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26 Commits
Author SHA1 Message Date
Nicola Soranzo 08bcea5370 Fix Makefile rule and update `run_tests_help.txt` 2022-09-09 17:20:23 +01:00
Nicola Soranzo 6a3804ba27 Update application documentation 
with:

```
make -C doc/ updaterst
```
 2022-08-14 18:39:19 +01:00
John Chilton ccdbc29160 Don't fail on sphinx warnings. 2021-01-12 09:35:19 -05:00
John Chilton 45ed317832 Rework docs to -W more aggressively but also provide a development Makefile target. 
Development target uses 4 cores (I use 8 locally), shows all warnings about issues (instead of failing on first), and skips the viewcode step which isn't parallelized and doesn't really exercise anything the developer has useful control over or would need to see during doc tweaking.
 2021-01-12 09:34:28 -05:00
John Chilton f674613f8f Allow setting sphinxopts via environment variables (-j 8 is fun) 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 1a7215b040 Documentation on writing Galaxy tests. 2021-01-10 18:52:26 -05:00
John Chilton 559b664b07 Refactor tool_shed webapp out of Galaxy. 2019-11-11 12:32:19 -05:00
Nicola Soranzo d2789add97 Restore docs building 
Broken in commit 42cf61fd36 .
 2019-07-10 16:01:44 +01:00
John Chilton fb7efea6ba Move tool XSD into galaxy-tool-util package. 2019-06-05 16:46:52 -04:00
Nicola Soranzo e97634739d Build tool XML schema docs using `sphinx_markdown_tables` 
instead of converting the Markdown to reStructuredText with pandoc.

Fix the broken tables, but code inside tables is not coloured as
in the rest of the document.
 2019-02-06 17:27:48 +00:00
Nate Coraor 37a9f2bcea Update logging config docs: 
- The example for split file logging was invalid (referenced the
  nonexistent "generic" formatter)

- Switch YAML dicts from 4- to 2-space indent to match the indentation
  style in galaxy.yml.sample

- Document setting the message format with the YAML config

- Reword a few things to hopefully be a bit clearer
 2019-01-07 16:16:32 -05:00
Nicola Soranzo e87d1aa79d More Python3 print function fixes 2018-01-25 11:52:11 +01:00
Nate Coraor 3cc1b25c18 Fix make docs when the virtualenv is not .venv 2018-01-24 12:50:22 -05:00
Nate Coraor db00f97175 Finish Galaxy logging configuration documentation 2018-01-10 16:26:09 -05:00
Nicola Soranzo fc9b3ad4a9 Generate api.rst and ts_api.rst during make 2017-06-02 16:47:30 +01:00
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
Nicola Soranzo 13ae374f84 Move sed commands to a script to resolve interferences with Make 
which happen only under OSX
 2016-12-08 20:46:06 +00:00
Nicola Soranzo 128a3174eb Use OSX-compatible sed syntax 2016-12-07 20:24:34 +00:00
Nicola Soranzo 7c030ebf2f Use sed instead of pandoc to insert TOC in schema doc 
pandoc < 1.14 adds the TOC depth as a float, which is not recognised by
Sphinx.
Also, move the TOC after the introduction, which looks nicer.
 2016-11-07 16:32:12 +00:00
John Chilton ce1c7e41c6 Restore XML formatting for schema document. 2016-11-01 13:18:47 -04:00
Nicola Soranzo 3180b63166 Properly integrate tool XML schema with docs 
Generate intermediate rst file instead of html
Move generation to doc/Makefile
Use pandoc to generate table of contents and fragment ids.
Remove nested inline markup (not supported by reStructuredText)
Fix https and other links.
 2016-10-24 19:42:19 +01:00
Nate Coraor 4227d0eabb Remove additional pieces from old genome index system. 2014-07-27 02:48:40 -04:00
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 d23cd8ea65 More work on docstrings to get them to be Sphinx compatible. Added dependency to Sphinx Makefile to get rid of errors when build files weren't there. 2012-11-01 01:23:56 -07:00
Dannon Baker 1a3a17056e Initial commit of Galaxy Documentation. 2012-06-13 11:31:00 -04:00