| b4cc0c7 | John Chilton | 14 September 2018, 14:48:11 UTC | Version 18.9.0 | 14 September 2018, 14:48:11 UTC |
| 81d4cce | John Chilton | 14 September 2018, 14:44:55 UTC | Prepare next release. | 14 September 2018, 14:46:05 UTC |
| fa343bd | John Chilton | 14 September 2018, 13:49:17 UTC | Merge pull request #132 from galaxyproject/conda_channel_mess change channel priority | 14 September 2018, 13:49:17 UTC |
| dfa5306 | John Chilton | 13 September 2018, 17:41:01 UTC | Merge pull request #135 from galaxyproject/update_to_galaxy_1809 Update to Galaxy 18.09. | 13 September 2018, 17:41:01 UTC |
| 96c083f | John Chilton | 13 September 2018, 17:12:04 UTC | Update to Galaxy 18.09. | 13 September 2018, 17:12:04 UTC |
| 4db7f39 | John Chilton | 13 September 2018, 17:00:06 UTC | Unicodify only once in mulled cmd handling. Version of this patch that was applied to galaxy. | 13 September 2018, 17:00:06 UTC |
| 080d672 | John Chilton | 13 September 2018, 15:35:27 UTC | Merge pull request #133 from galaxyproject/galaxy_update_last_1805 Bring in the latest 18.05, add XSD. | 13 September 2018, 15:35:27 UTC |
| fec5208 | John Chilton | 13 September 2018, 15:16:54 UTC | Merge pull request #134 from nsoranzo/fixes Fixes | 13 September 2018, 15:16:54 UTC |
| 5456847 | Nicola Soranzo | 13 September 2018, 15:10:24 UTC | Allow specifying `make_tool` also with newer cwltool | 13 September 2018, 15:10:24 UTC |
| 1f0cd6a | John Chilton | 13 September 2018, 14:57:00 UTC | Bring in the latest 18.05, add XSD. | 13 September 2018, 14:57:00 UTC |
| eabbe2e | Nicola Soranzo | 13 September 2018, 13:32:09 UTC | Removed unused `RuntimeContext` import | 13 September 2018, 13:32:09 UTC |
| d7d4975 | Nicola Soranzo | 13 September 2018, 10:47:39 UTC | Simplify stdio linter `_lint_level()` was missing `fatal_oom` as possible level, causing linting failures, e.g.: https://travis-ci.org/galaxyproteomics/tools-galaxyp/jobs/427283680#L573 Therefore remove checks already tested by the Planemo `tool_xsd` linter. | 13 September 2018, 10:57:17 UTC |
| dff3ae2 | Bjoern Gruening | 12 September 2018, 21:50:45 UTC | change channel priority | 12 September 2018, 21:50:45 UTC |
| 9cb0e7b | John Chilton | 12 September 2018, 18:27:19 UTC | Starting work on 18.5.16 | 12 September 2018, 18:27:19 UTC |
| f0f1f9f | John Chilton | 12 September 2018, 18:25:55 UTC | Version 18.5.15 | 12 September 2018, 18:25:55 UTC |
| abb4d3f | John Chilton | 12 September 2018, 18:25:49 UTC | Prep next release. | 12 September 2018, 18:25:49 UTC |
| c68f729 | John Chilton | 12 September 2018, 18:23:16 UTC | Another update to support newer cwltool compatiblity. | 12 September 2018, 18:24:46 UTC |
| a0c93de | John Chilton | 12 September 2018, 15:10:33 UTC | Starting work on 18.5.15 | 12 September 2018, 15:10:33 UTC |
| 5d5ad4a | John Chilton | 12 September 2018, 15:10:00 UTC | Version 18.5.14 | 12 September 2018, 15:10:00 UTC |
| 83f7a12 | John Chilton | 12 September 2018, 15:09:43 UTC | Prep next release. | 12 September 2018, 15:09:43 UTC |
| 1826344 | Björn Grüning | 04 September 2018, 18:14:54 UTC | Merge pull request #130 from pcm32/patch-1 Makes --test optional for involucro | 04 September 2018, 18:14:54 UTC |
