https://github.com/galaxyproject/galaxy

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438012b Bump galaxy-util version to 22.1.2 08 December 2022, 11:28:19 UTC
c818c1e Update changelog 08 December 2022, 11:27:36 UTC
e7b8e92 Merge pull request #15148 from mvdbeek/pin_packaging [22.01] Pin packaging to below 22 08 December 2022, 11:18:29 UTC
173177e Add missing pyparsing dependency to galaxy-util 08 December 2022, 11:01:55 UTC
b3eedc1 Update minikube-setup-action and use more recent k8s version The older minikube/k8s fail to launch under Ubuntu 22.04, which is being deployed on GitHub action workers: 08 December 2022, 11:01:55 UTC
dc7c8e7 Pin packaging to below 22 08 December 2022, 11:01:55 UTC
81ddf41 Merge pull request #15144 from martenson/tox4-allow [22.01] Rename removed tox configuration option 08 December 2022, 01:27:29 UTC
d251aa2 [22.01] Rename removed tox configuration option breaks our tox setup with 4.0.0 07 December 2022, 21:52:11 UTC
e5e6bda Contain directory traversal for static files to host static root. 05 December 2022, 19:35:56 UTC
7136d72 Merge pull request #15006 from nsoranzo/release_22.01_fix_LC_CTYPE_macOS [22.01] Fix setting ``LC_CTYPE`` variable in clean environment on macOS 17 November 2022, 17:18:52 UTC
c80577e Fix setting ``LC_CTYPE`` variable in clean environment on macOS Fix some older tools (not using `profile` or `stdio`) failing because of the following warning printed on stderr when run locally on macOS: ``` perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LC_ALL = (unset), LC_CTYPE = "C.UTF-8", LANG = (unset) are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). ``` 17 November 2022, 10:50:07 UTC
df77129 Start work on galaxy-tool-util 22.1.6 14 November 2022, 09:28:55 UTC
642c28a Release galaxy-tool-util-22.1.5 14 November 2022, 09:22:28 UTC
a8ab71f Merge pull request #14970 from mvdbeek/alt_fix_expected_failure_occurred [22.01] Set test status to success on expected failure 11 November 2022, 08:07:11 UTC
9570da5 Avoid negations 10 November 2022, 15:25:26 UTC
0687217 Set test status to success on expected failure Alternative to https://github.com/galaxyproject/galaxy/pull/14958 10 November 2022, 15:20:17 UTC
d75c0fd Merge pull request #14933 from mvdbeek/switch_back_to__run_workflow [22.01] Revert "Use _run_jobs instead of _run_workflows" 05 November 2022, 23:56:23 UTC
494bae8 Revert "Use _run_jobs instead of _run_workflows" This reverts commit a01c8c5a88debc7f9e0c7e2865a33acb9633acab. _run_workflow has the right type annotations, but 21.09 didn't have this. 05 November 2022, 17:14:18 UTC
6623f44 Merge branch 'release_21.09' into release_22.01 05 November 2022, 16:19:44 UTC
ce40058 Merge pull request #14908 from mvdbeek/backport_data_column_fix [21.09] Backport 14518: Always call strip() on data_column column values 05 November 2022, 16:17:37 UTC
a01c8c5 Use _run_jobs instead of _run_workflows 03 November 2022, 09:37:49 UTC
e6aeb21 Always call strip() on data_column column values Not just when they start with `c`. Should fix running workflows that were created by manually writing columns in the text area field and then hitting enter. 02 November 2022, 16:51:20 UTC
656751f Merge branch 'release_21.09' into release_22.01 02 November 2022, 15:43:16 UTC
e3d0561 Merge branch 'release_21.05' into release_21.09 02 November 2022, 15:40:57 UTC
d51d911 Merge branch 'release_21.01' into release_21.05 02 November 2022, 15:39:27 UTC
c8a514a Merge branch 'release_20.09' into release_21.01 02 November 2022, 15:37:59 UTC
9d31330 Merge branch 'release_20.05' into release_20.09 02 November 2022, 15:32:02 UTC
6df30d6 Merge branch 'release_20.01' into release_20.05 02 November 2022, 14:57:01 UTC
ae59839 Merge branch 'release_19.09' into release_20.01 02 November 2022, 14:55:38 UTC
f0a269c Merge branch 'release_19.05' into release_19.09 02 November 2022, 14:53:53 UTC
d48c4a4 Merge pull request #14900 from nsoranzo/release_19.05_backport_14882 [19.05] Backport fixes from #14882 02 November 2022, 14:48:21 UTC
