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22 May 2024, 15:32:24 UTC
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6b9f090 Nicola Soranzo 11 December 2022, 21:54:23 UTC Merge branch 'release_21.01' into release_21.05 11 December 2022, 21:54:23 UTC
2b79cf2 Dannon 11 December 2022, 20:25:50 UTC Merge pull request #15170 from nsoranzo/release_21.01_fix_passenv [21.01] Fix `passenv` option for tox 4.0 11 December 2022, 20:25:50 UTC
653b415 Nicola Soranzo 11 December 2022, 18:29:54 UTC Fix `passenv` option for tox 4.0 See https://tox.wiki/en/latest/faq.html#tox-4-changed-ini-rules 11 December 2022, 18:35:04 UTC
a59d4d4 Nicola Soranzo 08 December 2022, 12:39:45 UTC Merge branch 'release_21.01' into release_21.05 08 December 2022, 12:39:45 UTC
7d21208 Nicola Soranzo 08 December 2022, 08:13:16 UTC Merge pull request #15143 from martenson/release_21.01 [21.01] Rename removed tox configuration option 08 December 2022, 08:13:16 UTC
2887eb8 Martin Cech 07 December 2022, 20:47:41 UTC rename removed tox configuration option 07 December 2022, 20:47:41 UTC
d51d911 Nicola Soranzo 02 November 2022, 15:39:03 UTC Merge branch 'release_21.01' into release_21.05 02 November 2022, 15:39:27 UTC
c8a514a Nicola Soranzo 02 November 2022, 15:32:58 UTC Merge branch 'release_20.09' into release_21.01 02 November 2022, 15:37:59 UTC
9d31330 Nicola Soranzo 02 November 2022, 15:32:02 UTC Merge branch 'release_20.05' into release_20.09 02 November 2022, 15:32:02 UTC
6df30d6 Nicola Soranzo 02 November 2022, 14:57:01 UTC Merge branch 'release_20.01' into release_20.05 02 November 2022, 14:57:01 UTC
ae59839 Nicola Soranzo 02 November 2022, 14:55:38 UTC Merge branch 'release_19.09' into release_20.01 02 November 2022, 14:55:38 UTC
f0a269c Nicola Soranzo 02 November 2022, 14:53:53 UTC Merge branch 'release_19.05' into release_19.09 02 November 2022, 14:53:53 UTC
d48c4a4 Nicola Soranzo 02 November 2022, 14:48:21 UTC 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 Nicola Soranzo 01 November 2022, 02:29:07 UTC 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 Nicola Soranzo 01 November 2022, 01:31:08 UTC 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 Nicola Soranzo 31 October 2022, 22:28:16 UTC Fix mistakenly overwriting ``self._conda_version`` with conda-build version. Introduced in commit 0ed66646e1234a93193edbd4b5577c535ed32f99 . 01 November 2022, 11:57:07 UTC
85ad2a0 Nicola Soranzo 26 October 2022, 15:57:32 UTC Merge branch 'release_21.01' into release_21.05 26 October 2022, 15:57:32 UTC
cc0d811 Nicola Soranzo 26 October 2022, 15:55:05 UTC Merge branch 'release_20.09' into release_21.01 26 October 2022, 15:55:05 UTC
14f3fc2 Nicola Soranzo 26 October 2022, 13:18:20 UTC Merge branch 'release_20.05' into release_20.09 26 October 2022, 13:18:20 UTC
a99bea6 Nicola Soranzo 26 October 2022, 10:44:37 UTC Merge branch 'release_20.01' into release_20.05 26 October 2022, 10:44:37 UTC
68ba6fd Nicola Soranzo 26 October 2022, 10:30:22 UTC Merge branch 'release_19.09' into release_20.01 26 October 2022, 10:30:22 UTC
563b9e7 Nicola Soranzo 26 October 2022, 09:07:50 UTC Merge branch 'release_19.05' into release_19.09 26 October 2022, 09:07:50 UTC
e8eb248 Nicola Soranzo 26 October 2022, 09:03:07 UTC 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 Nicola Soranzo 25 October 2022, 18:28:57 UTC 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 Nicola Soranzo 25 October 2022, 18:21:41 UTC 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 Nicola Soranzo 25 October 2022, 18:18:11 UTC Rewrite `CondaContext._guess_conda_properties()` to use `conda info` 25 October 2022, 18:18:11 UTC
