rnaseq-cwl-training.git
6 years agoMerge pull request #163 from mawds/sortfigs
Raniere Silva [Tue, 8 Aug 2017 10:18:04 +0000 (11:18 +0100)]
Merge pull request #163 from mawds/sortfigs

Output episode figures in correct order

6 years agoSort HTML_DST output
David Mawdsley [Tue, 8 Aug 2017 09:29:39 +0000 (10:29 +0100)]
Sort HTML_DST output

6 years agoSort episodes before producing figures
David Mawdsley [Tue, 8 Aug 2017 09:17:50 +0000 (10:17 +0100)]
Sort episodes before producing figures

6 years agoMerge pull request #159 from rgaiacs/lc-svg-logo
Raniere Silva [Fri, 14 Jul 2017 10:34:14 +0000 (11:34 +0100)]
Merge pull request #159 from rgaiacs/lc-svg-logo

Add Library Carpentry SVG logo

6 years agoUpdate Library Carpentry logo
Raniere Silva [Fri, 14 Jul 2017 10:32:02 +0000 (11:32 +0100)]
Update Library Carpentry logo

6 years agoAdd Library Carpentry SVG logo
Raniere Silva [Thu, 6 Jul 2017 09:42:15 +0000 (10:42 +0100)]
Add Library Carpentry SVG logo

6 years agoMerge pull request #158 from rgaiacs/fix-logo-nav
Raniere Silva [Wed, 5 Jul 2017 09:14:48 +0000 (10:14 +0100)]
Merge pull request #158 from rgaiacs/fix-logo-nav

Fix logo at navbar

6 years agoFix logo at navbar
Raniere Silva [Wed, 5 Jul 2017 09:10:58 +0000 (10:10 +0100)]
Fix logo at navbar

by run

~~~
$ find _includes -type f -exec sed -i "s/page.carpentry/site.carpentry/g" {} \;
$ find _layouts -type f -exec sed -i "s/page.carpentry/site.carpentry/g" {} \;
$ find _extras -type f -exec sed -i "s/page.carpentry/site.carpentry/g" {} \;
$ find _episodes -type f -exec sed -i "s/page.carpentry/site.carpentry/g" {} \;
$ find bin -type f -exec sed -i "s/page.carpentry/site.carpentry/g" {} \;
$ find assets -type f -exec sed -i "s/page.carpentry/site.carpentry/g" {} \;
~~~

6 years agoMerge pull request #157 from rgaiacs/155
Raniere Silva [Wed, 5 Jul 2017 09:00:07 +0000 (10:00 +0100)]
Merge pull request #157 from rgaiacs/155

Unify Library Carpentry logo

6 years agoUnify Library Carpentry logo
Raniere Silva [Wed, 5 Jul 2017 08:58:54 +0000 (09:58 +0100)]
Unify Library Carpentry logo

Close #155

6 years agoMerge pull request #156 from jnothman/patch-1
Raniere Silva [Tue, 4 Jul 2017 08:45:55 +0000 (09:45 +0100)]
Merge pull request #156 from jnothman/patch-1

Link LC as for SWC and DC

6 years agoLink LC as for SWC and DC
Joel Nothman [Tue, 4 Jul 2017 05:07:12 +0000 (15:07 +1000)]
Link LC as for SWC and DC

6 years agoHandler for collaborative_notes
Raniere Silva [Sun, 18 Jun 2017 07:57:19 +0000 (08:57 +0100)]
Handler for collaborative_notes

See https://github.com/swcarpentry/workshop-template/issues/410

6 years agoRevert "Remove CONDUCT.md since it should be generate by bin/lesson_initialize.py"
Raniere Silva [Wed, 10 May 2017 10:05:10 +0000 (11:05 +0100)]
Revert "Remove CONDUCT.md since it should be generate by bin/lesson_initialize.py"

This reverts commit 1e56203d492a1a13d86756fb5e9d754ed2cae0f8.

