rnaseq-cwl-training.git
4 years agobump jekyll version to match github pages version
Allen Lee [Mon, 17 Jun 2019 22:57:56 +0000 (15:57 -0700)]
bump jekyll version to match github pages version

https://pages.github.com/versions/

4 years agolesson-check: exclude aio.md, fix read_references
Maxim Belkin [Sat, 1 Jun 2019 16:24:30 +0000 (11:24 -0500)]
lesson-check: exclude aio.md, fix read_references

4 years agoMerge branch 'gh-pages' of github.com:carpentries/styles into gh-pages
François Michonneau [Fri, 31 May 2019 18:23:34 +0000 (11:23 -0700)]
Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages

4 years ago[fix #408] remove aio from files that need to be initialized
François Michonneau [Fri, 31 May 2019 18:22:48 +0000 (11:22 -0700)]
[fix #408] remove aio from files that need to be initialized

4 years agoaio.md: multiple improvements
François Michonneau [Wed, 29 May 2019 23:10:23 +0000 (19:10 -0400)]
aio.md: multiple improvements

Pull Request: carpentries/styles#406

* change all-in-one file to have the same 'depth' as episode files

* move the core script of aio.md into _includes/aio-script.md

* include comment to inform maintainers to not edit the file

* move aio.md to the root of styles repository

4 years agolinks.md: include base_path.html
Maxim Belkin [Wed, 29 May 2019 19:28:02 +0000 (14:28 -0500)]
links.md: include base_path.html

4 years agolinks.md: fix lesson-setup link
Maxim Belkin [Wed, 29 May 2019 19:10:57 +0000 (14:10 -0500)]
links.md: fix lesson-setup link

4 years agoUpdate ISSUE_TEMPLATE.md
Rayna M Harris [Wed, 15 May 2019 23:07:35 +0000 (16:07 -0700)]
Update ISSUE_TEMPLATE.md

4 years agoUpdate PULL_REQUEST_TEMPLATE.md
Rayna M Harris [Wed, 15 May 2019 23:06:27 +0000 (16:06 -0700)]
Update PULL_REQUEST_TEMPLATE.md

4 years agoupdate coc incident reporting link
François Michonneau [Tue, 14 May 2019 09:37:15 +0000 (11:37 +0200)]
update coc incident reporting link

4 years agoMerge branch 'gh-pages' of github.com:carpentries/styles into gh-pages
François Michonneau [Mon, 13 May 2019 17:27:10 +0000 (19:27 +0200)]
Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages

4 years agoupgrade to bootstrap 3.4.1
François Michonneau [Mon, 13 May 2019 17:20:32 +0000 (19:20 +0200)]
upgrade to bootstrap 3.4.1

4 years agouse ndash as separator
François Michonneau [Mon, 13 May 2019 13:32:51 +0000 (15:32 +0200)]
use ndash as separator

display it only if both `page.title` and `site.title` are defined.

4 years agomake title show episode title first
maneesha sane [Tue, 7 May 2019 14:38:36 +0000 (10:38 -0400)]
make title show episode title first

5 years agoadd data-checker-ignore attributes to footer links
François Michonneau [Fri, 26 Apr 2019 18:57:59 +0000 (14:57 -0400)]
add data-checker-ignore attributes to footer links

5 years agoadd data-checker-ignore attributes to links that only work on GitHub
François Michonneau [Fri, 26 Apr 2019 18:51:30 +0000 (14:51 -0400)]
add data-checker-ignore attributes to links that only work on GitHub

5 years agoutil.py: hot fix for YAML loader
Maxim Belkin [Thu, 18 Apr 2019 19:26:28 +0000 (14:26 -0500)]
util.py: hot fix for YAML loader

5 years agobin/lesson_check.py: avoid inconsistent grammar
Katrin Leinweber [Thu, 18 Apr 2019 14:41:19 +0000 (16:41 +0200)]
bin/lesson_check.py: avoid inconsistent grammar

Pull Request: carpentries/styles#396

5 years agouse xenial on travis
François Michonneau [Wed, 27 Mar 2019 16:13:57 +0000 (17:13 +0100)]
use xenial on travis

5 years agoadd 'FIXME' so they will be picked up by checks
François Michonneau [Thu, 21 Mar 2019 10:54:01 +0000 (11:54 +0100)]
add 'FIXME' so they will be picked up by checks

5 years agogold colour to badge
Ana Costa [Thu, 21 Mar 2019 09:28:22 +0000 (09:28 +0000)]
gold colour to badge

gold looks more like the yellow from the original badge

5 years agoreference to the webpage of the lesson + goodfirst
Ana Costa [Wed, 20 Mar 2019 19:43:23 +0000 (19:43 +0000)]
reference to the webpage of the lesson + goodfirst

This contribution adds reference to the web page of the lesson in the Carpentries and makes it easier for visitors who want to contribute to get familiar with the good first issue badge.
This adds a list of current maintainers to the README.md.

