rnaseq-cwl-training.git
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 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 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 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

7 years agoNavigation links in footer
Greg Wilson [Mon, 5 Sep 2016 17:51:02 +0000 (13:51 -0400)]
Navigation links in footer

7 years agoSwitch to relative: setup default root and specific root for index.md
Rémi Emonet [Mon, 5 Sep 2016 17:28:26 +0000 (19:28 +0200)]
Switch to relative: setup default root and specific root for index.md

7 years agoSwitch to relative: in episode_title, use page.root + rewrite
Rémi Emonet [Mon, 5 Sep 2016 17:24:49 +0000 (19:24 +0200)]
Switch to relative: in episode_title, use page.root + rewrite

7 years agoSwitch to relative: use page.root in most templates
Rémi Emonet [Mon, 5 Sep 2016 17:22:11 +0000 (19:22 +0200)]
Switch to relative: use page.root in most templates

7 years agoMerge pull request #92 from swcarpentry/twitwi-patch-1
Greg Wilson [Fri, 26 Aug 2016 20:36:51 +0000 (16:36 -0400)]
Merge pull request #92 from swcarpentry/twitwi-patch-1

Fix "br" typo causing ugly rendering (epub only)

7 years agoFix "br" typo causing ugly rendering (epub only)
Rémi Emonet [Thu, 25 Aug 2016 15:55:55 +0000 (17:55 +0200)]
Fix "br" typo causing ugly rendering (epub only)

</br> instead of <br/> renders fine in the browser but not in an epub

7 years agoAdding a few more URLs
Greg Wilson [Thu, 28 Jul 2016 00:04:06 +0000 (20:04 -0400)]
Adding a few more URLs

7 years agoUpdating the lesson initializer's CONTRIBUTING.md
Greg Wilson [Tue, 26 Jul 2016 14:54:29 +0000 (10:54 -0400)]
Updating the lesson initializer's CONTRIBUTING.md

7 years agoChecking that internally-defined links resolve.
Greg Wilson [Sun, 24 Jul 2016 13:12:20 +0000 (09:12 -0400)]
Checking that internally-defined links resolve.

An internally-defined Markdown link has the form [xxx][yyy].  If the
ID 'yyy' doesn't resolve, the text is left as-is, so we check for
that, then subtract those that reference configuration values using
'{{'.  It's a hack, but it'll catch at least a few things.

7 years agoChecking future print
Greg Wilson [Thu, 21 Jul 2016 17:35:29 +0000 (13:35 -0400)]
Checking future print

7 years agoMoving from __future__ to start of file
Greg Wilson [Thu, 21 Jul 2016 17:29:27 +0000 (13:29 -0400)]
Moving from __future__ to start of file

7 years agoMerge pull request #85 from gdevenyi/gh-pages
Greg Wilson [Thu, 21 Jul 2016 14:56:18 +0000 (10:56 -0400)]
Merge pull request #85 from gdevenyi/gh-pages

Import future print in case of python2 environment

7 years agoImport future print in case of python2 environment
Gabriel A. Devenyi [Thu, 21 Jul 2016 13:52:21 +0000 (09:52 -0400)]
Import future print in case of python2 environment

7 years agoMerge pull request #83 from fmichonneau/check-r-packages
Greg Wilson [Thu, 21 Jul 2016 02:28:09 +0000 (22:28 -0400)]
Merge pull request #83 from fmichonneau/check-r-packages

[fix # 82] Check R packages required by the lesson

7 years agoLoading standard images via HTTPS
Greg Wilson [Thu, 21 Jul 2016 00:18:51 +0000 (20:18 -0400)]
Loading standard images via HTTPS

7 years agoForcing CSS and Javascript to be loaded via HTTPS.
Greg Wilson [Thu, 21 Jul 2016 00:01:47 +0000 (20:01 -0400)]
Forcing CSS and Javascript to be loaded via HTTPS.

Using `site.github.url` to refer to the repository fails to load resources when the GitHub Pages site is accessed via HTTPS, because `site.github.url` is `http` protocol.  This modifies loads of CSS and Javascript files to always use `https`.

7 years agosimplify code checking for knitr
Francois Michonneau [Wed, 20 Jul 2016 15:53:47 +0000 (11:53 -0400)]
simplify code checking for knitr

7 years agocheck packages required and install them if needed
Francois Michonneau [Wed, 20 Jul 2016 15:47:20 +0000 (11:47 -0400)]
check packages required and install them if needed

7 years agoIgnoring a few more things
Greg Wilson [Mon, 18 Jul 2016 10:31:01 +0000 (06:31 -0400)]
Ignoring a few more things

7 years agoCleaning up sorting of error messages.
Greg Wilson [Fri, 15 Jul 2016 23:23:58 +0000 (19:23 -0400)]
Cleaning up sorting of error messages.

Closes #75.