82a779e Force recomputation of conda properties after conda `install` conda version and conda-build availability may change after an `install` in the root environment. 01 November 2022, 12:03:54 UTC
3cbf332 Retry conda `install` and `create` commands without strict channel priority Restore the possibility to solve environments with packages present in multiple channels but whose requested version is not available in the highest priority one. The issue applies only when using conda >=4.7.5. Fix the following error for the `test/integration/test_resolvers.py::TestCondaResolutionIntegration::test_dependency_install` integration test: ``` ____________ TestCondaResolutionIntegration.test_dependency_install ____________ self = <integration.test_resolvers.TestCondaResolutionIntegration object at 0x7f7009682950> def test_dependency_install(self): """ Test installation of GNUPLOT dependency. """ data = GNUPLOT create_response = self._post("dependency_resolvers/dependency", data=data, admin=True) self._assert_status_code_is(create_response, 200) response = create_response.json() > self._assert_dependency_type(response) test/integration/test_resolvers.py:46: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <integration.test_resolvers.TestCondaResolutionIntegration object at 0x7f7009682950> response = {'cacheable': False, 'dependency_resolver': {'auto_init': True, 'auto_install': False, 'can_uninstall_dependencies': T...nda,defaults', ...}, 'dependency_type': 'conda', 'environment_path': '/tmp/tmp5f_37kj2/conda/envs/__gnuplot@_uv_', ...} type = 'conda', exact = True def _assert_dependency_type(self, response, type="conda", exact=True): if "dependency_type" not in response: raise Exception(f"Response [{response}] did not contain key 'dependency_type'") dependency_type = response["dependency_type"] assert dependency_type == type, f"Dependency type [{dependency_type}] not the expected value [{type}]" if "exact" not in response: raise Exception(f"Response [{response}] did not contain key 'exact'") > assert response["exact"] is exact E assert False is True test/integration/test_resolvers.py:150: AssertionError ``` due to the fact that this test tries to install version 4.6 of gnuplot, while in the highest priority conda-forge channel the oldest version available is 5.0.5. When trying to create the environment, conda fails to resolve it, so Galaxy falls back to create an environment with an unversioned gnuplot, which fails the exact version test. Introduced in commit bb000b2403e51b2ecf2a4dfe9d2ac560b333a437 . 01 November 2022, 11:57:29 UTC
c262156 Fix mistakenly overwriting ``self._conda_version`` with conda-build version. Introduced in commit 0ed66646e1234a93193edbd4b5577c535ed32f99 . 01 November 2022, 11:57:07 UTC
238ab85 Start work on galaxy-tool-util 22.1.5 28 October 2022, 08:31:56 UTC
52f60b5 Release tool-util package 22.1.4 28 October 2022, 08:30:23 UTC
ed6b054 Merge pull request #14877 from nsoranzo/release_22.01_fix_tool-util_package [22.01] Add missing ``unittest_utils`` package to galaxy-tool-util 28 October 2022, 08:21:24 UTC
895a18c Add missing ``unittest_utils`` package to galaxy-tool-util Fix: ``` ModuleNotFoundError: No module named 'galaxy.tool_util.unittest_utils' ``` in https://github.com/conda-forge/galaxy-tool-util-feedstock/pull/4 . 27 October 2022, 23:23:21 UTC
7ff1026 Start work on galaxy-tool-util 22.1.4 27 October 2022, 16:30:21 UTC
9bf0b4e Release tool-util package 22.1.3 27 October 2022, 16:29:48 UTC
e18ce25 Merge branch 'release_21.09' into release_22.01 26 October 2022, 18:17:27 UTC
3bc34bf Merge branch 'release_21.05' into release_21.09 26 October 2022, 17:43:18 UTC
85ad2a0 Merge branch 'release_21.01' into release_21.05 26 October 2022, 15:57:32 UTC
cc0d811 Merge branch 'release_20.09' into release_21.01 26 October 2022, 15:55:05 UTC
14f3fc2 Merge branch 'release_20.05' into release_20.09 26 October 2022, 13:18:20 UTC
a99bea6 Merge branch 'release_20.01' into release_20.05 26 October 2022, 10:44:37 UTC