5 years agoFix contrast of links in challenge blocks
Maxim Belkin [Tue, 12 Mar 2019 17:30:44 +0000 (12:30 -0500)]
Fix contrast of links in challenge blocks

5 years agoPrefix code blocks with language names
Maxim Belkin [Mon, 11 Mar 2019 19:17:31 +0000 (14:17 -0500)]
Prefix code blocks with language names

Also, improve contrast of comments

Signed-off-by: Maxim Belkin <maxim.belkin@gmail.com>
5 years agoImprove contrast of code elements
Maxim Belkin [Wed, 6 Mar 2019 19:56:33 +0000 (13:56 -0600)]
Improve contrast of code elements

5 years agoColorize all boxes
Maxim Belkin [Fri, 1 Mar 2019 19:03:05 +0000 (13:03 -0600)]
Colorize all boxes

Use the same colors but apply 12.5% opacity.

Solution boxes use 30% opacity

5 years agolesson_check.py: remove _config.yml from the list of required files
Alex Whan [Wed, 6 Feb 2019 05:26:04 +0000 (16:26 +1100)]
lesson_check.py: remove _config.yml from the list of required files

Pull Request: carpentries/styles#388

5 years agoMerge pull request #386 from gcapes/clarify-templates
Raniere Silva [Wed, 23 Jan 2019 15:57:10 +0000 (15:57 +0000)]
Merge pull request #386 from gcapes/clarify-templates

Clarify wording of PR & issue templates

5 years agoClarify wording of PR & issue templates
Gerard Capes [Wed, 23 Jan 2019 14:38:42 +0000 (14:38 +0000)]
Clarify wording of PR & issue templates

I see lots of contributions where none of this placeholder text has
been deleted, but also quite a lot where the first line has been deleted,
but the 'ext below' hasn't (exactly in accordance with the current
instructions).

5 years agoupdate link for coc reporting
François Michonneau [Thu, 20 Dec 2018 18:12:29 +0000 (13:12 -0500)]
update link for coc reporting

5 years agoMerge pull request #379 from maxim-belkin/lesson-links
Raniere Silva [Wed, 19 Dec 2018 15:11:19 +0000 (15:11 +0000)]
Merge pull request #379 from maxim-belkin/lesson-links

links.md: lesson-specific links

5 years agoknit_lessons.sh: require 2 inputs exactly
Maxim Belkin [Wed, 12 Dec 2018 08:13:23 +0000 (02:13 -0600)]
knit_lessons.sh: require 2 inputs exactly

5 years agolesson_check.py: require _config.yml too
Maxim Belkin [Wed, 12 Dec 2018 08:14:08 +0000 (02:14 -0600)]
lesson_check.py: require _config.yml too

5 years agolinks.md: sync with downstream (lesson-example)
Maxim Belkin [Fri, 7 Dec 2018 20:55:51 +0000 (14:55 -0600)]
links.md: sync with downstream (lesson-example)

5 years ago.travis.yml: use Python 3.7
Maxim Belkin [Fri, 7 Dec 2018 22:54:49 +0000 (16:54 -0600)]
.travis.yml: use Python 3.7

Signed-off-by: Maxim Belkin <maxim.belkin@gmail.com>
5 years agoadd meta tag for carpentry type
François Michonneau [Thu, 6 Dec 2018 16:38:26 +0000 (11:38 -0500)]
add meta tag for carpentry type

5 years agoCONTRIBUTING.md: remove repetitive text
Maxim Belkin [Mon, 3 Dec 2018 22:41:08 +0000 (22:41 +0000)]
CONTRIBUTING.md: remove repetitive text

5 years agolinks.md: lesson-specific links
Maxim Belkin [Tue, 4 Dec 2018 15:47:35 +0000 (09:47 -0600)]
links.md: lesson-specific links

5 years agoUpdate to inclusive language - roles
Chris Erdmann [Sun, 2 Dec 2018 11:56:25 +0000 (03:56 -0800)]
Update to inclusive language - roles

