rnaseq-cwl-training.git
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

7 years agoMerge pull request #62 from fmichonneau/fix-knitr-env
Francois Michonneau [Wed, 22 Jun 2016 21:13:02 +0000 (17:13 -0400)]
Merge pull request #62 from fmichonneau/fix-knitr-env

use anonymous function to generate markdown files

7 years agouse anonymous function to generate markdown files
Francois Michonneau [Wed, 22 Jun 2016 21:08:51 +0000 (17:08 -0400)]
use anonymous function to generate markdown files

7 years agoChecking metadata fields more carefully
Greg Wilson [Wed, 22 Jun 2016 19:09:02 +0000 (15:09 -0400)]
Checking metadata fields more carefully

7 years agoPrinting error messages in sorted order
Greg Wilson [Wed, 22 Jun 2016 18:53:32 +0000 (14:53 -0400)]
Printing error messages in sorted order

7 years agoChecking that episodes are numbered consecutively
Greg Wilson [Wed, 22 Jun 2016 18:10:31 +0000 (14:10 -0400)]
Checking that episodes are numbered consecutively

7 years agoMaking line-length checking optional for lessons.
Greg Wilson [Wed, 22 Jun 2016 17:57:22 +0000 (13:57 -0400)]
Making line-length checking optional for lessons.

1.  Modify `read_markdown` to return list of (index, line, line_length).
2.  Modify `lesson_check.py` to make line-length checking optional.

7 years agoRaising exception instead of printing error on bad YAML
Greg Wilson [Wed, 22 Jun 2016 17:17:02 +0000 (13:17 -0400)]
Raising exception instead of printing error on bad YAML

7 years agoMerge pull request #61 from fmichonneau/fix-rmd-formatting
Greg Wilson [Wed, 22 Jun 2016 14:59:22 +0000 (10:59 -0400)]
Merge pull request #61 from fmichonneau/fix-rmd-formatting

Fix Rmd formatting

7 years agoremove extra line return in knitr output
Francois Michonneau [Wed, 22 Jun 2016 14:48:53 +0000 (10:48 -0400)]
remove extra line return in knitr output

7 years agouse .r instead of .source for code chunks
Francois Michonneau [Wed, 22 Jun 2016 14:48:05 +0000 (10:48 -0400)]
use .r instead of .source for code chunks

7 years agoDirectory for R Markdown files
Greg Wilson [Wed, 22 Jun 2016 10:31:26 +0000 (06:31 -0400)]
Directory for R Markdown files

7 years agoRemoving legacy PHONY target lesson-single
Greg Wilson [Wed, 22 Jun 2016 09:05:43 +0000 (05:05 -0400)]
Removing legacy PHONY target lesson-single

7 years agoMerge pull request #56 from fmichonneau/rmarkdown-tools
Greg Wilson [Tue, 21 Jun 2016 22:51:46 +0000 (18:51 -0400)]
Merge pull request #56 from fmichonneau/rmarkdown-tools

add tools to deal with episodes written in Rmd

7 years agoadd tools to deal with episodes written in Rmd
Francois Michonneau [Tue, 21 Jun 2016 21:04:03 +0000 (17:04 -0400)]
add tools to deal with episodes written in Rmd

7 years agoMaking nav bar responsive
Greg Wilson [Tue, 21 Jun 2016 20:15:25 +0000 (16:15 -0400)]
Making nav bar responsive

7 years agoTidying up based on first contact with R maintainers.
Greg Wilson [Tue, 21 Jun 2016 19:26:09 +0000 (15:26 -0400)]
Tidying up based on first contact with R maintainers.

1.  Renaming Ruby file to use underscore in name (consistent with other `bin` scripts).
2.  Generating `_includes/all_figures.html` for the first time when creating a new lesson.

7 years agoPreparing for June 2016 release
Greg Wilson [Mon, 20 Jun 2016 22:45:37 +0000 (18:45 -0400)]
Preparing for June 2016 release

8 years agoFixing typo
Greg Wilson [Sun, 14 Jun 2015 23:31:48 +0000 (19:31 -0400)]
Fixing typo

8 years agoCSS cataloguing tool
Greg Wilson [Sun, 14 Jun 2015 21:04:37 +0000 (17:04 -0400)]
CSS cataloguing tool

8 years agoMerge pull request #30 from twitwi/master
Raniere Silva [Sat, 2 May 2015 11:11:13 +0000 (08:11 -0300)]
Merge pull request #30 from twitwi/master

fix #26: updated bundled deck.js, including the fix on browsercast

8 years agofix #26: updated bundled deck.js, including the fix on browsercast
Rémi Emonet [Fri, 1 May 2015 22:05:14 +0000 (00:05 +0200)]
fix #26: updated bundled deck.js, including the fix on browsercast

this bundle is used also for browsecast-less presentations
and thus browsercast should not unbind the space in this case
and that's solved now

