| a7f0a36 | mvdbeek | 13 June 2023, 15:58:13 UTC | Create version 23.0.2 | 13 June 2023, 15:58:13 UTC |
| a08a74f | mvdbeek | 13 June 2023, 15:27:59 UTC | Merge branch 'release_22.05' into release_23.0 | 13 June 2023, 15:27:59 UTC |
| 6d9b0fd | Marius van den Beek | 13 June 2023, 15:13:18 UTC | Merge pull request #16239 from nuwang/fix_dropbox_import [22.05] Fix dropbox import to support newer versions | 13 June 2023, 15:13:18 UTC |
| 8675451 | Marius van den Beek | 13 June 2023, 15:13:04 UTC | Comment on import fallback Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 13 June 2023, 15:13:04 UTC |
| 2622b9d | Marius van den Beek | 13 June 2023, 14:42:01 UTC | Merge pull request #16240 from mvdbeek/galaxy-release-util-ci [23.0] Use galaxy-release-util to upload python packages | 13 June 2023, 14:42:01 UTC |
| cbc7b91 | Marius van den Beek | 13 June 2023, 13:58:17 UTC | Merge pull request #16237 from bernt-matthias/topic/lint-expect-failure-and-numoutputs [23.0] linter: allow absent output counts in case of expected test failure | 13 June 2023, 13:58:17 UTC |
| 787b804 | mvdbeek | 13 June 2023, 13:39:03 UTC | Use galaxy-release-util to upload python packages | 13 June 2023, 13:49:37 UTC |
| cb412d1 | nuwang | 13 June 2023, 06:57:14 UTC | Fix dropbox import to support newer versions | 13 June 2023, 08:10:14 UTC |
| 54e54bb | Matthias Bernt | 12 June 2023, 21:08:04 UTC | linter: allow absent output counts in case of expected test failure otherwise we contradict that failing tests must nut have outputs fixes: https://github.com/galaxyproject/galaxy/issues/16235 | 12 June 2023, 21:08:04 UTC |
| 84d2ba8 | Martin Cech | 12 June 2023, 16:11:09 UTC | Merge pull request #16230 from mvdbeek/version_py_version_fix [23.0] Fix next version number | 12 June 2023, 16:11:09 UTC |
| 48573d3 | mvdbeek | 10 June 2023, 07:59:01 UTC | Fix next version number | 10 June 2023, 09:22:42 UTC |
| f16be61 | John Chilton | 09 June 2023, 20:06:33 UTC | Merge pull request #16219 from mvdbeek/fix_tool_util_dependency_on_cheetah [23.0] Don't fail CWL tool parsing when Cheetah not installed | 09 June 2023, 20:06:33 UTC |
| ad5b839 | mvdbeek | 09 June 2023, 12:41:32 UTC | Don't fail cwl tool parsing when Cheetah not installed | 09 June 2023, 15:07:01 UTC |
| a5ab850 | Marius van den Beek | 09 June 2023, 12:29:55 UTC | Merge pull request #16215 from mvdbeek/avoid_deprecated_selenium_options [23.0] Port selenium setup to non-deprecated selenium options | 09 June 2023, 12:29:55 UTC |
| b2138ea | Marius van den Beek | 09 June 2023, 07:43:08 UTC | Merge pull request #16216 from mvdbeek/rename_web_apps [23.0] Rename galaxy-webapps back to galaxy-web-apps | 09 June 2023, 07:43:08 UTC |
| 370a90d | mvdbeek | 08 June 2023, 19:14:20 UTC | Fix Safari setup | 08 June 2023, 19:21:51 UTC |
| d210aab | Marius van den Beek | 08 June 2023, 19:08:04 UTC | Make goog:loggingPrefs chrome specific Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com> | 08 June 2023, 19:08:04 UTC |
| 5d51742 | mvdbeek | 08 June 2023, 18:47:58 UTC | Rename galaxy-webapps back to galaxy-web-apps PyPI doesn't let us create projects with names that can be confused. | 08 June 2023, 18:48:03 UTC |
| 5b5f224 | mvdbeek | 08 June 2023, 17:12:30 UTC | Port to non-deprecated selenium options Should be compatible with new and old selenium package. The last release on PyPI removed some deprecated interfaces, which fails our packaging tests. | 08 June 2023, 18:40:50 UTC |