5 years agoAdd Carpentries, LC site, issues
Chris Erdmann [Sun, 2 Dec 2018 12:08:12 +0000 (04:08 -0800)]
Add Carpentries, LC site, issues

5 years agoAdd LC condition
Chris Erdmann [Sun, 2 Dec 2018 12:27:15 +0000 (04:27 -0800)]
Add LC condition

5 years agoInclude LC, Lesson Program date, update language
Chris Erdmann [Sun, 2 Dec 2018 12:23:17 +0000 (04:23 -0800)]
Include LC, Lesson Program date, update language

5 years agoUpdate to LC inclusive language
Chris Erdmann [Sun, 2 Dec 2018 12:38:30 +0000 (04:38 -0800)]
Update to LC inclusive language

5 years agoadd cp as template option
François Michonneau [Mon, 3 Dec 2018 14:14:52 +0000 (09:14 -0500)]
add cp as template option

5 years agoAdd lc to conditions, comments, text
Chris Erdmann [Sun, 2 Dec 2018 12:35:19 +0000 (04:35 -0800)]
Add lc to conditions, comments, text

5 years agoAdd LC to instruction material section
Chris Erdmann [Sun, 2 Dec 2018 12:13:44 +0000 (04:13 -0800)]
Add LC to instruction material section

5 years agolinks.md: Update link to Library Carpentry lessons
Chris Erdmann [Sun, 2 Dec 2018 21:06:22 +0000 (13:06 -0800)]
links.md: Update link to Library Carpentry lessons

Pull Request: carpentries/styles#374

5 years agoMerge pull request #368 from maxim-belkin/aio-fixes
Raniere Silva [Thu, 29 Nov 2018 23:15:31 +0000 (23:15 +0000)]
Merge pull request #368 from maxim-belkin/aio-fixes

aio.md: fix indentation and variable declaration

5 years agoMerge pull request #366 from katrinleinweber/patch-3
Erin Becker [Thu, 29 Nov 2018 22:00:54 +0000 (14:00 -0800)]
Merge pull request #366 from katrinleinweber/patch-3

ISSUE_TEMPLATE.md: Nudge contributors to specify episodes unambigously

5 years agoaio.md: fix indentation and variable declaration
Maxim Belkin [Thu, 29 Nov 2018 20:38:59 +0000 (14:38 -0600)]
aio.md: fix indentation and variable declaration

5 years agoNudge contributors to specify episodes unambigously
Katrin Leinweber [Wed, 14 Nov 2018 09:08:23 +0000 (10:08 +0100)]
Nudge contributors to specify episodes unambigously

See https://github.com/swcarpentry/r-novice-inflammation/issues/401 > 3.

5 years agoMerge pull request #359 from sdruskat/gh-pages
Raniere Silva [Wed, 10 Oct 2018 08:45:10 +0000 (09:45 +0100)]
Merge pull request #359 from sdruskat/gh-pages

Fix https://github.com/carpentries/workshop-template/issues/540

5 years agoFix https://github.com/carpentries/workshop-template/issues/540
Stephan Druskat [Wed, 10 Oct 2018 06:33:35 +0000 (08:33 +0200)]
Fix https://github.com/carpentries/workshop-template/issues/540

5 years agoRemove gh-variables from links.md
Maxim Belkin [Tue, 2 Oct 2018 16:29:03 +0000 (11:29 -0500)]
Remove gh-variables from links.md

5 years agoMerge branch 'gh-pages' into gh-pages
Sarah Brown [Mon, 24 Sep 2018 16:12:33 +0000 (12:12 -0400)]
Merge branch 'gh-pages' into gh-pages

5 years agoedit comment
François Michonneau [Tue, 11 Sep 2018 14:03:09 +0000 (10:03 -0400)]
edit comment

5 years agorefactor to avoid errors when rendering locally
François Michonneau [Mon, 27 Aug 2018 14:53:54 +0000 (10:53 -0400)]
refactor to avoid errors when rendering locally

5 years agouse github metadata to identify branch to use when editing files
François Michonneau [Fri, 24 Aug 2018 21:33:33 +0000 (17:33 -0400)]
use github metadata to identify branch to use when editing files

5 years agospelling corrections using en_US dictionary
Trevor Keller [Wed, 29 Aug 2018 22:56:02 +0000 (18:56 -0400)]
spelling corrections using en_US dictionary

5 years agouse quietly to avoid spurrious warnings
François Michonneau [Wed, 29 Aug 2018 20:37:41 +0000 (16:37 -0400)]
use quietly to avoid spurrious warnings

