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263 Commits
Author SHA1 Message Date
Nicola Soranzo e34590b687 Update deprecated Python import 
which doesn't work any more on Python 3.10 .
 2022-06-02 17:58:42 +01:00
Dannon Baker 03351d2a9f Apply black to tools as well 2022-02-03 09:12:13 -05:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
Nicola Soranzo bd0cefa020 Don't use triple-quoted strings as comments 
They are expressions that get uselessly evaluated.

These were reported as B018 errors by flake8-bugbear 21.11.28 , but B018 for
strings has then been disabled in 21.11.29 since these strings can also be
used as inline attribute doc strings or module variable docstrings (not our
case though).
 2021-11-29 23:02:34 +00:00
John Chilton 2a0474730b Rev mypy. 2021-04-23 14:49:53 -04:00
Nicola Soranzo 9d74bba7fb Drop support for retired Python 3.5 
Upgrade syntax using `pyupgrade --py36-plus` .

Manually drop several `six` imports.

Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
 2020-10-07 11:52:13 +01:00
Alexandru Mahmoud da860b09c8 filtering.py check_expression adding 'Constant' 2020-09-22 17:04:52 -04:00
Wolfgang Maier 41c547999b Bump tool wrapper version 2020-08-26 15:59:44 +02:00
Wolfgang Maier e003fbc081 Add doctests for additional allowed types 2020-08-26 14:17:43 +02:00
Wolfgang Maier 8639de2dee Allow unary plus and minus in filtering 2020-08-26 14:06:40 +02:00
Nicola Soranzo 739ab59eaa Merge branch 'release_20.01' into dev 2020-02-20 00:23:19 +00:00
Nicola Soranzo d4662fd952 Merge branch 'release_20.01' into dev 2020-02-19 12:43:07 +00:00
mvdbeek fb71055bfe Fix typo, other places that use wrong galaxy-util version 2020-02-19 09:56:02 +01:00
mvdbeek 05e8117995 Move aggregate_scores_in_intervals2 out of GALAXY_LIB_TOOLS_UNVERSIONED 2020-02-12 09:47:36 +01:00
Nicola Soranzo 0a26ed38b2 Merge branch 'release_20.01' into dev 2020-02-05 15:26:27 +00:00
Nicola Soranzo 1dc1e5f219 Python3: unicodify the output of `subprocess.check_output()` 
By default it's a bytestring.

Also:
- don't use `shell=True`
- add a `splitlines()` forgotten in commit 670897ec5c
- raise exception instead of returning `error_info` in `docker_to_singularity()`
- use a random temp dir in `singularity_container_test()`
 2020-02-05 12:13:39 +00:00
Nicola Soranzo f5cd88465e Make str.join()s more efficient 
by using generator expressions and tuples instead of lists.
 2020-01-23 11:06:32 +00:00
M Bernt 2ea05e81f8 grouping: redecided for the less intrusive rstrip 2019-11-11 11:17:20 +01:00
M Bernt 3a0d9325a6 grouping: strip newlines 
fixes https://github.com/galaxyproject/galaxy/issues/8383

more generally: if grouping is done on the last column then the newline
was retained and contained in the output.
 2019-11-10 22:16:00 +01:00
mvdbeek 16e244ad5a Quit gsummary script with non-zero exit code upon error 2019-06-24 11:07:00 +02:00
Nicola Soranzo c9f63ac2f8 Simplify code 2019-04-29 19:22:11 +01:00
mvdbeek 0c1334fea0 Fix grouping1 with modern sort, fix test data 
This tool currently fails with `sort: multi-character tab '$\\\\t'\n`
(https://jenkins.galaxyproject.org/view/All/job/docker-main-tools/lastCompletedBuild/testReport/test.functional/test_toolbox_pytest/test_tool_Grouping1_test_1_/).
This also removes test data that should be included in
galaxy-test-data instead (xref
https://github.com/galaxyproject/galaxy-test-data/pull/5),
and adds a test file that was missing from
https://github.com/galaxyproject/galaxy/pull/7205.
 2019-04-29 17:38:10 +02:00
John Chilton 00652f0b3a Merge pull request #7205 from bernt-matthias/topic/grouping-w-emptycells 
group: don't remove empty cells at the begin/start of lines
 2019-02-14 14:53:34 -05:00
Nicola Soranzo d5a406cef7 Fix errors reported by new flake8 3.7.3 2019-01-31 13:47:21 +00:00
bernt@informatik.uni-leipzig.de bc86e37d85 groupby: reenabled tests and added some, more bugfix 
- make script exit with code 1 in case of error
- removed one more strip
- adapted tool syntax to best practices
 2019-01-12 16:13:23 +01:00
M Bernt b18aa199aa group: don't remove empty cells at the begin/start of lines 
currently group removes empty cells at the begin and end of lines

