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Author SHA1 Message Date
Nicola Soranzo 527e332aa3 Fix a bunch of errors reported by Sphinx 2016-10-24 19:42:19 +01:00
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 e6d0b69ec8 Add and use local images for build runner doc 2016-10-24 19:40:42 +01:00
Nicola Soranzo 8a17143bc7 Remove unused files 2016-10-24 19:40:42 +01:00
Nicola Soranzo a21ed34efb Move png in the right directory 
Broken in #2543.
 2016-10-24 19:40:41 +01:00
Nicola Soranzo 4bfac45369 Fix flake8 errors and Python3 compatibility for doc/patch.py 2016-10-24 19:40:41 +01:00
Nicola Soranzo 05be84ba47 Merge pull request #3087 from martenson/fix-makefile 
fix bad merge in #3060
 2016-10-24 19:39:24 +01:00
Martin Cech 00c48e4878 remove the rest of the badle merged target 2016-10-24 14:09:16 -04:00
Martin Cech 0f0bcb6a08 fix bad merge in #3060 2016-10-24 13:39:56 -04:00
John Chilton 5662a6a5c6 Merge pull request #3071 from nsoranzo/fix__all__ 
Change __all__ from list to tuple [2/2]
 2016-10-24 13:07:01 -04:00
Dannon Baker a6d52cdbdc Merge remote-tracking branch 'bgruening/feature/plugin-system' into dev 2016-10-23 19:00:43 +02:00
Martin Cech cfeb0135ac Merge pull request #3072 from jmchilton/default_value_legacy_xsd 
Add deprecated, legacy attribute default_value to XSD.
 2016-10-19 13:14:05 -04:00
John Chilton 05f792edcd Specify actual parameter to use in lieu of default_value in XSD. 
As suggested by @nsoranzo.
 2016-10-19 12:48:21 -04:00
John Chilton 3a99bbae07 Add deprecated, legacy attribute default_value to XSD. 
Cleanup use of ``gxdocs:deprecated``.
 2016-10-19 11:52:42 -04:00
Nicola Soranzo e4b3766c1b Change remaining __all__ from list to tuple 
Also fix import order and Python3 compatibility.
 2016-10-18 19:24:31 +01:00
Daniel Blankenberg 2a7e4f79c0 Merge pull request #3062 from guerler/fix_dataset_caching 
Dataset metadata should not be cached when building chart visualizations
 2016-10-18 14:18:49 -04:00
John Chilton 569723a4e5 Merge pull request #3060 from martenson/remimarenco-gcc2015_talk 
Add Galaxy Architecture slides in .md
 2016-10-18 11:23:14 -04:00
guerler bdc8829dd2 Dataset metadata should not be cached when building chart visualizations 2016-10-17 15:20:25 -04:00
Martin Cech 564aeeccd7 remove the duplicated variable 2016-10-17 14:13:01 -04:00
Remi Marenco 3e737c99ea Add Galaxy Architecture slides in .md 
+ 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.
 2016-10-17 14:02:06 -04:00
John Chilton 1dc2d6a4ea Merge pull request #2875 from guerler/remote_chart_plugins 
Link charts to external repo, adjust interface
 2016-10-17 13:33:33 -04:00
Martin Cech 7eb413f4e8 Merge pull request #2961 from jmchilton/xsd_fixes_1 
Improve ``version_command`` tag.
 2016-10-17 13:31:52 -04:00
John Chilton 22839eeee0 Merge pull request #3052 from guerler/always_display_text 
Always display text
 2016-10-17 13:27:12 -04:00
John Chilton 7207c15090 Merge pull request #3033 from nsoranzo/fix_for_3001 
Increase min number of columns for pileup sniffing to 5
 2016-10-17 13:23:40 -04:00
Martin Cech 4bf1994fc3 Merge pull request #3059 from jmchilton/import_update 
Fix import orders for updates to flake8_import_order.
