rnaseq-cwl-training.git
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

5 years agocenter images
François Michonneau [Tue, 3 Jul 2018 20:21:46 +0000 (16:21 -0400)]
center images

5 years agoMerge pull request #318 from carpentries/tracykteal-patch-1
François Michonneau [Thu, 28 Jun 2018 13:12:02 +0000 (09:12 -0400)]
Merge pull request #318 from carpentries/tracykteal-patch-1

added about the discussion stage to the LC description

5 years agoMerge branch 'gh-pages' into tracykteal-patch-1
François Michonneau [Thu, 28 Jun 2018 13:11:48 +0000 (09:11 -0400)]
Merge branch 'gh-pages' into tracykteal-patch-1

5 years agoMerge pull request #317 from carpentries/fix-311
Belinda Weaver [Thu, 28 Jun 2018 01:04:24 +0000 (11:04 +1000)]
Merge pull request #317 from carpentries/fix-311

[fix carpentries/styles#311] update descriptions of the carpentries

5 years agoadded about the discussion stage to the LC description
Tracy Teal [Wed, 27 Jun 2018 21:36:30 +0000 (14:36 -0700)]
added about the discussion stage to the LC description

5 years ago[fix carpentries/styles#311] update descriptions of the carpentries
François Michonneau [Wed, 27 Jun 2018 19:40:40 +0000 (15:40 -0400)]
[fix carpentries/styles#311] update descriptions of the carpentries

5 years ago_config.yml: fix link to the Library Carpentry website
Maxim Belkin [Sat, 23 Jun 2018 14:00:41 +0000 (14:00 +0000)]
_config.yml: fix link to the Library Carpentry website

Pull Request: carpentries/styles#313

5 years agoUpdate Library Carpentry link, resolve #304
trk [Sat, 23 Jun 2018 13:54:36 +0000 (13:54 +0000)]
Update Library Carpentry link, resolve #304

5 years agolesson_check.py: check YAML headers in Rmd episodes
François Michonneau [Wed, 20 Jun 2018 17:22:51 +0000 (13:22 -0400)]
lesson_check.py: check YAML headers in Rmd episodes

Check that Rmd episode files include `source: Rmd`

Fixes carpentries/styles#273

5 years agoMerge pull request #303 from katrinleinweber/patch-3
Raniere Silva [Wed, 20 Jun 2018 13:35:33 +0000 (14:35 +0100)]
Merge pull request #303 from katrinleinweber/patch-3

links.md: add links to carpentries' lessons overview pages

5 years agoSort alphabetically
Katrin Leinweber [Wed, 20 Jun 2018 05:57:03 +0000 (07:57 +0200)]
Sort alphabetically

5 years agoLink to lessons (closes swcarpentry/r-novice-inflammation/#371)
Katrin Leinweber [Wed, 20 Jun 2018 05:26:48 +0000 (07:26 +0200)]
Link to lessons (closes swcarpentry/r-novice-inflammation/#371)

5 years agobump version number
François Michonneau [Tue, 19 Jun 2018 17:41:35 +0000 (13:41 -0400)]
bump version number

5 years ago[fix carpentries/styles#300] add CODE_OF_CONDUCT.md to root
François Michonneau [Tue, 19 Jun 2018 17:40:37 +0000 (13:40 -0400)]
[fix carpentries/styles#300] add CODE_OF_CONDUCT.md to root

5 years agoswitch contact email to team@carpentries.org
François Michonneau [Tue, 19 Jun 2018 16:00:38 +0000 (12:00 -0400)]
switch contact email to team@carpentries.org

5 years agoMerge branch 'gh-pages' of github.com:carpentries/styles into gh-pages
François Michonneau [Mon, 18 Jun 2018 20:56:21 +0000 (16:56 -0400)]
Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages

5 years agobump version in footer
François Michonneau [Fri, 15 Jun 2018 16:32:34 +0000 (12:32 -0400)]
bump version in footer

5 years agoAdd 'cp' (Carpentry) as a new lesson type
François Michonneau [Fri, 15 Jun 2018 15:55:22 +0000 (11:55 -0400)]
Add 'cp' (Carpentry) as a new lesson type

* Add 'cp' (Carpentry) as a lesson type (for instructor training)
* Explain lesson type abbreviations (swc, dc, lc, cp)
* Emphasize the fact that there is no need to edit "repository" variable in front matter

5 years ago[fix carpentries/styles#281] add missing include links.md
François Michonneau [Fri, 15 Jun 2018 13:10:04 +0000 (09:10 -0400)]
[fix carpentries/styles#281] add missing include links.md