6 years agoFix bug with Python script
Raniere Silva [Sat, 6 May 2017 09:19:56 +0000 (10:19 +0100)]
Fix bug with Python script

6 years agoRemove CONDUCT.md since it should be generate by bin/lesson_initialize.py
Raniere Silva [Sat, 6 May 2017 09:07:40 +0000 (10:07 +0100)]
Remove CONDUCT.md since it should be generate by bin/lesson_initialize.py

6 years agoRemove extra link to Library Carpentry
Raniere Silva [Sat, 6 May 2017 08:45:55 +0000 (09:45 +0100)]
Remove extra link to Library Carpentry

6 years agoMerge pull request #149 from rgaiacs/styles-print
Raniere Silva [Sat, 6 May 2017 08:26:10 +0000 (09:26 +0100)]
Merge pull request #149 from rgaiacs/styles-print

Add all in one lesson build with Javascript

6 years agoAdd all in one lesson build with Javascript
Raniere Silva [Tue, 2 May 2017 10:41:18 +0000 (11:41 +0100)]
Add all in one lesson build with Javascript

6 years agoMerge pull request #148 from rgaiacs/show-challenges
Raniere Silva [Sat, 6 May 2017 08:14:39 +0000 (09:14 +0100)]
Merge pull request #148 from rgaiacs/show-challenges

Make challenges and discussion visibles

6 years agoMake challenges and discussion visibles
Raniere Silva [Sat, 6 May 2017 08:12:36 +0000 (09:12 +0100)]
Make challenges and discussion visibles

This is based on
https://github.com/swcarpentry/instructor-training/pull/437/files and
https://github.com/swcarpentry/instructor-training/pull/439/files,
both write by @ErinBecker.

6 years agoMerge pull request #147 from rgaiacs/update-coc
Raniere Silva [Sat, 6 May 2017 08:04:42 +0000 (09:04 +0100)]
Merge pull request #147 from rgaiacs/update-coc

Updated CONDUCT.md

6 years agoUpdated CONDUCT.md
Raniere Silva [Sat, 6 May 2017 08:03:26 +0000 (09:03 +0100)]
Updated CONDUCT.md

Rebased of https://github.com/swcarpentry/lesson-example/pull/116/.

Thanks to @tracyteal.

6 years agoMerge pull request #143 from ErinBecker/gh-pages
Raniere Silva [Sat, 6 May 2017 07:51:00 +0000 (08:51 +0100)]
Merge pull request #143 from ErinBecker/gh-pages

Suggest template language

6 years agoMerge pull request #142 from rgaiacs/styles-library-carpentry
Raniere Silva [Sat, 6 May 2017 07:50:26 +0000 (08:50 +0100)]
Merge pull request #142 from rgaiacs/styles-library-carpentry

Add Library Carpentry to the workshop template

6 years agoMerge pull request #146 from fmichonneau/check-version-checkpoint
Raniere Silva [Fri, 5 May 2017 06:59:40 +0000 (07:59 +0100)]
Merge pull request #146 from fmichonneau/check-version-checkpoint

make sure that checkpoint version is 0.4.0 or higher

6 years agomake sure that checkpoint version is 0.4.0 or higher
Francois Michonneau [Thu, 4 May 2017 15:58:52 +0000 (11:58 -0400)]
make sure that checkpoint version is 0.4.0 or higher

6 years agoMerge pull request #145 from fmichonneau/fix-checkpoint
Raniere Silva [Tue, 2 May 2017 09:08:20 +0000 (10:08 +0100)]
Merge pull request #145 from fmichonneau/fix-checkpoint

fix swcarpentry/lesson-example#118: use checkpoint::scanForPackages

7 years agofix swcarpentry/lesson-examples#118: use checkpoint::scanForPackages
Francois Michonneau [Sat, 29 Apr 2017 22:26:45 +0000 (18:26 -0400)]
fix swcarpentry/lesson-examples#118: use checkpoint::scanForPackages

7 years agoSuggest template language
ErinBecker [Tue, 25 Apr 2017 20:36:15 +0000 (13:36 -0700)]
Suggest template language

7 years agoAdd Library Carpentry to the workshop template
Raniere Silva [Tue, 4 Apr 2017 07:02:53 +0000 (08:02 +0100)]
Add Library Carpentry to the workshop template

Includes @drjwbaker's description of Library Carpentry.