| 9fcfeda | Marius van den Beek | 08 June 2023, 16:34:59 UTC | Merge pull request #16214 from mvdbeek/point_release_deps_fixes_and_docs [23.0] Point release deps fixes and docs | 08 June 2023, 16:34:59 UTC |
| f6bb46a | Marius van den Beek | 08 June 2023, 16:34:45 UTC | Merge pull request #16212 from mvdbeek/text_file_busy_fix [23.0] Fix ``Text File Busy`` errors at the source | 08 June 2023, 16:34:45 UTC |
| 5475121 | mvdbeek | 08 June 2023, 14:54:54 UTC | Add build and twine to dev dependencies | 08 June 2023, 15:34:24 UTC |
| 06c8fc0 | mvdbeek | 08 June 2023, 14:53:27 UTC | Add `--skip-existing` flag to twine upload | 08 June 2023, 14:53:38 UTC |
| 9cb86a9 | mvdbeek | 08 June 2023, 14:53:01 UTC | More documentation for point release process | 08 June 2023, 14:53:01 UTC |
| aa9cc5b | Matthias Bernt | 08 June 2023, 13:54:32 UTC | Start work on 23.1.dev0 | 08 June 2023, 13:54:32 UTC |
| f722e12 | Matthias Bernt | 08 June 2023, 13:54:28 UTC | Create version 23.0.1 | 08 June 2023, 13:54:28 UTC |
| 1ee21e3 | Marius van den Beek | 08 June 2023, 12:05:43 UTC | Merge pull request #16205 from guerler/verify_default_value [23.0] Verify existence of default value attribute for user forms fields | 08 June 2023, 12:05:43 UTC |
| 409aef5 | mvdbeek | 08 June 2023, 09:47:48 UTC | Fix ``Text File Busy`` errors at the source Comment in line explains the source of the errors. I've created https://gist.github.com/mvdbeek/682f3495e31275b5f8ed121fabd7103f to verify that we can reproduce the issue and that the additional locking fixes it. I think it's reasonable to block on aquiring the second lock, however https://stackoverflow.com/a/5255473 is an option we could implement. | 08 June 2023, 10:35:20 UTC |
| 95f85c4 | Aysam Guerler | 08 June 2023, 09:26:45 UTC | Update lib/galaxy/model/__init__.py Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 08 June 2023, 09:26:45 UTC |
| a6597f7 | Aysam Guerler | 08 June 2023, 09:26:37 UTC | Update lib/galaxy/model/__init__.py Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 08 June 2023, 09:26:37 UTC |
| 7c1e01b | guerler | 07 June 2023, 17:34:42 UTC | Verify existence of default value attribute for user forms fields | 07 June 2023, 18:07:35 UTC |
| b995180 | John Chilton | 07 June 2023, 17:16:49 UTC | Merge pull request #16201 from mvdbeek/pin_minimum_tpv [23.0] Pin minimum tpv version | 07 June 2023, 17:16:49 UTC |
| 2339e8e | mvdbeek | 07 June 2023, 08:53:14 UTC | Pin minimum tpv version Fixes https://sentry.galaxyproject.org/organizations/galaxy/issues/116691/?project=3&query=is%3Aunresolved&referrer=issue-stream&statsPeriod=14d | 07 June 2023, 13:36:09 UTC |
| 5c24606 | Marius van den Beek | 06 June 2023, 13:53:54 UTC | Merge pull request #16195 from mvdbeek/quit_if_branches_not_updated [23.0] Assert that local branches are up to date in release point script | 06 June 2023, 13:53:54 UTC |
| 133b0a5 | Marius van den Beek | 06 June 2023, 13:41:59 UTC | Merge pull request #16193 from mvdbeek/support_ro_crate_0_8_0_and_0_7_0 [23.0] Support ro crate 0.8.0 and 0.7.0 | 06 June 2023, 13:41:59 UTC |
| 2a5b442 | Marius van den Beek | 06 June 2023, 13:39:10 UTC | Merge pull request #16190 from mvdbeek/docutils_fallback [23.0] Make point release script compatible with docutils 0.16 | 06 June 2023, 13:39:10 UTC |
| 7056942 | mvdbeek | 06 June 2023, 11:20:37 UTC | Fail if local branch doesn't match remote branch | 06 June 2023, 13:04:43 UTC |
