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2a0474730bd3a52cab7a1dbcd16b990b2b7ac0b4
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259 Commits
Author SHA1 Message Date
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
Nicola Soranzo 11b4f3a60c Fix import order and Python3 compatibility for tools/ 
xref #1715
 2016-09-29 19:26:22 +01:00
nturaga 4fabf51f4b typo in summary statistics tool 2016-07-20 15:27:24 -04:00
Gildas Le Corguillé f951249c79 Update gsummary.xml 
Delete r and rpy deps
 2016-07-12 13:28:42 +02:00
Gildas Le Corguillé e862067332 Update gsummary.xml 2016-07-07 16:41:06 +02:00