Commit Graph
58 Commits
Author SHA1 Message Date
Nicola Soranzo 5ca0aea54a Drop nose
It's deprecated and unmaintained, and is broken under Python 3.10 .
2022-11-01 18:45:07 +00:00
Nicola Soranzo 95326249cd Update application documentation
with:

```
make -C doc/ updaterst
```
2022-08-19 17:37:27 +01:00
Nicola Soranzo 961472cfff Merge branch 'release_22.01' into release_22.05 2022-08-16 23:25:42 +01:00
Nicola Soranzo 6a3804ba27 Update application documentation
with:

```
make -C doc/ updaterst
```
2022-08-14 18:39:19 +01:00
John Chilton 2613512327 Remove job metrics CollectL plugin.
The project seems to be a deadend and it was never adopted in production as far as I am aware. The cgroup plugin seems to provide similar information with much less overhead and with easier to manage dependencies.
2022-03-31 09:25:52 -04:00
mvdbeek 6794d6be93 Resolve circular dependency for ToolEvaluator
by placing ComputeEnvironment and ActionBox under job_execution.
2021-11-29 11:22:42 +01:00
John Chilton 5661e0db9f Exploratory Jupyter environment for `galaxy-selenium`.
The new Makefile-based command ``make serve-selenium-notebooks`` will serve notebooks in lib/galaxy_test/selenium/jupyter.

The notebooks will target a Galaxy host running on port 8080 - but are parameterized to be run with papermill (https://papermill.readthedocs.io/) for automate targeting different Galaxy servers, remote Selenium servers, etc..

Screenshots will be embedded right into the notebook.

Example notebooks setup to target just the library code in ``galaxy-selenium`` as well as one appropriate to leverage the Galaxy testing framework are included and documented in depth via modules docstring for ``galaxy_test.selenium.jupyter``.
2021-01-18 17:24:28 -05:00
John Chilton 99186b6294 Remove sphinx stub generated due to local, non-branch changes. 2021-01-12 09:34:28 -05:00
John Chilton 8d06cffae4 Remove now unused .gitignore file.
Or am I missing how that file is generated in someway...
2021-01-12 09:29:54 -05:00
John Chilton 9bd66edc0b Re-do API documentation to avoid duplicate labels. 2021-01-12 09:29:53 -05:00
John Chilton e1d0a1d049 Rebuild rst lib structure. 2021-01-11 13:03:57 -05:00
Nicola Soranzo 79210e8ed7 Update application documentation
with:

```
make -C doc/ updaterst
```
2020-12-18 02:37:10 +00:00
mvdbeek 8be1ac07e6 Merge branch 'release_20.01' into dev 2020-05-05 21:04:03 +02:00
mvdbeek f6a79f6341 Rename galaxy.util.logging to galaxy.util.custom_logging
Otherwise there may be import issues:
```
==================================== ERRORS ====================================

________________________ ERROR collecting test session _________________________

.tox/py27-unit/lib/python2.7/site-packages/py/_path/common.py:383: in visit

    for x in Visitor(fil, rec, ignore, bf, sort).gen(self):

.tox/py27-unit/lib/python2.7/site-packages/py/_path/common.py:425: in gen

    if p.check(dir=1) and (rec is None or rec(p))])

.tox/py27-unit/lib/python2.7/site-packages/_pytest/main.py:667: in _recurse

    ihook = self.gethookproxy(dirpath)

.tox/py27-unit/lib/python2.7/site-packages/_pytest/main.py:482: in gethookproxy

    my_conftestmodules = pm._getconftestmodules(fspath)

.tox/py27-unit/lib/python2.7/site-packages/_pytest/config/__init__.py:424: in _getconftestmodules

    mod = self._importconftest(conftestpath.realpath())

.tox/py27-unit/lib/python2.7/site-packages/_pytest/config/__init__.py:463: in _importconftest

    raise ConftestImportFailure(conftestpath, sys.exc_info())

E   ConftestImportFailure: (local('/home/circleci/repo/test/unit/queue_worker/conftest.py'), (<type 'exceptions.AttributeError'>, AttributeError("'module' object has no attribute 'getLogger'",), <traceback object at 0x7fabd96b7eb0>))

----- generated html file: file:///home/circleci/repo/run_unit_tests.html ------

!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!

=========================== 1 error in 1.83 seconds ============================

```
2020-05-03 21:50:12 +02:00
Nicola Soranzo addb73c1c4 Update documentation
- Fixes for `interactivetools.rst`
- Run `make updaterst`
2020-05-01 01:20:06 +01:00
John Chilton 559b664b07 Refactor tool_shed webapp out of Galaxy. 2019-11-11 12:32:19 -05:00
Sergey Golitsynskiy df5252c887 Update RST files to reflect code structure changes
Also, clean out obsolete RST files.
2019-07-21 12:42:58 -04:00
Dannon Baker 3072975897 Drop mimeparse docs 2019-07-09 14:14:37 +01:00
Marius van den Beek d22d7beaf4 Merge pull request #8305 from jmchilton/axe_log_tempfile
Remove log_tempfile.
2019-07-09 14:42:43 +02:00
Dannon Baker f5f15e2dfc Drop log_tempfile docs 2019-07-08 20:04:03 -04:00
Dannon Baker ae11aaa5ec Drop psyco_full docs 2019-07-08 16:08:20 -04:00
Sergey Golitsynskiy b5f19e8466 Rerun make updaterst
First rm doc/source/lib/*, then rerun sphinx. Cleans out obsolete files.
2019-07-06 10:10:56 +02:00
Sergey Golitsynskiy 17beaef624 Update Sphinx RST files for lib/
Running sphinx 1.8.5 updates all files (one known update: periods are no
longer escaped)
2019-07-05 17:21:31 +02:00
Nicola Soranzo 57af073813 Update application documentation
with:
```
make -C doc/ updaterst
```