8069584 Nicola Soranzo 06 September 2022, 10:12:59 UTC Merge branch 'release_21.01' into release_21.05 06 September 2022, 10:12:59 UTC
50bdd35 Marius van den Beek 05 September 2022, 17:18:56 UTC 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 Dannon 31 August 2022, 12:11:58 UTC 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
9b66e46 Matthias Bernt 26 August 2022, 15:04:01 UTC always use default=0 for strandCol just for consistency 26 August 2022, 15:04:01 UTC
fe30308 Matthias Bernt 26 August 2022, 10:55:08 UTC 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 Matthias Bernt 26 August 2022, 10:01:54 UTC Revert "set metadata default to no_value if default is None" This reverts commit dff9d4087bdcd500912eb4a7e5512b9b26ab9879. 26 August 2022, 10:01:54 UTC
dff9d40 Matthias Bernt 25 August 2022, 15:30:13 UTC set metadata default to no_value if default is None 25 August 2022, 15:30:13 UTC
59f7704 Matthias Bernt 25 August 2022, 14:43:31 UTC test case showing failing set_meta broke in https://github.com/galaxyproject/galaxy/commit/7d0ec29fa06ae6f04c0ae6fc193a390bc11cddcd 25 August 2022, 14:45:26 UTC
05cad6d mvdbeek 23 August 2022, 13:47:56 UTC 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
00ba0a9 Marius van den Beek 23 June 2022, 13:35:52 UTC Merge pull request #13907 from davelopez/21.05_fix_anonymous_import_histories [21.05] Fix condition importing histories anonymously 23 June 2022, 13:35:52 UTC
42b3c6e davelopez 11 May 2022, 14:31:46 UTC Fix condition importing histories anonymously 11 May 2022, 14:31:46 UTC
06d37d9 Marius van den Beek 04 April 2022, 13:52:53 UTC Merge pull request #13664 from nsoranzo/release_21.05_backport_dbf7ac364a20835acf16ccdffea3018a58023e2d [21.05] Partially backport #13532 to fix `test_github_search` mulled unit test 04 April 2022, 13:52:53 UTC
2cbbf1e Nicola Soranzo 10 March 2022, 19:42:10 UTC Check GitHub API rate limit in GitHubSearch. Deprecate `get_json()` search Follow-up on https://github.com/galaxyproject/galaxy/pull/13509 . 04 April 2022, 11:56:07 UTC
58d7e3c Nicola Soranzo 20 July 2021, 14:26:30 UTC Raise exception if GET request returned an unsuccessful status code 04 April 2022, 11:40:16 UTC
bad8ecb Nicola Soranzo 16 March 2022, 18:00:25 UTC Merge pull request #13554 from mvdbeek/fix_sff_extractor_tool 16 March 2022, 18:00:25 UTC
e2d4380 mvdbeek 16 March 2022, 14:13:40 UTC Fix ``sff_extract`` tool, drop type annotation I don't think this tool is really used much, but it is loaded in `tool_conf.xml`. https://github.com/galaxyproject/galaxy/pull/11877 added type annotations, and that's a syntax error on 2.7 The alternative would be to fix the rest of the tool for 3.x, but I think we're just wasting our time there and we shouldn't touch this again. 16 March 2022, 14:24:55 UTC
99835a8 Björn Grüning 14 March 2022, 20:30:26 UTC Merge pull request #13537 from davelopez/patch_21.05_allow_admins_access_datasets [21.05] Allow admin access to datasets API (before refactoring) 14 March 2022, 20:30:26 UTC
1330da2 John Chilton 25 October 2021, 15:48:05 UTC Fixes for LDDA manager - clearly that didn't work at all. 14 March 2022, 17:21:03 UTC
71742ac davelopez 14 March 2022, 13:50:22 UTC Allow admin access to datasets API (before refactoring) This patch contains the changes in #13060 and it is meant to be applied only to 21.05 do not merge forward this commit into 22.01 since it is already fixed there 14 March 2022, 13:50:22 UTC