9 years agoMerge branch 'styles-compatible' into new-style
Raniere Silva [Sat, 25 Apr 2015 11:40:43 +0000 (08:40 -0300)]
Merge branch 'styles-compatible' into new-style

9 years agoMerge branch 'style-img-responsive' into new-style
Raniere Silva [Sat, 25 Apr 2015 11:40:31 +0000 (08:40 -0300)]
Merge branch 'style-img-responsive' into new-style

9 years agoMerge branch 'upgrade-bootstrap' into new-style
Raniere Silva [Sat, 25 Apr 2015 11:40:21 +0000 (08:40 -0300)]
Merge branch 'upgrade-bootstrap' into new-style

9 years agoMerge pull request #24 from fmichonneau/merge-badge-classes
Raniere Silva [Sat, 25 Apr 2015 11:39:01 +0000 (08:39 -0300)]
Merge pull request #24 from fmichonneau/merge-badge-classes

consolidate badge classes to swc.css

9 years agoFix path of fonts
Raniere Silva [Sun, 19 Apr 2015 17:24:47 +0000 (14:24 -0300)]
Fix path of fonts

9 years agoCSS compatible with different versions of Pandoc
Raniere Silva [Sun, 19 Apr 2015 15:28:51 +0000 (12:28 -0300)]
CSS compatible with different versions of Pandoc

9 years agoImprove figures
Raniere Silva [Sun, 19 Apr 2015 14:50:52 +0000 (11:50 -0300)]
Improve figures

Figures should be centered
and not overflow the screen.

9 years agoBootstrap v3.3.4
Raniere Silva [Sun, 19 Apr 2015 14:25:27 +0000 (11:25 -0300)]
Bootstrap v3.3.4

9 years agoconsolidate badge classes to swc.css
Francois Michonneau [Tue, 24 Mar 2015 02:05:27 +0000 (22:05 -0400)]
consolidate badge classes to swc.css

the class removed are unused as we take advantage of classes provided by
Bootstrap instead.

9 years agoMerge pull request #18 from r-gaia-cs/styles-card
Greg Wilson [Sat, 21 Mar 2015 21:28:20 +0000 (17:28 -0400)]
Merge pull request #18 from r-gaia-cs/styles-card

Add documentation about card class

9 years agoAdd documentation about card class
Raniere Silva [Sat, 21 Mar 2015 20:02:25 +0000 (17:02 -0300)]
Add documentation about card class

9 years agoMerge pull request #17 from r-gaia-cs/style-panels
Greg Wilson [Sat, 21 Mar 2015 16:48:38 +0000 (12:48 -0400)]
Merge pull request #17 from r-gaia-cs/style-panels

Better style for challenges

9 years agoMerge pull request #16 from r-gaia-cs/styles-fix-background
Greg Wilson [Sat, 21 Mar 2015 16:48:30 +0000 (12:48 -0400)]
Merge pull request #16 from r-gaia-cs/styles-fix-background

Fix background for lessons

9 years agoFix: styles for panel heading
Piotr Banaszkiewicz [Wed, 18 Feb 2015 19:30:08 +0000 (20:30 +0100)]
Fix: styles for panel heading

There's a note in
https://github.com/swcarpentry/lesson-template/pull/182
explaining why we need to fix style for panel heading.

9 years agoAdd Bootstrap theme
Piotr Banaszkiewicz [Wed, 18 Feb 2015 19:26:10 +0000 (20:26 +0100)]
Add Bootstrap theme

This makes some things look nicer (e.g. adds gradients, etc).

9 years agoFix background for lessons
Raniere Silva [Sat, 21 Mar 2015 07:52:51 +0000 (04:52 -0300)]
Fix background for lessons

9 years agoMerge pull request #12 from fmichonneau/site-update
Francois Michonneau [Mon, 2 Mar 2015 19:40:09 +0000 (14:40 -0500)]
Merge pull request #12 from fmichonneau/site-update

Update CSS to go with the SWC site template update

9 years agoMerge pull request #10 from pbanaszkiewicz/fix-table-styles
Raniere Silva [Wed, 25 Feb 2015 19:51:57 +0000 (20:51 +0100)]
Merge pull request #10 from pbanaszkiewicz/fix-table-styles

Fix: styles for tables in SQL lessons

9 years agofix footer for small displays
Francois Michonneau [Mon, 23 Feb 2015 16:57:00 +0000 (11:57 -0500)]
fix footer for small displays

