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1284 Commits
Author SHA1 Message Date
Marius van den BeekandNicola Soranzo d61321d872 Improve enable_tool_cache option description 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-02-23 10:22:52 +01:00
mvdbeek 82f26d40ac Disable tool document cache by default 
It's kind of brittle, and https://github.com/galaxyproject/galaxy/pull/10804
has improved the parsing so much that it doesn't add much benefit.
Instances on Anvil start up in ~ 32 seconds, with all of main's toolbox.
 2021-02-23 08:53:45 +01:00
mvdbeek 7d0ec29fa0 Drop legacy metadata mode 
And always serialize input dataset metadata using the model exports.
This means we don't have to pickle anymore, which breaks with weakrefs
used by sqlalchemy-json's Mutable class.
 2021-02-05 11:38:50 +01:00
mvdbeek 4d984c5132 Add setting that lets admins enable/disable the tool document cache 
Closes https://github.com/galaxyproject/galaxy/issues/11082
 2021-01-20 10:12:07 +01:00
Nicola Soranzo e225de9b00 Merge pull request #11103 from jmchilton/more_docs_stuff_3 2021-01-12 17:58:24 +00:00
Sergey GolitsynskiyandNicola Soranzo 64139e9bb3 Update doc/source/dev/writing_tests.md 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-01-12 10:04:27 -05:00
Sergey GolitsynskiyandNicola Soranzo f9b38719fd Update doc/source/dev/writing_tests.md 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-01-12 10:03:41 -05:00
John Chilton b8c11ab21a Link in MQ docs stub. 2021-01-12 09:34:28 -05:00
John Chilton 955c6a8053 Index the user release notes when available by default. 
https://github.com/galaxyproject/galaxy/pull/11103#discussion_r555514754
 2021-01-12 09:34:28 -05:00
John Chilton 99186b6294 Remove sphinx stub generated due to local, non-branch changes. 2021-01-12 09:34:28 -05:00
John Chilton ee3280ad52 Mark pre-annoucnement page as orphan. 
I guess I always imagined we would link these but then I was told we shouldn't - so I don't even know why we're generating them to be honest then.
 2021-01-12 09:29:55 -05:00
John Chilton 8d06cffae4 Remove now unused .gitignore file. 
Or am I missing how that file is generated in someway...
 2021-01-12 09:29:54 -05:00
John Chilton eef17877d1 Link to user announcements to eliminate sphinx warnings. 2021-01-12 09:29:54 -05:00
John Chilton 6c79073eb4 Mark some Sphinx as orphans - they seem to be not linked to TOC for reasons. 2021-01-12 09:29:54 -05:00
John Chilton e643c09806 Fixup more sphinx warning in config option doc generation. 2021-01-12 09:29:53 -05:00
John Chilton f5648e2025 Fixup some linking between documents in sphinx. 2021-01-12 09:29:53 -05:00
John Chilton 9bd66edc0b Re-do API documentation to avoid duplicate labels. 2021-01-12 09:29:53 -05:00
John Chilton 61188ca27b Hook requests up to intersphinx. 2021-01-12 09:29:53 -05:00
John Chilton 386470789f A couple new ways to speed up doc building locally. 2021-01-12 09:29:53 -05:00
Sergey GolitsynskiyandNicola Soranzo 0b0ec0cada Update doc/source/dev/writing_tests.md 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-01-12 00:37:06 -05:00
Sergey Golitsynskiy 204538c387 Add more edits 2021-01-12 00:35:45 -05:00
Sergey Golitsynskiy dad51dee87 Make minor improvements, add ToC 2021-01-11 23:28:15 -05:00
Nicola Soranzo ed084a77c3 Add framework tests to Overview 
Also fix some typos.