| 09c1d93 | Pablo Moreno | 04 September 2018, 14:25:38 UTC | Missing bracket | 04 September 2018, 14:25:38 UTC |
| d6146c7 | Pablo Moreno | 04 September 2018, 14:14:26 UTC | Makes --test optional for involucro | 04 September 2018, 14:14:26 UTC |
| 892dcf9 | John Chilton | 04 September 2018, 12:39:59 UTC | Merge pull request #129 from nsoranzo/support_cwltool_1.0.20180611202326 Add support for cwltool 1.0.20180611202326 | 04 September 2018, 12:39:59 UTC |
| 5d5ab4d | Nicola Soranzo | 31 August 2018, 19:22:18 UTC | Add support for cwltool 1.0.20180611202326 | 31 August 2018, 19:53:56 UTC |
| dca663c | Björn Grüning | 24 July 2018, 14:11:52 UTC | Merge pull request #121 from natefoo/lint-name Support passing a name through to the lint context so that error messages can be more useful | 24 July 2018, 14:11:52 UTC |
| d0170c5 | Björn Grüning | 24 July 2018, 14:11:01 UTC | Merge pull request #128 from nsoranzo/test_output_name_error Report a lint error if test output name does not match tool outputs | 24 July 2018, 14:11:01 UTC |
| 35dc456 | Nicola Soranzo | 16 July 2018, 09:26:39 UTC | Report a lint error if test output name does not match tool outputs not a warning. Fix https://github.com/galaxyproject/planemo/issues/858 . | 16 July 2018, 09:27:50 UTC |
| a6935b9 | Nate Coraor | 26 June 2018, 17:51:49 UTC | Support passing a name through to the lint context so that error messages can be more useful | 26 June 2018, 17:51:49 UTC |
| 11c46b7 | John Chilton | 23 May 2018, 12:19:52 UTC | Starting work on 18.5.14 | 23 May 2018, 12:19:52 UTC |
| 1b1a6b8 | John Chilton | 23 May 2018, 12:19:27 UTC | Version 18.5.13 | 23 May 2018, 12:19:27 UTC |
| a0f7203 | John Chilton | 23 May 2018, 12:19:01 UTC | Prep next version. | 23 May 2018, 12:19:01 UTC |
| 82f3b91 | John Chilton | 23 May 2018, 12:17:55 UTC | Merge pull request #120 from jmchilton/explicit_galaxy_style_collection Add support for explicit Galaxy-style collections as test inputs. | 23 May 2018, 12:17:55 UTC |
| 0682855 | John Chilton | 23 May 2018, 10:51:56 UTC | Add support for explicit Galaxy-style collections as test inputs. There is some support for a direct list syntax already from the CWL work, but it doesn't support explicit element identifiers or collection type annotation. This format should feel a bit more like Galaxy tool test collection inputs I think. | 23 May 2018, 10:51:56 UTC |
| 6db297c | John Chilton | 23 May 2018, 10:48:06 UTC | Merge pull request #119 from galaxyproject/filetype add filetype support to the workflow-job.yml test script | 23 May 2018, 10:48:06 UTC |
| 46be221 | Björn Grüning | 23 May 2018, 09:55:24 UTC | add filetype support to the workflow-job.yml test script | 23 May 2018, 09:55:24 UTC |
| 3f37a5c | John Chilton | 22 May 2018, 15:32:06 UTC | Starting work on 18.5.13 | 22 May 2018, 15:32:06 UTC |
| 2cb5f31 | John Chilton | 22 May 2018, 15:31:35 UTC | Version 18.5.12 | 22 May 2018, 15:31:35 UTC |
| cb06532 | John Chilton | 22 May 2018, 15:30:44 UTC | Prep release. | 22 May 2018, 15:31:27 UTC |
