rnaseq-cwl-training.git
5 years agoMerge pull request #250 from fmichonneau/favicons
Raniere Silva [Wed, 16 May 2018 21:37:10 +0000 (22:37 +0100)]
Merge pull request #250 from fmichonneau/favicons

Favicons and logos

5 years agoremove unneeded files
François Michonneau [Wed, 16 May 2018 16:20:44 +0000 (12:20 -0400)]
remove unneeded files

5 years agochange alt text for Carpentries logo
François Michonneau [Wed, 16 May 2018 16:15:50 +0000 (12:15 -0400)]
change alt text for Carpentries logo

5 years agoremove unused .ico in root folder
François Michonneau [Tue, 15 May 2018 16:11:49 +0000 (12:11 -0400)]
remove unused .ico in root folder

5 years agouse favicons for workshop page
François Michonneau [Tue, 15 May 2018 16:00:42 +0000 (12:00 -0400)]
use favicons for workshop page

5 years agoadd cp as option in footers
François Michonneau [Tue, 15 May 2018 16:00:34 +0000 (12:00 -0400)]
add cp as option in footers

5 years agofix/add logos and icons for navbar
François Michonneau [Tue, 15 May 2018 15:50:38 +0000 (11:50 -0400)]
fix/add logos and icons for navbar

5 years agofix logos and add Carpentries as an option
François Michonneau [Tue, 15 May 2018 15:50:21 +0000 (11:50 -0400)]
fix logos and add Carpentries as an option

5 years agoadd html for favicons
François Michonneau [Tue, 15 May 2018 15:49:55 +0000 (11:49 -0400)]
add html for favicons

5 years agorename cc to cp for carpentries
François Michonneau [Tue, 15 May 2018 15:45:26 +0000 (11:45 -0400)]
rename cc to cp for carpentries

5 years agoadd favicons for all flavors
François Michonneau [Tue, 15 May 2018 15:30:38 +0000 (11:30 -0400)]
add favicons for all flavors

5 years agoMerge pull request #242 from rgaiacs/add-version-to-footer
Raniere Silva [Sun, 13 May 2018 09:46:17 +0000 (10:46 +0100)]
Merge pull request #242 from rgaiacs/add-version-to-footer

Add note about the version of the style

5 years agoMerge branch 'gh-pages' into add-version-to-footer
Raniere Silva [Sun, 13 May 2018 09:46:10 +0000 (10:46 +0100)]
Merge branch 'gh-pages' into add-version-to-footer

5 years agoMerge pull request #239 from rgaiacs/237
Raniere Silva [Sun, 13 May 2018 09:45:07 +0000 (10:45 +0100)]
Merge pull request #239 from rgaiacs/237

Fix Copyright information

5 years agoMerge branch 'gh-pages' into 237
Raniere Silva [Sun, 13 May 2018 09:44:57 +0000 (10:44 +0100)]
Merge branch 'gh-pages' into 237

5 years agoMerge pull request #247 from rgaiacs/styles-246
Raniere Silva [Fri, 11 May 2018 15:20:56 +0000 (16:20 +0100)]
Merge pull request #247 from rgaiacs/styles-246

Fix search

5 years agoFix search
Raniere Silva [Fri, 11 May 2018 15:19:03 +0000 (16:19 +0100)]
Fix search

Probably because of change on GitHub API.

Close swcarpentry/styles#246

5 years agoAdd note about the version of the style
Raniere Silva [Tue, 8 May 2018 15:32:39 +0000 (16:32 +0100)]
Add note about the version of the style

5 years agoMerge pull request #241 from rgaiacs/clean-footer
Raniere Silva [Tue, 8 May 2018 15:26:19 +0000 (16:26 +0100)]
Merge pull request #241 from rgaiacs/clean-footer

Clean footer HTML

5 years agoClean footer HTML
Raniere Silva [Tue, 8 May 2018 15:21:52 +0000 (16:21 +0100)]
Clean footer HTML

5 years agoMerge pull request #240 from rgaiacs/favicon
Raniere Silva [Tue, 8 May 2018 15:09:42 +0000 (16:09 +0100)]
Merge pull request #240 from rgaiacs/favicon

Fix favicon

5 years agoFix favicon
David Perez Suarez [Tue, 8 May 2018 15:08:43 +0000 (16:08 +0100)]
Fix favicon

5 years agoFix Copyright information
Raniere Silva [Tue, 8 May 2018 14:52:24 +0000 (15:52 +0100)]
Fix Copyright information

