Commit Graph
52 Commits
Author SHA1 Message Date
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
Dannon Baker 51b6811867 Placeholder in api documentation for Return Codes and Format standards. 2013-12-16 15:17:51 -05:00
Dave Clements 2935ca8e42 New RST files describing Sphinx doc for tool shed changes. 2013-04-01 14:49:17 -07:00
Dannon Baker fd5358bb5a Sphinx Doc: Remove enable_api step from the api quickstart as it is no longer necessary. 2013-01-18 10:26:57 -05:00
Dave Clements c85177860d Update Sphinx RST structural doc to reflect recent code changes. 2013-01-14 17:01:17 -08:00
Dave Clements a3dac95afc First iteration of updating Sphinx RST files. These describe classes and modules (and ...) and are used to generate the Sphinx code documentation. However, they are not updated automatically.
Add the patch.py to automate some of the RST update process, but it is still pretty brutal.  Look for cleanup in the next few releases.
2012-12-18 13:27:20 -08:00
Dave Clements 9ece96cc8f All Sphinx related changes:
- Changed from Galaxy Documentation to Galaxy Code Documentation to be clearer
- Dropped galaxy.jobs.rules, as it is now empty.
2012-11-03 08:51:09 -07:00