5 years agofix URL
François Michonneau [Tue, 12 Jun 2018 19:19:11 +0000 (15:19 -0400)]
fix URL

5 years agoMerge pull request #295 from carpentries/update-urls
François Michonneau [Tue, 12 Jun 2018 16:24:07 +0000 (12:24 -0400)]
Merge pull request #295 from carpentries/update-urls

update URLs to reflect consolidation to carpentries organization

5 years agoupdate URLs to reflect consolidation to carpentries organization
François Michonneau [Tue, 12 Jun 2018 16:22:00 +0000 (12:22 -0400)]
update URLs to reflect consolidation to carpentries organization

5 years agoMerge pull request #284 from maxim-belkin/fix-links-md
Raniere Silva [Tue, 12 Jun 2018 13:54:29 +0000 (14:54 +0100)]
Merge pull request #284 from maxim-belkin/fix-links-md

Add links.md to files in boilerplate

5 years agoMerge pull request #243 from alee/docker
François Michonneau [Mon, 11 Jun 2018 19:59:12 +0000 (15:59 -0400)]
Merge pull request #243 from alee/docker

Makefile: add docker-serve target

5 years agoMerge pull request #285 from maxim-belkin/fix-conduct
Raniere Silva [Wed, 6 Jun 2018 07:22:21 +0000 (08:22 +0100)]
Merge pull request #285 from maxim-belkin/fix-conduct

Move CODE_OF_CONDUCT.md to boilerplate

5 years agoAdd CODE_OF_CONDUCT.md to boilerplate
Maxim Belkin [Tue, 5 Jun 2018 15:58:35 +0000 (08:58 -0700)]
Add CODE_OF_CONDUCT.md to boilerplate

5 years agoRemove CODE_OF_CONDUCT.md
Maxim Belkin [Fri, 1 Jun 2018 12:50:15 +0000 (07:50 -0500)]
Remove CODE_OF_CONDUCT.md

5 years agoMerge pull request #282 from mr-c/patch-1
Raniere Silva [Sat, 2 Jun 2018 18:34:30 +0000 (19:34 +0100)]
Merge pull request #282 from mr-c/patch-1

remove permalink that breaks asset includes

5 years agoMerge pull request #286 from mzc9/gitIgnoreChanges
Raniere Silva [Sat, 2 Jun 2018 18:27:35 +0000 (19:27 +0100)]
Merge pull request #286 from mzc9/gitIgnoreChanges

gitIgnore for R

5 years agogitIgnore for R
mzc9 [Fri, 1 Jun 2018 20:02:57 +0000 (16:02 -0400)]
gitIgnore for R

5 years agoAdd several FIXMEs to the template episode
Maxim Belkin [Fri, 1 Jun 2018 13:00:41 +0000 (13:00 +0000)]
Add several FIXMEs to the template episode

5 years agoRemove extra blank lines
Maxim Belkin [Fri, 1 Jun 2018 12:59:13 +0000 (12:59 +0000)]
Remove extra blank lines

5 years agoAdd links.md to files in boilerplate
Maxim Belkin [Fri, 1 Jun 2018 12:44:24 +0000 (07:44 -0500)]
Add links.md to files in boilerplate

5 years ago_config.yml: no 'mailto' in 'email'
Michael R. Crusoe [Wed, 30 May 2018 11:43:05 +0000 (14:43 +0300)]
_config.yml: no 'mailto' in 'email'

Closes swcarpentry/styles#283

`site.email` is used as:

_includes/lesson_footer.html:         <a href="mailto:{{ site.email }}">Contact</a>
_includes/workshop_footer.html: <a href="mailto:{{ site.email }}">Contact</a>

Therefore, it does not make sense to have `mailto` in the `email` itself.

5 years agoremove permalink that breaks asset includes
Michael R. Crusoe [Wed, 30 May 2018 09:16:56 +0000 (12:16 +0300)]
remove permalink that breaks asset includes

Will also match https://raw.githubusercontent.com/swcarpentry/lesson-example/gh-pages/CONDUCT.md

5 years agoMerge pull request #280 from katrinleinweber/patch-3
Raniere Silva [Sun, 27 May 2018 20:08:08 +0000 (21:08 +0100)]
Merge pull request #280 from katrinleinweber/patch-3

Rename CoC file to align with GitHub's Community Profile expectation

5 years agoUpgrade repo's Community Profile
Katrin Leinweber [Sun, 27 May 2018 08:04:48 +0000 (10:04 +0200)]
Upgrade repo's Community Profile

See https://help.github.com/articles/about-community-profiles-for-public-repositories/.