Close swcarpentry/lesson-example/193

5 years agoMerge pull request #234 from mr-c/py34
Raniere Silva [Tue, 8 May 2018 14:32:29 +0000 (15:32 +0100)]
Merge pull request #234 from mr-c/py34

convert to py3.4 syntax, a few cleanups

6 years agoconvert to py3.4 syntax, a few cleanups
Michael R. Crusoe [Fri, 20 Apr 2018 09:50:50 +0000 (12:50 +0300)]
convert to py3.4 syntax, a few cleanups

6 years agoMerge pull request #231 from maxim-belkin/fix-util
Raniere Silva [Fri, 20 Apr 2018 07:38:00 +0000 (08:38 +0100)]
Merge pull request #231 from maxim-belkin/fix-util

bin/util.py: fix error handling for Python 2

6 years agoMerge pull request #230 from maxim-belkin/fix-links
Raniere Silva [Fri, 20 Apr 2018 07:31:56 +0000 (08:31 +0100)]
Merge pull request #230 from maxim-belkin/fix-links

links.md: remove duplicate line

6 years agobin/util.py: fix error handling for Python 2
Maxim Belkin [Thu, 19 Apr 2018 21:20:58 +0000 (16:20 -0500)]
bin/util.py: fix error handling for Python 2

6 years agolinks.md: remove duplicate line
Maxim Belkin [Thu, 19 Apr 2018 18:01:40 +0000 (13:01 -0500)]
links.md: remove duplicate line

6 years agoMerge pull request #228 from rgaiacs/gh-pages
Raniere Silva [Tue, 17 Apr 2018 15:57:55 +0000 (16:57 +0100)]
Merge pull request #228 from rgaiacs/gh-pages

Some commits from (lesson-example/186) Assorted minor fixes to spelling, whitespace, hyperlinks & sorting

6 years agoConvert CRAN links to preferred, canonical form
Katrin Leinweber [Sun, 18 Mar 2018 17:47:22 +0000 (18:47 +0100)]
Convert CRAN links to preferred, canonical form

https://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Specifying-URLs

6 years agoReflect merger
Katrin Leinweber [Sun, 18 Mar 2018 17:38:26 +0000 (18:38 +0100)]
Reflect merger

6 years agoResort hyperlinks alphabetically
Katrin Leinweber [Sun, 18 Mar 2018 17:38:17 +0000 (18:38 +0100)]
Resort hyperlinks alphabetically

6 years agoSecure hyperlinks
Katrin Leinweber [Sun, 18 Mar 2018 17:35:40 +0000 (18:35 +0100)]
Secure hyperlinks

6 years agoMerge pull request #227 from fmichonneau/fix-gh-metadata
Raniere Silva [Tue, 17 Apr 2018 15:24:55 +0000 (16:24 +0100)]
Merge pull request #227 from fmichonneau/fix-gh-metadata

fix github meta data

6 years agofix github meta data
François Michonneau [Tue, 17 Apr 2018 14:53:24 +0000 (10:53 -0400)]
fix github meta data

6 years agoMerge pull request #225 from swcarpentry/jduck-coc
Raniere Silva [Fri, 13 Apr 2018 08:27:57 +0000 (09:27 +0100)]
Merge pull request #225 from swcarpentry/jduck-coc

Updating to handbook as canonical source for CoC

6 years agoUpdating to handbook as canonical source for CoC
Jonah Duckles [Fri, 13 Apr 2018 01:09:19 +0000 (13:09 +1200)]
Updating to handbook as canonical source for CoC

6 years agoMerge pull request #223 from fmichonneau/no-hyphens-code
Raniere Silva [Wed, 11 Apr 2018 14:57:22 +0000 (15:57 +0100)]
Merge pull request #223 from fmichonneau/no-hyphens-code

don't break words in code

6 years agouse CRAN canonical addresses for packages
François Michonneau [Wed, 11 Apr 2018 13:26:04 +0000 (09:26 -0400)]
use CRAN canonical addresses for packages

6 years agoMerge pull request #224 from fmichonneau/update-gh-labels
Raniere Silva [Wed, 11 Apr 2018 10:11:49 +0000 (11:11 +0100)]
Merge pull request #224 from fmichonneau/update-gh-labels

Update repo_check.py with new GitHub labels

6 years agoupdate github labels
François Michonneau [Mon, 9 Apr 2018 20:07:20 +0000 (16:07 -0400)]
update github labels

6 years agocheck hex color using lowercase
François Michonneau [Mon, 9 Apr 2018 20:06:44 +0000 (16:06 -0400)]
check hex color using lowercase

6 years agodon't break words in code
François Michonneau [Wed, 4 Apr 2018 14:01:36 +0000 (10:01 -0400)]
don't break words in code

6 years agoImprove language on CONTRIBUTING file
Raniere Silva [Thu, 22 Mar 2018 19:21:39 +0000 (19:21 +0000)]
Improve language on CONTRIBUTING file

As @marwahaha said

> "master repository" feels overloaded,
> since typically "master" refers to a branch name.