7 years agoMerge pull request #139 from rgaiacs/improve-wording
Raniere Silva [Tue, 14 Mar 2017 14:25:35 +0000 (14:25 +0000)]
Merge pull request #139 from rgaiacs/improve-wording

Improve wording on syllabus.html

7 years agoImprove wording on syllabus.html
Raniere Silva [Tue, 14 Mar 2017 14:22:16 +0000 (14:22 +0000)]
Improve wording on syllabus.html

As suggested by @gcapes.

7 years agoMerge pull request #138 from swcarpentry/revert-129-dt-ids
Raniere Silva [Fri, 3 Mar 2017 21:37:47 +0000 (21:37 +0000)]
Merge pull request #138 from swcarpentry/revert-129-dt-ids

Revert "ensure dt elements have an id set"

7 years agoRevert "ensure dt elements have an id set"
Raniere Silva [Fri, 3 Mar 2017 21:37:22 +0000 (21:37 +0000)]
Revert "ensure dt elements have an id set"

7 years agoMerge pull request #137 from rgaiacs/styles-numbering
Raniere Silva [Fri, 3 Mar 2017 21:08:11 +0000 (21:08 +0000)]
Merge pull request #137 from rgaiacs/styles-numbering

Numbering the lessons in the schedule

7 years agoNumbering the lessons in the schedule
Raniere Silva [Sat, 18 Feb 2017 17:14:20 +0000 (17:14 +0000)]
Numbering the lessons in the schedule

Related with https://github.com/swcarpentry/styles/issues/80.

7 years agoMerge pull request #136 from rgaiacs/styles-edit-on-github
Raniere Silva [Fri, 3 Mar 2017 21:04:32 +0000 (21:04 +0000)]
Merge pull request #136 from rgaiacs/styles-edit-on-github

Edit on GitHub

7 years agoFix issue with link to GitHub from RMarkdown files
Raniere Silva [Fri, 3 Mar 2017 20:52:49 +0000 (20:52 +0000)]
Fix issue with link to GitHub from RMarkdown files

Jekyll doesn't export the _episodes_rmd so we need to flag the files.
Each Rmd file must have in the YAML header

    source: Rmd

7 years agoAdopt @lexnederbragt suggestion for Edit link
Raniere Silva [Fri, 3 Mar 2017 20:44:12 +0000 (20:44 +0000)]
Adopt @lexnederbragt suggestion for Edit link

https://github.com/swcarpentry/lesson-example/pull/104#issuecomment-283310978

7 years agoChange Edit on GitHub link to edit page
Raniere Silva [Fri, 3 Mar 2017 20:42:00 +0000 (20:42 +0000)]
Change Edit on GitHub link to edit page

7 years agoAdd link to Edit on GitHub
Raniere Silva [Thu, 23 Feb 2017 17:22:53 +0000 (17:22 +0000)]
Add link to Edit on GitHub

7 years agoMerge pull request #135 from rgaiacs/106
Raniere Silva [Thu, 2 Mar 2017 22:03:07 +0000 (22:03 +0000)]
Merge pull request #135 from rgaiacs/106

Update copyright year with current year

7 years agoUpdate copyright year with current year
Raniere Silva [Thu, 2 Mar 2017 22:01:47 +0000 (22:01 +0000)]
Update copyright year with current year

7 years agoMerge pull request #133 from rgaiacs/styles-round-corners
Raniere Silva [Sat, 18 Feb 2017 18:05:42 +0000 (18:05 +0000)]
Merge pull request #133 from rgaiacs/styles-round-corners

Improve round corners on block input and output

7 years agoImprove round corners on block input and output
Raniere Silva [Sat, 18 Feb 2017 17:49:06 +0000 (17:49 +0000)]
Improve round corners on block input and output

7 years agoMerge pull request #132 from rgaiacs/table
Raniere Silva [Sat, 18 Feb 2017 17:57:35 +0000 (17:57 +0000)]
Merge pull request #132 from rgaiacs/table

Make tables wider

7 years agoMake tables wider
Raniere Silva [Sat, 18 Feb 2017 17:56:38 +0000 (17:56 +0000)]
Make tables wider

Close https://github.com/swcarpentry/styles/issues/101.