a4b5bfd Nicola Soranzo 02 March 2022, 19:06:55 UTC Merge branch 'release_21.01' into release_21.05 02 March 2022, 19:06:55 UTC
2d535ed Nicola Soranzo 02 March 2022, 19:01:57 UTC Merge pull request #13468 from mvdbeek/quay_io_fix 02 March 2022, 19:01:57 UTC
16cb094 Marius van den Beek 02 March 2022, 15:57:42 UTC Fix trailing whitespace 02 March 2022, 15:57:42 UTC
831a077 Marius van den Beek 02 March 2022, 15:30:28 UTC Move header definition out of while loop Co-authored-by: Sergey Golitsynskiy <sgolitsynskiy@gmail.com> 02 March 2022, 15:30:28 UTC
2511b64 Nuwan Goonasekera 22 February 2022, 16:59:33 UTC Initial fix for quay.io repo query issue Fixes not getting a full list of images in a repo. Without this fix some container images are not resolvable. 02 March 2022, 12:17:42 UTC
5b62953 Dannon Baker 16 February 2022, 18:51:59 UTC Merge remote-tracking branch 'upstream/release_21.01' into release_21.05 16 February 2022, 18:51:59 UTC
3f59f59 Dannon Baker 16 February 2022, 18:51:28 UTC Merge remote-tracking branch 'upstream/release_20.09' into release_21.01 16 February 2022, 18:51:28 UTC
9e4463e Dannon Baker 16 February 2022, 18:50:51 UTC Merge remote-tracking branch 'upstream/release_20.05' into release_20.09 16 February 2022, 18:50:51 UTC
d4384ba Dannon 16 February 2022, 18:12:07 UTC Merge pull request #13387 from mvdbeek/fix_history_export_include_hidden_handling [20.05] Fix history export include hidden handling 16 February 2022, 18:12:07 UTC
c58f443 Marius van den Beek 16 February 2022, 15:00:06 UTC Make test assertions more precise Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 16 February 2022, 15:00:06 UTC
baed73d mvdbeek 16 February 2022, 10:38:36 UTC Fix history_export include_hidden=False handling Fixes https://github.com/galaxyproject/galaxy/issues/13386 16 February 2022, 10:41:47 UTC
cea780c mvdbeek 16 February 2022, 10:36:06 UTC Test that include_hidden is handled correctly 16 February 2022, 10:41:44 UTC
d27ded4 Nicola Soranzo 08 February 2022, 11:14:26 UTC Merge pull request #13315 from mvdbeek/restore_metadata_size_limit 08 February 2022, 11:14:26 UTC
83c0683 mvdbeek 07 February 2022, 10:12:54 UTC Restore Metadata size limit Broke in https://github.com/galaxyproject/galaxy/pull/11902 07 February 2022, 14:02:02 UTC
9ade7a2 Marius van den Beek 17 December 2021, 14:27:04 UTC Merge pull request #13077 from mvdbeek/fix_mulled_tests [21.05] Fix mulled unit tests by checking that known versions are returned 17 December 2021, 14:27:04 UTC
4176e79 Nicola Soranzo 09 December 2021, 20:06:23 UTC Fix test_singularity_search unit test in a way that it doesn't break when a new version of the container is released. 17 December 2021, 13:30:57 UTC
b4238f9 mvdbeek 13 December 2021, 14:18:13 UTC Merge branch 'release_21.01' into release_21.05 13 December 2021, 14:18:13 UTC
6928436 Marius van den Beek 13 December 2021, 14:15:33 UTC Merge pull request #13055 from mvdbeek/lift_version_check_in_toolshed [21.01] Only check profile version in Galaxy 13 December 2021, 14:15:33 UTC
b4a29f2 mvdbeek 13 December 2021, 11:49:47 UTC Only check profile version in Galaxy Should fix https://github.com/galaxyproject/galaxy/issues/13008 13 December 2021, 11:49:50 UTC
35dda33 Nicola Soranzo 03 December 2021, 12:49:44 UTC Merge pull request #13028 from nsoranzo/release_21.05_min_pip_version 03 December 2021, 12:49:44 UTC