We are going to use "originating repository".

6 years agoUpdate Trademark
Raniere Silva [Thu, 22 Mar 2018 19:17:17 +0000 (19:17 +0000)]
Update Trademark

Close #211

6 years agoAdd swc-releases to _includes/links
Raniere Silva [Thu, 22 Mar 2018 19:13:00 +0000 (19:13 +0000)]
Add swc-releases to _includes/links

Close #217

6 years agoMerge pull request #219 from katrinleinweber/patch-2
Raniere Silva [Mon, 19 Mar 2018 09:14:12 +0000 (09:14 +0000)]
Merge pull request #219 from katrinleinweber/patch-2

Fix source of typo #646

6 years agoFix source of typo #646
Katrin Leinweber [Mon, 19 Mar 2018 07:11:15 +0000 (08:11 +0100)]
Fix source of typo #646

6 years agoMerge pull request #214 from katrinleinweber/resolve-DOIs-securely
Raniere Silva [Mon, 5 Mar 2018 11:10:12 +0000 (11:10 +0000)]
Merge pull request #214 from katrinleinweber/resolve-DOIs-securely

Link DOIs to preferred resolver

6 years agoLink DOIs to preferred resolver
Katrin Leinweber [Sat, 3 Mar 2018 12:01:39 +0000 (13:01 +0100)]
Link DOIs to preferred resolver

6 years agoMerge pull request #213 from ErinBecker/update-coc
Raniere Silva [Wed, 28 Feb 2018 12:10:39 +0000 (12:10 +0000)]
Merge pull request #213 from ErinBecker/update-coc

Remove out-of-date CoC language

6 years agoRemove out-of-date CoC language
Erin Becker [Tue, 27 Feb 2018 23:29:55 +0000 (15:29 -0800)]
Remove out-of-date CoC language

6 years agoMerge pull request #203 from swcarpentry/fix-svg
Raniere Silva [Mon, 19 Feb 2018 16:17:53 +0000 (16:17 +0000)]
Merge pull request #203 from swcarpentry/fix-svg

fix svg files

6 years agoFix issue with CSS
Raniere Silva [Mon, 19 Feb 2018 16:10:30 +0000 (16:10 +0000)]
Fix issue with CSS

6 years agoMerge pull request #209 from rgaiacs/gh-pages
Raniere Silva [Fri, 16 Feb 2018 13:42:42 +0000 (13:42 +0000)]
Merge pull request #209 from rgaiacs/gh-pages

Related with lesson-example/pull/172

6 years agoRequested changes
Andrew Sanchez [Thu, 15 Feb 2018 20:51:04 +0000 (13:51 -0700)]
Requested changes

6 years agoMerge pull request #206 from rgaiacs/gh-pages
Raniere Silva [Thu, 15 Feb 2018 10:50:48 +0000 (10:50 +0000)]
Merge pull request #206 from rgaiacs/gh-pages

Fix broken link for Contact

6 years agoFix broken link for Contact
Raniere Silva [Thu, 15 Feb 2018 10:49:12 +0000 (10:49 +0000)]
Fix broken link for Contact

6 years agoMerge pull request #205 from rgaiacs/gh-pages
Raniere Silva [Wed, 14 Feb 2018 17:38:20 +0000 (17:38 +0000)]
Merge pull request #205 from rgaiacs/gh-pages

Add current year to copyright of workshop footer

6 years agoAdd current year to copyright of workshop footer
jcoliver [Wed, 10 Jan 2018 18:15:19 +0000 (11:15 -0700)]
Add current year to copyright of workshop footer

6 years agoMerge pull request #188 from wclose/update_lesson_initialize
Raniere Silva [Wed, 14 Feb 2018 17:31:23 +0000 (17:31 +0000)]
Merge pull request #188 from wclose/update_lesson_initialize

Updated lesson_initialize

6 years agoMerge pull request #202 from rgaiacs/gh-pages
Raniere Silva [Wed, 14 Feb 2018 17:29:00 +0000 (17:29 +0000)]
Merge pull request #202 from rgaiacs/gh-pages

