| 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 |
| 0c69916 | John Chilton | 22 February 2018, 16:20:26 UTC | Fix bad merge in 600d5d71590443ba66aee472b1960a3ea5f4c76d. Lost this change from #84. | 22 February 2018, 16:20:26 UTC |
| f23d619 | John Chilton | 22 February 2018, 15:40:41 UTC | Starting work on 17.9.12 | 22 February 2018, 15:40:41 UTC |
| e6d2daf | John Chilton | 22 February 2018, 15:40:12 UTC | Version 17.9.11 | 22 February 2018, 15:40:12 UTC |
| fe40e8f | John Chilton | 22 February 2018, 15:39:13 UTC | Prep the next release. | 22 February 2018, 15:39:13 UTC |
| bdb73ea | John Chilton | 22 February 2018, 14:59:29 UTC | Merge pull request #88 from jmchilton/read1_hack Small Fixes | 22 February 2018, 14:59:29 UTC |
| 1800916 | John Chilton | 22 February 2018, 04:18:01 UTC | Add missing modules to list of packages in setup.py. | 22 February 2018, 04:18:01 UTC |
| 17d1676 | John Chilton | 22 February 2018, 04:17:20 UTC | Python 3 fix. | 22 February 2018, 04:17:20 UTC |
| 119a201 | John Chilton | 18 January 2018, 21:57:41 UTC | Merge pull request #86 from jmchilton/read1_hack Restore gzip read1 hack. | 18 January 2018, 21:57:41 UTC |
| be839c1 | John Chilton | 18 January 2018, 21:35:35 UTC | Restore gzip read1 hack. Accidentally dropped it out. | 18 January 2018, 21:36:00 UTC |
| 72ad9ba | John Chilton | 18 January 2018, 20:45:01 UTC | Merge pull request #85 from galaxyproject/update_to_latest_galaxy Upgrade to latest galaxy. | 18 January 2018, 20:45:01 UTC |
| c7cc9ca | John Chilton | 18 January 2018, 20:39:36 UTC | Another Python 3 test fix. | 18 January 2018, 20:39:36 UTC |
| c056e39 | John Chilton | 18 January 2018, 20:27:41 UTC | Fix Python 3 issue with galaxy.util.path. | 18 January 2018, 20:27:41 UTC |
| 600d5d7 | John Chilton | 18 January 2018, 17:02:37 UTC | Upgrade to latest galaxy. | 18 January 2018, 19:50:35 UTC |
| 763e6ca | John Chilton | 23 November 2017, 16:58:20 UTC | Starting work on 17.9.11 | 23 November 2017, 16:58:20 UTC |
| 064cb5b | John Chilton | 23 November 2017, 16:57:55 UTC | Version 17.9.10 | 23 November 2017, 16:57:55 UTC |
| 164891c | John Chilton | 23 November 2017, 16:57:41 UTC | Prepare next release. | 23 November 2017, 16:57:41 UTC |
| 9470e3a | John Chilton | 23 November 2017, 16:53:25 UTC | Merge pull request #84 from galaxyproject/tripple make multitool-container generation a little bit more stable | 23 November 2017, 16:53:25 UTC |
| 73e35b1 | John Chilton | 23 November 2017, 16:52:01 UTC | Merge pull request #83 from galaxyproject/catch_error catches an error when conda search does not find the package at all | 23 November 2017, 16:52:01 UTC |
| 8412943 | Björn Grüning | 22 November 2017, 17:36:40 UTC | catches an error when conda search does not find the package at all This was causing bad error messages in planemo-monitor: https://travis-ci.org/galaxyproject/planemo-monitor#L892 | 22 November 2017, 17:36:40 UTC |
| e067e01 | Björn Grüning | 22 November 2017, 16:59:52 UTC | remove r-channel | 22 November 2017, 16:59:52 UTC |
| c12ad29 | Björn Grüning | 22 November 2017, 16:05:04 UTC | missing imports | 22 November 2017, 16:05:04 UTC |
| eefaf60 | Björn Grüning | 22 November 2017, 16:00:43 UTC | smaller then 10 | 22 November 2017, 16:00:43 UTC |
| 7b9b5b8 | Björn Grüning | 22 November 2017, 15:55:12 UTC | use PrintProgress() | 22 November 2017, 15:55:12 UTC |
| d000016 | Björn Grüning | 22 November 2017, 15:52:14 UTC | add PrintProgress class to trick travis for long running downloads | 22 November 2017, 15:52:14 UTC |
| ca9d70c | Björn Grüning | 22 November 2017, 15:45:08 UTC | ok, smallest container is 20 | 22 November 2017, 15:45:08 UTC |
| 31cf7e4 | Björn Grüning | 22 November 2017, 14:15:08 UTC | import sys | 22 November 2017, 14:15:08 UTC |
| 09f0417 | Björn Grüning | 22 November 2017, 14:06:24 UTC | fail early | 22 November 2017, 14:06:24 UTC |
| 60a4d58 | Björn Grüning | 22 November 2017, 13:18:47 UTC | use miniconda3 woth python3 as default | 22 November 2017, 13:18:47 UTC |
| 75e2f4f | Björn Grüning | 22 November 2017, 13:00:08 UTC | tripple the size for small containers | 22 November 2017, 13:00:08 UTC |
| ed5421c | Björn Grüning | 22 November 2017, 09:46:18 UTC | Merge pull request #82 from jerowe/feature/docs-mulled Feature/docs mulled | 22 November 2017, 09:46:18 UTC |
| 0855fef | Jillian Rowe | 20 November 2017, 05:15:25 UTC | fixed up a few things | 20 November 2017, 05:15:25 UTC |