9 years agofix swcarpentry/site#844 reposition button on small displays
Francois Michonneau [Mon, 23 Feb 2015 16:56:20 +0000 (11:56 -0500)]
fix swcarpentry/site#844 reposition button on small displays

9 years agofix navbar
Francois Michonneau [Thu, 19 Feb 2015 05:01:57 +0000 (00:01 -0500)]
fix navbar

9 years agofix blockquote
Francois Michonneau [Thu, 19 Feb 2015 05:01:44 +0000 (00:01 -0500)]
fix blockquote

9 years agoswc.css: Add striped rows to tables
Piotr Banaszkiewicz [Sat, 14 Feb 2015 10:56:02 +0000 (11:56 +0100)]
swc.css: Add striped rows to tables

Now the style is matching closely `.table-bordered` from Bootstrap.
I decided to leave the header row background blank because it was too
close in color to `#F9F9F9` - our new rule for even rows in the table.

I also increased horizontal padding by 5px on both sides, because now
that we have vertical borders it was too cramped.

Additionaly I introduced borders for every cell in the table.

9 years agoFix: styles for tables in SQL lessons
Piotr Banaszkiewicz [Fri, 13 Feb 2015 19:58:35 +0000 (20:58 +0100)]
Fix: styles for tables in SQL lessons

Previously: table cells had no padding, which caused a visual collapse
(cell content was too close to cell neighbors). Table header rows had
dark blue background and black letters.  Tables had no space between
them and following paragraphs.

Changes:
* added 5px padding to cell contents
* changed header row background to gray-ish (I considered switching text
  color to white, but it didn't look good)
* 15px margin on the bottom of the tables (similarly to bottom margin
  used by paragraph style).

9 years agofix #8 (font size for code in headings)
Francois Michonneau [Fri, 13 Feb 2015 14:17:00 +0000 (09:17 -0500)]
fix #8 (font size for code in headings)

9 years agofix navbar on smaller displays
Francois Michonneau [Thu, 12 Feb 2015 03:05:00 +0000 (22:05 -0500)]
fix navbar on smaller displays

9 years agobump z-index for ribbon
Francois Michonneau [Thu, 12 Feb 2015 02:32:57 +0000 (21:32 -0500)]
bump z-index for ribbon

9 years agofix footer
Francois Michonneau [Thu, 12 Feb 2015 01:57:07 +0000 (20:57 -0500)]
fix footer

9 years agofix swcarpentry/styles#4 github ribbon position
Francois Michonneau [Thu, 5 Feb 2015 04:24:48 +0000 (23:24 -0500)]
fix swcarpentry/styles#4 github ribbon position

9 years agoMerge github.com:swcarpentry/styles into site-update
Francois Michonneau [Thu, 5 Feb 2015 03:58:29 +0000 (22:58 -0500)]
Merge github.com:swcarpentry/styles into site-update

9 years agomodify CSS for navbar
Francois Michonneau [Wed, 4 Feb 2015 22:12:04 +0000 (17:12 -0500)]
modify CSS for navbar

9 years agofix urls for location of glyphicons
Francois Michonneau [Wed, 4 Feb 2015 22:11:51 +0000 (17:11 -0500)]
fix urls for location of glyphicons

9 years agoremove unneeded classes
Francois Michonneau [Wed, 4 Feb 2015 19:49:51 +0000 (14:49 -0500)]
remove unneeded classes

9 years agofix class for navbar
Francois Michonneau [Mon, 2 Feb 2015 05:22:46 +0000 (00:22 -0500)]
fix class for navbar

9 years agoMerge pull request #6 from fmichonneau/fix-typo
Francois Michonneau [Mon, 2 Feb 2015 03:21:37 +0000 (22:21 -0500)]
Merge pull request #6 from fmichonneau/fix-typo

add missing bracket

9 years agoadd missing bracket
Francois Michonneau [Mon, 2 Feb 2015 03:21:02 +0000 (22:21 -0500)]
add missing bracket

9 years agoMerge pull request #3 from fmichonneau/upgrade-bootstrap
Raniere Silva [Sun, 1 Feb 2015 01:25:58 +0000 (23:25 -0200)]
Merge pull request #3 from fmichonneau/upgrade-bootstrap

Upgrade bootstrap

9 years agoMerge github.com:swcarpentry/styles into upgrade-bootstrap
Francois Michonneau [Sat, 31 Jan 2015 17:14:52 +0000 (12:14 -0500)]
Merge github.com:swcarpentry/styles into upgrade-bootstrap

Conflicts:
css/swc-bootstrap.css
css/swc.css

9 years agoMerge pull request #5 from swcarpentry/join-site-lesson
Raniere Silva [Wed, 28 Jan 2015 20:29:40 +0000 (18:29 -0200)]
Merge pull request #5 from swcarpentry/join-site-lesson

Join CSS from site and lessons

9 years agoMerge branch 'site'
Raniere Silva [Wed, 28 Jan 2015 20:13:07 +0000 (18:13 -0200)]
Merge branch 'site'

9 years agoUse unified CSS from site.
James Allen [Mon, 26 Jan 2015 10:00:10 +0000 (10:00 +0000)]
Use unified CSS from site.

