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.
- Add some labels that have been added to Github but not this list (tool-dependencies, i18n, security).
- Add subworkflows which was added to Github as ``area/subworkflows`` but which I think should be ``area/workflows/subworkflows``.
- Add various specific testing areas (integration, selenium, and api) and a general testing area for bugs and enhancements for other parts of testing.*
- Add labels I think should be there but aren't (cwl, objectstore, upload, webhooks)
* I know there is a kind/testing, but I initially thought it should be an area and I still do. I'm either making enhancements or bug fixes to testing - I think ``kind/bug``, ``kind/enhancement``, and ``kind/refactoring`` apply to the ``area`` of testing. Maybe the new more specific areas for testing make that clear? I wanted to see all the recent Selenium changes but I didn't have a real clear way to do that without this. Maybe a compromise if others haven't come around to my way of seeing things is to keep the area sub-types of testing (e.g. ``area/testing/selenium``) but drop ``area/testing`` from this list.
John Chilton