| 5552214 | Jillian Rowe | 20 November 2017, 05:13:24 UTC | adding in docs for involucro on your own quay namespace | 20 November 2017, 05:13:24 UTC |
| 041d04c | John Chilton | 08 October 2017, 14:07:37 UTC | More docs... - Add some mulled docs sync-ed up with Galaxy. - Add some dependency resolution docs refactored from Galaxy docs. | 09 October 2017, 01:55:55 UTC |
| b3a3304 | John Chilton | 08 October 2017, 11:49:14 UTC | Docs improvements. - Rename CODE_OF_CONDUCT.md to CODE_OF_CONDUCT.rst so it shows up in the docs. - Fill out installation docs. - Add a header element to README.rst so it renders as part of the sphinx docs. - Remove uninitialized coverage testing badge. | 08 October 2017, 12:03:20 UTC |
| 3c920e8 | John Chilton | 08 October 2017, 11:36:44 UTC | Add D107 to lint ignore list. Some things in a docstring linted module don't conform to this. | 08 October 2017, 11:36:44 UTC |
| 9bbb56b | John Chilton | 08 October 2017, 11:29:51 UTC | Fix docs link on README and rebuild RST docs. | 08 October 2017, 11:29:51 UTC |
| fcb00ed | John Chilton | 27 September 2017, 18:00:21 UTC | Starting work on 17.9.10 | 27 September 2017, 18:00:21 UTC |
| a25e9af | John Chilton | 27 September 2017, 17:59:35 UTC | Version 17.9.9 | 27 September 2017, 17:59:35 UTC |
| eafbd1f | John Chilton | 27 September 2017, 17:58:52 UTC | Merge pull request #79 from jmchilton/17.9.9 Update to the latest 17.09 upstream changes. | 27 September 2017, 17:58:52 UTC |
| 2c758b6 | John Chilton | 27 September 2017, 17:41:23 UTC | Merge pull request #1 from natefoo/17.9.9 Reapply #76. | 27 September 2017, 17:41:23 UTC |
| 91944fc | Nate Coraor | 27 September 2017, 17:34:07 UTC | Reapply #76. | 27 September 2017, 17:34:07 UTC |
| 7621d07 | John Chilton | 27 September 2017, 17:19:35 UTC | Another fix for bz2. | 27 September 2017, 17:19:35 UTC |
| cd15faf | John Chilton | 27 September 2017, 17:02:29 UTC | Fix bz2file unavailable in galaxy-lib. | 27 September 2017, 17:02:29 UTC |
| 675b9dd | John Chilton | 27 September 2017, 16:51:41 UTC | Update to the latest Galaxy version. | 27 September 2017, 16:55:14 UTC |
| 7b6597a | John Chilton | 26 September 2017, 14:18:23 UTC | Starting work on 17.9.9 | 26 September 2017, 14:18:23 UTC |
| c0cff97 | John Chilton | 26 September 2017, 14:17:56 UTC | Version 17.9.8 | 26 September 2017, 14:17:56 UTC |
| 3d380e8 | John Chilton | 26 September 2017, 14:17:28 UTC | Rev next release. | 26 September 2017, 14:17:49 UTC |
| 3feba1e | John Chilton | 26 September 2017, 14:16:56 UTC | Merge pull request #78 from jmchilton/cwl_update_5 Update CWL utilities to latest CWL branch. | 26 September 2017, 14:16:56 UTC |
| 8e4e324 | John Chilton | 26 September 2017, 14:11:10 UTC | Update CWL utilities to latest CWL branch. | 26 September 2017, 14:11:10 UTC |
| 3b1e54d | John Chilton | 19 September 2017, 10:59:25 UTC | Merge remote-tracking branch 'origin/master' | 19 September 2017, 10:59:25 UTC |
| ad8c93e | John Chilton | 19 September 2017, 10:58:50 UTC | Starting work on 17.9.8 | 19 September 2017, 10:58:50 UTC |
| a5abb20 | John Chilton | 19 September 2017, 10:58:26 UTC | Version 17.9.7 | 19 September 2017, 10:58:26 UTC |
| c0bb6da | John Chilton | 19 September 2017, 10:58:12 UTC | Prep next release. | 19 September 2017, 10:58:12 UTC |
| c72d6db | John Chilton | 19 September 2017, 10:56:51 UTC | Merge pull request #77 from jmchilton/cwl_update_4 More CWL updates. | 19 September 2017, 10:56:51 UTC |
| ea959ac | John Chilton | 19 September 2017, 00:59:37 UTC | More CWL updates. | 19 September 2017, 00:59:37 UTC |
| 3a1c6a3 | John Chilton | 15 September 2017, 14:24:49 UTC | Starting work on 17.9.7 | 15 September 2017, 14:24:49 UTC |
| 898047d | John Chilton | 15 September 2017, 14:22:54 UTC | Version 17.9.6 | 15 September 2017, 14:22:54 UTC |
| c4ad7f2 | John Chilton | 15 September 2017, 14:22:42 UTC | Update HISTORY.rst for next release. | 15 September 2017, 14:22:42 UTC |
| 3797907 | John Chilton | 15 September 2017, 14:20:13 UTC | Merge pull request #76 from jmchilton/remove_defunct_command_check Remove defunct command attribute checks. | 15 September 2017, 14:20:13 UTC |
| ce5ea4e | John Chilton | 15 September 2017, 13:44:59 UTC | Remove defunct command attribute checks. Better just to use the XSD - fixes https://github.com/galaxyproject/planemo/issues/726. | 15 September 2017, 13:44:59 UTC |