| 02d9f7f | John Chilton | 22 May 2018, 15:29:34 UTC | Merge pull request #118 from jmchilton/uri_test_data Allow URIs in test data inputs. | 22 May 2018, 15:29:34 UTC |
| 87c4ec6 | John Chilton | 22 May 2018, 15:19:17 UTC | Allow URIs in test data inputs. | 22 May 2018, 15:19:44 UTC |
| da3497c | John Chilton | 18 May 2018, 15:15:31 UTC | Merge pull request #116 from jmchilton/py3fixmulled Python 3 fix for mulled container resolver. | 18 May 2018, 15:15:31 UTC |
| e5fd913 | John Chilton | 18 May 2018, 15:06:01 UTC | Python 3 fix for mulled container resolver. | 18 May 2018, 15:06:01 UTC |
| 9ad63b2 | John Chilton | 16 May 2018, 16:52:40 UTC | Starting work on 18.5.12 | 16 May 2018, 16:52:40 UTC |
| 6646bec | John Chilton | 16 May 2018, 16:52:04 UTC | Version 18.5.11 | 16 May 2018, 16:52:04 UTC |
| e2ff498 | John Chilton | 16 May 2018, 16:49:23 UTC | Merge pull request #115 from jmchilton/cwl_parse_req Rough pass at parsing CWL software requirements to Galaxy requirements. | 16 May 2018, 16:49:23 UTC |
| 7863464 | John Chilton | 16 May 2018, 16:03:17 UTC | Rough pass at parsing CWL software requirements to Galaxy requirements. Required to fix various Planemo conda functionality for CWL tools (linting Conda requirements, biocontainers, conda_install, conda_env, etc...). | 16 May 2018, 16:05:02 UTC |
| 4b58ea5 | John Chilton | 12 May 2018, 05:01:40 UTC | Merge pull request #114 from galaxyproject/quiet --quiet = Do not display progress bar. | 12 May 2018, 05:01:40 UTC |
| c0d15df | Björn Grüning | 11 May 2018, 20:58:48 UTC | --quiet = Do not display progress bar. | 11 May 2018, 20:58:48 UTC |
| 7336674 | John Chilton | 11 May 2018, 00:09:33 UTC | Starting work on 18.5.11 | 11 May 2018, 00:09:33 UTC |
| a5210a2 | John Chilton | 11 May 2018, 00:08:58 UTC | Version 18.5.10 | 11 May 2018, 00:08:58 UTC |
| 1e9c14a | John Chilton | 11 May 2018, 00:08:50 UTC | Prep the next release. | 11 May 2018, 00:08:50 UTC |
| 91c001d | John Chilton | 10 May 2018, 23:41:26 UTC | Merge pull request #113 from jmchilton/docker_fixes Fix for docker_util logs_command used by Planemo. | 10 May 2018, 23:41:26 UTC |
| e203831 | John Chilton | 10 May 2018, 23:26:12 UTC | Fix for docker_util logs_command used by Planemo. | 10 May 2018, 23:26:12 UTC |
| 14360da | John Chilton | 07 May 2018, 16:45:39 UTC | Starting work on 18.5.10 | 07 May 2018, 16:45:39 UTC |
| cf0707e | John Chilton | 07 May 2018, 16:45:13 UTC | Version 18.5.9 | 07 May 2018, 16:45:13 UTC |
| 4d2cb6a | John Chilton | 07 May 2018, 16:44:46 UTC | Prep next release. | 07 May 2018, 16:45:05 UTC |
| 5758046 | John Chilton | 07 May 2018, 16:43:55 UTC | Merge pull request #112 from jmchilton/cwl_lint_1.0 Update cwl tool linting to 1.0. | 07 May 2018, 16:43:55 UTC |
| 34d7bc4 | John Chilton | 05 March 2018, 02:45:24 UTC | Update cwl tool linting to 1.0. | 07 May 2018, 15:25:37 UTC |
| c2098e0 | John Chilton | 06 May 2018, 15:00:25 UTC | Starting work on 18.5.9 | 06 May 2018, 15:00:25 UTC |
| 6a967b2 | John Chilton | 06 May 2018, 14:59:51 UTC | Version 18.5.8 | 06 May 2018, 14:59:51 UTC |
