rnaseq-cwl-training.git
3 years agoIgnore .jekyll-metatada
Kilian [Thu, 17 Dec 2020 11:03:48 +0000 (12:03 +0100)]
Ignore .jekyll-metatada

3 years agolesson.scss: wildcard selectors for code blocks
Maxim Belkin [Fri, 20 Nov 2020 14:42:26 +0000 (08:42 -0600)]
lesson.scss: wildcard selectors for code blocks

3 years ago404 page for better learner experience
Maxim Belkin [Tue, 24 Nov 2020 21:06:38 +0000 (15:06 -0600)]
404 page for better learner experience

3 years agoadd control structure
Zhian N. Kamvar [Mon, 7 Dec 2020 17:54:36 +0000 (09:54 -0800)]
add control structure

3 years agorun R-based lessons in forks
Zhian N. Kamvar [Mon, 7 Dec 2020 17:47:46 +0000 (09:47 -0800)]
run R-based lessons in forks

This is a modification for #501

3 years agoaccept any base filename for Rmd episodes
Toby Hodges [Tue, 8 Dec 2020 18:09:16 +0000 (19:09 +0100)]
accept any base filename for Rmd episodes

3 years agoFix Ruby style
Maxim Belkin [Tue, 24 Nov 2020 22:41:26 +0000 (16:41 -0600)]
Fix Ruby style

3 years agoset CRAN url if default is "@CRAN@"
Zhian N. Kamvar [Wed, 2 Dec 2020 17:35:13 +0000 (09:35 -0800)]
set CRAN url if default is "@CRAN@"

This will fix #526

3 years agoMatlab -> MATLAB
Toby Hodges [Mon, 9 Nov 2020 10:33:14 +0000 (11:33 +0100)]
Matlab -> MATLAB

3 years ago_config.yml: mention Carpentries Incubator
Maxim Belkin [Thu, 5 Nov 2020 14:57:54 +0000 (08:57 -0600)]
_config.yml: mention Carpentries Incubator

3 years agoremoving contractions from CONTRIBUTING (#512)
Christina K [Mon, 2 Nov 2020 10:14:44 +0000 (04:14 -0600)]
removing contractions from CONTRIBUTING (#512)

3 years agodrop patch version, fix at v1
François Michonneau [Wed, 28 Oct 2020 14:03:09 +0000 (15:03 +0100)]
drop patch version, fix at v1

3 years agobump ruby version (as specified in github-pages v209)
François Michonneau [Wed, 28 Oct 2020 13:44:35 +0000 (14:44 +0100)]
bump ruby version (as specified in github-pages v209)

3 years agolesson.scss: no borders around unrecognized code (#510)
Maxim Belkin [Thu, 22 Oct 2020 04:34:27 +0000 (21:34 -0700)]
lesson.scss: no borders around unrecognized code (#510)

3 years agoupdate expected reference filename (#508)
Toby Hodges [Wed, 21 Oct 2020 16:20:39 +0000 (18:20 +0200)]
update expected reference filename (#508)

3 years agoadd warning code block
François Michonneau [Tue, 20 Oct 2020 06:16:35 +0000 (08:16 +0200)]
add warning code block

3 years agoRevert "Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages"
François Michonneau [Tue, 20 Oct 2020 05:16:30 +0000 (07:16 +0200)]
Revert "Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages"

This reverts commit 2c6b97e57dce86830bdbde8d9f8a871c0b46a035, reversing
changes made to 53e991355f617c108912a21eae00cfe46823aca4.

3 years agoadd warning blockquote
François Michonneau [Wed, 7 Oct 2020 07:55:41 +0000 (09:55 +0200)]
add warning blockquote

3 years agoMerge branch 'gh-pages' of github.com:carpentries/styles into gh-pages
François Michonneau [Tue, 20 Oct 2020 05:06:26 +0000 (07:06 +0200)]
Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages

3 years agoadd default repository to install_required_packages() (#509)
Zhian N. Kamvar [Mon, 19 Oct 2020 06:45:35 +0000 (23:45 -0700)]
add default repository to install_required_packages() (#509)

3 years agoupdate link to discuss mailing list (#507)
Toby Hodges [Thu, 8 Oct 2020 09:06:10 +0000 (11:06 +0200)]
update link to discuss mailing list (#507)

3 years agolesson.scss: styling for DIVs for embedding Youtube videos (#503)
Maxim Belkin [Mon, 21 Sep 2020 13:45:18 +0000 (06:45 -0700)]
lesson.scss: styling for DIVs for embedding Youtube videos (#503)

3 years agoGH Website action: rename + don't use lesson directory (#504)
Maxim Belkin [Mon, 21 Sep 2020 13:22:51 +0000 (06:22 -0700)]
GH Website action: rename + don't use lesson directory (#504)

When 'Website' action tests a lesson, it checks out repositories into the current working directory: 'lesson' directory doesn't exist.
As a result, steps that use "lesson" as the working directory fail.