| 7cb93b3 | mvdbeek | 06 June 2023, 09:53:42 UTC | Support ro-crate >=0.8.0 and 0.7.0 I guess there's a chance downstream users may run into version conflicts if we pin ro-cate to 0.7.0, and we also don't really want to bump stable version dependencies. | 06 June 2023, 09:55:52 UTC |
| e2e7cbc | mvdbeek | 05 June 2023, 14:02:17 UTC | Make point release script compatible with docutils 0.16 | 05 June 2023, 14:02:17 UTC |
| 0f670d7 | Marius van den Beek | 04 June 2023, 15:45:46 UTC | Merge pull request #16175 from mvdbeek/startup_fix_when_tool_removed_between_reboot [23.0] Startup fix when tool removed between reboot | 04 June 2023, 15:45:46 UTC |
| e14c2d1 | Marius van den Beek | 04 June 2023, 09:32:21 UTC | Merge pull request #16183 from guerler/tool_warnings_type_error [23.0] Tool warnings can either be None or a Dictionary but not a String | 04 June 2023, 09:32:21 UTC |
| 13d644f | Björn Grüning | 04 June 2023, 07:28:59 UTC | Merge pull request #16141 from jmchilton/fix_optional_fields [23.0] Fix optional fields being validated as missing in ts api | 04 June 2023, 07:28:59 UTC |
| cb1f4eb | guerler | 03 June 2023, 14:45:10 UTC | Tool warnings can be either None or a dictionary but not a string | 03 June 2023, 14:45:10 UTC |
| 2088717 | mvdbeek | 05 April 2023, 14:36:57 UTC | Fix job handler startup when tool not available | 02 June 2023, 12:32:37 UTC |
| 498bf14 | mvdbeek | 05 April 2023, 10:40:08 UTC | Don't fail startup if monitored tool not installed anymore Fixes ``` galaxy.jobs.handler WARNING 2023-04-05 12:33:46,660 [pN:main,p:6422,tN:MainThread] (42544) Tool 'toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2' removed from tool config, unable to recover job galaxy.jobs DEBUG 2023-04-05 12:33:46,666 [pN:main,p:6422,tN:MainThread] (42544) fail(): Job destination raised JobMappingException('Can't map job to destination, tool 'toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2' is unavailable'), caching fake '__fail__' destination for completion of fail method Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 59, in app_pair app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "/Users/mvandenb/src/galaxy/lib/galaxy/app.py", line 714, in __init__ self.application_stack.register_postfork_function(self.job_manager.start) File "/Users/mvandenb/src/galaxy/lib/galaxy/web_stack/__init__.py", line 46, in register_postfork_function f(*args, **kwargs) File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/manager.py", line 41, in start self.job_handler.start() File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/handler.py", line 93, in start self.job_queue.start() File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/handler.py", line 248, in start self.__check_jobs_at_startup() File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/handler.py", line 295, in __check_jobs_at_startup self.job_wrapper(job).fail( File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1416, in fail for dataset_path in self.job_io.get_output_fnames(): File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1069, in job_io tool_directory=self.tool_directory(), File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1050, in tool_directory tool_dir = self.tool.tool_dir AttributeError: 'NoneType' object has no attribute 'tool_dir' ``` | 02 June 2023, 11:17:21 UTC |