7 years agoMerge pull request #129 from neon-ninja/dt-ids
Raniere Silva [Sat, 18 Feb 2017 17:04:36 +0000 (17:04 +0000)]
Merge pull request #129 from neon-ninja/dt-ids

ensure dt elements have an id set

7 years agoMerge pull request #127 from rgaiacs/fix-syllabus
Raniere Silva [Sat, 18 Feb 2017 17:04:22 +0000 (17:04 +0000)]
Merge pull request #127 from rgaiacs/fix-syllabus

Fix layout of syllabus table

7 years agoMerge pull request #109 from gvwilson/adding-jquery-debugging
Raniere Silva [Sat, 18 Feb 2017 17:01:39 +0000 (17:01 +0000)]
Merge pull request #109 from gvwilson/adding-jquery-debugging

Adding JQuery debugging

7 years agoMerge pull request #117 from maxim-belkin/patch-2
Raniere Silva [Wed, 8 Feb 2017 17:41:00 +0000 (17:41 +0000)]
Merge pull request #117 from maxim-belkin/patch-2

Visually separate inline code blocks

7 years agoMerge pull request #126 from gvwilson/consolidating-links
Raniere Silva [Sat, 4 Feb 2017 14:28:41 +0000 (14:28 +0000)]
Merge pull request #126 from gvwilson/consolidating-links

Checking consolidated links

7 years agoAdd javascript comments to the dt-ids snippet
Nick Young [Tue, 31 Jan 2017 21:19:36 +0000 (10:19 +1300)]
Add javascript comments to the dt-ids snippet

7 years agoensure dt elements have an id set
Nick Young [Tue, 31 Jan 2017 04:10:48 +0000 (17:10 +1300)]
ensure dt elements have an id set

7 years agoMerge pull request #128 from wking/example-site-reference
Raniere Silva [Tue, 24 Jan 2017 10:26:08 +0000 (10:26 +0000)]
Merge pull request #128 from wking/example-site-reference

bin/lesson_initialize.py: Remove 'example-site' reference

7 years agobin/lesson_initialize.py: Remove 'example-site' reference
W. Trevor King [Mon, 23 Jan 2017 22:54:50 +0000 (14:54 -0800)]
bin/lesson_initialize.py: Remove 'example-site' reference

The consumer was removed by 079d7d50 (Updating contribution guidelines
in boilerplate, 2016-06-26).

7 years agoEnforce Bootstrap's 12 column layout
Raniere Silva [Wed, 18 Jan 2017 22:50:09 +0000 (22:50 +0000)]
Enforce Bootstrap's 12 column layout

7 years agoAdd multiday condition on _includes/syllabus.html
Raniere Silva [Wed, 18 Jan 2017 22:39:47 +0000 (22:39 +0000)]
Add multiday condition on _includes/syllabus.html

7 years agoAdd missing class on _includes/syllabus.html
Raniere Silva [Wed, 18 Jan 2017 22:37:17 +0000 (22:37 +0000)]
Add missing class on _includes/syllabus.html

7 years agoAddition of link to setup had one too few columns.
Greg Wilson [Wed, 18 Jan 2017 12:27:55 +0000 (07:27 -0500)]
Addition of link to setup had one too few columns.

Rev 7da36a56c0ee added a new row to the syllabus table with only 11 columns (instead of 12), which broke layout.
This fix adds the missing space.

7 years agoChecking consolidated links
Greg Wilson [Sun, 15 Jan 2017 20:02:34 +0000 (15:02 -0500)]
Checking consolidated links

7 years agoMerge pull request #123 from gvwilson/mentioning-library-carpentry
Raniere Silva [Tue, 10 Jan 2017 13:21:22 +0000 (13:21 +0000)]
Merge pull request #123 from gvwilson/mentioning-library-carpentry

Including mention of Library Carpentry in include files

7 years agoMerging changes from other branches
Greg Wilson [Tue, 10 Jan 2017 00:59:11 +0000 (19:59 -0500)]
Merging changes from other branches

