Nicola Soranzo
7fee81607c
Add linting with ruff
...
ruff (https://github.com/charliermarsh/ruff ) is a new and extremely fast
Python linter, written in Rust.
Ruff can be used to replace Flake8 (plus a variety of plugins), isort,
pydocstyle, yesqa, eradicate, pyupgrade, and autoflake.
Here ruff is added to our current linters (flake8, flake8-bugbear and isort)
while we assess its reliability.
I've not enabled the isort rules because many of the options we use are not
implemented yet. I have instead enabled the pyupgrade rules (a tool which I
run manually every few months).
Also:
- Fix new linting errors reported by ruff.
2023-01-16 14:34:56 +00:00
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
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
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
f4203ca051
Fix errors reported by flake8 3.6.0
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Ignore W504.
2018-10-24 23:22:19 +01:00
Anthony Bretaudeau
0b191abaf1
pass the condition by a json file instead of arg
2018-04-19 15:24:29 +02:00
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
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
Nicola Soranzo
8a43b2b492
Python 3: use "as" instead of comma in except clause
2016-05-17 23:53:16 +01:00
Nicola Soranzo
ed4132d9c0
Python3: Use open() instead of file()
2016-05-17 23:53:16 +01:00
Nicola Soranzo
69cda48690
Remove remaining references to galaxy.eggs . flake8 some files in tools/ .
2015-10-26 19:29:13 +00:00
John Chilton
be172fdfda
Merge Pull Request #244 .
2013-11-04 23:42:06 -06:00
John Chilton
4fb2b89347
White-list expressions executed by filtering and dna_filtering tools.
2013-11-04 14:55:00 -05:00
Bjoern Gruening
b172b602ad
add [ and ] to mapped strings and advanced filters
2013-10-25 10:34:28 +02:00
Jeremy Goecks
ea8d337316
Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.
2013-01-29 10:37:16 -05:00
Jeremy Goecks
a4b56c0b74
Improve filtering tool's stdout reporting of lines filtered; fixes #536
2011-06-15 13:22:18 -04:00
Kanwei Li
34155271b3
[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537 . Fixes #535
2011-05-27 10:47:17 +02:00
Jeremy Goecks
ccf07c72aa
Enable filter tool to operate correctly on files with a variable number of columns (such as SAM files). Tool prepares and processes only columns up to and including the right-most column (i.e. column with the largest index) in the filtering condition, and subsequent columns are ignored. New functional test added for this functionality as well.
2010-11-04 16:30:34 -04:00
Greg Von Kuster
a14492c491
Added from __future__ import division to the Filter tool and increased the version, and fixed the URL in the new bx_browser tool config.
2010-01-14 11:26:08 -05:00
Greg Von Kuster
d0d7875192
Deprecated code corrections for supporting Python 2.6. Many of the Python 2.6 eggs are still throwing DeprecationWarning messages, so some things still won't work. Eggs for 2.6 need to be re-scrambled after corrections are made.
2009-08-14 15:37:31 -04:00
Guruprasad Anada
b88df9bdc3
Bug fixes for compare, Group and filter tools.
2008-12-02 11:41:25 -05:00
Daniel Blankenberg
b9e242e4eb
Add a new metadata type of Metadata Files.
...
These are now used to store the list of chromosomes for species as well as the index for MAF files.
MAF tools have been enhanced to make use of index files when available.
TODO: When datasets are purged from disk, these files should also be purged.
2008-10-22 13:49:22 -04:00
Greg Von Kuster
7aace9ccaa
Convert metadata unicode strings to ascii ( previous code doesn't seem to do anything, am I missing something? ). Add no_value metadata attribute to columns and column_types metadata. Fix for column_maker and filter tools.
2008-09-24 11:14:44 -04:00
Greg Von Kuster
bfabec75a0
Fixes for column_maker and filtering tool to use new approach for handling metadata in the tool params - functional tests should now pass.
2008-07-23 17:12:01 -04:00
Greg Von Kuster
bb4b6c63b1
Improved information in filtering tool.
2008-05-15 12:38:30 +00:00
Greg Von Kuster
160c9d9a4f
Fix for the filter tool, also improved the way we determine column_types meta data.
2008-05-13 18:51:00 +00:00
Greg Von Kuster
bb3cd06be1
Extensive fixes for filtering tool, now uses column_types metadata, no more MemoryErrors!
2008-05-09 14:57:19 +00:00
Nate Coraor
7560751dc8
Separate framework and tool environments.
...
Whether running locally or via PBS, $PATH should now be handled in your
user's environment.
This also fixes problems like PYTHONPATH on the new blast nodes being
wrong (because they are x86_64 and the frontends are i686).
Note that you can actually start Galaxy without having an eggs dir now.
2008-04-11 20:11:21 +00:00
Greg Von Kuster
135c9a0377
Removed the remainder of the tool version subdirectories.
2008-03-03 18:38:57 +00:00
Greg Von Kuster
78b2d4b78e
Added tool version directories for stats tools directory.
2008-02-22 20:26:57 +00:00
Greg Von Kuster
e54be223b2
Better way to skip invalid comment lines in filtering tool. Better numerical value checks in interval.py.
2007-12-18 14:52:04 +00:00
Greg Von Kuster
7718b28839
Better error condition handling for some tools. I've made these changes because anything printed to stderr now results in the tool state being "error" and tools with this state are no longer allowed as input datasets for tools.
2007-12-12 19:30:26 +00:00
Greg Von Kuster
65aeb6ec40
Better behavior in filter tool if filtering condition includes improper syntax (like commas).
2007-07-13 13:08:36 +00:00
Greg Von Kuster
437399fc66
Added expression validation for column_maker, filter.
2007-06-01 14:31:13 +00:00
Greg Von Kuster
c2d1d0189f
Some corrections for tracking referrals. Eliminated the referer column from the event table as it is not needed.
2007-04-10 16:07:53 +00:00
Greg Von Kuster
baacb7c67c
Enhanced security measures for condition entered as free text - should make tool more useful and reduce job errors.
2007-04-05 18:24:47 +00:00
Greg Von Kuster
f42b4c6742
Re-added the safety measures.
2007-03-27 13:56:16 +00:00
Greg Von Kuster
5cfc24d89e
Cleaned up the behavior of the filter tool and eliminated restrictions on filtering on words in the data. Should eliminate most job errors.
2007-03-27 13:18:33 +00:00
Greg Von Kuster
e34fff8ff8
Added a corner-case fix for auto-detect file formats. Updated info displayed to user on upload and filter tools and added more valid words to filter tool.
2007-03-23 17:46:06 +00:00
Greg Von Kuster
2b05ca975f
Fixed a bug in sniff.py and added a new unit test case to cover it. Added the hpvar data source tool to tool_conf.xml.sample. Slightly enhanced the filter and compute tools.
2007-03-19 19:55:57 +00:00
Greg Von Kuster
7ab5369033
Corrected the way these tools read input datasets to keep them from entering infinite loops if the dataset is empty.
2007-02-27 16:32:05 +00:00
Greg Von Kuster
5a8135f56c
Minor correction to the message for the location of the first invalid line in a dataset, if there is in fact one.
2007-02-21 21:44:22 +00:00
Greg Von Kuster
67e1bb8846
Enhanced the Filter tool to handle invalid data and to display more useful, informative messages to the user.
2007-02-21 18:41:58 +00:00
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
Nicola Soranzo