262ab83 Nicola Soranzo 03 December 2021, 10:28:42 UTC Increase pip minimum version in startup script Pip <19.0 cannot install abi3 wheels, so for example on Python >3.6 it would (try to) build a cryptography wheel, which is not needed since cp36-abi3 wheels are already available on PyPI: https://cryptography.io/en/latest/faq/#why-are-there-no-wheels-for-my-python3-x-version Fix https://github.com/galaxyproject/galaxy/issues/13023 . xref: https://github.com/galaxyproject/planemo/issues/1208#issuecomment-984831111 03 December 2021, 11:02:20 UTC
6c97e48 Nuwan Goonasekera 16 November 2021, 02:54:22 UTC Merge pull request #12925 from nuwang/fix_docker_image_build_output_name Fix output step name in docker image build 16 November 2021, 02:54:22 UTC
52cbc86 Nuwan Goonasekera 15 November 2021, 20:00:07 UTC Fix output step name in docker image build 15 November 2021, 20:00:07 UTC
55acdf9 Nuwan Goonasekera 15 November 2021, 19:08:00 UTC Merge pull request #12922 from nuwang/fix_docker_repo_names [21.05] Update docker autobuilds to use correct repos 15 November 2021, 19:08:00 UTC
3d7b713 Nuwan Goonasekera 15 November 2021, 15:05:31 UTC Update docker autobuilds to use correct repos 15 November 2021, 15:08:59 UTC
fffde08 Marius van den Beek 15 November 2021, 09:36:33 UTC Merge pull request #12837 from nuwang/fixes_for_galaxy_min_ci_build [21.05] Fixes for docker galaxy-min ci build 15 November 2021, 09:36:33 UTC
f9e1fe8 Marius van den Beek 15 November 2021, 09:35:02 UTC Merge pull request #12850 from mvdbeek/dont_fail_sending_activation_token_for_emails_with_escaped_characters [21.05] Fix activation token sending for emails with characters that are escaped in html 15 November 2021, 09:35:02 UTC
48d5431 mvdbeek 04 November 2021, 08:32:10 UTC Fix action token sending for chracters that are escaped in html The function body of escape is ``` def escape(s): """Replace the characters ``&``, ``<``, ``>``, ``'``, and ``"`` in the string with HTML-safe sequences. Use this if you need to display text that might contain such characters in HTML. If the object has an ``__html__`` method, it is called and the return value is assumed to already be safe for HTML. :param s: An object to be converted to a string and escaped. :return: A :class:`Markup` string with the escaped text. """ if hasattr(s, "__html__"): return Markup(s.__html__()) return Markup( text_type(s) .replace("&", "&amp;") .replace(">", "&gt;") .replace("<", "&lt;") .replace("'", "&#39;") .replace('"', "&#34;") ) ``` It doesn't make sense to lookup the replaced values in the database, and it breaks single-quotes in the email username portion, which is valid https://en.wikipedia.org/wiki/Email_address#Syntax 04 November 2021, 08:32:13 UTC
9283865 Nuwan Goonasekera 04 November 2021, 05:56:31 UTC Merge pull request #4 from almahmoud/patch-16 Change anvil branche to dev 04 November 2021, 05:56:31 UTC
6a54fe0 Alexandru Mahmoud 04 November 2021, 02:01:14 UTC Change anvil branche to dev 04 November 2021, 02:01:14 UTC
e5b50d1 Nuwan Goonasekera 02 November 2021, 15:49:16 UTC Add open container labels to image 02 November 2021, 15:53:45 UTC
9d54c2b Nuwan Goonasekera 02 November 2021, 15:23:01 UTC Remove -auto from end of tag 02 November 2021, 15:23:01 UTC
33af0e3 Nuwan Goonasekera 02 November 2021, 13:54:09 UTC Only tag by branch name for now, to avoid too many images 02 November 2021, 14:46:33 UTC
101d956 Nuwan Goonasekera 02 November 2021, 13:52:33 UTC Use correct repo name on quay.io 02 November 2021, 14:46:24 UTC
2b25c37 Martin Cech 02 November 2021, 10:20:09 UTC Merge pull request #12832 from mvdbeek/disable_dockerhub_push [21.05] Disable dockerhub pushes 02 November 2021, 10:20:09 UTC