7 years agoMerge pull request #119 from itcarroll/gh-pages
Raniere Silva [Mon, 9 Jan 2017 23:47:24 +0000 (23:47 +0000)]
Merge pull request #119 from itcarroll/gh-pages

Knit episodes only when any one RMarkdown source changes

7 years agoMerge pull request #122 from gvwilson/commenting-includes
Raniere Silva [Mon, 9 Jan 2017 23:35:18 +0000 (23:35 +0000)]
Merge pull request #122 from gvwilson/commenting-includes

Adding comments on purposes of include files

7 years agoMerge pull request #121 from gvwilson/prev-next
Raniere Silva [Mon, 9 Jan 2017 23:34:13 +0000 (23:34 +0000)]
Merge pull request #121 from gvwilson/prev-next

Using page.previous and page.next for links instead of loop

7 years agoIncluding mention of Library Carpentry in include files
Greg Wilson [Mon, 9 Jan 2017 20:15:58 +0000 (15:15 -0500)]
Including mention of Library Carpentry in include files

7 years agoAdding comments on include files purposes
Greg Wilson [Mon, 9 Jan 2017 20:14:44 +0000 (15:14 -0500)]
Adding comments on include files purposes

7 years agoUsing page.previous and page.next for links instead of loop
Greg Wilson [Mon, 9 Jan 2017 20:12:30 +0000 (15:12 -0500)]
Using page.previous and page.next for links instead of loop

7 years agoMerge pull request #116 from maxim-belkin/patch-1
Raniere Silva [Mon, 9 Jan 2017 13:02:15 +0000 (13:02 +0000)]
Merge pull request #116 from maxim-belkin/patch-1

lesson.scss: 2em left padding for lists

7 years agochanges lesson-rmd target to lesson-md with new recipe
Ian Carroll [Sat, 31 Dec 2016 01:49:20 +0000 (20:49 -0500)]
changes lesson-rmd target to lesson-md with new recipe

7 years agoVisually separate inline code blocks
Maxim Belkin [Wed, 14 Dec 2016 17:40:19 +0000 (11:40 -0600)]
Visually separate inline code blocks

Change text color, background color and padding around inline code blocks

7 years agolesson.scss: 2em left padding for lists
Maxim Belkin [Wed, 14 Dec 2016 17:08:17 +0000 (11:08 -0600)]
lesson.scss: 2em left padding for lists

Example of the problem: see "Ten Things You Need To Know" from http://swcarpentry.github.io/lesson-example/
For numbered lists that have more that 9 elements 1 em padding on the left is not sufficient. The result is that "1" in numbers "10" and above is printed on top of the border of encapsulating HTML block. 2 em padding solves this problem for lists with less that 100 elements. It should be safe to safe to assume that numbered lists in Carpentries' lessons should not have more than 99 items.

7 years agoMerge pull request #108 from gvwilson/library-carpentry
Greg Wilson [Tue, 8 Nov 2016 22:24:45 +0000 (17:24 -0500)]
Merge pull request #108 from gvwilson/library-carpentry

Starting to incorporate Library Carpentry materials

7 years agoWeb site for Library Carpentry
Greg Wilson [Tue, 8 Nov 2016 22:23:11 +0000 (17:23 -0500)]
Web site for Library Carpentry

7 years agoMerge branch 'gh-pages' into library-carpentry
Greg Wilson [Tue, 8 Nov 2016 22:20:21 +0000 (17:20 -0500)]
Merge branch 'gh-pages' into library-carpentry

7 years agoMerge pull request #110 from rgaiacs/setup
Raniere Silva [Mon, 31 Oct 2016 03:23:56 +0000 (03:23 +0000)]
Merge pull request #110 from rgaiacs/setup

Add link to setup from schedule

7 years agoAdd link to setup from schedule
Raniere Silva [Tue, 18 Oct 2016 15:44:48 +0000 (16:44 +0100)]
Add link to setup from schedule

7 years agoUpdating lesson checker to include Library Carpentry values
Greg Wilson [Sat, 8 Oct 2016 19:38:11 +0000 (15:38 -0400)]
Updating lesson checker to include Library Carpentry values