68ba6fd Merge branch 'release_19.09' into release_20.01 26 October 2022, 10:30:22 UTC
563b9e7 Merge branch 'release_19.05' into release_19.09 26 October 2022, 09:07:50 UTC
e8eb248 Merge pull request #14856 from nsoranzo/release_19.05_fix_14848 [19.05] Require also a recent pyOpenSSL package when installing conda 26 October 2022, 09:03:07 UTC
bb000b2 Add `--strict-channel-priority` to conda create/install commands Fix https://github.com/galaxyproject/galaxy/issues/12790 . This is added only if using conda >=4.7.5 , which includes this bug fix: https://github.com/conda/conda/pull/8819 25 October 2022, 18:29:14 UTC
32e3287 Require also a recent pyOpenSSL package when installing conda Fix https://github.com/galaxyproject/galaxy/issues/14848 . 25 October 2022, 18:26:59 UTC
0ed6664 Rewrite `CondaContext._guess_conda_properties()` to use `conda info` 25 October 2022, 18:18:11 UTC
330eb07 Merge branch 'release_21.09' into release_22.01 17 October 2022, 12:49:11 UTC
cf036f1 Merge pull request #14530 from bernt-matthias/correct-fail [21.09] JobWrapper: use correct fail method 17 October 2022, 10:13:56 UTC
577a7d1 Merge pull request #14773 from nsoranzo/release_22.01_fix_provenance_follow [22.01] Fix dataset provenance API when ``follow=False`` 11 October 2022, 12:01:10 UTC
bb3006d Fix dataset provenance API when ``follow=False`` 10 October 2022, 23:45:37 UTC
cd4ae46 JobWrapper: use correct fail method if the JobWrapper.fail method is called directly exit code (etc) are lost. fixes https://github.com/galaxyproject/galaxy/issues/14206 not sure why this error popped up now, probably a change in tool verification ..? 16 September 2022, 11:05:23 UTC
7b870dc Merge pull request #14607 from nsoranzo/release_22.01_pin_CacheControl [22.01] Pin CacheControl to prevent missing dependency 13 September 2022, 11:07:02 UTC
77553d1 Pin CacheControl to prevent missing dependency schema-salad currently requires: - "CacheControl >= 0.11.7, < 0.13" - "lockfile >= 0.9", which is needed for CacheControl's FileCache until 0.12.11 but CacheControl 0.12.12 replaced lockfile with filelock. Prevent the following traceback: ``` self = <cachecontrol.caches.file_cache.FileCache object at 0x7fe36ac5d190> directory = PosixPath('/tmp/.cache/salad'), forever = False, filemode = 384 dirmode = 448, lock_class = None def __init__( self, directory, forever=False, filemode=0o0600, dirmode=0o0700, lock_class=None, ): try: if lock_class is None: > from filelock import FileLock E ModuleNotFoundError: No module named 'filelock' /tmp/gxpkgtestenvcy0lxY/lib/python3.7/site-packages/cachecontrol/caches/file_cache.py:74: ModuleNotFoundError ``` 12 September 2022, 20:57:43 UTC
eb33760 Merge pull request #14590 from mvdbeek/fix_systemd_sample_unit [22.01] Include /bin in sample systemd unit path 09 September 2022, 12:17:59 UTC
b05462a Add sbin to PATH Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 09 September 2022, 11:06:35 UTC
0256b34 Include /bin in sample systemd unit path 09 September 2022, 10:52:05 UTC
9f1d8d0 Merge branch 'release_21.09' into release_22.01 06 September 2022, 10:36:36 UTC
06baa27 Merge branch 'release_21.05' into release_21.09 06 September 2022, 10:24:20 UTC
8069584 Merge branch 'release_21.01' into release_21.05 06 September 2022, 10:12:59 UTC
50bdd35 Merge pull request #14513 from bernt-matthias/topic/bed-metadata [21.01] fix metadata setting for bed and interval 05 September 2022, 17:18:56 UTC
f3eb503 Merge pull request #14497 from mvdbeek/fix_finding_repository_directory [21.05] Fix finding repository directory if repository is repeated in path 31 August 2022, 12:11:58 UTC
afebb89 Merge pull request #14528 from mvdbeek/tool_util_packaging_fixes [22.01] Fix tool-util packaging 30 August 2022, 18:22:30 UTC
609c90f Update packages/tool_util/HISTORY.rst 30 August 2022, 15:25:10 UTC
6519604 Add some type annotations 30 August 2022, 13:34:54 UTC
2f15059 Skip the quay.io lookup if we have a valid cache entry Good thing we had tests that made sure the cache was getting used ... 29 August 2022, 14:54:23 UTC
