rnaseq-cwl-training.git
3 years agoImprove issue template (#463)
Maxim Belkin [Mon, 15 Jun 2020 14:13:24 +0000 (09:13 -0500)]
Improve issue template (#463)

Co-authored-by: Sarah Brown <sarah_m_brown@brown.edu>
3 years agoUse renv (#462)
Zhian N. Kamvar [Fri, 29 May 2020 13:01:17 +0000 (06:01 -0700)]
Use renv (#462)

3 years agoUse carpentries/lesson-docker for docker-serve make rule (#461)
Zhian N. Kamvar [Thu, 28 May 2020 09:18:22 +0000 (02:18 -0700)]
Use carpentries/lesson-docker for docker-serve make rule (#461)

4 years ago_includes/links.md: Update PyYAML link (#457)
Maxim Belkin [Wed, 12 Feb 2020 17:19:47 +0000 (11:19 -0600)]
_includes/links.md: Update PyYAML link (#457)

4 years agoUpdate PyPI link
Katrin Leinweber [Wed, 12 Feb 2020 16:00:11 +0000 (17:00 +0100)]
Update PyPI link

4 years agoadd warning hook + CSS class for Rmd-based lessons (#455)
François Michonneau [Mon, 10 Feb 2020 14:35:22 +0000 (09:35 -0500)]
add warning hook + CSS class for Rmd-based lessons (#455)

4 years agospecify YAML loader
François Michonneau [Wed, 18 Dec 2019 19:25:25 +0000 (14:25 -0500)]
specify YAML loader

Co-authored-by: Daniel McCloy <dan.mccloy@gmail.com>c
4 years agoUpdate R install in .travis.yml (#430)
Anthony Gitter [Mon, 16 Dec 2019 19:39:10 +0000 (13:39 -0600)]
Update R install in .travis.yml (#430)

* Update R install in .travis.yml

See https://cran.r-project.org/bin/linux/ubuntu/README.html

* update .travis.yml

4 years agoMakefile: improve commands target and commands categories (#450)
Maxim Belkin [Fri, 13 Dec 2019 22:30:00 +0000 (16:30 -0600)]
Makefile: improve commands target and commands categories (#450)

* Makefile: improve commands target and commands categories

* replace 'files' with 'website'

4 years agoMakefile: use Python to execute repo_check.py
Maxim Belkin [Fri, 13 Dec 2019 18:12:16 +0000 (12:12 -0600)]
Makefile: use Python to execute repo_check.py

4 years agoMakefile: Specify shell. Don't include commands.mk
Maxim Belkin [Fri, 13 Dec 2019 17:48:58 +0000 (11:48 -0600)]
Makefile: Specify shell. Don't include commands.mk

4 years agoadd .bundle to .gitignore
François Michonneau [Fri, 13 Dec 2019 20:50:42 +0000 (15:50 -0500)]
add .bundle to .gitignore

4 years agoadd @maxim-belkin suggestions
François Michonneau [Fri, 13 Dec 2019 17:09:40 +0000 (12:09 -0500)]
add @maxim-belkin suggestions

4 years agorefactor use of docker
François Michonneau [Wed, 11 Dec 2019 20:06:25 +0000 (15:06 -0500)]
refactor use of docker

Co-authored-by: Allen Lee <allen.lee@asu.edu>
4 years agoinstall gems locally
François Michonneau [Wed, 11 Dec 2019 19:59:47 +0000 (14:59 -0500)]
install gems locally

4 years agouse bundler to render lessons
François Michonneau [Thu, 12 Sep 2019 14:41:02 +0000 (16:41 +0200)]
use bundler to render lessons

4 years agoMerge pull request carpentries/styles#446
Maxim Belkin [Thu, 12 Dec 2019 15:58:29 +0000 (09:58 -0600)]
Merge pull request carpentries/styles#446

4 years agofix urls in _config.yml
François Michonneau [Wed, 11 Dec 2019 19:02:49 +0000 (14:02 -0500)]
fix urls in _config.yml

4 years agoMakefile: fix two more syntax errors in conditionals
Maxim Belkin [Mon, 9 Dec 2019 22:55:00 +0000 (16:55 -0600)]
Makefile: fix two more syntax errors in conditionals

4 years agoMakefile: fix syntax in conditional
Maxim Belkin [Mon, 9 Dec 2019 22:51:12 +0000 (16:51 -0600)]
Makefile: fix syntax in conditional

4 years agoMakefile: handle MS Store's Python 3
Maxim Belkin [Mon, 9 Dec 2019 22:45:16 +0000 (16:45 -0600)]
Makefile: handle MS Store's Python 3

4 years agoMakefile: suppress another error message on Windows
Maxim Belkin [Fri, 6 Dec 2019 21:11:48 +0000 (15:11 -0600)]
Makefile: suppress another error message on Windows

These '2>/dev/null' are important on Windows because without them
a mere `make` stalls.