7 years agoTidying up references to LC
Greg Wilson [Fri, 7 Oct 2016 17:23:18 +0000 (13:23 -0400)]
Tidying up references to LC

7 years agoAdding link to citation
Greg Wilson [Fri, 7 Oct 2016 17:20:16 +0000 (13:20 -0400)]
Adding link to citation

7 years agoContact address
Greg Wilson [Fri, 7 Oct 2016 16:46:44 +0000 (12:46 -0400)]
Contact address

7 years agoMerge branch 'gh-pages' into adding-jquery-debugging
Greg Wilson [Fri, 7 Oct 2016 16:41:55 +0000 (12:41 -0400)]
Merge branch 'gh-pages' into adding-jquery-debugging

7 years agoMerge pull request #107 from gvwilson/training-survey
Greg Wilson [Fri, 7 Oct 2016 16:41:08 +0000 (12:41 -0400)]
Merge pull request #107 from gvwilson/training-survey

Adding link to training survey to config

7 years agoFixing typo in license file
Greg Wilson [Fri, 7 Oct 2016 14:58:59 +0000 (10:58 -0400)]
Fixing typo in license file

7 years agoStarting to incorporate Library Carpentry materials
Greg Wilson [Fri, 7 Oct 2016 14:38:42 +0000 (10:38 -0400)]
Starting to incorporate Library Carpentry materials

7 years agoAdding link to training survey to config
Greg Wilson [Wed, 5 Oct 2016 19:09:16 +0000 (15:09 -0400)]
Adding link to training survey to config

7 years agoMerge pull request #105 from gvwilson/analytics
Jonah Duckles [Mon, 26 Sep 2016 20:09:00 +0000 (15:09 -0500)]
Merge pull request #105 from gvwilson/analytics

Adding Google Analytics code

7 years agoAdding Google Analytics code
Greg Wilson [Mon, 26 Sep 2016 20:06:57 +0000 (16:06 -0400)]
Adding Google Analytics code

7 years agoMerge pull request #103 from evanwill/accessibility-fix
Raniere Silva [Fri, 23 Sep 2016 13:41:13 +0000 (14:41 +0100)]
Merge pull request #103 from evanwill/accessibility-fix

accessibility fixes.

7 years agoMerge pull request #104 from evanwill/search-fix
Raniere Silva [Fri, 23 Sep 2016 13:39:00 +0000 (14:39 +0100)]
Merge pull request #104 from evanwill/search-fix

fix search meta tag.

7 years agofix search meta tag.
evanwill [Fri, 23 Sep 2016 04:52:27 +0000 (21:52 -0700)]
fix search meta tag.

7 years agoaccessibility fixes.
evanwill [Fri, 23 Sep 2016 04:46:11 +0000 (21:46 -0700)]
accessibility fixes.
Add label to search box and navigation arrows.

7 years agoAdding checks for things that commonly go wrong during template conversion.
Greg Wilson [Thu, 15 Sep 2016 18:37:58 +0000 (14:37 -0400)]
Adding checks for things that commonly go wrong during template conversion.

1. Checking that `index.md` has `root` set to '.'
2. Checking that `_config.yml` has `root` set to '..'

7 years agoRemoving trailing space in Ruby file
Greg Wilson [Mon, 12 Sep 2016 15:57:22 +0000 (11:57 -0400)]
Removing trailing space in Ruby file

7 years agoDisplaying break information in a box
Greg Wilson [Mon, 12 Sep 2016 15:57:02 +0000 (11:57 -0400)]
Displaying break information in a box

7 years agoAdding ID attribute to schedule
Greg Wilson [Wed, 7 Sep 2016 21:16:12 +0000 (17:16 -0400)]
Adding ID attribute to schedule

7 years agoChanging name of instructor's guide to 'instructor notes'
Greg Wilson [Wed, 7 Sep 2016 19:15:12 +0000 (15:15 -0400)]
Changing name of instructor's guide to 'instructor notes'

7 years agoAdding footnote about syllabus
Greg Wilson [Wed, 7 Sep 2016 19:10:19 +0000 (15:10 -0400)]
Adding footnote about syllabus