7 years agoAlways checking upstream
Greg Wilson [Fri, 15 Jul 2016 14:44:29 +0000 (10:44 -0400)]
Always checking upstream

7 years agoUsing 00:00 as a start time
Greg Wilson [Fri, 15 Jul 2016 14:12:27 +0000 (10:12 -0400)]
Using 00:00 as a start time

7 years agoCleaning up prev/next logic
Greg Wilson [Thu, 14 Jul 2016 17:40:18 +0000 (13:40 -0400)]
Cleaning up prev/next logic

7 years agoSynchronizing lesson checker with late changes
Greg Wilson [Thu, 14 Jul 2016 14:43:35 +0000 (10:43 -0400)]
Synchronizing lesson checker with late changes

7 years agoLesson initializer
Greg Wilson [Thu, 14 Jul 2016 14:38:48 +0000 (10:38 -0400)]
Lesson initializer

7 years agoSwitching to GitHub-defined variables
Greg Wilson [Thu, 14 Jul 2016 14:28:36 +0000 (10:28 -0400)]
Switching to GitHub-defined variables

7 years agoMaking the code a little more robust
Greg Wilson [Wed, 13 Jul 2016 11:19:05 +0000 (07:19 -0400)]
Making the code a little more robust

7 years agoAdding support for MATLAB
Greg Wilson [Fri, 8 Jul 2016 21:04:05 +0000 (17:04 -0400)]
Adding support for MATLAB

7 years agoHandling anchors by ignoring them
Greg Wilson [Fri, 8 Jul 2016 11:07:18 +0000 (07:07 -0400)]
Handling anchors by ignoring them

7 years agoTighter checks for figures
Greg Wilson [Thu, 7 Jul 2016 20:46:22 +0000 (16:46 -0400)]
Tighter checks for figures

7 years agoChecking for links to figures
Greg Wilson [Thu, 7 Jul 2016 19:35:33 +0000 (15:35 -0400)]
Checking for links to figures

7 years agoStarting on tool to check repository settings.
Greg Wilson [Thu, 7 Jul 2016 14:59:38 +0000 (10:59 -0400)]
Starting on tool to check repository settings.

1.  Created `bin/repo_check.py`.
2.  Moved `require()` to `util.py`.
3.  Updated `Makefile` with new target.

7 years agoChecking more configuration values
Greg Wilson [Wed, 6 Jul 2016 00:48:45 +0000 (20:48 -0400)]
Checking more configuration values

7 years agoMust provide permalinks in pages, not layouts
Greg Wilson [Sun, 3 Jul 2016 21:51:10 +0000 (17:51 -0400)]
Must provide permalinks in pages, not layouts

7 years agoChecking for .nojekyll file
Greg Wilson [Sun, 3 Jul 2016 21:43:08 +0000 (17:43 -0400)]
Checking for .nojekyll file

7 years agoImages cannot be wider than the page
Greg Wilson [Sun, 3 Jul 2016 18:52:02 +0000 (14:52 -0400)]
Images cannot be wider than the page

7 years agoMerge branch '2016-06' of github.com:swcarpentry/styles into 2016-06
Greg Wilson [Sat, 2 Jul 2016 21:34:09 +0000 (17:34 -0400)]
Merge branch '2016-06' of github.com:swcarpentry/styles into 2016-06

7 years agoLooking for missing or superfluous images
Greg Wilson [Sat, 2 Jul 2016 21:30:22 +0000 (17:30 -0400)]
Looking for missing or superfluous images

7 years agoMerge pull request #73 from fmichonneau/knitr_fig_path
Greg Wilson [Sat, 2 Jul 2016 13:05:56 +0000 (09:05 -0400)]
Merge pull request #73 from fmichonneau/knitr_fig_path

add function knitr_fig_path

7 years agoLesson checking parameter handling
Greg Wilson [Fri, 1 Jul 2016 18:10:07 +0000 (14:10 -0400)]
Lesson checking parameter handling

7 years agoadd function knitr_fig_path
Francois Michonneau [Fri, 1 Jul 2016 18:08:58 +0000 (14:08 -0400)]
add function knitr_fig_path

7 years agoChecking ends of lines
Greg Wilson [Thu, 30 Jun 2016 03:16:39 +0000 (23:16 -0400)]
Checking ends of lines

7 years agoMerge branch 'move-data' of https://github.com/fmichonneau/styles into fmichonneau...
Greg Wilson [Tue, 28 Jun 2016 16:01:44 +0000 (12:01 -0400)]
Merge branch 'move-data' of https://github.com/fmichonneau/styles into fmichonneau-move-data

7 years agore-add ./data folder
Francois Michonneau [Tue, 28 Jun 2016 15:35:08 +0000 (11:35 -0400)]
re-add ./data folder

7 years agosimplify to single _episodes_rmd/data folder
Francois Michonneau [Tue, 28 Jun 2016 15:27:31 +0000 (11:27 -0400)]
simplify to single _episodes_rmd/data folder

7 years agoMerge branch 'styling-workshops' into 2016-06
Greg Wilson [Mon, 27 Jun 2016 01:39:12 +0000 (21:39 -0400)]
Merge branch 'styling-workshops' into 2016-06

7 years agoMerge branch 'markdownify' into 2016-06
Greg Wilson [Mon, 27 Jun 2016 01:39:01 +0000 (21:39 -0400)]
Merge branch 'markdownify' into 2016-06