4 years agofix typo in lesson_initialize.py
Maxim Belkin [Fri, 6 Dec 2019 20:20:31 +0000 (14:20 -0600)]
fix typo in lesson_initialize.py

4 years agoMakefile: suppress error message on Windows
Maxim Belkin [Fri, 6 Dec 2019 19:43:11 +0000 (13:43 -0600)]
Makefile: suppress error message on Windows

4 years agotest_lesson_check.py: skip unnecessary steps
Maxim Belkin [Fri, 6 Dec 2019 19:31:55 +0000 (13:31 -0600)]
test_lesson_check.py: skip unnecessary steps

4 years agoMakefile: Windows does not like single quotes
Maxim Belkin [Fri, 6 Dec 2019 19:31:19 +0000 (13:31 -0600)]
Makefile: Windows does not like single quotes

4 years agoclarify comment on python check block
Sarah Brown [Fri, 6 Dec 2019 16:53:29 +0000 (11:53 -0500)]
clarify comment on python check block

4 years agorepo_check.py: enforce utf-8 encoding
Maxim Belkin [Thu, 5 Dec 2019 21:36:51 +0000 (15:36 -0600)]
repo_check.py: enforce utf-8 encoding

... for compatibility with Windows

4 years agolesson_check.py: Windows-compatible regular expression pattern
Maxim Belkin [Thu, 5 Dec 2019 21:20:52 +0000 (15:20 -0600)]
lesson_check.py: Windows-compatible regular expression pattern

4 years agolesson_initialize: windows compatibility
Maxim Belkin [Thu, 5 Dec 2019 20:13:05 +0000 (14:13 -0600)]
lesson_initialize: windows compatibility

4 years agoRemove executable bits from Python scripts
Maxim Belkin [Thu, 5 Dec 2019 19:37:44 +0000 (13:37 -0600)]
Remove executable bits from Python scripts

We can't use a single shebang:
* on some platforms `python` may mean Python 2, on others - Python 3
* on some platforms `python3` does not exist at all

Therefore, we're removing the shebangs altogether.

4 years agoUndo optimizations to read_all_markdown
Maxim Belkin [Thu, 5 Dec 2019 19:36:50 +0000 (13:36 -0600)]
Undo optimizations to read_all_markdown

These will be submitted in a separate PR

4 years agoutil.py: remove empty line
Maxim Belkin [Thu, 5 Dec 2019 16:49:09 +0000 (10:49 -0600)]
util.py: remove empty line

4 years agoMakefile: detect Python 3
Maxim Belkin [Thu, 5 Dec 2019 16:46:38 +0000 (10:46 -0600)]
Makefile: detect Python 3

4 years agoSilenced output of PYTHON calls
Joao Rodrigues [Thu, 5 Dec 2019 12:50:49 +0000 (06:50 -0600)]
Silenced output of PYTHON calls

4 years agoFixes encoding problem on Windows systems, with minimal changes to existing code.
Joao Rodrigues [Thu, 5 Dec 2019 12:47:00 +0000 (06:47 -0600)]
Fixes encoding problem on Windows systems, with minimal changes to existing code.

4 years agoRemoved shebang lines from Python scripts to avoid cross-OS problems
Joao Rodrigues [Wed, 4 Dec 2019 22:45:44 +0000 (16:45 -0600)]
Removed shebang lines from Python scripts to avoid cross-OS problems

4 years agoReverted variable names
Joao Rodrigues [Wed, 4 Dec 2019 22:45:02 +0000 (16:45 -0600)]
Reverted variable names

4 years agoAdded PYTHON variable to define executable to run python scripts
Joao Rodrigues [Wed, 4 Dec 2019 22:43:59 +0000 (16:43 -0600)]
Added PYTHON variable to define executable to run python scripts

4 years agoCleaned leftover debug code and old implementations.
Joao Rodrigues [Wed, 4 Dec 2019 20:15:05 +0000 (14:15 -0600)]
Cleaned leftover debug code and old implementations.

4 years agoReverted change of permissiveness on lesson_check
Joao Rodrigues [Tue, 3 Dec 2019 23:23:09 +0000 (17:23 -0600)]
Reverted change of permissiveness on lesson_check

4 years agoModified shebang to use python, not python3.
Joao Rodrigues [Tue, 3 Dec 2019 23:20:32 +0000 (17:20 -0600)]
Modified shebang to use python, not python3.