additionally the sort command line is changed (hoping that this looks a bit
more obvious)
 2019-01-11 14:41:11 +01:00
John Chilton bf550da2af Merge pull request #6684 from nsoranzo/deprecate_param_size 
Deprecate `size` attribute of `<param/>` and remove it from tools
 2018-12-12 10:51:28 -05:00
John Chilton d06718ef24 Merge pull request #6577 from bernt-matthias/topic/grouping-wreplace 
improved grouping tool
 2018-12-12 10:45:53 -05:00
Nicola Soranzo f4203ca051 Fix errors reported by flake8 3.6.0 
Ignore W504.
 2018-10-24 23:22:19 +01:00
Nicola Soranzo 0c931235af Change all remaining old-style classes to new style 2018-09-17 12:26:07 +01:00
M Bernt 7b027d8a1f improved grouping 
- replaces non 'floatable' values to a user supplied default value
- do not strip lines because this removes empty cells at the ends
- added some comments to python code
 2018-09-10 12:05:15 +01:00
Nicola Soranzo f865e8359f Deprecate size attribute of <param/> and remove it from tools 
Also:
- dos2unix test/functional/tools/for_workflows/head.xml
- Single-quote text and data params in `<command/>`
- Remove deprecated `interpreter` attribute of `<command />`
 2018-09-10 11:34:37 +01:00
mvdbeek c939e7bb61 Bump version of Summary Statistics for rpy2 version update 2018-09-05 18:24:05 +02:00
mvdbeek 918634f1fb Switch rpy2 to 2.9.4, 2.7.8 can't be resolved 2018-09-05 14:22:00 +02:00
mvdbeek 2d732715ff Fix grouping tool 2018-09-05 14:22:00 +02:00
mvdbeek 6405aeb86c Comment out tests with unavailable test data 2018-09-05 14:22:00 +02:00
mvdbeek 00e8d4ee76 Quote Filter1 input and output 2018-08-13 16:16:55 +02:00
Anthony Bretaudeau dadb4fcda7 change back version 2018-04-20 09:45:06 +02:00
Anthony Bretaudeau dc4902353f add test case for fixed bug 2018-04-20 09:44:27 +02:00
Anthony Bretaudeau 0b191abaf1 pass the condition by a json file instead of arg 2018-04-19 15:24:29 +02:00
Anthony Bretaudeau bb9963dddc fix quote escaping 2018-04-10 14:20:53 +02:00
Anthony Bretaudeau 16f9e58af5 quotes 2018-04-10 12:02:18 +02:00
Anthony Bretaudeau de5ac42fa9 more tolerant sanitizing 2018-04-10 11:36:08 +02:00
Nicola Soranzo b3dc7923db Python3: use collections.Mapping instead of removed DictMixin 2017-12-12 15:30:53 +00:00
M Bernt b2cc634e8a python3 fix (#5043) 
strings can not be written to byte mode file handlers.
writing resulted in: TypeError: a bytes-like object is required, not 'str'

Alternative would be to make string byte.
 2017-11-20 22:34:02 +01:00
Nicola Soranzo 9b4de72ca6 Fix all E722 errors and ignore E741 
Introduced in flake8 3.5.0
Fix import order.
 2017-10-24 11:29:09 +01:00
Nicola Soranzo 21b44bf348 Fix all E201 and E202 style errors 
using the following command:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 .
```
 2017-08-17 11:35:39 +01:00
Nicola Soranzo 03a807e374 Lint some tools 2017-01-23 21:11:43 +00:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Daniel Blankenberg ba07956117 Fix tabular filtering tool broken in #2983 2016-10-13 10:40:40 -04:00