 2021-01-11 19:07:39 +00:00
Nicola Soranzo 8b67c2cc05 Remove broken link 2021-01-11 18:48:42 +00:00
Nicola Soranzo 57305c2184 Fix Sphinx warnings 2021-01-11 18:48:10 +00:00
John Chilton e1d0a1d049 Rebuild rst lib structure. 2021-01-11 13:03:57 -05:00
John Chilton 6fd6100285 Various sphinx warning fixes. 2021-01-11 12:58:45 -05:00
Marius van den Beek 75ae4264dc Merge pull request #11088 from jmchilton/test_docs_1 
Documentation for Writing Tests
 2021-01-11 09:50:00 +01:00
John Chilton 1a7215b040 Documentation on writing Galaxy tests. 2021-01-10 18:52:26 -05:00
John Chilton 1d63a3abd5 Link to high-quality developer documentation. 2021-01-10 18:52:26 -05:00
John Chilton 02380a88a8 A couple small fixes for docs generation. 
- 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.
 2021-01-10 18:52:26 -05:00
John Chilton 0482543402 Merge pull request #10822 from jmchilton/conda_readonly_2 
Implement read-only conda resolver (alternative)
 2021-01-10 12:43:59 -05:00
Marius van den Beek af4d041dc9 Merge pull request #10592 from hexylena/edam-tool-panel 
EDAM tool panel
 2021-01-08 18:56:28 +01:00
John Chilton 22aa23e1db Implement read-only conda resolver. 2021-01-08 11:09:10 -05:00
Dannon 02f6e028bb Merge pull request #10960 from astrovsky01/new_version_tab 
Add version tab which links to release notes to help tab
 2021-01-08 11:08:38 -05:00
Dannon c0b45fde61 Merge pull request #10701 from linnil1/fix-ftp-doc 
Update ftp document for rounds=100000
 2021-01-07 19:20:12 -05:00
Helena Rasche f5a3545541 Merge branch 'dev' into edam-tool-panel 2021-01-07 19:54:12 +01:00
Marius van den Beek 6bed4e8d4d Merge pull request #10573 from brinkmanlab/doc_data_manager 
Document data manager repository layout
 2021-01-07 19:12:13 +01:00
John Chilton b7cb74c600 Merge pull request #11067 from nsoranzo/clarify_master_api_key 
Clarify `master_api_key` intended use
 2021-01-06 22:21:50 -05:00
Marius van den Beek 683bb54183 Merge pull request #10347 from brinkmanlab/mq_doc 
Stub MQ docs
 2021-01-06 22:12:22 +01:00
Nicola Soranzo 967ad305dc Clarify master_api_key intended use 
xref. https://github.com/galaxyproject/galaxy/issues/11065
 2021-01-06 20:26:44 +00:00
John Chilton 9b5526a998 Merge pull request #10959 from ic4f/dev_issue10607 
Add custom activation email message
 2021-01-04 10:51:27 -05:00
John Chilton c7d6f286e5 Merge pull request #10919 from mvdbeek/zipstream_replace_tarball 
Replace StreamBall, replace tarballs with zip
 2020-12-21 10:27:51 -05:00
Marius van den Beek 1501fa9a65 Merge pull request #10497 from natefoo/gxit-stop 
Support stopping Interactive Tools without deleting their outputs
 2020-12-21 10:06:07 +01:00
mvdbeek 64b75e074c Restore upstream_gzip option, rename upstream_zip to upstream_mod_zip 2020-12-19 19:03:53 +01:00
Alexander OSTROVSKY b6891f9f99 different return if running a dev instance 2020-12-18 14:21:48 -08:00
Alexander OSTROVSKY 249e8744eb updated config name 2020-12-18 09:06:16 -08:00
Marius van den BeekandNicola Soranzo f3bf548da5 Improve mod-zip documentation 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2020-12-18 17:04:00 +01:00
mvdbeek ad655b9e52 Fix grammar and clarify internal statement 2020-12-18 16:45:37 +01:00
mvdbeek d4552d31cb Enable archive creating via mod-zip 2020-12-18 14:09:31 +01:00