7 years agoMerge branch 'converting-to-reporter' into 2016-06
Greg Wilson [Mon, 27 Jun 2016 01:38:50 +0000 (21:38 -0400)]
Merge branch 'converting-to-reporter' into 2016-06

7 years agoMerge branch '2016-06' of github.com:swcarpentry/styles into 2016-06
Greg Wilson [Mon, 27 Jun 2016 00:46:42 +0000 (20:46 -0400)]
Merge branch '2016-06' of github.com:swcarpentry/styles into 2016-06

7 years agoUpdating contribution guidelines in boilerplate
Greg Wilson [Mon, 27 Jun 2016 00:45:43 +0000 (20:45 -0400)]
Updating contribution guidelines in boilerplate

7 years agoMerge pull request #67 from gvwilson/clean-rmd
Francois Michonneau [Mon, 27 Jun 2016 00:28:24 +0000 (20:28 -0400)]
Merge pull request #67 from gvwilson/clean-rmd

Only cleaning intermediate R files on demand.

7 years agoMaking pages work for workshops as well as lessons
Greg Wilson [Sun, 26 Jun 2016 23:14:01 +0000 (19:14 -0400)]
Making pages work for workshops as well as lessons

7 years agoStyling workshops correctly.
Greg Wilson [Sun, 26 Jun 2016 22:54:18 +0000 (18:54 -0400)]
Styling workshops correctly.

1.  Use site.root for root path if set, otherwise use site.github.url.
2.  Display extra files for workshop-template repo as well as for lessons.

7 years agoMarkdownifying questions, keypoints, etc.
Greg Wilson [Sun, 26 Jun 2016 04:25:00 +0000 (00:25 -0400)]
Markdownifying questions, keypoints, etc.

7 years agoAdding error handling for YAML import.
Greg Wilson [Sun, 26 Jun 2016 02:23:19 +0000 (22:23 -0400)]
Adding error handling for YAML import.

1.  Moving all YAML library usage into 'util.py' via utility function.
2.  Wrapping 'import yaml' in error handling to report what library to install.

7 years agoChecking CONTRIBUTING.md (without YAML)
Greg Wilson [Sun, 26 Jun 2016 00:56:47 +0000 (20:56 -0400)]
Checking CONTRIBUTING.md (without YAML)

7 years agoConverting workshop checker to use Reporter class.
Greg Wilson [Sun, 26 Jun 2016 00:52:47 +0000 (20:52 -0400)]
Converting workshop checker to use Reporter class.

1.  Converting error reporting.
2.  Simplifying checking logic.
3.  Refactoring metadata loading.
4.  Modifying lesson checker to reflect refactoring.

Closes #47.

7 years agoChecking for non-Markdown files.
Greg Wilson [Sat, 25 Jun 2016 23:55:00 +0000 (19:55 -0400)]
Checking for non-Markdown files.

Closes #55.

7 years agoOnly cleaning intermediate R files on demand.
Greg Wilson [Sat, 25 Jun 2016 14:24:34 +0000 (10:24 -0400)]
Only cleaning intermediate R files on demand.

1.  Splitting commands to clean intermediate R files into separate target.  These files must be committed to the repo, so they shouldn't be deleted under normal circumstances.
2.  Modifying intermediate file generation to create fig/rmd-* rather than fig/swc-rmd-*, since this template is used by other carpentries (not just SWC).

7 years agomove data/ into _episodes/ and _episodes_rmd/
Francois Michonneau [Fri, 24 Jun 2016 17:13:26 +0000 (13:13 -0400)]
move data/ into _episodes/ and _episodes_rmd/

`generate_md_episodes()` is modified such that datasets storred into
_episodes_rmd/data/ needed to knit the episodes, are copied into
_episodes/data/, and are made available at the root of the site.

7 years agoMerge pull request #64 from gvwilson/building-r
Greg Wilson [Fri, 24 Jun 2016 16:37:47 +0000 (12:37 -0400)]
Merge pull request #64 from gvwilson/building-r

Only try building R files if there are some

7 years agoChanging text of auto-generated file
Greg Wilson [Thu, 23 Jun 2016 21:07:18 +0000 (17:07 -0400)]
Changing text of auto-generated file

7 years agoMerge branch '2016-06' into building-r
Greg Wilson [Thu, 23 Jun 2016 21:03:27 +0000 (17:03 -0400)]
Merge branch '2016-06' into building-r

7 years agoUpdating _config_dev.yml to match changes to root and repo vars
Greg Wilson [Thu, 23 Jun 2016 21:01:00 +0000 (17:01 -0400)]
Updating _config_dev.yml to match changes to root and repo vars

7 years agoSwitching to site.root and site.repo
Greg Wilson [Thu, 23 Jun 2016 20:50:38 +0000 (16:50 -0400)]
Switching to site.root and site.repo

7 years agoOnly try building R files if there are some
Greg Wilson [Thu, 23 Jun 2016 19:43:47 +0000 (15:43 -0400)]
Only try building R files if there are some

7 years agoBetter display of file groups in Makefile
Greg Wilson [Thu, 23 Jun 2016 14:54:58 +0000 (10:54 -0400)]
Better display of file groups in Makefile