5 years agoinstall remotes instead of failing if package not available
François Michonneau [Wed, 29 Aug 2018 20:21:17 +0000 (16:21 -0400)]
install remotes instead of failing if package not available

5 years agoReflect Apple's rebranding
Katrin Leinweber [Mon, 27 Aug 2018 13:30:13 +0000 (15:30 +0200)]
Reflect Apple's rebranding

See apple.com/macos

5 years agoinclude base_path where needed
François Michonneau [Fri, 24 Aug 2018 18:19:50 +0000 (14:19 -0400)]
include base_path where needed

5 years agoMerge pull request #345 from maxim-belkin/margin0
Raniere Silva [Fri, 24 Aug 2018 15:41:47 +0000 (16:41 +0100)]
Merge pull request #345 from maxim-belkin/margin0

Code/callout/prereq/etc blocks: set left and right margins to 0

5 years agomake relative_base_path available to syllabus
François Michonneau [Thu, 23 Aug 2018 23:02:03 +0000 (19:02 -0400)]
make relative_base_path available to syllabus

5 years agomake sure relative_root_path is in scope in the episode navbar
François Michonneau [Thu, 23 Aug 2018 21:22:03 +0000 (17:22 -0400)]
make sure relative_root_path is in scope in the episode navbar

5 years agouse requirements package to find lesson dependencies
François Michonneau [Thu, 23 Aug 2018 20:00:11 +0000 (16:00 -0400)]
use requirements package to find lesson dependencies

5 years agofix variable names
François Michonneau [Thu, 23 Aug 2018 19:49:40 +0000 (15:49 -0400)]
fix variable names

5 years agoClone images instead of creating new ones
Maxim Belkin [Wed, 22 Aug 2018 19:58:07 +0000 (14:58 -0500)]
Clone images instead of creating new ones

5 years agoReplace page.root (#310)
François Michonneau [Thu, 23 Aug 2018 00:08:58 +0000 (20:08 -0400)]
Replace page.root (#310)

* replace page.root with 'base' variable that knows path level

* deal with case of trailing / in URL

* use link to figure out path for logos

* simplify path building for favicons

* baseurl isn't used in our template so it can removed
* use 'base' variable for path root instead of unecessary http request to
  site.url

* replace page.root with 'base' variable that knows path level

* deal with case of trailing / in URL

* use link to figure out path for logos

* simplify path building for favicons

* baseurl isn't used in our template so it can removed
* use 'base' variable for path root instead of unecessary http request to
  site.url

* rename variable, consolidate comments

* rename variable in template files

5 years agomake figures a little larger and higher definition
François Michonneau [Wed, 22 Aug 2018 19:28:49 +0000 (15:28 -0400)]
make figures a little larger and higher definition

5 years agofigures.md: fixes and improvements
Maxim Belkin [Wed, 22 Aug 2018 17:28:59 +0000 (17:28 +0000)]
figures.md: fixes and improvements

Pull Request carpentries/styles#330
Closes carpentries/styles#343

1. Fix the script so that all figures are displayed.
2. Add image numbers.
3. Don't add headers for episodes without images.
4. Add horizontal rulers to better separate adjacent images.
   Don't add a ruler after the last image in the episode.
5. Add empty lines to `figures.md` to improve code readability.
6. Use classes for styling text and figures

5 years agoSet left/right margins to 0
Maxim Belkin [Wed, 22 Aug 2018 16:32:44 +0000 (11:32 -0500)]
Set left/right margins to 0

5 years agoAdjust spacing of headers
Maxim Belkin [Wed, 22 Aug 2018 16:20:01 +0000 (16:20 +0000)]
Adjust spacing of headers

Pull Request: carpentries/styles#327

5 years agochange shell parameter to "$@"
François Michonneau [Tue, 21 Aug 2018 21:24:40 +0000 (17:24 -0400)]
change shell parameter to "$@"

5 years agoupdate test checking src and dest are provided
François Michonneau [Tue, 21 Aug 2018 16:51:35 +0000 (12:51 -0400)]
update test checking src and dest are provided

5 years agoonly knit rmd files to md if they have changed
jsta [Sun, 1 Jul 2018 14:23:24 +0000 (10:23 -0400)]
only knit rmd files to md if they have changed

5 years ago.editorconfig: code style guidelines for text editors
Katrin Leinweber [Tue, 21 Aug 2018 16:02:31 +0000 (18:02 +0200)]
.editorconfig: code style guidelines for text editors