As per swcarpentry/lesson-template#140, but only the core CSS
changes.

9 years agoMove files (from site) into css
Raniere Silva [Wed, 28 Jan 2015 20:02:25 +0000 (18:02 -0200)]
Move files (from site) into css

9 years agoMerging @r-gaia-cs improvements
Greg Wilson [Thu, 22 Jan 2015 01:19:24 +0000 (20:19 -0500)]
Merging @r-gaia-cs improvements

9 years agoSmall improvements to CSS
Raniere Silva [Sun, 4 Jan 2015 12:45:14 +0000 (10:45 -0200)]
Small improvements to CSS

-   Remove extra space before title of boxes
-   Remove background color of boxes when printing
-   Add "Input", "Output" and "Error" tips for code blocks
    when printing
-   Avoid duplicate lines

9 years agoadded some challenge CSS
Bill Mills [Wed, 31 Dec 2014 06:06:23 +0000 (22:06 -0800)]
added some challenge CSS

9 years agoImprove callout box
Raniere Silva [Sun, 16 Nov 2014 13:53:38 +0000 (11:53 -0200)]
Improve callout box

and "learning objectives" box.

9 years agoBlockquote margins
Timothée Poisot [Fri, 14 Nov 2014 00:38:43 +0000 (13:38 +1300)]
Blockquote margins

9 years agoSet up code color
Raniere Silva [Sun, 16 Nov 2014 13:03:14 +0000 (11:03 -0200)]
Set up code color

9 years agoRemove border bottom from title
Raniere Silva [Sun, 16 Nov 2014 11:51:03 +0000 (09:51 -0200)]
Remove border bottom from title

9 years agoClean CSS file
Raniere Silva [Thu, 13 Nov 2014 21:28:48 +0000 (19:28 -0200)]
Clean CSS file

9 years agouse correct swc.css file
Francois Michonneau [Tue, 27 Jan 2015 17:40:30 +0000 (12:40 -0500)]
use correct swc.css file

9 years agoconsolidate CSS files
Francois Michonneau [Tue, 27 Jan 2015 16:21:31 +0000 (11:21 -0500)]
consolidate CSS files

9 years agoupgrade to bootstrap 3.3.2
Francois Michonneau [Tue, 27 Jan 2015 16:20:52 +0000 (11:20 -0500)]
upgrade to bootstrap 3.3.2

9 years agoSeparate out some specific workshop classes.
James Allen [Wed, 21 Jan 2015 21:14:36 +0000 (21:14 +0000)]
Separate out some specific workshop classes.

The workshop template is mostly plain bootstrap, so getting it work
alongside the site CSS seems mostly straightforward. We only need to
add in a .workshop class to the body, and a .card class to the
.container in the workshop. Everything else is bootstrap content.

This commit also removes the banner.html include since this did not
seem to be removed in the main site, but was referenced in the CSS.
Removing it makes it clear the .banner class is only needed in the
workshop, not here.

9 years agoCleaning up nav bar
Greg Wilson [Sun, 21 Dec 2014 01:53:11 +0000 (20:53 -0500)]
Cleaning up nav bar

9 years agoReformatting instructor bios
Greg Wilson [Fri, 28 Nov 2014 12:25:58 +0000 (07:25 -0500)]
Reformatting instructor bios

9 years agoInstructor training registration form
Abigail Cabunoc [Mon, 24 Nov 2014 20:23:52 +0000 (15:23 -0500)]
Instructor training registration form
* add Country drop down select
* add Gender

9 years agoMove files into css
Raniere Silva [Fri, 24 Oct 2014 12:53:31 +0000 (10:53 -0200)]
Move files into css

9 years agoReplace bootcamp with workshop
Raniere Silva [Thu, 25 Sep 2014 15:59:59 +0000 (12:59 -0300)]
Replace bootcamp with workshop

~~~
$ for file in $(grep -r -l 'bootcamp' .); do sed -i 's/bootcamp/workshop/g' $file; done
$ for file in $(grep -r -l 'boot camp' .); do sed -i 's/boot camp/workshop/g' $file; done
~~~

and others minors changes.