Fix CSS to use .language-X class

6 years agofix svg files
François Michonneau [Mon, 12 Feb 2018 20:52:11 +0000 (15:52 -0500)]
fix svg files

6 years agoMerge pull request #200 from mawds/commentgenerated
Raniere Silva [Tue, 30 Jan 2018 13:49:00 +0000 (13:49 +0000)]
Merge pull request #200 from mawds/commentgenerated

Advise users not to edit .md files generated from .Rmd files

6 years agoImplement using @naupaka 's suggestions
David Mawdsley [Tue, 30 Jan 2018 10:08:00 +0000 (10:08 +0000)]
Implement using @naupaka 's suggestions

6 years agoFix CSS to use .language-X class
Raniere Silva [Mon, 29 Jan 2018 11:29:15 +0000 (11:29 +0000)]
Fix CSS to use .language-X class

6 years agoInsert comment in YAML header advising not to edit
David Mawdsley [Thu, 25 Jan 2018 09:38:50 +0000 (09:38 +0000)]
Insert comment in YAML header advising not to edit

6 years agoMerge pull request #196 from katrinleinweber/patch-1
Raniere Silva [Thu, 21 Dec 2017 10:13:15 +0000 (10:13 +0000)]
Merge pull request #196 from katrinleinweber/patch-1

secure hyperlinks to pre-empt server-side HTTPS redirects

6 years agopre-empt server-side redirects
Katrin Leinweber [Wed, 20 Dec 2017 11:50:31 +0000 (12:50 +0100)]
pre-empt server-side redirects

6 years agoMade minor revision to order of information
William L. Close [Thu, 7 Dec 2017 02:31:30 +0000 (21:31 -0500)]
Made minor revision to order of information

Reorganized description of process for contributing to clarify/increase readability

6 years agoMade requested revisions to lesson_initialize
William L. Close [Thu, 7 Dec 2017 02:20:27 +0000 (21:20 -0500)]
Made requested revisions to lesson_initialize

Changed the keyword for emailing from 'contact' to 'email' per https://github.com/swcarpentry/styles/issues/178 and changed the description for how to use GitHub to reflect usage of the web interface.

6 years agoFix problem with {% link reference.md %}
Raniere Silva [Fri, 1 Dec 2017 10:38:52 +0000 (10:38 +0000)]
Fix problem with {% link reference.md %}

6 years agoMerge pull request #193 from rgaiacs/gh-pages
Raniere Silva [Fri, 24 Nov 2017 00:14:27 +0000 (00:14 +0000)]
Merge pull request #193 from rgaiacs/gh-pages

Fix bin/lesson_initialize.py

6 years agoFix bin/lesson_initialize.py
Raniere Silva [Fri, 24 Nov 2017 00:02:07 +0000 (00:02 +0000)]
Fix bin/lesson_initialize.py

If _extras/figures.md exists,

    $ ./bin/lesson_initialize.py

will return

    Warning: _extras/figures.md already exists.
    **Exiting without creating files.**

6 years agoCopy _extras/figures.md from lesson example
Raniere Silva [Thu, 23 Nov 2017 08:55:23 +0000 (08:55 +0000)]
Copy _extras/figures.md from lesson example

6 years agoPort changes from workshop
Raniere Silva [Thu, 23 Nov 2017 08:22:52 +0000 (08:22 +0000)]
Port changes from workshop

6 years agoPort changes from workshop
Raniere Silva [Thu, 23 Nov 2017 08:20:23 +0000 (08:20 +0000)]
Port changes from workshop

6 years agoRename _includes/lc/syllabys.html to _includes/lc/syllabus.html
Raniere Silva [Sun, 19 Nov 2017 20:34:48 +0000 (20:34 +0000)]
Rename _includes/lc/syllabys.html to _includes/lc/syllabus.html

Close #150

6 years agoFix usage instruction at bin/workshop_check.py
Raniere Silva [Sun, 19 Nov 2017 20:27:33 +0000 (20:27 +0000)]
Fix usage instruction at bin/workshop_check.py

Close #152.

