- Don't use 'sphinx.ext.autodoc' if existing option GALAXY_DOCS_SKIP_SOURCE=1 is used to speed up the build.
- Add a matching option to GALAXY_DOCS_SKIP_SOURCE called GALAXY_DOCS_SKIP_RELEASES to further speed up development of just the core rst/md docs.
- Fix an markdown link added to the rst index this release.
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
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.
This is a bugfix for the future bug of missing documentation for 17.09 and before. 18.01 will require a significant rewrite of these pages for the uWSGI and configuration changes to Galaxy and the release_17.09 branch of these docs is now being hosted https://docs.galaxyproject.org/en/release_17.09/, so backporting this configuration documentation will allow us to provide permenant links to this 17.09 varaint of all this documentation (with information about paste and galaxy.ini for instance).
This content currently includes:
- the production configuration page
- the cluster configuration page
- the job configuration page
- the scaling information page
- the ftp configuration page
- the top-level nginx page (for external auth content still linking out to the hub)
- the top-level apache page (for external auth content still linking out to the hub)
- the job metrics configuration page
Includes small tweaks to sphinx documentation generation.
- Add a quick build mode that skips source generation / Python docs (export GALAXY_DOCS_SKIP_SOURCE=1 to build this way). This speeds up review of core Sphinx docs.
- Use AutoStructify for better Markdown integration.
Updates to the documentation above and beyond what is on the corresponding Hub pages to reflect more of the state of art as of 17.09 including:
- Update the job configuration page with information about XML macros.
- Mention and link to newer style resubmission condition expressions (not just an enumerated string anymore).
- Updated list of dynamic job runner configuration parameters.
- Mention the ``raw`` attribute for ``env`` directives in the job configuration page.
- Mention the ``total_walltime`` limit added in #3217.
- Drop mentions of older URL-based job conf configuration stuff.
- Mention newer Local and Paramiko based shell runners in CLI section.
- Mention newer slurm job styles in CLI section.
- Improved Pulsar links.
- Fix dataset security link in Apache display sites config.
- Update job metrics page to link to a new Github issue instead of old Trello issues.
+ the plumbing for slides creation
Init of #2244, second part: Python converter md to html + wip on GCC 2015 talk conversion
Add the 2. Galaxy app architecture. Need images
Add the 3. Galaxy components and object model
Add more content in md
Fix linting error by adding newline at the end of build_slideshow.py
Moved the galaxyArchitecture.md into a folder dedicated to it
Add 7th and 17th image + add style.css to have a better management of layout + added first slide as the first in GCC2015 slide
Set properly the CSS used in the whole presentation + add special to p and first slide
Add special orange for regular text and green emphasis (emphasis_2_galaxy)
Changed the font to PT Sans
Add 3. with images + few modifications
Removed the images integrated using background-image by now Markdown imaging (still need work, image's size seems not good by default
Add Makefile target to build architecture slides...
2016 Updates to 2015 architecture talk.
More intro slides for Galaxy architecture.
Update author line.
Progress on architecture slides...
- Improved styling (use Oxygen - closer to Galaxy font)
- Add ability to generate SVG diagrams to slide infrastructure
- Add newer client-server sequence diagram based on that.
Improved logging when there are problems with SQL migrations.
More misc work on architecture talk.
More images, slides, slide formatting, and initial work on an IPython notebook.
Improved styling for architecture slides...
Updates to architecture talk...
- Infrastructure for building class diagrams with plantuml
- Bring in move SVGs from last year's google docs.
- Fill out section on client architecture.
More work on slides for architecture talk.
Add startup_output.
Replace mermaid diagrams with plantuml diagrams.
Fill out these diagrams more and style them for a black background in Galaxy oranges.
John Chilton