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Commit Graph
415 Commits
Author SHA1 Message Date
mvdbeek 50fe6a9cfb Add missing requirements to perl tools 2023-10-06 13:43:55 -04:00
Björn Grüning a9f5400eae FileInput no longer accept 'U' in the file mode 2023-09-16 18:33:07 +02:00
Nicola Soranzo 64af46c4ae Fix new B018 errors raised by ruff 0.0.260 2023-04-13 16:53:01 +01:00
mvdbeek 73dc126e67 Use format_source="input" instead of format="input" 
Fixes https://github.com/galaxyproject/galaxy/issues/15302
 2023-01-13 10:58:57 +01:00
mvdbeek 350508909d Fix more tests 
Include a perl dependency and profile version for the `addValue` tool.
It otherwise fails on OSX with
```
INFO     galaxy.tool_util.output_checker:output_checker.py:155 Job failed because of contents in the standard error stream: [perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
	LC_ALL = (unset),
	LC_CTYPE = "C.UTF-8",
	LANG = (unset)
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
]
```

Also fix CollectionTypeDescription when collection_type is already CollectionTypeDescription
and fix some wrong type annotations in lib/galaxy/tools/actions/__init__.py

Into more fixes
 2022-11-09 15:35:31 +01:00
Wolfgang Maier ddebbd97b2 Bump wrapper version and declare updates to it WF-safe 2022-10-31 23:03:32 +01:00
Wolfgang Maier 74b7ed8b10 Simplify head wrapper - same functionality, no pipe 2022-10-31 15:27:40 +01:00
jancrichter 912dc47c8a bump version 2022-08-18 17:49:06 +02:00
jancrichter f9f7e97043 adjust tests to correctly test for retainment of header 2022-08-18 17:49:05 +02:00
jancrichter 7b10be9cb8 Append grep results to avoid overwriting header 
Currently, if "keep_header" is true, the header is copied to the output file, but is then overwritten by the grep results.
 2022-08-18 17:49:04 +02:00
Nicola Soranzo 00f7522e7e Merge branch 'release_22.01' into dev 2022-03-19 01:57:33 +00:00
Nicola Soranzo 5114b67902 Merge branch 'release_21.09' into release_22.01 2022-03-18 18:28:15 +00:00
Nicola Soranzo 8e4bdb58e4 Merge branch 'release_21.05' into release_21.09 2022-03-18 18:08:10 +00:00
mvdbeek e2d43806dc Fix `sff_extract` tool, drop type annotation 
I don't think this tool is really used much, but it is loaded in
`tool_conf.xml`.
https://github.com/galaxyproject/galaxy/pull/11877 added type
annotations, and that's a syntax error on 2.7

The alternative would be to fix the rest of the tool for 3.x,
but I think we're just wasting our time there and we shouldn't
touch this again.
 2022-03-16 15:24:55 +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
Dannon Baker c3605c7112 Merge remote-tracking branch 'upstream/release_21.09' into dev 2021-10-19 09:59:21 -04:00
John Chilton 54e8d22fa7 Check types of modules without type annotations in the their signatures on new modules. 
https://mypy.readthedocs.io/en/stable/command_line.html#cmdoption-mypy-check-untyped-defs

> it type checks the body of every function, regardless of whether it has type annotations. (By default the bodies of functions without annotations are not type checked.)
 2021-10-11 16:08:26 -04:00
Nate Coraor 6c39e132e7 Modernize sorter (sort1) tool: 
- Don't use shell, pipe with subprocess.PIPE instead
- Switch optparse for argparse
- Add missing coreutils requirement for `sort` command
- Change Python requirement from 2.7 to 3.8
 2021-10-01 12:47:14 -04:00
mvdbeek dcac61fd1d Fix linting in grep.py script 2021-07-12 18:29:26 +02:00
mvdbeek 4eda692eae Restore Grep1 version 1.0.1 
The select option value for inverting results changed from `true` to
`-v`, so if you don't update your workflow you'll run grep without
the `-v` flag.
I don't think there's a way around this change (that is now part of
21.05 for a while, so we can't just switch the option value back).