| f07c801 | John Chilton | 06 May 2018, 14:57:25 UTC | Prep next relaese. | 06 May 2018, 14:58:59 UTC |
| dad6afe | John Chilton | 06 May 2018, 14:49:16 UTC | Merge pull request #109 from galaxyproject/catch_errors catch error during conda search | 06 May 2018, 14:49:16 UTC |
| de40459 | Bjoern Gruening | 06 May 2018, 11:46:52 UTC | catch real Exception | 06 May 2018, 11:46:52 UTC |
| 04da969 | Bjoern Gruening | 06 May 2018, 11:13:24 UTC | catch error during conda search | 06 May 2018, 11:13:24 UTC |
| f3b1abc | John Chilton | 19 April 2018, 19:58:48 UTC | Merge pull request #107 from jmchilton/update-dev-20180419 Update to latest galaxy dev. | 19 April 2018, 19:58:48 UTC |
| 5c89c8b | John Chilton | 19 April 2018, 19:47:46 UTC | Update to latest galaxy dev. | 19 April 2018, 19:56:03 UTC |
| 57352da | John Chilton | 22 March 2018, 10:53:03 UTC | Merge pull request #106 from davebx/version_lint_pep440 Emit a linter warning if tool version is not pep 440 compliant. | 22 March 2018, 10:53:03 UTC |
| 81a04d3 | Dave Bouvier | 21 March 2018, 20:35:51 UTC | Failed linting, ironically. | 21 March 2018, 20:35:51 UTC |
| af652eb | Dave Bouvier | 21 March 2018, 20:16:54 UTC | Emit a linter warning if tool version is not pep 440 compliant. | 21 March 2018, 20:16:54 UTC |
| fde42ae | Nicola Soranzo | 12 March 2018, 22:40:17 UTC | Merge pull request #105 from jmchilton/admin_key_fix Use admin=True when getting test data path. | 12 March 2018, 22:40:17 UTC |
| 10543e2 | John Chilton | 12 March 2018, 20:54:11 UTC | Use admin=True when getting test data path. Fixes abstraction leakage introduced in #104 caught by @nsoranzo. | 12 March 2018, 20:54:11 UTC |
| 015f84d | John Chilton | 12 March 2018, 20:12:59 UTC | Starting work on 18.5.8 | 12 March 2018, 20:12:59 UTC |
| 9ab1cbf | John Chilton | 12 March 2018, 20:12:37 UTC | Version 18.5.7 | 12 March 2018, 20:12:37 UTC |
| ef02e6b | John Chilton | 12 March 2018, 20:12:30 UTC | Prep next release. | 12 March 2018, 20:12:30 UTC |
| 4cf661d | John Chilton | 12 March 2018, 20:11:30 UTC | Merge pull request #104 from jmchilton/tool_test_enhancements Fixes for tool testing client. | 12 March 2018, 20:11:30 UTC |
| c4249c0 | John Chilton | 12 March 2018, 20:06:04 UTC | Fixes for tool testing client. From testing within ephemeris. | 12 March 2018, 20:06:04 UTC |
| 569e262 | John Chilton | 12 March 2018, 14:53:25 UTC | Starting work on 18.5.7 | 12 March 2018, 14:53:25 UTC |
| 9cb55ad | John Chilton | 12 March 2018, 14:52:59 UTC | Version 18.5.6 | 12 March 2018, 14:52:59 UTC |
| ee3cef5 | John Chilton | 12 March 2018, 14:51:54 UTC | Merge pull request #103 from jmchilton/external_tool_testing Provide more test data when running verify_tool. | 12 March 2018, 14:51:54 UTC |
| 009d825 | John Chilton | 12 March 2018, 14:18:32 UTC | Fix up HISTORY.rst. | 12 March 2018, 14:18:32 UTC |
| f9bb57a | John Chilton | 12 March 2018, 14:16:50 UTC | Bring in updates from galaxy review process for tool testing code. | 12 March 2018, 14:17:10 UTC |
| 4ce51f2 | John Chilton | 08 March 2018, 13:27:32 UTC | Implement verbose flag on verify script. | 08 March 2018, 13:27:32 UTC |
