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17 Commits
Author SHA1 Message Date
Matthias Bernt d89987c748 schema doc: add attribute table to all assertions 2022-01-20 11:39:26 +01:00
Matthias Bernt 4496311bb2 followup on xsd restructuring 
doc parsing: asserts are now choice
 2022-01-20 11:39:26 +01:00
Matthias Bernt 6a4381cc78 xml assertions: tests, small improvements + xsd reformatting 
- added unit tests for all xml assertions
- restructured xsd:
  - grouped general, text, tabular, archive, xml, and h5 assertions
  - full definition of all assertions in xsd
  - allow for "recursion" in xsd for has_archive_member and element_text
- restructured schema doc: instead of the table its now a
  definition list (no more horizontal scrolling in the wide table)
  also here assertions are grouped
 2022-01-20 11:39:26 +01:00
Nicola Soranzo 0e43c82a49 Fix tool profile details in schema docs 
Per the GitHub Flavored Markdown Spec: "Block-level elements cannot be
inserted in a table.", see
https://github.github.com/gfm/#tables-extension-
 2021-04-07 17:34:47 +01:00
Nicola Soranzo 9d74bba7fb Drop support for retired Python 3.5 
Upgrade syntax using `pyupgrade --py36-plus` .

Manually drop several `six` imports.

Also:
- Remove broken pr_cache in scripts/bootstrap_history.py
- Fix broken prefix removal in lib/galaxy/tool_util/deps/mulled/mulled_build.py
 2020-10-07 11:52:13 +01:00
Nicola Soranzo f5cd88465e Make str.join()s more efficient 
by using generator expressions and tuples instead of lists.
 2020-01-23 11:06:32 +00:00
John Chilton 41f6584e6f Refactor XSD output elements to share output attributes. 2019-03-18 15:06:48 -04:00
Nicola Soranzo 394ce04c37 Merge branch 'release_19.01' into dev 2019-02-20 11:20:15 +00:00
John Chilton 2033535976 Fix HDF5 test assert docs 
Alternative to https://github.com/galaxyproject/galaxy/pull/7382, fix documentation without giving up better validation one gets with actual types for assertion XML elements.
 2019-02-18 13:09:12 -05:00
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
Nicola Soranzo 59c1ed2266 Various doc fixes 2018-09-03 14:34:13 +01:00
Martin Cech 9a840537cb pass the check for pipe presence in details 
the docs build fine and the table renders fine too
 2018-05-22 14:15:36 -04:00
Martin Cech a00bd8bf8e escape pipe in details 
so we can have pipes inside markdown tables
 2018-05-21 16:12:36 -04:00
Nicola Soranzo 1d17a29c79 Fixes for pycodestyle 2.2.0 2016-11-15 16:56:50 +00:00
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
Nicola Soranzo 1e32c0926c Fix import order and Python3 compatibility for most of test/ 2016-10-10 19:06:22 +01:00
John Chilton a8bc9d5d16 XSD Generated Tool Documentation. 
- Add script to generate Markdown documentation from the XSD.
 - Add Makefile target to build these docs, convert to HTML, and open respectively.
 2016-09-21 08:41:12 -04:00