Addresses https://github.com/galaxyproject/galaxy/issues/12249.
We should also require an additional confirmation.
 2021-07-12 18:20:43 +02:00
mvdbeek 0f88e4a9da Fix patterns in Grep1 tool 
Fixes https://github.com/galaxyproject/galaxy/issues/12165
 2021-06-18 13:11:39 +02:00
mvdbeek 326e4c9c63 Ignore sigpipe in Show beginning1 tool 
Fixes https://github.com/galaxyproject/galaxy/issues/12093
 2021-06-09 11:28:41 +02:00
mvdbeek a6f5745ffa Add test that triggers sigpipe 2021-06-09 11:23:06 +02:00
Marius van den Beek d8e261dbc2 Merge pull request #11859 from bernt-matthias/topic/grep-header 
grep, tail, head: add option to keep header
 2021-05-04 19:07:46 +02:00
Matthias Bernt a94b8816f6 Merge branch 'topic/grep-header' of https://github.com/bernt-matthias/galaxy into topic/grep-header 2021-05-04 15:00:19 +02:00
Matthias Bernt a45f06b881 fix test 3 and error detection 
only error for exit code > 1:
 2021-05-04 14:59:23 +02:00
M BerntandMarius van den Beek 181b862250 Apply suggestions from code review 
- add profile
- add requirement

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2021-05-04 13:47:29 +02:00
Matthias Bernt 85f643bc66 remove python wrapper for grep tool 
and fix cli (`-n +2`) for head, tail, grep
 2021-05-04 10:49:23 +02:00
Matthias Bernt 8cc1c3bc0f some updates for grep, tail, head 
- CDATA for all
- exit code
- remove interpreter
- bump versions
- and add the tools to WORKFLOW_SAFE_TOOL_VERSION_UPDATES
 2021-05-03 13:15:08 +02:00
John Chilton 2a0474730b Rev mypy. 2021-04-23 14:49:53 -04:00
Matthias Bernt d1e3edfb68 consider header in tail/head wrapper 
and remove pl wrapper
 2021-04-19 13:57:57 +02:00
Matthias Bernt fc3c6eef97 grep: add option to keep header 
https://github.com/galaxyproject/tools-iuc/issues/3511
 2021-04-18 22:18:14 +02:00
mvdbeek d6954bdd22 Merge branch 'release_21.01' into dev 2021-02-23 08:59:14 +01:00
mvdbeek 53ede0c2e4 Merge branch 'release_20.09' into release_21.01 2021-02-23 08:58:14 +01:00
mvdbeek a20919edaa Make hash selection mandatory 2021-02-22 11:13:02 +01:00
Matthias Bernt 610e31147a add python requirement 2021-02-13 23:04:17 +01:00
Matthias Bernt 30fb1e2c2d Merge branch 'ccedmendoza_patch-1' of https://github.com/bernt-matthias/galaxy into ccedmendoza_patch-1 2021-02-13 22:03:16 +01:00
Matthias Bernt 4be9bc6430 bump tool version 2021-02-13 22:02:57 +01:00
M BerntandNicola Soranzo e4d9e1a29e Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-02-13 20:38:05 +01:00
Matthias Bernt faed88a1bd remove interpreter 2021-02-13 16:34:09 +01:00
Matthias Bernt cec6e6926b revert to a less intrusive change 2021-02-13 14:54:26 +01:00
ccedmendoza 765e700803 remove trailing white space 2021-02-13 14:47:24 +01:00
ccedmendoza 8491730b83 Corrent linting 2021-02-13 14:47:24 +01:00
ccedmendoza f44c0b311c Simplify script while adding empty lines and comments handling 2021-02-13 14:47:24 +01:00
ccedmendoza f9cf7e640c Make filter work with file containing header 2021-02-13 14:47:24 +01:00
Nicola Soranzo d26b3d9848 Fix all E203, E741 and W504 flake8 errors 2021-01-18 10:35:41 +00:00
Nicola Soranzo 452aba9ee3 Fix remaining issues reported by bugbear; add it to flake8 reqs 2021-01-16 05:58:15 +00:00
Helena Rasche f5a3545541 Merge branch 'dev' into edam-tool-panel 2021-01-07 19:54:12 +01:00
Nicola Soranzo 1e9f83b53e Add missing single-quotes in tools Cheetah 2020-11-10 19:29:22 +00:00