Nicola Soranzo
5ab560068d
Update lib documentation
...
Also simplify updaterst target in doc/Makefile
Partially revert commit b4feb85f11
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
Dave Clements
f39c2cb970
Bringing Sphinx RST files up to date; changing generated doc so all modules are documented, not just galaxy.*
2012-10-31 15:41:13 -07:00
Dannon Baker
1a3a17056e
Initial commit of Galaxy Documentation.
2012-06-13 11:31:00 -04:00
Nicola Soranzo