Pull Request: carpentries/styles#216

5 years agoadd missing <article> tags
François Michonneau [Tue, 21 Aug 2018 14:12:02 +0000 (10:12 -0400)]
add missing <article> tags

5 years agoupgrade version number
François Michonneau [Tue, 21 Aug 2018 13:50:55 +0000 (09:50 -0400)]
upgrade version number

5 years agoadd lesson life cycle stage indicator
François Michonneau [Tue, 21 Aug 2018 13:45:12 +0000 (09:45 -0400)]
add lesson life cycle stage indicator

5 years agolesson.scss: center images
Maxim Belkin [Mon, 20 Aug 2018 18:18:04 +0000 (18:18 +0000)]
lesson.scss: center images

Pull Request: carpentries/styles#323

5 years agoFix footer and copyright notice
Raniere Silva [Wed, 15 Aug 2018 15:51:58 +0000 (16:51 +0100)]
Fix footer and copyright notice

Close carpentries/styles#325

5 years agoMerge pull request #340 from tracykteal/calendar
Raniere Silva [Wed, 15 Aug 2018 16:20:42 +0000 (17:20 +0100)]
Merge pull request #340 from tracykteal/calendar

added workshop calendar

5 years agoMerge pull request #326 from carpentries/callout-margins
Raniere Silva [Wed, 15 Aug 2018 16:05:18 +0000 (17:05 +0100)]
Merge pull request #326 from carpentries/callout-margins

space out callout elements better

5 years agouse site.github.url only in production
François Michonneau [Tue, 14 Aug 2018 21:58:44 +0000 (17:58 -0400)]
use site.github.url only in production

5 years agoavoid warnings and errors around github metadata for local rendering
François Michonneau [Tue, 14 Aug 2018 14:58:33 +0000 (10:58 -0400)]
avoid warnings and errors around github metadata for local rendering

5 years agoadded workshop calendar
Tracy Teal [Mon, 6 Aug 2018 13:33:35 +0000 (09:33 -0400)]
added workshop calendar

5 years agoMerge pull request #338 from rgaiacs/336
Raniere Silva [Fri, 3 Aug 2018 07:34:33 +0000 (08:34 +0100)]
Merge pull request #338 from rgaiacs/336

Fix lesson_initialize.py to initialize new lessons

5 years agoFix lesson_initialize.py to initialize new lessons
Raniere Silva [Fri, 3 Aug 2018 07:32:39 +0000 (08:32 +0100)]
Fix lesson_initialize.py to initialize new lessons

CODE_OF_CONDUCT.md is already at the root of the repository.

5 years agoMerge pull request #334 from carpentries/add-surveys
François Michonneau [Fri, 20 Jul 2018 13:14:44 +0000 (09:14 -0400)]
Merge pull request #334 from carpentries/add-surveys

Add surveys

5 years ago[fix #332] add instructor training survey links
François Michonneau [Fri, 20 Jul 2018 13:13:00 +0000 (09:13 -0400)]
[fix #332] add instructor training survey links

5 years agoadd LC survey links
François Michonneau [Fri, 20 Jul 2018 13:09:25 +0000 (09:09 -0400)]
add LC survey links

5 years agoMerge pull request #333 from maxim-belkin/fix-makefile
Raniere Silva [Wed, 18 Jul 2018 08:31:32 +0000 (09:31 +0100)]
Merge pull request #333 from maxim-belkin/fix-makefile

Makefile: fix typo in clean-rmd rule

5 years agoMakefile: fix typo in clean-rmd rule
Maxim Belkin [Tue, 17 Jul 2018 21:53:56 +0000 (16:53 -0500)]
Makefile: fix typo in clean-rmd rule

5 years agoMerge pull request #328 from carpentries/fix-survey
Raniere Silva [Thu, 12 Jul 2018 12:15:53 +0000 (13:15 +0100)]
Merge pull request #328 from carpentries/fix-survey

fix survey link variables

5 years agofix survey link variables
François Michonneau [Thu, 12 Jul 2018 05:02:15 +0000 (15:02 +1000)]
fix survey link variables

5 years agospace out callout elements better
François Michonneau [Tue, 3 Jul 2018 21:45:43 +0000 (17:45 -0400)]
space out callout elements better

5 years agorestrict to article
François Michonneau [Tue, 3 Jul 2018 20:44:33 +0000 (16:44 -0400)]
restrict to article

5 years agouse 20px margin
François Michonneau [Tue, 3 Jul 2018 20:30:31 +0000 (16:30 -0400)]
use 20px margin