Close #240.

9 years agoChanging wording in everything except blog posts
Greg Wilson [Mon, 29 Sep 2014 16:52:33 +0000 (12:52 -0400)]
Changing wording in everything except blog posts

9 years agoMerge pull request #535 from gvwilson/rewriting-shell-lesson-using-nelle
Greg Wilson [Tue, 22 Jul 2014 19:52:11 +0000 (15:52 -0400)]
Merge pull request #535 from gvwilson/rewriting-shell-lesson-using-nelle

Rewriting novice shell lesson so that everything refers to Nelle instead of Vlad.

9 years agoUpdate IPython Notebook template
Raniere Silva [Sat, 14 Jun 2014 03:10:02 +0000 (00:10 -0300)]
Update IPython Notebook template

- Improve to handle err class
- Improve pandoc support

9 years agoShrink the font size for print version
Raniere Silva [Mon, 23 Jun 2014 21:09:47 +0000 (18:09 -0300)]
Shrink the font size for print version

9 years agoAdd CSS for printing
Raniere Silva [Sun, 22 Jun 2014 14:51:55 +0000 (11:51 -0300)]
Add CSS for printing

The CSS was add at our main CSS and remove from printing:

- Logo at header
- GitHub ribbon
- Footnote

Close #561.

9 years agoUpdate template for book to rely on CSS
Raniere Silva [Fri, 13 Jun 2014 17:15:42 +0000 (14:15 -0300)]
Update template for book to rely on CSS

Use h2 tag for "subtitle" will break any tool used to convert HTML
for another format. This commit replace h2 with span and rely on
CSS for have the same look.

9 years agoMerge pull request #447 from r-gaia-cs/github
Greg Wilson [Tue, 10 Jun 2014 15:49:38 +0000 (11:49 -0400)]
Merge pull request #447 from r-gaia-cs/github

Add GitHub Ribbon to our lessons

9 years agoNovice shell lesson is now written in terms of Nelle instead of Vlad.
Greg Wilson [Mon, 9 Jun 2014 17:29:58 +0000 (13:29 -0400)]
Novice shell lesson is now written in terms of Nelle instead of Vlad.

9 years agoImprove CSS for GitHub ribbon
Raniere Silva [Sat, 7 Jun 2014 16:43:05 +0000 (13:43 -0300)]
Improve CSS for GitHub ribbon

- For small screen, preserve margin.
- Use css-beautify

9 years agoAdd GitHub Ribbon to our lessons
Raniere Silva [Fri, 18 Apr 2014 13:52:12 +0000 (10:52 -0300)]
Add GitHub Ribbon to our lessons

Backport of 9a19e91 from swcarpentry/site.

All credits to Abigail Cabunoc <abigail.cabunoc@oicr.on.ca>
for the awesome work with CSS.

9 years agoCross browser - stop text wrap in ff
Abigail Cabunoc [Mon, 2 Jun 2014 13:24:52 +0000 (09:24 -0400)]
Cross browser - stop text wrap in ff
* #462

9 years agoChange to a css github ribbon
Abigail Cabunoc [Mon, 2 Jun 2014 02:09:54 +0000 (22:09 -0400)]
Change to a css github ribbon
* responsive for smaller screens
* move menu over more - click will always open menu
* #462

9 years agoFix btn-nav position due GitHub Ribbon
Raniere Silva [Fri, 18 Apr 2014 14:31:06 +0000 (11:31 -0300)]
Fix btn-nav position due GitHub Ribbon

9 years agoConverting to individual challenge div's in the novice shell lessons
Greg Wilson [Mon, 26 May 2014 16:44:43 +0000 (12:44 -0400)]
Converting to individual challenge div's in the novice shell lessons

10 years agoMerge pull request #385 from r-gaia-cs/css-mobile
Greg Wilson [Sun, 6 Apr 2014 13:50:02 +0000 (09:50 -0400)]
Merge pull request #385 from r-gaia-cs/css-mobile

Add CSS media query to improve logo position

10 years agoCleaning up novice extras
Greg Wilson [Tue, 25 Mar 2014 18:06:49 +0000 (14:06 -0400)]
Cleaning up novice extras

10 years agoAdd CSS media query to improve logo
Raniere Silva [Mon, 17 Mar 2014 16:52:50 +0000 (13:52 -0300)]
Add CSS media query to improve logo

10 years agoGetting the pre-formatted code's color right
Greg Wilson [Mon, 3 Mar 2014 16:12:54 +0000 (11:12 -0500)]
Getting the pre-formatted code's color right