3 years agoGitHub Action: website.yml: don't run in forks (#501)
Maxim Belkin [Wed, 2 Sep 2020 16:18:48 +0000 (11:18 -0500)]
GitHub Action: website.yml: don't run in forks (#501)

3 years agoGitHub Actions: better workflow and job names (#500)
Maxim Belkin [Tue, 25 Aug 2020 08:17:56 +0000 (03:17 -0500)]
GitHub Actions: better workflow and job names (#500)

3 years agoGitHub Actions: website (#488)
Maxim Belkin [Tue, 25 Aug 2020 08:16:36 +0000 (03:16 -0500)]
GitHub Actions: website (#488)

3 years agoSync styles first (#494)
François Michonneau [Sat, 22 Aug 2020 05:11:22 +0000 (07:11 +0200)]
Sync styles first (#494)

Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com>
3 years agoremove unused code highlight classes (#498)
François Michonneau [Thu, 20 Aug 2020 12:56:01 +0000 (14:56 +0200)]
remove unused code highlight classes (#498)

3 years agoadd three more common languages (#497)
Henry Schreiner [Wed, 19 Aug 2020 16:27:24 +0000 (12:27 -0400)]
add three more common languages (#497)

3 years agofix: tighten definitions of highlighter (#496)
Henry Schreiner [Wed, 19 Aug 2020 14:48:29 +0000 (10:48 -0400)]
fix: tighten definitions of highlighter (#496)

3 years agoGitHub Actions: check lesson template (#489)
Maxim Belkin [Fri, 14 Aug 2020 16:34:28 +0000 (11:34 -0500)]
GitHub Actions: check lesson template (#489)

Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com>
Co-authored-by: François Michonneau <francois.michonneau@gmail.com>
3 years agofix variable name
François Michonneau [Thu, 13 Aug 2020 05:51:56 +0000 (07:51 +0200)]
fix variable name

3 years agoonly display Episodes drop-down if we have episodes to show (#491)
François Michonneau [Tue, 11 Aug 2020 14:36:48 +0000 (16:36 +0200)]
only display Episodes drop-down if we have episodes to show (#491)

3 years agoFix Python scripts for Windows: UTF-8 encoding (#485)
Maxim Belkin [Tue, 11 Aug 2020 13:03:52 +0000 (08:03 -0500)]
Fix Python scripts for Windows: UTF-8 encoding (#485)

To avoid problems with various symbols, we have to specify the encoding
when we read files.
The actual codec name is `utf_8` but aliases like `utf8`, `utf-8`, etc
are accepted. Here, I'm using `utf-8` alias.
https://docs.python.org/3.8/library/codecs.html#standard-encodings

This fixes `make lesson-check` when running under 'Git for Windows' for
lessons that have non-cp1252 characters.

3 years agoMakefile: fix 'lesson-fixme' target for Windows (#486)
Maxim Belkin [Tue, 11 Aug 2020 13:03:01 +0000 (08:03 -0500)]
Makefile: fix 'lesson-fixme' target for Windows (#486)

Git for Windows doesn't provide fgrep, which is a shortcut
to call `grep -F` on Mac and Linux. Instead, we have to use
full arguments.