| 8b14c96 | Marius van den Beek | 01 June 2023, 16:47:37 UTC | Merge pull request #16168 from dannon/fix-toolbox-flattening [23.0] Tool filtering fix for label handling | 01 June 2023, 16:47:37 UTC |
| 54cfd48 | Marius van den Beek | 01 June 2023, 13:14:25 UTC | Merge pull request #16170 from mvdbeek/fix_hashed_test_search [23.0] Fix test search for mulled container hashes | 01 June 2023, 13:14:25 UTC |
| 59dbb25 | John Chilton | 01 June 2023, 12:52:13 UTC | Merge pull request #16165 from dannon/failed-meta-bugreport [23.0] Show bug error for failed_meta state | 01 June 2023, 12:52:13 UTC |
| 5c7b458 | John Chilton | 01 June 2023, 12:37:35 UTC | Merge pull request #16160 from jmchilton/release_script [23.0] Converge release process auth discovery. | 01 June 2023, 12:37:35 UTC |
| eff2f6e | Dannon Baker | 01 June 2023, 11:11:22 UTC | Backport ignore dist for jest discovery | 01 June 2023, 11:11:22 UTC |
| 4e4bdaa | Dannon Baker | 01 June 2023, 11:10:12 UTC | Tweak toolbox test data to cover testing w/ empty labels. | 01 June 2023, 11:10:12 UTC |
| cc43c50 | mvdbeek | 01 June 2023, 10:51:18 UTC | Fix test search for mulled container hashes Fixes ``` FAILED test/unit/tool_util/mulled/test_get_tests.py::test_hashed_test_search - AssertionError: assert ['bamtools --help'] == ['bamtools --help', 'samtools --help'] Right contains one more item: 'samtools --help' Full diff: - ['bamtools --help', 'samtools --help'] + ['bamtools --help'] ``` (again). The test broke with the addition of `osx-64/samtools-1.3.1-h0840685_11.tar.bz2` 4 days ago. | 01 June 2023, 10:51:21 UTC |
| a9c7220 | Dannon Baker | 01 June 2023, 03:16:08 UTC | Better testing of whether or not a thing is a tool for toolbox normalization/flattening | 01 June 2023, 03:16:08 UTC |
| 8a2327d | Dannon Baker | 30 May 2023, 19:51:15 UTC | Show bug error for failed_meta state | 31 May 2023, 18:11:01 UTC |
| 2103eb0 | John Chilton | 30 May 2023, 15:25:32 UTC | Converge release process auth discovery. | 30 May 2023, 17:11:27 UTC |
| 8ec95d3 | John Chilton | 30 May 2023, 15:24:49 UTC | Merge pull request #16076 from mvdbeek/release_script Add script for creating (point) releases | 30 May 2023, 15:24:49 UTC |
| d5508f5 | Marius van den Beek | 30 May 2023, 07:34:33 UTC | Merge pull request #16139 from dannon/ctx_rev_optional [23.0] Make ``ctx_rev`` optional in InstalledToolShedRepository response model | 30 May 2023, 07:34:33 UTC |
| 6de151f | Dannon Baker | 23 May 2023, 13:08:40 UTC | In practice this is not always defined and should be treated as optional, I think | 29 May 2023, 20:28:29 UTC |
| 66ca4d5 | mvdbeek | 28 May 2023, 06:23:01 UTC | Run only on galaxyproject.org owner | 28 May 2023, 09:16:00 UTC |
| a4f43ca | mvdbeek | 28 May 2023, 06:00:27 UTC | Drop package_repository argument, just use TWINE_REPOSITORY_URL | 28 May 2023, 09:15:59 UTC |
| 827d9b6 | mvdbeek | 27 May 2023, 23:06:50 UTC | Fix prerelease event | 28 May 2023, 09:15:59 UTC |
| c4548d0 | mvdbeek | 27 May 2023, 22:38:43 UTC | --no-build-packages | 28 May 2023, 09:15:59 UTC |
| 521d144 | mvdbeek | 27 May 2023, 22:09:56 UTC | Fix twine upload command | 28 May 2023, 09:15:59 UTC |
| d79f819 | mvdbeek | 27 May 2023, 19:48:11 UTC | Add publishing workflow | 28 May 2023, 09:15:59 UTC |
| ebf5b73 | mvdbeek | 27 May 2023, 15:30:16 UTC | Set default galaxy-root option to CWD | 28 May 2023, 09:15:59 UTC |
| cc7e902 | mvdbeek | 26 May 2023, 17:15:21 UTC | Fix no_confirm logic | 28 May 2023, 09:15:59 UTC |
| f1d0be7 | mvdbeek | 26 May 2023, 15:45:45 UTC | Fail on build errors | 28 May 2023, 09:15:59 UTC |
