rnaseq-cwl-training.git
7 years agoMerge pull request #108 from gvwilson/library-carpentry
Greg Wilson [Tue, 8 Nov 2016 22:24:45 +0000 (17:24 -0500)]
Merge pull request #108 from gvwilson/library-carpentry

Starting to incorporate Library Carpentry materials

7 years agoWeb site for Library Carpentry
Greg Wilson [Tue, 8 Nov 2016 22:23:11 +0000 (17:23 -0500)]
Web site for Library Carpentry

7 years agoMerge branch 'gh-pages' into library-carpentry
Greg Wilson [Tue, 8 Nov 2016 22:20:21 +0000 (17:20 -0500)]
Merge branch 'gh-pages' into library-carpentry

7 years agoMerge pull request #110 from rgaiacs/setup
Raniere Silva [Mon, 31 Oct 2016 03:23:56 +0000 (03:23 +0000)]
Merge pull request #110 from rgaiacs/setup

Add link to setup from schedule

7 years agoAdd link to setup from schedule
Raniere Silva [Tue, 18 Oct 2016 15:44:48 +0000 (16:44 +0100)]
Add link to setup from schedule

7 years agoUpdating lesson checker to include Library Carpentry values
Greg Wilson [Sat, 8 Oct 2016 19:38:11 +0000 (15:38 -0400)]
Updating lesson checker to include Library Carpentry values

7 years agoTidying up references to LC
Greg Wilson [Fri, 7 Oct 2016 17:23:18 +0000 (13:23 -0400)]
Tidying up references to LC

7 years agoAdding link to citation
Greg Wilson [Fri, 7 Oct 2016 17:20:16 +0000 (13:20 -0400)]
Adding link to citation

7 years agoContact address
Greg Wilson [Fri, 7 Oct 2016 16:46:44 +0000 (12:46 -0400)]
Contact address

7 years agoMerge pull request #107 from gvwilson/training-survey
Greg Wilson [Fri, 7 Oct 2016 16:41:08 +0000 (12:41 -0400)]
Merge pull request #107 from gvwilson/training-survey

Adding link to training survey to config

7 years agoFixing typo in license file
Greg Wilson [Fri, 7 Oct 2016 14:58:59 +0000 (10:58 -0400)]
Fixing typo in license file

7 years agoStarting to incorporate Library Carpentry materials
Greg Wilson [Fri, 7 Oct 2016 14:38:42 +0000 (10:38 -0400)]
Starting to incorporate Library Carpentry materials

7 years agoAdding link to training survey to config
Greg Wilson [Wed, 5 Oct 2016 19:09:16 +0000 (15:09 -0400)]
Adding link to training survey to config

7 years agoMerge pull request #105 from gvwilson/analytics
Jonah Duckles [Mon, 26 Sep 2016 20:09:00 +0000 (15:09 -0500)]
Merge pull request #105 from gvwilson/analytics

Adding Google Analytics code

7 years agoAdding Google Analytics code
Greg Wilson [Mon, 26 Sep 2016 20:06:57 +0000 (16:06 -0400)]
Adding Google Analytics code

7 years agoMerge pull request #103 from evanwill/accessibility-fix
Raniere Silva [Fri, 23 Sep 2016 13:41:13 +0000 (14:41 +0100)]
Merge pull request #103 from evanwill/accessibility-fix

accessibility fixes.

7 years agoMerge pull request #104 from evanwill/search-fix
Raniere Silva [Fri, 23 Sep 2016 13:39:00 +0000 (14:39 +0100)]
Merge pull request #104 from evanwill/search-fix

fix search meta tag.

7 years agofix search meta tag.
evanwill [Fri, 23 Sep 2016 04:52:27 +0000 (21:52 -0700)]
fix search meta tag.

7 years agoaccessibility fixes.
evanwill [Fri, 23 Sep 2016 04:46:11 +0000 (21:46 -0700)]
accessibility fixes.
Add label to search box and navigation arrows.

7 years agoAdding checks for things that commonly go wrong during template conversion.
Greg Wilson [Thu, 15 Sep 2016 18:37:58 +0000 (14:37 -0400)]
Adding checks for things that commonly go wrong during template conversion.

1. Checking that `index.md` has `root` set to '.'
2. Checking that `_config.yml` has `root` set to '..'

7 years agoRemoving trailing space in Ruby file
Greg Wilson [Mon, 12 Sep 2016 15:57:22 +0000 (11:57 -0400)]
Removing trailing space in Ruby file

7 years agoDisplaying break information in a box
Greg Wilson [Mon, 12 Sep 2016 15:57:02 +0000 (11:57 -0400)]
Displaying break information in a box

7 years agoAdding ID attribute to schedule
Greg Wilson [Wed, 7 Sep 2016 21:16:12 +0000 (17:16 -0400)]
Adding ID attribute to schedule

7 years agoChanging name of instructor's guide to 'instructor notes'
Greg Wilson [Wed, 7 Sep 2016 19:15:12 +0000 (15:15 -0400)]
Changing name of instructor's guide to 'instructor notes'

