproject/planemo issues and pull requests

#1481 - Fix repository category update

Pull Request - State: closed - Opened by mvdbeek 7 days ago - 3 comments

#1480 - New toolshed categories are not updating for the existing tools

Issue - State: closed - Opened by pavanvidem 8 days ago - 14 comments

#1478 - planemo autoupdate may fail on tools but exit code is 0

Issue - State: open - Opened by lldelisle about 1 month ago

#1477 - Don't assume default master key works

Pull Request - State: open - Opened by mvdbeek about 1 month ago - 1 comment

#1475 - Synchronize with Galaxy Post 24.2 Publication

Issue - State: open - Opened by jmchilton about 1 month ago - 1 comment

#1474 - Fix up autopygen type annotation

Pull Request - State: closed - Opened by mvdbeek about 1 month ago

#1473 - Display last lines of logs

Pull Request - State: closed - Opened by mvdbeek 3 months ago

#1472 - Rewrite tool linters defined in planemo

Pull Request - State: open - Opened by bernt-matthias 3 months ago
Labels: help wanted

#1471 - add extended-assertions requirements

Pull Request - State: closed - Opened by bernt-matthias 4 months ago

#1470 - Pin galaxy-tool-util to >=24.0.2

Pull Request - State: closed - Opened by nsoranzo 4 months ago - 1 comment

#1469 - Planemo error upload1

Issue - State: open - Opened by marieBvr 4 months ago

#1468 - Planemo test : Failed to install Galaxy via command

Issue - State: closed - Opened by marieBvr 4 months ago - 1 comment

#1467 - use target_str_to_targets from tool-util package

Pull Request - State: open - Opened by bernt-matthias 4 months ago

#1466 - Run CI tests against newer Galaxy versions

Pull Request - State: closed - Opened by bernt-matthias 4 months ago

#1465 - Check lint skip types only for tool linting

Pull Request - State: closed - Opened by bernt-matthias 4 months ago - 3 comments

#1463 - Increase worflow linting

Pull Request - State: closed - Opened by lldelisle 4 months ago - 17 comments

#1462 - Add option to create a minimal markdown test report

Pull Request - State: closed - Opened by bernt-matthias 4 months ago - 4 comments

#1461 - Add the option to provide a history id to run the workflow in

Pull Request - State: closed - Opened by Delphine-L 4 months ago

#1460 - Update pinning for Galaxy 24.1

Pull Request - State: closed - Opened by bernt-matthias 4 months ago - 3 comments

#1459 - Search function on readthedocs is not Working

Issue - State: closed - Opened by Delphine-L 4 months ago

#1458 - Workflow best practices: check that creator identifiers are URIs

Pull Request - State: closed - Opened by elichad 4 months ago - 1 comment

#1457 - Add a new single cell category

Pull Request - State: closed - Opened by pavanvidem 4 months ago - 2 comments

#1454 - Remove myself from committer list

Pull Request - State: closed - Opened by simonbray 5 months ago - 1 comment

#1453 - Make sure that skip list does not get `['']` (if no skip is given)

Pull Request - State: closed - Opened by bernt-matthias 5 months ago - 3 comments

#1452 - Fix autoupdate for workflows with overlapping tool updates

Pull Request - State: closed - Opened by bernt-matthias 5 months ago - 2 comments

#1450 - Install prebuilt client by default

Pull Request - State: closed - Opened by mvdbeek 6 months ago

#1449 - Return inputs ID in --test_output_json outputs

Issue - State: open - Opened by Delphine-L 6 months ago

#1448 - Allow planemo run to send invocation to an existing history

Issue - State: closed - Opened by Delphine-L 6 months ago - 1 comment

#1447 - replace dead link in conclusions

Pull Request - State: closed - Opened by martenson 7 months ago

#1446 - replace dead docs link

Pull Request - State: closed - Opened by martenson 7 months ago

#1444 - Add text to autopygen exceptions

Pull Request - State: closed - Opened by bernt-matthias 7 months ago

#1443 - Drop circleci config

Pull Request - State: closed - Opened by mvdbeek 7 months ago - 1 comment

#1442 - Fix linting of asserts with children

Pull Request - State: closed - Opened by bernt-matthias 7 months ago

#1441 - Bump galaxy packages to allow for 24.0

Pull Request - State: closed - Opened by bernt-matthias 7 months ago

#1440 - Fix markdown template: add missing closing details tag

Pull Request - State: closed - Opened by bernt-matthias 7 months ago - 4 comments

#1439 - Fix parsing of training ``metadata.yaml`` files

Pull Request - State: closed - Opened by nsoranzo 7 months ago - 2 comments

#1438 - Use proper tmpdir for jobfiles

Pull Request - State: open - Opened by bernt-matthias 8 months ago - 2 comments

#1437 - Misc workflow linting improvements

Pull Request - State: closed - Opened by bernt-matthias 8 months ago

#1436 - Test against existing invocation

Issue - State: closed - Opened by bernt-matthias 8 months ago - 1 comment

#1434 - Addition of metadata generation for planemo run

Pull Request - State: open - Opened by Delphine-L 8 months ago - 3 comments

#1433 - Don't skip requirements with an environment marker

Pull Request - State: closed - Opened by nsoranzo 8 months ago

#1432 - autopygen: missing module stdlib-list

Issue - State: closed - Opened by thorstenwagner 8 months ago - 2 comments

#1431 - Output files detected with size 0 on planemo tests

Issue - State: open - Opened by pcm32 9 months ago - 2 comments

#1430 - Add `--host` parameter to allow listening on non-default hosts

Pull Request - State: closed - Opened by selten 9 months ago

#1429 - Planemo serve: --host not utilised

Issue - State: closed - Opened by selten 9 months ago - 1 comment
Labels: bug

#1428 - Add option to pass extra arguments to `docker run`

Pull Request - State: closed - Opened by bernt-matthias 9 months ago - 6 comments