| 4464ef9 | mvdbeek | 26 May 2023, 15:40:34 UTC | Implement pushing to upstream git url | 28 May 2023, 09:15:58 UTC |
| 20a28bf | mvdbeek | 26 May 2023, 14:46:11 UTC | Split functionality into subcommands | 28 May 2023, 09:15:58 UTC |
| 93dae39 | mvdbeek | 25 May 2023, 10:50:45 UTC | Ensure that merges will not conflict | 28 May 2023, 09:15:58 UTC |
| d8e62f8 | mvdbeek | 11 May 2023, 19:06:32 UTC | Add script for creating (point) releases Still working on it, but it's minimally useful already. | 28 May 2023, 09:15:57 UTC |
| 7fea2db | Nicola Soranzo | 25 May 2023, 11:25:30 UTC | Merge branch 'release_22.05' into release_23.0 | 25 May 2023, 12:53:52 UTC |
| 766f093 | Nicola Soranzo | 25 May 2023, 10:58:59 UTC | Merge pull request #16125 from nsoranzo/release_22.05_fix_get_file_from_conda_package [22.05] Fix ``get_test_from_anaconda()`` and ``base_image_for_targets()`` functions | 25 May 2023, 10:58:59 UTC |
| ffb5291 | Nicola Soranzo | 24 May 2023, 19:38:42 UTC | Fix parsing of mulled tsv files containing comments and tabs | 25 May 2023, 07:32:22 UTC |
| cc35a28 | Nicola Soranzo | 23 May 2023, 17:39:11 UTC | Add test for conda ``best_search_result()`` | 25 May 2023, 07:32:21 UTC |
| a0d6e87 | Nicola Soranzo | 23 May 2023, 14:30:49 UTC | Fix testing importing modules in containers | 25 May 2023, 07:32:21 UTC |
| 1fedac7 | Nicola Soranzo | 23 May 2023, 11:15:15 UTC | Fix ``mulled-update-singularity-containers`` documentation The `mulled-singularity-testing` command was never added to the `galaxy-tool-util` package. | 25 May 2023, 07:32:20 UTC |
| 95c6e4b | Nicola Soranzo | 21 May 2023, 21:06:47 UTC | Fix ``get_test_from_anaconda()`` and ``base_image_for_targets()`` functions by extracting all specified files in ``get_files_from_conda_package()`` and processing them in order of precedence. Fix broken mulled unit test: ``` FAILED test/unit/tool_util/mulled/test_get_tests.py::test_hashed_test_search - AssertionError: assert ['bamtools --help'] == ['bamtools --help', 'samtools --help'] Right contains one more item: 'samtools --help' Full diff: - ['bamtools --help', 'samtools --help'] + ['bamtools --help'] ``` which failed because, after a new build of samtools 1.3.1 was released, ``get_file_from_conda_package()`` started returning the content of ``info/recipe/meta.yaml.template`` instead of ``info/recipe/meta.yaml`` when called inside ``get_test_from_anaconda()``. Then parsing the content of ``info/recipe/meta.yaml.template`` in ``get_commands_from_yaml()`` failed with ``` jinja2.exceptions.UndefinedError: 'compiler' is undefined ``` because that file contains ``{{ compiler('c') }}`` . Broken in https://github.com/galaxyproject/galaxy/pull/15682 . | 25 May 2023, 07:32:20 UTC |
| 5889ae0 | Nicola Soranzo | 27 September 2022, 08:40:17 UTC | Run ToolShed tests on ubuntu-latest | 25 May 2023, 07:28:58 UTC |
| 0901ad7 | Marius van den Beek | 24 May 2023, 12:44:48 UTC | Merge pull request #16133 from mvdbeek/implicit_converter_fix [23.0] Fix implicit converters with optional parameters | 24 May 2023, 12:44:48 UTC |
| dca783b | mvdbeek | 24 May 2023, 08:47:49 UTC | Add test tool for triggering implicit bigwig to wig converter | 24 May 2023, 08:54:31 UTC |