60cda23 Mock quay.io API calls, pass `install=False` to not pull docker images 29 August 2022, 14:38:31 UTC
c4f576c Fix cache lookup condition 29 August 2022, 14:38:31 UTC
c4a9050 Fix _namespace_has_repo if cache namespace cache key not present 29 August 2022, 12:08:49 UTC
c07fd27 Touch up tool util packaging fixes 29 August 2022, 11:12:01 UTC
9b66e46 always use default=0 for strandCol just for consistency 26 August 2022, 15:04:01 UTC
fe30308 bed, interval: set default for strandCol bed and interval datatypes `check element_is_set` before overwriting metadata. since the having `default=None` and `no_value=0` makes `element_is_set` return True (since `None!=0`). Therefore metadata values are never set 26 August 2022, 13:53:40 UTC
4e23fbb Revert "set metadata default to no_value if default is None" This reverts commit dff9d4087bdcd500912eb4a7e5512b9b26ab9879. 26 August 2022, 10:01:54 UTC
dff9d40 set metadata default to no_value if default is None 25 August 2022, 15:30:13 UTC
59f7704 test case showing failing set_meta broke in https://github.com/galaxyproject/galaxy/commit/7d0ec29fa06ae6f04c0ae6fc193a390bc11cddcd 25 August 2022, 14:45:26 UTC
7a9e83c Merge pull request #14496 from bernt-matthias/topic/lint_level [22.01] fix lint context fail function 23 August 2022, 17:06:47 UTC
05cad6d Fix finding repository directory if repository directory is repeated in path As happens for instance for toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/0e3cf9594bb7/ncbi_blast_plus/tools/ncbi_blast_plus 23 August 2022, 13:49:48 UTC
0b3f8af fix lint context fail function error introduced here https://github.com/galaxyproject/galaxy/pull/13186 found this while working on https://github.com/galaxyproject/planemo/pull/1264 23 August 2022, 13:46:16 UTC
0a69d3d Update version to 22.1.2.dev0 22 August 2022, 19:57:17 UTC
dc56fc4 Update version to 22.01.1 22 August 2022, 19:47:47 UTC
30dc1bf Merge pull request #14440 from qiagu/dynamic_options [22.01] Revert startswith of tool parameter options 18 August 2022, 17:21:23 UTC
5f0fbb0 fix docs 18 August 2022, 12:30:14 UTC
8ef9ef4 fix test 18 August 2022, 12:28:55 UTC
ea85cab Revert startswith of tool parameter options 18 August 2022, 09:04:12 UTC
6db3224 Merge pull request #14466 from nsoranzo/release_22.01_fix_docs [22.01] Fix doc versioning banner and other doc fixes 16 August 2022, 20:26:41 UTC
11c0c7b Fix doc versioning banner Currently doc builds for `release_22.01` and `master` branches incorrectly show the "This document is for an in-development version of Galaxy." warning banner. Partially backport commit 318a1d7056cc8a5b9f6b83ef1cd186d6ef8939d4 and drop the unused `TARGET_BRANCH` variable from `Makefile` which shadows the shell environment variable of the same name set in `.github/workflows/docs.yaml` and used in `doc/source/conf.versioning.py` . 16 August 2022, 14:33:26 UTC
69defb7 Doc fixes 15 August 2022, 18:15:02 UTC
6a3804b Update application documentation with: ``` make -C doc/ updaterst ``` 14 August 2022, 17:39:19 UTC
6c43d66 Merge pull request #14373 from cat-bro/fix-IMPLICITLY_REQUIRED_TOOL_FILES-for-maxquant [22.01] Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools 26 July 2022, 12:26:15 UTC
25e847e Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools 25 July 2022, 17:07:36 UTC
a20d796 Merge pull request #14332 from bernt-matthias/topic/options-var [22.01] fix `startswith` attribute of `<options>` 24 July 2022, 16:22:21 UTC
21a7ad2 Merge pull request #14363 from davelopez/fix_enable_account_interface [22.01] Fix enable_account_interface option hiding too much 24 July 2022, 16:17:39 UTC
f2bdee4 Display correct description in Manage Information 22 July 2022, 16:11:14 UTC
b004c32 Display Manage Cloud Auth user preferences always 22 July 2022, 16:10:19 UTC
e775648 Disable only specific inputs in user information 22 July 2022, 16:09:23 UTC
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