4 years agoRefactored paths to make use of OS agnostic methods
Joao Rodrigues [Tue, 3 Dec 2019 23:20:12 +0000 (17:20 -0600)]
Refactored paths to make use of OS agnostic methods

4 years agoForced re-encoding of text to UTF-8, to avoid issues on Windows
Joao Rodrigues [Tue, 3 Dec 2019 23:19:44 +0000 (17:19 -0600)]
Forced re-encoding of text to UTF-8, to avoid issues on Windows

4 years agoremove Jekyll command markers from comment block
François Michonneau [Mon, 2 Dec 2019 17:48:29 +0000 (12:48 -0500)]
remove Jekyll command markers from comment block

fix carpentries/lesson-example#281

4 years agoEnable 'Sponsor' button on GitHub repos
Maxim Belkin [Wed, 13 Nov 2019 20:45:35 +0000 (14:45 -0600)]
Enable 'Sponsor' button on GitHub repos

4 years agomanual_episode_order.html: fix typo in a comment
Maxim Belkin [Mon, 11 Nov 2019 20:29:38 +0000 (14:29 -0600)]
manual_episode_order.html: fix typo in a comment

4 years agoUse Jekyll to generate the 'all-in-one' page (carpentries/styles#438)
François Michonneau [Fri, 8 Nov 2019 23:50:32 +0000 (00:50 +0100)]
Use Jekyll to generate the 'all-in-one' page (carpentries/styles#438)

4 years agobin/boilerplate/README.md: fix typo
Michael Joseph [Fri, 8 Nov 2019 19:41:27 +0000 (14:41 -0500)]
bin/boilerplate/README.md: fix typo

carpentries/styles#441

4 years agoSwitch to Liquid comments
Maxim Belkin [Wed, 6 Nov 2019 22:40:35 +0000 (16:40 -0600)]
Switch to Liquid comments

HTML comments end up in the generated HTML pages: they're not displayed by the browsers but they're still present there. Liquid comments do not end up in the generated HTML pages

4 years agoupdate survey links
François Michonneau [Mon, 28 Oct 2019 10:19:41 +0000 (11:19 +0100)]
update survey links

4 years ago[fix carpentries/workshop-template#513] remove site.title outside
François Michonneau [Fri, 11 Oct 2019 14:19:24 +0000 (16:19 +0200)]
[fix carpentries/workshop-template#513] remove site.title outside

lessons

4 years agoManual ordering of episodes and extras
Maxim Belkin [Fri, 27 Sep 2019 16:52:26 +0000 (11:52 -0500)]
Manual ordering of episodes and extras

Co-authored-by: stamper <tbyhdgs@gmail.com>
4 years agorestore lost CSS settings
Maxim Belkin [Fri, 30 Aug 2019 15:06:46 +0000 (10:06 -0500)]
restore lost CSS settings

4 years agoassets/css/lesson.scss: add proper padding to the top of paragraphs in blockquotes...
K.E. Koziar [Fri, 30 Aug 2019 17:29:57 +0000 (10:29 -0700)]
assets/css/lesson.scss: add proper padding to the top of paragraphs in blockquotes (#425)

4 years agoIgnore Jekyll 4's cache
Katrin Leinweber [Wed, 21 Aug 2019 20:33:09 +0000 (22:33 +0200)]
Ignore Jekyll 4's cache

See https://jekyllrb.com/news/2019/08/20/jekyll-4-0-0-released/#cache-all-the-things- & https://github.com/jekyll/jekyll/releases/tag/v4.0.0

It appears during `make site` & `make serve`.

4 years agospecify language based on engine
François Michonneau [Fri, 21 Jun 2019 13:57:37 +0000 (15:57 +0200)]
specify language based on engine

- fix swcarpentry/r-novice-inflammation#436

4 years agoUse 1px borders: fix Google Chrome & Edge
Maxim Belkin [Thu, 20 Jun 2019 16:04:24 +0000 (11:04 -0500)]
Use 1px borders: fix Google Chrome & Edge

See https://github.com/swcarpentry/git-novice/pull/662#issuecomment-499555724

4 years agoUse darker purple for code blocks
Maxim Belkin [Tue, 18 Jun 2019 15:38:20 +0000 (10:38 -0500)]
Use darker purple for code blocks

4 years agoCallout (and other) blocks: proper font size, margins
Maxim Belkin [Tue, 18 Jun 2019 15:43:16 +0000 (10:43 -0500)]
Callout (and other) blocks: proper font size, margins

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