rnaseq-cwl-training.git
6 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

6 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

6 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

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

6 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

6 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.

6 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

6 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

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

6 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

6 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

6 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

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

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

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

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

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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

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

6 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)

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

6 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

6 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

6 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

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

6 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

6 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

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

6 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

6 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

6 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

6 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

6 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

6 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

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

6 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

6 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

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

6 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

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

6 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

6 years agoMerge pull request #1 from swcarpentry/gh-pages
Sarah Brown [Fri, 1 Jun 2018 09:54:30 +0000 (02:54 -0700)]
Merge pull request #1 from swcarpentry/gh-pages

_config.yml: no 'mailto' in 'email'

6 years agofix typos and add clarifying text to boilerplate
Sarah Brown [Fri, 1 Jun 2018 09:52:21 +0000 (02:52 -0700)]
fix typos and add clarifying text to boilerplate

6 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.

6 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

6 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

6 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/.

6 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

6 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

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

6 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

6 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

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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

6 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

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

6 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

6 years agoRemove unnecessary super call
Maxim Belkin [Tue, 22 May 2018 12:09:33 +0000 (07:09 -0500)]
Remove unnecessary super call

6 years agoMerge pull request #267 from jsta/patch-2
Raniere Silva [Mon, 21 May 2018 17:37:59 +0000 (18:37 +0100)]
Merge pull request #267 from jsta/patch-2

missing comma in boilerplate generation

6 years agomissing comma in boilerplate generation
Joseph Stachelek [Mon, 21 May 2018 16:49:04 +0000 (12:49 -0400)]
missing comma in boilerplate generation

6 years agoMerge pull request #265 from maxim-belkin/not-implmntd
Raniere Silva [Mon, 21 May 2018 06:16:28 +0000 (07:16 +0100)]
Merge pull request #265 from maxim-belkin/not-implmntd

lesson_check: fix create_checker function

6 years agoMerge pull request #266 from maxim-belkin/simple-report
Raniere Silva [Mon, 21 May 2018 06:15:49 +0000 (07:15 +0100)]
Merge pull request #266 from maxim-belkin/simple-report

utils.py: simplify report function

6 years agoutils.py: simplify report function
Maxim Belkin [Sun, 20 May 2018 13:38:12 +0000 (08:38 -0500)]
utils.py: simplify report function

6 years agolesson_check: fix create_checker function
Maxim Belkin [Sun, 20 May 2018 13:34:42 +0000 (08:34 -0500)]
lesson_check: fix create_checker function

6 years agoMerge pull request #263 from rgaiacs/244
Raniere Silva [Fri, 18 May 2018 15:31:00 +0000 (16:31 +0100)]
Merge pull request #263 from rgaiacs/244

Fix font size of h2 in call out box

6 years agoFix font size of h2 in call out box
Raniere Silva [Fri, 18 May 2018 15:29:49 +0000 (16:29 +0100)]
Fix font size of h2 in call out box

Close swcarpentry/styles#244

6 years agoMerge pull request #262 from rgaiacs/248
Raniere Silva [Fri, 18 May 2018 15:26:38 +0000 (16:26 +0100)]
Merge pull request #262 from rgaiacs/248

Add README to bin/lesson_initialize.py

6 years agoAdd README to bin/lesson_initialize.py
Andy Boughton [Fri, 18 May 2018 15:25:27 +0000 (16:25 +0100)]
Add README to bin/lesson_initialize.py

This is a revamp of swcarpentry/styles#248.

Thanks to Andy Boughton.

6 years agoMerge pull request #261 from rgaiacs/249
Raniere Silva [Fri, 18 May 2018 15:13:56 +0000 (16:13 +0100)]
Merge pull request #261 from rgaiacs/249

Fix line wrap after dash in code block

6 years agoFix line wrap after dash in code block
Raniere Silva [Fri, 18 May 2018 15:12:58 +0000 (16:12 +0100)]
Fix line wrap after dash in code block

Close swcarpentry/styles#249

6 years agoMerge pull request #260 from rgaiacs/shutil
Raniere Silva [Fri, 18 May 2018 14:04:12 +0000 (15:04 +0100)]
Merge pull request #260 from rgaiacs/shutil

Move boilerplate files to their own file

6 years agoMove boilerplate files to their own file
Raniere Silva [Fri, 18 May 2018 13:52:45 +0000 (14:52 +0100)]
Move boilerplate files to their own file

6 years agoMerge pull request #259 from maxim-belkin/fix-repocheck
Raniere Silva [Fri, 18 May 2018 10:45:20 +0000 (11:45 +0100)]
Merge pull request #259 from maxim-belkin/fix-repocheck

repo_check: use argparse and remove unused variable

6 years agoMerge pull request #256 from maxim-belkin/static-get-val
Raniere Silva [Fri, 18 May 2018 10:44:20 +0000 (11:44 +0100)]
Merge pull request #256 from maxim-belkin/static-get-val

lesson_check: get_val is a static method

6 years agorepo_check: use argparse and remove unused variable
Maxim Belkin [Fri, 18 May 2018 09:49:54 +0000 (04:49 -0500)]
repo_check: use argparse and remove unused variable

6 years agoMerge pull request #257 from maxim-belkin/py3-inits
Raniere Silva [Fri, 18 May 2018 08:20:46 +0000 (09:20 +0100)]
Merge pull request #257 from maxim-belkin/py3-inits

lesson_check: Python3-style inits

6 years agoMerge pull request #258 from maxim-belkin/add-docstring
Raniere Silva [Fri, 18 May 2018 08:19:54 +0000 (09:19 +0100)]
Merge pull request #258 from maxim-belkin/add-docstring

lesson_check: add missing docstring

6 years agoMerge pull request #255 from maxim-belkin/use-argparse
Raniere Silva [Fri, 18 May 2018 08:14:39 +0000 (09:14 +0100)]
Merge pull request #255 from maxim-belkin/use-argparse

lesson_check: switch to argparse

6 years agolesson_check: add missing docstring
Maxim Belkin [Fri, 18 May 2018 06:12:08 +0000 (01:12 -0500)]
lesson_check: add missing docstring

6 years agoPython3-style inits
Maxim Belkin [Fri, 18 May 2018 06:01:29 +0000 (01:01 -0500)]
Python3-style inits

6 years agolesson_check: get_val is a static method
Maxim Belkin [Fri, 18 May 2018 05:30:09 +0000 (00:30 -0500)]
lesson_check: get_val is a static method

6 years agolesson_check: switch to argparse
Maxim Belkin [Fri, 18 May 2018 04:52:46 +0000 (23:52 -0500)]
lesson_check: switch to argparse

6 years agoMerge pull request #253 from maxim-belkin/error-out
Raniere Silva [Thu, 17 May 2018 20:44:43 +0000 (21:44 +0100)]
Merge pull request #253 from maxim-belkin/error-out

lesson_check.py: Exit with a status of 1 if something was wrong