| b346c82 | mvdbeek | 22 May 2023, 15:32:06 UTC | Inject None in optional parameters when buidling implicit converter params Fixes: ``` KeyError: 'chrom' File "galaxy/tools/__init__.py", line 1909, in handle_single_execution rval = self.execute( File "galaxy/tools/__init__.py", line 2005, in execute return self.tool_action.execute( File "galaxy/tools/actions/__init__.py", line 392, in execute ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info) File "galaxy/tools/actions/__init__.py", line 327, in _collect_inputs inp_data, all_permissions = self._collect_input_datasets( File "galaxy/tools/actions/__init__.py", line 268, in _collect_input_datasets tool.visit_inputs(param_values, visitor) File "galaxy/tools/__init__.py", line 1748, in visit_inputs visit_input_values(self.inputs, values, callback) File "galaxy/tools/parameters/__init__.py", line 224, in visit_input_values callback_helper( File "galaxy/tools/parameters/__init__.py", line 159, in callback_helper new_value = callback(**args) File "galaxy/tools/actions/__init__.py", line 191, in visitor input_datasets[prefix + input.name] = process_dataset(value) File "galaxy/tools/actions/__init__.py", line 126, in process_dataset data = data.get_converted_dataset(trans, target_ext, target_context=parent, history=history) File "galaxy/model/__init__.py", line 4211, in get_converted_dataset self.datatype.convert_dataset( File "galaxy/datatypes/data.py", line 795, in convert_dataset job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history) File "galaxy/tools/__init__.py", line 2005, in execute return self.tool_action.execute( File "galaxy/tools/actions/__init__.py", line 453, in execute params=wrapped_params.params, File "galaxy/tools/parameters/wrapped.py", line 43, in params self.wrap_values(self.tool.inputs, params, skip_missing_values=not self.tool.check_values) File "galaxy/tools/parameters/wrapped.py", line 58, in wrap_values value = input_values[input.name] ``` in https://sentry.galaxyproject.org/share/issue/4f2171798f214f7ba8b947eaaebe2776/ | 24 May 2023, 08:54:31 UTC |
| c910931 | John Chilton | 23 May 2023, 15:22:35 UTC | Fix optional fields being validated as missing. Fixes https://github.com/galaxyproject/galaxy/issues/16135 | 23 May 2023, 20:30:30 UTC |
| 8b926e6 | Martin Cech | 23 May 2023, 15:12:22 UTC | Merge pull request #16128 from mvdbeek/fix_bulk_endpoint_with_related_filter [23.0] Fix related-hid in bulk contents API | 23 May 2023, 15:12:22 UTC |
| 1d59dcb | Nicola Soranzo | 03 November 2022, 23:51:33 UTC | Fix the ``singularity_container_test()`` function Fix ``test_singularity_container_test`` unit test, which failed with: ``` test/unit/tool_util/mulled/test_mulled_update_singularity_containers.py:48: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ lib/galaxy/tool_util/deps/mulled/mulled_update_singularity_containers.py:62: in singularity_container_test check_output(exec_command.extend(["bash", "-c", test_command]), stderr=subprocess.STDOUT) /usr/lib/python3.8/subprocess.py:415: in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, /usr/lib/python3.8/subprocess.py:493: in run with Popen(*popenargs, **kwargs) as process: /usr/lib/python3.8/subprocess.py:858: in __init__ self._execute_child(args, executable, preexec_fn, close_fds, > args = list(args) E TypeError: 'NoneType' object is not iterable /usr/lib/python3.8/subprocess.py:1569: TypeError ``` Broken in commit 1dc1e5f219e7824bfb3167678423f7dd191ba823 . Also: - Use `tmp_path` pytest fixture. - Add type annotations. - Code refactorings. - Install singularity in the mulled GitHub workflow so that the 2 singularity unit tests are not skipped any more. | 23 May 2023, 11:17:23 UTC |