3a7324c mvdbeek 02 November 2021, 08:59:36 UTC Disable dockerhub pushes 02 November 2021, 08:59:36 UTC
fae99b9 Marius van den Beek 01 November 2021, 12:19:54 UTC Merge pull request #12520 from almahmoud/2105-imagebuild [21.05] Add image auto-building through GA 01 November 2021, 12:19:54 UTC
aa7b10e mvdbeek 01 November 2021, 12:11:29 UTC Only build docker image for galaxyproject repo limit concurrency and only build for release and anvil branches. 01 November 2021, 12:16:22 UTC
d41bb73 Oleg Zharkov 29 October 2021, 17:25:59 UTC Merge pull request #12807 from mvdbeek/display_unknown_datatype [21.05] If datatype is unknown display warning when trying to connect nodes 29 October 2021, 17:25:59 UTC
6d1edce mvdbeek 29 October 2021, 12:23:35 UTC If datatype is unknown display warning when trying to connect nodes 29 October 2021, 14:04:14 UTC
69ca27e Marius van den Beek 29 October 2021, 12:37:31 UTC Merge pull request #12806 from mvdbeek/diable_library_uploads_using_master_api_key [21.05] Disable library uploads using master API key 29 October 2021, 12:37:31 UTC
2f89e55 Marius van den Beek 29 October 2021, 10:20:23 UTC Fix typo Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 29 October 2021, 10:20:23 UTC
c151af0 mvdbeek 29 October 2021, 09:02:52 UTC Exclude invalid LibraryDataset items from folder 29 October 2021, 09:03:26 UTC
629abab mvdbeek 29 October 2021, 08:00:51 UTC Disable library uploads using master API key and cleanup some of the parameter validation. 29 October 2021, 08:42:04 UTC
0bd899a Marius van den Beek 28 October 2021, 14:49:34 UTC Merge pull request #12712 from bernt-matthias/topic/rds [21.05] Add support for RDS files and improvements for RData 28 October 2021, 14:49:34 UTC
ea2d8d7 mvdbeek 28 October 2021, 11:01:58 UTC Use build_sniff_from_prefix for rds and rdata 28 October 2021, 11:01:58 UTC
5d83ea6 Marius van den Beek 28 October 2021, 09:18:31 UTC Merge pull request #12799 from nsoranzo/release_21.05_genomes_api_allow_sessionless [21.05] Allow sessionless access to genomes API 28 October 2021, 09:18:31 UTC
37c75a4 Marius van den Beek 28 October 2021, 09:17:09 UTC Merge pull request #12793 from davelopez/fix_bootstrap_admin_run_jobs [21.05] Raise Bad Request when bootstrap admins (master key) try to run jobs/tools 28 October 2021, 09:17:09 UTC
3941659 Nicola Soranzo 27 October 2021, 18:17:00 UTC Fix broken f-strings 27 October 2021, 18:17:00 UTC
4467a27 Nicola Soranzo 27 October 2021, 18:15:09 UTC Allow sessionless access to genomes API Broken in commit 47e37cddda77a053b9283574ae444cb54834fcff Reported by @innovate-invent 27 October 2021, 18:16:16 UTC
d779b61 davelopez 27 October 2021, 16:42:58 UTC Raise Bad Request when bootstrap admin try to run/create workflows 27 October 2021, 16:42:58 UTC
b9f7a61 davelopez 27 October 2021, 14:10:21 UTC Raise Bad Request when bootstrap admins try to run jobs/tools 27 October 2021, 15:57:49 UTC
c7ceec9 Marius van den Beek 26 October 2021, 14:12:31 UTC Merge pull request #12782 from dannon/fix-msa [21.05] Fix msa visualization 26 October 2021, 14:12:31 UTC
c8d6d39 Dannon Baker 25 October 2021, 22:10:59 UTC Manually hack the built static, too -- this needs followup in dev to be clean and remove artifacts 26 October 2021, 12:42:08 UTC
c220f6d Dannon Baker 25 October 2021, 21:15:14 UTC The surgical in-place fix to prebuilt msa.js to account for 'at' being in array now in ff/chrome 26 October 2021, 12:42:08 UTC
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