5 years agoIncrease version to v9.5.0
Raniere Silva [Thu, 24 May 2018 07:51:31 +0000 (08:51 +0100)]
Increase version to v9.5.0

5 years agoMerge pull request #279 from rgaiacs/lesson-check
Raniere Silva [Thu, 24 May 2018 07:48:51 +0000 (08:48 +0100)]
Merge pull request #279 from rgaiacs/lesson-check

Fix lesson_check.py

5 years agoFix lesson_check.py
Raniere Silva [Thu, 24 May 2018 07:47:52 +0000 (08:47 +0100)]
Fix lesson_check.py

5 years agoMerge pull request #278 from maxim-belkin/fix264
Raniere Silva [Thu, 24 May 2018 07:10:53 +0000 (08:10 +0100)]
Merge pull request #278 from maxim-belkin/fix264

Run lesson-fixme from within lesson-check

5 years agoRun lesson-fixme from within lesson-check
Maxim Belkin [Wed, 23 May 2018 18:05:40 +0000 (13:05 -0500)]
Run lesson-fixme from within lesson-check

5 years agoUpdate Makefile
Raniere Silva [Wed, 23 May 2018 17:38:12 +0000 (18:38 +0100)]
Update Makefile

5 years agoMerge pull request #277 from rgaiacs/bin-python3
Raniere Silva [Wed, 23 May 2018 17:32:44 +0000 (18:32 +0100)]
Merge pull request #277 from rgaiacs/bin-python3

Change shebang to Python3

5 years agoChange shebang to Python3
Raniere Silva [Wed, 23 May 2018 17:31:15 +0000 (18:31 +0100)]
Change shebang to Python3

Close swcarpentry/styles#271

5 years agoMerge pull request #276 from rgaiacs/274
Raniere Silva [Wed, 23 May 2018 17:21:41 +0000 (18:21 +0100)]
Merge pull request #276 from rgaiacs/274

Make Jekyll ignore .Rproj

5 years agoMake Jekyll ignore .Rproj
Raniere Silva [Wed, 23 May 2018 17:19:46 +0000 (18:19 +0100)]
Make Jekyll ignore .Rproj

Port of https://github.com/swcarpentry/r-novice-inflammation/commit/9da857efb16d7351127f2d5c46fc0af660654506.

Close swcarpentry/styles#274

5 years agoMerge pull request #275 from rgaiacs/travis-build
Raniere Silva [Wed, 23 May 2018 17:17:08 +0000 (18:17 +0100)]
Merge pull request #275 from rgaiacs/travis-build

Improve .travis.yml to build the lesson

5 years agoImprove .travis.yml to build the lesson
Raniere Silva [Wed, 23 May 2018 17:15:52 +0000 (18:15 +0100)]
Improve .travis.yml to build the lesson

5 years agoMerge pull request #272 from rgaiacs/remove-root-and-layout
Raniere Silva [Wed, 23 May 2018 12:45:35 +0000 (13:45 +0100)]
Merge pull request #272 from rgaiacs/remove-root-and-layout

Remove root and layout from YAML for boilerplate

5 years agoRemove root and layout from YAML for boilerplate
Raniere Silva [Wed, 23 May 2018 12:44:08 +0000 (13:44 +0100)]
Remove root and layout from YAML for boilerplate

5 years agoMerge pull request #269 from maxim-belkin/fix-super-call
Raniere Silva [Wed, 23 May 2018 08:29:17 +0000 (09:29 +0100)]
Merge pull request #269 from maxim-belkin/fix-super-call

Remove unnecessary super call

5 years agoMerge pull request #270 from maxim-belkin/py3-classes
Raniere Silva [Wed, 23 May 2018 07:55:12 +0000 (08:55 +0100)]
Merge pull request #270 from maxim-belkin/py3-classes

Use Python3-style class declaration

5 years agoMerge pull request #268 from maxim-belkin/fix-returns
Raniere Silva [Wed, 23 May 2018 07:43:07 +0000 (08:43 +0100)]
Merge pull request #268 from maxim-belkin/fix-returns

util.py: make functions return NotImplemented

5 years agoUse Python3-style class declaration
Maxim Belkin [Tue, 22 May 2018 13:23:43 +0000 (08:23 -0500)]
Use Python3-style class declaration

5 years agoutil.py: make functions return NotImplemented
Maxim Belkin [Tue, 22 May 2018 12:25:02 +0000 (07:25 -0500)]
util.py: make functions return NotImplemented