#1427 - Fix workflow_edit

Pull Request - State: closed - Opened by mvdbeek 9 months ago - 1 comment

#1426 - Improve docs with regards to running and testing workflows

Pull Request - State: open - Opened by wm75 9 months ago - 7 comments

#1425 - Update to black 2024 stable style

Pull Request - State: closed - Opened by nsoranzo 9 months ago

#1424 - Fix use of `package_name` attribute on `CondaTarget` objects

Pull Request - State: closed - Opened by nsoranzo 9 months ago - 4 comments

#1423 - Input staging problem: History not found

Issue - State: open - Opened by bernt-matthias 10 months ago

#1422 - Don't crash autoupdate on non-PEP440-compliant tool versions

Pull Request - State: closed - Opened by nsoranzo 10 months ago

#1421 - planemo lint fails with lxml version 5.0.0

Issue - State: closed - Opened by patrick-austin 10 months ago - 3 comments

#1420 - Tool linting add `--skip_file` and remove lxml schema validation

Pull Request - State: closed - Opened by bernt-matthias 11 months ago - 1 comment

#1419 - Add now mandatory readthedocs config files

Pull Request - State: closed - Opened by nsoranzo 11 months ago - 1 comment

#1418 - readthedocs is out of date

Issue - State: closed - Opened by lldelisle 11 months ago

#1417 - Validate with jsonschema

Pull Request - State: open - Opened by mvdbeek 11 months ago - 1 comment

#1416 - Update action versions

Pull Request - State: closed - Opened by nsoranzo 11 months ago - 1 comment

#1415 - planemo training_init creates maintainers not editorial_board

Issue - State: closed - Opened by patrick-austin 11 months ago - 2 comments

#1414 - planemo test_workflow with list:list collections

Issue - State: closed - Opened by lldelisle 11 months ago - 1 comment

#1413 - planemo lint workflow tests improvement

Issue - State: open - Opened by lldelisle 11 months ago

#1412 - Fix workflow download when using instance id

Pull Request - State: closed - Opened by mvdbeek 11 months ago

#1411 - planemo lint multiple

Issue - State: open - Opened by lldelisle 12 months ago

#1410 - Remove introduction header from training init

Pull Request - State: closed - Opened by hexylena 12 months ago

#1409 - Uploading/mirroring of test data

Issue - State: open - Opened by mvdbeek 12 months ago - 1 comment

#1407 - Fix running workflow tests when there are multiple tests

Pull Request - State: closed - Opened by mvdbeek 12 months ago - 3 comments

#1406 - Fix matching of tool ids to autoupdate

Pull Request - State: closed - Opened by nsoranzo 12 months ago

#1404 - planemo autoupdate workflows improvements

Issue - State: open - Opened by lldelisle 12 months ago

#1403 - planemo autoupdate report bug

Issue - State: closed - Opened by lldelisle 12 months ago - 2 comments

#1402 - Fix test result download

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

#1401 - Implement running tests against existing invocation

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

#1400 - Make test reports more resilient to failing invocations

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

#1399 - Fix zenodo test, drop explicit datatype mapping

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

#1398 - Change info message for markdown readme in repo

Pull Request - State: closed - Opened by bernt-matthias about 1 year ago - 5 comments

#1396 - Fix linting rule selection

Pull Request - State: closed - Opened by bernt-matthias about 1 year ago

#1395 - Fix workflow_lint for json output values

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

#1394 - add --skip to shed_lint

Pull Request - State: closed - Opened by bernt-matthias about 1 year ago

#1393 - Remove API key requirement from training_init

Pull Request - State: closed - Opened by hexylena about 1 year ago

#1392 - planemo should catch when Python isn't there

Issue - State: open - Opened by jmchilton about 1 year ago - 1 comment

#1391 - Try to fix planemo test workflow when output is collection with identical name

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

#1390 - planemo serve breaks with new docker version when running tools

Issue - State: open - Opened by pcm32 about 1 year ago - 5 comments

#1389 - Track subworkflow invocations after main invocation is scheduled

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

#1388 - Update upper bound for galaxy packages to < 23.2

Pull Request - State: closed - Opened by bernt-matthias about 1 year ago - 15 comments

#1387 - Support for testing workflows with conditional steps

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

#1386 - Sync planemo and planemo virtual appliance docs

Pull Request - State: open - Opened by bernt-matthias about 1 year ago

#1385 - Add pick_value to distro_tools

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

#1384 - Allow missing conda_exec

Pull Request - State: closed - Opened by mstabrin about 1 year ago - 1 comment

#1383 - Fix profile version test

Pull Request - State: closed - Opened by bernt-matthias about 1 year ago

#1382 - Fix type comparisons

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

#1381 - Run galaxy with default tools included

Pull Request - State: closed - Opened by bernt-matthias over 1 year ago - 5 comments