Also fix 2 links in `doc/source/api/guidelines.rst` .
2019-02-20 14:56:21 +00:00
Nicola Soranzo d5b306dd21 Remove OpenID auth from docs
Follow-up on https://github.com/galaxyproject/galaxy/pull/7028 .
2019-01-21 17:44:34 +00:00
Nicola Soranzo 77706a8e62 Update application documentation
With
```
make -C doc/ updaterst
```
2018-09-03 11:25:42 +01:00
Dannon Baker 02ffdf0be9 This strips the graphite-specific middleware; statistic functionality is provided by the statsd middleware and we don't need two separate mechanisms to maintain. 2018-04-30 13:50:05 -04:00
Nicola Soranzo 5ab560068d Update lib documentation
Also simplify updaterst target in doc/Makefile

Partially revert commit b4feb85f11 : re-add
doc/source/lib/galaxy.webapps.galaxy.api.rst and
doc/source/lib/galaxy.webapps.tool_shed.api.rst and include them in
doc/source/api/api.rst and doc/source/api/ts_api.rst respectively to
simplify doc maintenance.
2017-06-02 15:09:44 +01:00
Martin Cech b4feb85f11 improve accessibility of API docs
for both Galaxy and TS
2017-03-27 15:21:37 -04:00
John Chilton f9edf39f58 Migrate galaxy_utils to a wheel.
Alternative approach to #3542 which was not future proof with Conda dependencies. I think this should be now.

xref #3364 #2994 http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td4670472.html

Rebased with fixes from @nsoranzo and @mvdbeek.
2017-02-03 10:38:24 -05:00
Nicola Soranzo 527e332aa3 Fix a bunch of errors reported by Sphinx 2016-10-24 19:42:19 +01:00
Nicola Soranzo 8a17143bc7 Remove unused files 2016-10-24 19:40:42 +01:00
Alexander Lenail 0a49f17411 Modified galaxy.objectstore.rst
Not sure how RST works — would appreciate some guidance here.
2016-07-19 15:27:01 -04:00
John Chilton 51f63a7d3e Replace embedded Pulsar code with dependency.
Pulsar's setup.py has been parameterized to allow it build a special wheel that doesn't depend on galaxy-lib (https://github.com/galaxyproject/pulsar/commit/ce9d4f9e80936407fe4f793afa6688d75635e827) and instead expects it to come from the environment.

This special dependency has been published to PyPI here (https://pypi.python.org/pypi/pulsar-galaxy-lib) and added to StarForge here (https://github.com/galaxyproject/starforge/pull/79). These are now available on wheels.galaxyproject.org.

In addition to removing the source dirctories - I have removed doc and CI references to these directories.
2016-03-31 08:17:06 -04:00
Mark Iskander 825a20ef81 Modified more names, added bcf_bgzip to datatypes, added converters going both ways 2015-11-20 13:49:04 -06:00
Mark Iskander 6cd550e0c7 Added the bcf_bgzip_to_bcf converter to datatype.converters.rst, renamed files to follow standard naming scheme 2015-11-20 12:25:00 -06:00
Nicola Soranzo 3c7082c64a Fix doc/source/lib using "sphinx-apidoc -M -f -o doc/source/lib/ lib/" 2015-10-26 19:29:13 +00:00
John Chilton c3ef5467c7 Eliminate LWR from Galaxy. 2015-10-06 12:33:36 +01:00
Nicola Soranzo ee0ce040ce Update to sphinx-apidoc v1.3.1 .
sphinx-apidoc -M -o doc/source/lib/ lib/
2015-06-29 15:39:12 +01:00
Nicola Soranzo f339cc1631 Fix doc/source/ using sphinx-apidoc v1.1.3 . 2015-06-29 15:30:49 +01:00
Nicola Soranzo 025930bfd1 Move the additional API doc out of autogenerated docs. 2015-06-29 15:30:26 +01:00
Nicola Soranzo 416785e16d Update rst docs for bab978a4f4 . 2015-06-24 16:24:25 +01:00
Dannon Baker 3af3bf5742 Per IRC discussion, remove demo_sequencer webapp. 2015-02-21 13:29:58 -05:00
Martin Cech 5a9259d773 updated sphinx documentation: added managers; added new API controllers; cleanup 2014-10-22 17:55:45 -04:00
Nate Coraor 8fadc6392b Rename universe_wsgi.ini -> galaxy.ini everywhere. 2014-09-15 16:43:51 -04:00
Trevor Wennblom 195017daf7 remove misc files that slipped past hgignore 2014-04-10 22:54:34 -05:00
Nate Coraor 9c64fc123e Remove broken and/or obsolete tools. 2014-01-27 13:58:31 -05:00
Martin Cech 87c84e8c5e Merged in martenson/galaxy-central-marten (pull request #273)
Initial Data Libraries
2013-12-19 12:48:22 -05:00
Martin Cech 3317e25ee1 refactor + docs 2013-12-19 12:44:34 -05:00
John Chilton 1653efcf6e RFC: API design guidelines and considerations. 2013-12-16 15:57:31 -06:00