| 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 |
| 92cb104 | Marcel Bargull | 01 March 2018, 23:36:12 UTC | mulled: use shlex_quote from six.moves | 01 March 2018, 23:36:12 UTC |
| 570837d | Marcel Bargull | 01 March 2018, 22:41:00 UTC | mulled: use shlex.quote to escape single quotes in test | 01 March 2018, 22:41:00 UTC |
| 53810d9 | Marcel Bargull | 01 March 2018, 19:29:10 UTC | mulled: make CONDA_IMAGE configurable via env variable | 01 March 2018, 19:29:10 UTC |
| 3f34998 | John Chilton | 01 March 2018, 15:04:34 UTC | Starting work on 18.5.4 | 01 March 2018, 15:04:34 UTC |
| 6ef2839 | John Chilton | 01 March 2018, 03:22:24 UTC | Version 18.5.3 | 01 March 2018, 03:22:24 UTC |
| bd228ff | John Chilton | 01 March 2018, 03:22:11 UTC | Prep next release. | 01 March 2018, 03:22:11 UTC |
| d91169d | John Chilton | 01 March 2018, 03:21:08 UTC | Merge pull request #98 from jmchilton/windows_fix Fix galaxy.util.path for Windows import. | 01 March 2018, 03:21:08 UTC |
| afa243c | John Chilton | 01 March 2018, 00:17:36 UTC | Fix galaxy.util.path for Windows import. These modules are not available under Windows, just throw a NotImplementedError if they are attempted to be used. | 01 March 2018, 00:17:36 UTC |
| 46166e9 | John Chilton | 28 February 2018, 13:33:10 UTC | Starting work on 18.5.3 | 28 February 2018, 13:33:10 UTC |
| c78237e | John Chilton | 28 February 2018, 13:32:36 UTC | Version 18.5.2 | 28 February 2018, 13:32:36 UTC |
| 4cc48ec | John Chilton | 28 February 2018, 13:31:44 UTC | Prep next release. | 28 February 2018, 13:32:08 UTC |
| af58e90 | John Chilton | 28 February 2018, 13:30:11 UTC | Merge pull request #95 from jmchilton/conda_fix_nsoranzo_will_hate More Conda fixes for Planemo | 28 February 2018, 13:30:11 UTC |
| 3c8c7da | Nicola Soranzo | 28 February 2018, 13:09:25 UTC | Open/close stdout file in exec_command() | 28 February 2018, 13:09:25 UTC |
| b1a221c | John Chilton | 28 February 2018, 02:04:32 UTC | Second attempt at fix for stdout in conda_util. | 28 February 2018, 02:11:46 UTC |
| 8284191 | John Chilton | 27 February 2018, 20:24:19 UTC | Bugfix for conda commands with shell redirection included. Fixes Planemo's conda_env command. | 27 February 2018, 20:25:27 UTC |
| 461ae2c | John Chilton | 27 February 2018, 19:39:59 UTC | Fix "UnboundLocalError: local variable 'tempdir' referenced before assignment" | 27 February 2018, 20:25:27 UTC |
| 0f5e07f | John Chilton | 27 February 2018, 20:23:20 UTC | Merge pull request #94 from jmchilton/py3fix Python 3 fix for galaxy.tools.verify.test_data. | 27 February 2018, 20:23:20 UTC |
| 0aff54e | John Chilton | 27 February 2018, 19:21:53 UTC | Redo Python 3 fix with smart_str (as suggested by @nsoranzo). | 27 February 2018, 19:21:53 UTC |
| da0ba86 | John Chilton | 27 February 2018, 19:20:21 UTC | Do not lint against W503. xref https://github.com/galaxyproject/galaxy/pull/2594 | 27 February 2018, 19:20:21 UTC |
| dc96206 | John Chilton | 27 February 2018, 19:19:57 UTC | Revert "Lint fix - fix a W503 error in galaxy.web.stack." This reverts commit 1e90c7b6d659e4141f803d79947c772741c5bd23. | 27 February 2018, 19:19:57 UTC |
| db66bd0 | John Chilton | 26 February 2018, 13:22:05 UTC | Python 3 fix for galaxy.tools.verify.test_data. | 27 February 2018, 15:11:20 UTC |
| bf750c9 | John Chilton | 27 February 2018, 03:08:38 UTC | Starting work on 18.5.2 | 27 February 2018, 03:08:38 UTC |
| 46a49a0 | John Chilton | 27 February 2018, 03:08:14 UTC | Version 18.5.1 | 27 February 2018, 03:08:14 UTC |
| 180c923 | John Chilton | 27 February 2018, 03:08:00 UTC | Prep next release. | 27 February 2018, 03:08:00 UTC |
| cbc94f3 | John Chilton | 27 February 2018, 03:06:03 UTC | Starting work on 18.5.1 | 27 February 2018, 03:06:26 UTC |
| d3e80b2 | John Chilton | 27 February 2018, 03:05:26 UTC | Version 18.5.0 | 27 February 2018, 03:06:26 UTC |
| ad1ae5b | John Chilton | 27 February 2018, 03:05:12 UTC | Prep next release. | 27 February 2018, 03:06:26 UTC |
| 9e657e3 | John Chilton | 27 February 2018, 03:01:44 UTC | Merge pull request #93 from jmchilton/py3_hashing_outputs Yet another Python 3 fix, best not to loop indefinitely here. | 27 February 2018, 03:01:44 UTC |
| 07540b6 | John Chilton | 27 February 2018, 02:45:35 UTC | Yet another Python 3 fix, best not to loop indefinitely here. Now with a simple test. | 27 February 2018, 02:59:26 UTC |
| 8ae8264 | John Chilton | 26 February 2018, 19:15:41 UTC | Starting work on 18.1.1 | 26 February 2018, 19:15:41 UTC |
| f526420 | John Chilton | 26 February 2018, 19:15:17 UTC | Version 18.1.0 | 26 February 2018, 19:15:17 UTC |
| e6994da | John Chilton | 26 February 2018, 19:15:07 UTC | Prep next release. | 26 February 2018, 19:15:07 UTC |