 2016-10-17 12:39:47 -04:00
John Chilton 762337e110 Fix import orders for updates to flake8_import_order. 2016-10-17 11:54:56 -04:00
John Chilton 31cb477e1a Merge pull request #2771 from Takadonet/dev 
Collection Operator tools
 2016-10-17 11:38:27 -04:00
Philip Mabon 7d938e2a23 Merge pull request #1 from jmchilton/collection_tools 
Enhance the Merge Collections Tool
 2016-10-17 08:57:35 -05:00
John Chilton 49eac93882 Cleanup merge collection and get test cases working again. 2016-10-16 14:11:40 -04:00
John Chilton 448a27a4a1 Merge remote-tracking branch 'jmchilton/dev' into collection_tools 2016-10-16 09:49:31 -04:00
John Chilton 15ad14e662 Enhance merge collection work from @Takadonet with more merge conflict actions. 
And allow it to work over any number of input collections.
 2016-10-16 09:48:38 -04:00
Evgeny Anatskiy ebaffa2e0d fix failing Travis tests #2 (TOX_ENV=py27-lint) and #6 (TOX_ENV=py27-lint-imports) 2016-10-14 22:29:55 +02:00
guerler f053f9bb3d Merge branch 'dev' into remote_chart_plugins 2016-10-14 16:24:39 -04:00
guerler 868658c7e7 Always display text, with test cases 2016-10-14 15:32:56 -04:00
Martin Cech a895c823da Merge pull request #3019 from blankenberg/collection-wf-resume-error 
Fix for rerunning tool with workflow resume that is part of a collection.
 2016-10-14 10:38:37 -04:00
Dannon Baker 28bb83f0ab Merge pull request #3055 from dannon/cherrypick_masthead_fix 
Cherrypick masthead fix
 2016-10-14 09:57:50 -04:00
Dannon Baker 6312d8052b Rebuild cilent. 2016-10-14 09:43:41 -04:00
Scott Szakonyi 36134bca69 Added code to adjust top setting of tool search if messagebox is visible, issue 2907 2016-10-14 09:40:34 -04:00
Martin Cech e5913a49e2 Merge pull request #3047 from galaxyproject/tool_tarball_fix 
Fix downloading tool tarball with boolean test input values.
 2016-10-14 09:22:03 -04:00
Björn Grüning 4bbab51c05 Add note about interface stability. 2016-10-14 12:43:28 +02:00
Nicola Soranzo d26f46423e Merge pull request #3042 from dannon/image_detection_fixes 
Image detection fixes
 2016-10-14 10:27:17 +01:00
Bjoern Gruening 3d4f302c47 change default settings in galaxy.ini.sample 2016-10-14 02:02:57 +02:00
Evgeny Anatskiy bd20ab1aa5 pep8 2016-10-14 01:12:15 +02:00
Evgeny Anatskiy 3770239281 Merge branch 'feature/plugin-system' of github.com:bgruening/galaxy into feature/plugin-system 2016-10-14 00:29:39 +02:00
Dannon Baker 4446ccc98c Merge pull request #3045 from blankenberg/value_to_display_text-fix 
Fix for displaying parameters to the user, that have a False value.
 2016-10-13 17:54:21 -04:00
Bjoern Gruening 3cb8189e1f Merge branch 'dev' into feature/plugin-system 2016-10-13 23:33:25 +02:00
Bjoern Gruening 0dc2c95bd0 Merge branch 'feature/plugin-system' of https://github.com/bgruening/galaxy into feature/plugin-system 2016-10-13 23:28:18 +02:00
Bjoern Gruening 3aadd84b80 add case where no user is logged in 2016-10-13 23:28:02 +02:00
Björn Grüning 8694356ab7 Adopt help to the latest changes 2016-10-13 23:20:51 +02:00
Evgeny Anatskiy 2703ba1a0c activate all demo plugins in testing purposes 2016-10-13 22:37:02 +02:00