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42 Commits
Author SHA1 Message Date
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
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