6 years agoMerge pull request #192 from rgaiacs/syntax-highlight
Raniere Silva [Thu, 16 Nov 2017 22:50:01 +0000 (22:50 +0000)]
Merge pull request #192 from rgaiacs/syntax-highlight

Syntax highlight

6 years agoRemove check for all_figures.html now that we are using Javascript
Raniere Silva [Thu, 16 Nov 2017 22:38:49 +0000 (22:38 +0000)]
Remove check for all_figures.html now that we are using Javascript

6 years agoFix validation for syntax highlight
Raniere Silva [Thu, 16 Nov 2017 22:31:07 +0000 (22:31 +0000)]
Fix validation for syntax highlight

6 years agoChange bin/chunk-options.R to use .language-r instead of r
Raniere Silva [Thu, 16 Nov 2017 22:16:26 +0000 (22:16 +0000)]
Change bin/chunk-options.R to use .language-r instead of r

6 years agoEnable syntax highlighting
naught101 [Thu, 16 Nov 2017 22:46:57 +0000 (22:46 +0000)]
Enable syntax highlighting

Based on https://github.com/swcarpentry/lesson-example/pull/144/files

6 years agoFix broken link
Raniere Silva [Wed, 15 Nov 2017 18:23:00 +0000 (18:23 +0000)]
Fix broken link

Close https://github.com/swcarpentry/lesson-example/issues/145.

6 years agoUpdated lesson_initialize
William L. Close [Tue, 7 Nov 2017 21:31:26 +0000 (16:31 -0500)]
Updated lesson_initialize

Clarified instructions for using GitHub to contribute, altered link for [issues] to direct to GitHub page on navigating issues to avoid FIXME issue with link when initializing, removed link to master repo to avoid FIXME issue with link when initializing. These suggestions were based on a pull request initially done elsewhere swcarpentry/shell-novice#639

6 years agoFix root YAML variable in bin/lesson_initialize.py
Raniere Silva [Tue, 7 Nov 2017 16:30:34 +0000 (16:30 +0000)]
Fix root YAML variable in bin/lesson_initialize.py

Close #186

6 years agoFix email as keyword in bin/lesson_check.py
Raniere Silva [Sun, 5 Nov 2017 10:05:53 +0000 (10:05 +0000)]
Fix email as keyword in bin/lesson_check.py

6 years agoMerge pull request #185 from rgaiacs/178
Raniere Silva [Sun, 5 Nov 2017 10:01:05 +0000 (10:01 +0000)]
Merge pull request #185 from rgaiacs/178

Adopt email instead of contact as keyword

6 years agoAdopt email instead of contact as keyword
Raniere Silva [Sun, 5 Nov 2017 09:59:48 +0000 (09:59 +0000)]
Adopt email instead of contact as keyword

Close #178

6 years agoMerge pull request #184 from rgaiacs/styles-js-load-images
Raniere Silva [Sun, 5 Nov 2017 09:31:10 +0000 (09:31 +0000)]
Merge pull request #184 from rgaiacs/styles-js-load-images

Replace extract_figures.py with Javacript

6 years agoReplace extract_figures.py with Javacript
Raniere Silva [Sun, 5 Nov 2017 09:29:51 +0000 (09:29 +0000)]
Replace extract_figures.py with Javacript

Demo at https://github.com/swcarpentry/lesson-example/pull/132/.

6 years agoMerge pull request #165 from brandoncurtis/keyboard-keys
Raniere Silva [Sun, 5 Nov 2017 09:00:47 +0000 (09:00 +0000)]
Merge pull request #165 from brandoncurtis/keyboard-keys

add keyboard key style

6 years agoMerge pull request #183 from rgaiacs/gh-pages
Raniere Silva [Sun, 5 Nov 2017 08:58:11 +0000 (08:58 +0000)]
Merge pull request #183 from rgaiacs/gh-pages

Fix concept-maps link

6 years agoFix concept-maps link
Raniere Silva [Sun, 5 Nov 2017 08:57:09 +0000 (08:57 +0000)]
Fix concept-maps link

Close #176

6 years agoMerge pull request #182 from rgaiacs/gh-pages
Raniere Silva [Sun, 5 Nov 2017 08:55:47 +0000 (08:55 +0000)]
Merge pull request #182 from rgaiacs/gh-pages

Fix github-importer link

6 years agoFix github-importer link
Raniere Silva [Sun, 5 Nov 2017 08:53:46 +0000 (08:53 +0000)]
Fix github-importer link

Close #177

6 years agoMerge pull request #181 from rgaiacs/styles-offline
Raniere Silva [Sun, 5 Nov 2017 08:38:21 +0000 (08:38 +0000)]
Merge pull request #181 from rgaiacs/styles-offline

Add "Offline" Capable

6 years agoAdd "Offline" Capable
Raniere Silva [Sun, 5 Nov 2017 08:36:25 +0000 (08:36 +0000)]
Add "Offline" Capable

This is based on https://github.com/swcarpentry/lesson-example/pull/127/.