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43 Commits
Author SHA1 Message Date
Nicola Soranzo 30f60493c3 Format Python code with black 23.1.0 
with manual fixes to 3 files to make them compatible with black 22.12.0 .

We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
 2023-02-01 23:51:03 +00:00
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
Nicola Soranzo 3b03237b94 Remove redundant licensing info 
to simplify future license migration.
 2022-08-28 19:11:09 +01:00
mvdbeek a9420d24b5 Drop remaining references to uWSGI 2022-03-21 13:44:37 +01:00
mvdbeek d7ddc95943 Drop init scripts that are likely unused 2022-03-15 21:59:21 +01:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
Nicola Soranzo 90a729e431 New pyupgrade fixes 
Found by running `ack --type=python -f | grep -v '^tools/' | xargs pyupgrade --py36-plus`
 2021-10-24 12:10:34 +01:00
mvdbeek 9d45e2b0db Remove unused legacy controller things 2021-06-19 16:28:56 +02:00
Nicola Soranzo d26b3d9848 Fix all E203, E741 and W504 flake8 errors 2021-01-18 10:35:41 +00:00
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
Nicola Soranzo 0c931235af Change all remaining old-style classes to new style 2018-09-17 12:26:07 +01:00
Nicola Soranzo 18221ae931 paster.pid/log to galaxy.pid/log reference update 
Fix errors in `first_startup` jobs:
https://travis-ci.org/galaxyproject/galaxy/jobs/316342622#L1029

Introduced in https://github.com/galaxyproject/galaxy/pull/4475
 2017-12-15 15:34:47 +00:00
Nicola Soranzo 6f722861cf Python3: fix moved imports 
Add `.ci/check_py3_compatibility.sh` script to find library modules
that have been moved in Python3. Fix errors found by the script.
 2017-12-15 01:03:28 +00:00
Nicola Soranzo d1bc98dfcb Python3: fix remaining print statements 
Remove some debugging prints.
Fix import order.
Consolidate exception logging in ToolShed database migrations.
 2017-10-12 18:34:29 +01:00
Nicola Soranzo a353b2e88f Fix E127 errors introduced by previous commit 
using:
```
autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E127 .
```
 2017-08-17 11:35:39 +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
E Rasche 2f992d90ae Rebase 2017-06-01 16:43:21 +00:00
Nate Coraor 86a7880e48 Update Nagios check 2017-02-07 11:25:59 +11:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
Nicola Soranzo cc336f61c0 Make some files compatible with Python3 
Also enlarge the set of files tested with flake8 under Python3
 2016-06-03 19:24:46 +01:00
Nicola Soranzo 6ba6f798ec Fix more E203 flake8 errors 2016-05-17 23:53:16 +01:00
Nicola Soranzo 8a43b2b492 Python 3: use "as" instead of comma in except clause 2016-05-17 23:53:16 +01:00
John Chilton f0272e02f7 Merge pull request #2109 from mvdbeek/fix_debian_init_script 
Update debian init script
 2016-04-08 13:18:03 -04:00
Marius van den Beek d6a7acab99 Update debian init script 
to include instructions for starting galaxy >= 16.01.
 2016-04-08 16:55:45 +02:00
Marius van den Beek 0de8832715 Change program name to galaxy_web 2016-04-06 14:46:12 +02:00
Marius van den Beek 974a9adc1b Add sample supervisor config 
for galaxy served by uwsgi, with seperate handlers.
 2016-04-06 12:02:38 +02:00
Mikael Loaec 1aaf65e8b6 missing ;; in case stop 2016-03-11 20:43:24 +01:00
Mikael Loaec d9c00771d0 adding blank line to separate function 2016-03-11 18:24:43 +01:00
Mikael Loaec 6d6b637299 removing lock files creation and deletion because of rigths problems in case of using galaxy user 2016-03-11 18:20:17 +01:00
Mikael Loaec 0697364f9d adding contrib init for reports and modifying status check to have output by process in case multiprocess 2016-03-11 17:21:22 +01:00
Nicola Soranzo af2f93b236 flake8 contrib/ . 2015-09-09 19:34:42 +01:00
Nicola Soranzo cc9b0bed85 Fix all E712 errors. Standardize sqlalchemy imports. 2015-07-14 20:49:34 +01:00
Nate Coraor 8fadc6392b Rename universe_wsgi.ini -> galaxy.ini everywhere. 2014-09-15 16:43:51 -04:00
Nate Coraor 1b6f2bf27a Fix check_galaxy for recent framework changes. 2012-11-27 15:57:05 -05:00
Nate Coraor 624fa70cbc Remove contrib/multiprocess.sh since run.sh can run all of the processes itself now. 2012-08-08 11:12:42 -04:00
Nate Coraor f866c529a8 Provide a modified check_galaxy.py that is suitable for use with nagios. 2012-05-26 15:00:36 -04:00
Greg Von Kuster e00f7d04fc Add script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample contributed by Anne Pajon. 2012-03-28 10:58:19 -04:00
Nate Coraor 9b5e9992f0 Fedora(/RHEL/SL/CentOS) init script, thanks Brad Chapman! 2011-12-05 14:55:00 -05:00
Nate Coraor e8ab977d8b Add the "Galaxy ls" script to contrib/. Thanks, Simon McGowan. 2011-09-06 11:51:01 -04:00
Greg Von Kuster 3eacfa47ea Add Assaf Gordon's collect_job_timings.sh script. 
This shell script produces the report, combining information from SGE's QACCT with the galaxy job/dataset information.

The output contains:
job, user, tool name, dbkey, total input size in bytes, waiting time in SGE queue, actual SGE executiong running time, and some other tidbits.

This allows finding how much running time each user had on the cluster,
how much time each tool/user spend idly waiting,
and some possible correlations between tools, dbkeys, input size and running time.

The script is tightly coupled with SGE and PostgreSQL, but can probably be adapted to PBS/MySQL.
 2011-07-21 13:55:24 -04:00
Florent Angly a26e479b86 MacOS X daemon launcher: 
* fixed bad XML
  * better default parameters
  * improved documentation
 2010-12-13 13:54:22 +10:00
Nate Coraor d8281a6e77 add multiprocess.sh example script for running multiple galaxy processes. instructions coming later. 2010-05-20 17:00:12 -04:00
Nate Coraor a51ce47c40 Add contributed Debian init script and OS X LaunchDaemon plist from James Casbon, and my Solaris SMF manifest. 2009-10-30 12:41:17 -04:00