3 years agoOS stripe: adjust line height (#490)
Maxim Belkin [Tue, 11 Aug 2020 07:59:17 +0000 (02:59 -0500)]
OS stripe: adjust line height (#490)

3 years agoadd vendor folder to gitignore and _config.yml
François Michonneau [Fri, 7 Aug 2020 13:34:05 +0000 (15:34 +0200)]
add vendor folder to gitignore and _config.yml

3 years ago[fix carpentries/styles#477] rewrite travis script
François Michonneau [Fri, 7 Aug 2020 09:26:30 +0000 (11:26 +0200)]
[fix carpentries/styles#477] rewrite travis script

3 years agoMakefile: don't use /bin/bash shell (#484)
Maxim Belkin [Fri, 7 Aug 2020 09:09:53 +0000 (04:09 -0500)]
Makefile: don't use /bin/bash shell (#484)

3 years agorepo_check.py: match https repositories (#483)
Maxim Belkin [Wed, 5 Aug 2020 13:52:34 +0000 (08:52 -0500)]
repo_check.py: match https repositories (#483)

3 years agoMakefile: fix comment in front of `lesson-check` (#481)
Maxim Belkin [Wed, 5 Aug 2020 09:06:30 +0000 (04:06 -0500)]
Makefile: fix comment in front of `lesson-check` (#481)

Comments prepended with `##` appear in the output of `make commands`.
This commit changes `#` to `##` in front of `lesson-check` so that it
appears in the output of `make commands`.

3 years agorepo_check.py: allow URLs not ending with .git (#482)
Maxim Belkin [Wed, 5 Aug 2020 09:05:45 +0000 (04:05 -0500)]
repo_check.py: allow URLs not ending with .git (#482)

3 years ago_config.yml: link to Lesson Life Cycle chapter of CDH
Toby Hodges [Tue, 28 Jul 2020 13:31:04 +0000 (15:31 +0200)]
_config.yml: link to Lesson Life Cycle chapter of CDH

To help users of the lesson template understand how to choose/when to update the value of life_cycle

3 years agoMake links in code tags distinguishable (#478)
Renato Alves [Sat, 25 Jul 2020 04:29:51 +0000 (06:29 +0200)]
Make links in code tags distinguishable (#478)

3 years agoadd warning blockquote style, carpentries/styles#49 (#475)
Joseph Stachelek [Fri, 24 Jul 2020 06:36:59 +0000 (02:36 -0400)]
add warning blockquote style, carpentries/styles#49 (#475)

3 years agoDeprecated use of --path when installing bundle (#473)
ocaisa [Fri, 10 Jul 2020 17:08:06 +0000 (19:08 +0200)]
Deprecated use of --path when installing bundle (#473)

3 years agofix AMY's URL
François Michonneau [Fri, 10 Jul 2020 08:45:51 +0000 (04:45 -0400)]
fix AMY's URL

3 years agoLicense is not a copyright. License info ID (#472)
Maxim Belkin [Mon, 6 Jul 2020 14:52:50 +0000 (09:52 -0500)]
License is not a copyright. License info ID (#472)

3 years agoassets/js/lesson.js: use .length instead of .size()
Maxim Belkin [Mon, 6 Jul 2020 01:45:44 +0000 (20:45 -0500)]
assets/js/lesson.js: use .length instead of .size()

.size() was deprecated in jQuery 3.0 in favor of .length attribute.
https://jquery.com/upgrade-guide/3.0/#breaking-change-deprecated-size-removed

Co-Authored-By: Thomas Green <tomgreen66@hotmail.com>
3 years agoUpgrade jQuery to 3.5.1 (#469)
Maxim Belkin [Tue, 30 Jun 2020 10:31:19 +0000 (05:31 -0500)]
Upgrade jQuery to 3.5.1 (#469)

```
cd assets/js
wget https://code.jquery.com/jquery-3.5.1.min.js
wget https://code.jquery.com/jquery-3.5.1.min.map
mv -f jquery-3.5.1.min.js jquery.min.js
mv -f jquery-3.5.1.min.map jquery.min.map
```

Fixes carpentries/styles#460

3 years agobump ruby version
François Michonneau [Mon, 29 Jun 2020 14:07:09 +0000 (10:07 -0400)]
bump ruby version

3 years agoOS stripe color (#468)
Maxim Belkin [Mon, 29 Jun 2020 08:12:43 +0000 (03:12 -0500)]
OS stripe color (#468)

3 years agoImprove pull request template (#465)
Maxim Belkin [Mon, 22 Jun 2020 16:15:46 +0000 (11:15 -0500)]
Improve pull request template (#465)

3 years agolesson.scss: style tab panels on setup pages (#464)
Maxim Belkin [Fri, 19 Jun 2020 12:58:25 +0000 (07:58 -0500)]
lesson.scss: style tab panels on setup pages (#464)

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