| d24b871 | John Chilton | 26 February 2018, 19:13:06 UTC | Merge pull request #92 from nsoranzo/python3_fixes Python3 fixes | 26 February 2018, 19:13:06 UTC |
| eea2b79 | Nicola Soranzo | 26 February 2018, 18:19:37 UTC | Python3: unicodify before json.loads() Fix `planemo lint --conda_requirements`, see the following test traceback: ``` ====================================================================== FAIL: test_lint_dependencies_okay (tests.test_lint.LintTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/build/galaxyproject/planemo/tests/test_lint.py", line 101, in test_lint_dependencies_okay self._check_exit_code(lint_cmd) File "/home/travis/build/galaxyproject/planemo/tests/test_utils.py", line 100, in _check_exit_code raise AssertionError(message) nose.proxy.AssertionError: Planemo command [lint --conda_requirements /home/travis/build/galaxyproject/planemo/tests/../project_templates/seqtk_complete/seqtk_seq.xml] resulted in unexpected exit code [-1], expected exit code [0]]. Command output [Linting tool /home/travis/build/galaxyproject/planemo/project_templates/seqtk_complete/seqtk_seq.xml ... Traceback (most recent call last): File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/testing.py", line 279, in invoke prog_name=self.get_default_prog_name(cli), **extra) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 697, in main rv = self.invoke(ctx) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 895, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 535, in invoke return callback(*args, **kwargs) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/decorators.py", line 64, in new_func return ctx.invoke(f, obj, *args[1:], **kwargs) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/click/core.py", line 535, in invoke return callback(*args, **kwargs) File "/home/travis/build/galaxyproject/planemo/planemo/cli.py", line 177, in handle_blended_options return f(*args, **kwds) File "/home/travis/build/galaxyproject/planemo/planemo/commands/cmd_lint.py", line 58, in cli recursive=kwds["recursive"] File "/home/travis/build/galaxyproject/planemo/planemo/tool_lint.py", line 31, in lint_tools_on_path if not lint_tool_source(tool_xml, **lint_args): File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/lint.py", line 17, in lint_tool_source lint_tool_source_with(lint_context, tool_source, extra_modules) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/lint.py", line 53, in lint_tool_source_with lint_context.lint(name, value, tool_source) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/lint.py", line 81, in lint lint_func(lint_target, self) File "/home/travis/build/galaxyproject/planemo/planemo/linters/conda_requirements.py", line 18, in lint_requirements_in_conda (best_hit, exact) = best_practice_search(conda_target) File "/home/travis/build/galaxyproject/planemo/planemo/conda.py", line 155, in best_practice_search return conda_util.best_search_result(conda_target, conda_context=conda_context, channels_override=BEST_PRACTICE_CHANNELS, offline=offline) File "/home/travis/build/galaxyproject/planemo/.tox/py34/lib/python3.4/site-packages/galaxy/tools/deps/conda_util.py", line 462, in best_search_result hits = json.loads(res).get(conda_target.package, []) File "/usr/lib/python3.4/json/__init__.py", line 312, in loads s.__class__.__name__)) TypeError: the JSON object must be str, not 'bytes' ``` | 26 February 2018, 18:19:41 UTC |
| fc6c3d6 | Nicola Soranzo | 26 February 2018, 17:40:31 UTC | Cleaner imports | 26 February 2018, 17:40:31 UTC |
| 3cfdd1f | John Chilton | 23 February 2018, 23:45:24 UTC | Merge pull request #90 from jmchilton/update_galaxy Update against the latest Galaxy dev, update version to track 18.1.XXX. | 23 February 2018, 23:45:24 UTC |
| 1e90c7b | John Chilton | 23 February 2018, 23:38:04 UTC | Lint fix - fix a W503 error in galaxy.web.stack. | 23 February 2018, 23:38:04 UTC |
| cdaab5a | John Chilton | 23 February 2018, 20:39:13 UTC | Update against the latest Galaxy dev, update version to track 18.1.XXX. | 23 February 2018, 23:36:19 UTC |
| 052fb81 | John Chilton | 23 February 2018, 02:20:28 UTC | Starting work on 17.9.13 | 23 February 2018, 02:20:28 UTC |
| 4612266 | John Chilton | 23 February 2018, 02:20:02 UTC | Version 17.9.12 | 23 February 2018, 02:20:02 UTC |
| b115bfa | John Chilton | 23 February 2018, 02:19:46 UTC | Prep next release. | 23 February 2018, 02:19:46 UTC |
| 9f3e744 | John Chilton | 23 February 2018, 02:18:36 UTC | Merge pull request #89 from nsoranzo/fixes_for_py3_planemo Fixes for Python3 planemo | 23 February 2018, 02:18:36 UTC |
| fcfb1ae | Nicola Soranzo | 22 February 2018, 20:54:40 UTC | Python3: unicodify before writing to stdout/stderr | 22 February 2018, 20:54:40 UTC |
| 704b240 | Nicola Soranzo | 22 February 2018, 20:53:48 UTC | Fix redirecting_io for io.StringIO objects | 22 February 2018, 20:53:48 UTC |