| 6c4141b | Marius van den Beek | 23 May 2023, 07:32:15 UTC | Merge pull request #15981 from guerler/fix_rerun [23.0] Fix backbone-based data selector to materialize consistent attribute set | 23 May 2023, 07:32:15 UTC |
| 995d2d3 | John Davis | 23 May 2023, 01:23:32 UTC | Merge pull request #16137 from jdavcs/release_23.0_fix_job_rank [23.0] Release 23.0 fix job rank | 23 May 2023, 01:23:32 UTC |
| 248d03f | John Davis | 22 May 2023, 20:41:59 UTC | Fix rank calculation for jobs run by anonymous users | 22 May 2023, 21:08:55 UTC |
| 001f140 | guerler | 22 May 2023, 17:13:07 UTC | Augment test case | 22 May 2023, 18:45:35 UTC |
| e96689f | guerler | 22 May 2023, 16:26:28 UTC | Fix naming of input match helper to avoid confusion | 22 May 2023, 16:26:28 UTC |
| 5ee0180 | guerler | 22 May 2023, 16:14:46 UTC | Reset previous errors when new set of errors is provided | 22 May 2023, 16:17:25 UTC |
| a9636fb | John Chilton | 22 May 2023, 14:24:32 UTC | Merge pull request #16126 from mvdbeek/rerun_dce_fix [23.0] Fix sort error when re-running job with DCE collection input | 22 May 2023, 14:24:32 UTC |
| 900dec0 | John Chilton | 22 May 2023, 14:23:41 UTC | Merge pull request #16116 from mvdbeek/backport_collection_edit_selenium_fix [23.0] Backport Improve robustness and abstractions used by collection edit tests. | 22 May 2023, 14:23:41 UTC |
| 591ace5 | Nicola Soranzo | 14 October 2022, 10:00:32 UTC | Fix ``test_get_alternative_versions`` unit test Fix the following error: ``` > assert versions == ["recipes/bamtools/2.3.0/meta.yaml"] E AssertionError: assert [] == ['recipes/bam....0/meta.yaml'] E Right contains one more item: 'recipes/bamtools/2.3.0/meta.yaml' E Full diff: E - ['recipes/bamtools/2.3.0/meta.yaml'] E + [] test/unit/tool_util/mulled/test_get_tests.py:80: AssertionError ``` due to the removal of the `recipes/bamtools/2.3.0/meta.yaml` file in https://github.com/bioconda/bioconda-recipes/commit/b94d1bd9a146dcf0ddcf4224ffd265f17ff0a489#diff-d7df16f707f82264802dbbed7b281cb9a3d9053c21cd9bd79f3c8e56612bdc81 | 22 May 2023, 11:05:59 UTC |
| b4095a0 | guerler | 22 May 2023, 08:49:30 UTC | Prioritize errors over warnings | 22 May 2023, 08:49:30 UTC |
| 8ed600a | guerler | 22 May 2023, 08:08:19 UTC | Fix linting | 22 May 2023, 08:08:19 UTC |
| ea3de3b | guerler | 22 May 2023, 07:58:19 UTC | Build out warning alerts, add tests | 22 May 2023, 07:58:19 UTC |
| c7d48a2 | mvdbeek | 22 May 2023, 07:45:14 UTC | Fix related-hid in bulk contents API Fixes https://github.com/galaxyproject/galaxy/issues/16127 | 22 May 2023, 07:45:23 UTC |
| cac52b6 | mvdbeek | 22 May 2023, 07:27:50 UTC | Fix sort error when re-running job with DCE collection input Otherwise fails with ``` TypeError: '<' not supported between instances of 'NoneType' and 'int' File "galaxy/tools/__init__.py", line 2542, in populate_model tool_dict = input.to_dict(request_context, other_values=other_values) File "galaxy/tools/parameters/basic.py", line 2536, in to_dict d["options"]["hdca"] = sorted(d["options"]["hdca"], key=lambda k: k.get("hid", -1), reverse=True) ``` From https://sentry.galaxyproject.org/share/issue/1b0bcc83846b4b1891824776b0099545/ | 22 May 2023, 07:28:54 UTC |
| 024d94f | Björn Grüning | 20 May 2023, 13:59:12 UTC | Merge pull request #16120 from mvdbeek/dce_resume [23.0] Extract HDA for code_file validate_input hook | 20 May 2023, 13:59:12 UTC |