| 82a4b7f | John Chilton | 07 March 2018, 23:38:57 UTC | Improvements to external testing script. | 07 March 2018, 23:38:57 UTC |
| bccf8ca | John Chilton | 07 March 2018, 20:58:07 UTC | Provide more test data when running verify_tool. This is information Planemo generates from Galaxy's XUnit report and inserts back into the result JSON, with this change I think one can simply run ``planemo test_reports result.json`` on the result of the driver script here to generate Planemo-style reports for tool test runs. ``` pip install galaxy-lib galaxy-tool-test -u http://localhost:8080 -a dccd838ad8f46637e0d7661d849806a1 -k dccd838ad8f46637e0d7661d849806a1 -t inputs_as_json -j output.json planemo test_reports --test_output output.html --test_output_markdown output.md output.json ``` Requires some small changes to Planemo's test_reports command contained within https://github.com/galaxyproject/planemo/pull/781. | 07 March 2018, 21:47:03 UTC |
| 073e6e5 | John Chilton | 07 March 2018, 20:57:24 UTC | Add a few HISTORY entries for 18.5.6. | 07 March 2018, 20:57:24 UTC |
| 124c5d8 | John Chilton | 07 March 2018, 16:16:03 UTC | Merge pull request #91 from jmchilton/tool_testing Bring in Galaxy updates to run externally-driven tool tests. | 07 March 2018, 16:16:03 UTC |
| 012cacc | John Chilton | 26 February 2018, 02:06:29 UTC | Bring in Galaxy dev branch updates. Raise max-complexity for tool output verification code. | 07 March 2018, 15:44:04 UTC |
| 6abf375 | John Chilton | 07 March 2018, 02:52:26 UTC | Starting work on 18.5.6 | 07 March 2018, 02:52:26 UTC |
| 4826e30 | John Chilton | 07 March 2018, 02:52:01 UTC | Version 18.5.5 | 07 March 2018, 02:52:01 UTC |
| c1783e1 | John Chilton | 07 March 2018, 02:50:25 UTC | Prep next release. | 07 March 2018, 02:51:46 UTC |
| dc32d7c | John Chilton | 07 March 2018, 02:48:30 UTC | Merge pull request #101 from jmchilton/py3_fix Python 3 fix for test assertion checking. | 07 March 2018, 02:48:30 UTC |
| f79cbf1 | Björn Grüning | 06 March 2018, 17:57:39 UTC | Merge pull request #102 from mbargull/dep-markupsafe add missing markupsafe dependency | 06 March 2018, 17:57:39 UTC |
| ab83486 | Marcel Bargull | 06 March 2018, 17:29:59 UTC | add missing markupsafe dependency | 06 March 2018, 17:29:59 UTC |
| b38f69e | John Chilton | 05 March 2018, 18:37:12 UTC | Python 3 fix for test assertion checking. | 05 March 2018, 18:37:56 UTC |
| 543f6c7 | Björn Grüning | 02 March 2018, 18:42:38 UTC | Merge pull request #100 from mbargull/mulled-shlex-quote mulled: use shlex.quote to escape single quotes in test | 02 March 2018, 18:42:38 UTC |
| 78572fa | John Chilton | 02 March 2018, 00:55:55 UTC | Starting work on 18.5.5 | 02 March 2018, 00:55:55 UTC |
| 3354f36 | John Chilton | 02 March 2018, 00:55:31 UTC | Version 18.5.4 | 02 March 2018, 00:55:31 UTC |
| b25168c | John Chilton | 02 March 2018, 00:55:14 UTC | Prep next release. | 02 March 2018, 00:55:14 UTC |
| 1ed56f6 | John Chilton | 02 March 2018, 00:53:51 UTC | Merge pull request #99 from mbargull/mulled-conda-image mulled: make CONDA_IMAGE configurable via env variable | 02 March 2018, 00:53:51 UTC |