7 years agoAdding footnote about syllabus
Greg Wilson [Wed, 7 Sep 2016 19:10:19 +0000 (15:10 -0400)]
Adding footnote about syllabus

7 years agoNavigation links in footer
Greg Wilson [Mon, 5 Sep 2016 17:51:02 +0000 (13:51 -0400)]
Navigation links in footer

7 years agoSwitch to relative: setup default root and specific root for index.md
Rémi Emonet [Mon, 5 Sep 2016 17:28:26 +0000 (19:28 +0200)]
Switch to relative: setup default root and specific root for index.md

7 years agoSwitch to relative: in episode_title, use page.root + rewrite
Rémi Emonet [Mon, 5 Sep 2016 17:24:49 +0000 (19:24 +0200)]
Switch to relative: in episode_title, use page.root + rewrite

7 years agoSwitch to relative: use page.root in most templates
Rémi Emonet [Mon, 5 Sep 2016 17:22:11 +0000 (19:22 +0200)]
Switch to relative: use page.root in most templates

7 years agoMerge pull request #92 from swcarpentry/twitwi-patch-1
Greg Wilson [Fri, 26 Aug 2016 20:36:51 +0000 (16:36 -0400)]
Merge pull request #92 from swcarpentry/twitwi-patch-1

Fix "br" typo causing ugly rendering (epub only)

7 years agoFix "br" typo causing ugly rendering (epub only)
Rémi Emonet [Thu, 25 Aug 2016 15:55:55 +0000 (17:55 +0200)]
Fix "br" typo causing ugly rendering (epub only)

</br> instead of <br/> renders fine in the browser but not in an epub

7 years agoAdding a few more URLs
Greg Wilson [Thu, 28 Jul 2016 00:04:06 +0000 (20:04 -0400)]
Adding a few more URLs

7 years agoUpdating the lesson initializer's CONTRIBUTING.md
Greg Wilson [Tue, 26 Jul 2016 14:54:29 +0000 (10:54 -0400)]
Updating the lesson initializer's CONTRIBUTING.md

7 years agoChecking that internally-defined links resolve.
Greg Wilson [Sun, 24 Jul 2016 13:12:20 +0000 (09:12 -0400)]
Checking that internally-defined links resolve.

An internally-defined Markdown link has the form [xxx][yyy].  If the
ID 'yyy' doesn't resolve, the text is left as-is, so we check for
that, then subtract those that reference configuration values using
'{{'.  It's a hack, but it'll catch at least a few things.

7 years agoChecking future print
Greg Wilson [Thu, 21 Jul 2016 17:35:29 +0000 (13:35 -0400)]
Checking future print

7 years agoMoving from __future__ to start of file
Greg Wilson [Thu, 21 Jul 2016 17:29:27 +0000 (13:29 -0400)]
Moving from __future__ to start of file

7 years agoMerge pull request #85 from gdevenyi/gh-pages
Greg Wilson [Thu, 21 Jul 2016 14:56:18 +0000 (10:56 -0400)]
Merge pull request #85 from gdevenyi/gh-pages

Import future print in case of python2 environment

7 years agoImport future print in case of python2 environment
Gabriel A. Devenyi [Thu, 21 Jul 2016 13:52:21 +0000 (09:52 -0400)]
Import future print in case of python2 environment

7 years agoMerge pull request #83 from fmichonneau/check-r-packages
Greg Wilson [Thu, 21 Jul 2016 02:28:09 +0000 (22:28 -0400)]
Merge pull request #83 from fmichonneau/check-r-packages

[fix # 82] Check R packages required by the lesson

7 years agoLoading standard images via HTTPS
Greg Wilson [Thu, 21 Jul 2016 00:18:51 +0000 (20:18 -0400)]
Loading standard images via HTTPS

7 years agoForcing CSS and Javascript to be loaded via HTTPS.
Greg Wilson [Thu, 21 Jul 2016 00:01:47 +0000 (20:01 -0400)]
Forcing CSS and Javascript to be loaded via HTTPS.

Using `site.github.url` to refer to the repository fails to load resources when the GitHub Pages site is accessed via HTTPS, because `site.github.url` is `http` protocol.  This modifies loads of CSS and Javascript files to always use `https`.

7 years agosimplify code checking for knitr
Francois Michonneau [Wed, 20 Jul 2016 15:53:47 +0000 (11:53 -0400)]
simplify code checking for knitr

7 years agocheck packages required and install them if needed
Francois Michonneau [Wed, 20 Jul 2016 15:47:20 +0000 (11:47 -0400)]
check packages required and install them if needed

7 years agoIgnoring a few more things
Greg Wilson [Mon, 18 Jul 2016 10:31:01 +0000 (06:31 -0400)]
Ignoring a few more things

7 years agoCleaning up sorting of error messages.
Greg Wilson [Fri, 15 Jul 2016 23:23:58 +0000 (19:23 -0400)]
Cleaning up sorting of error messages.

Closes #75.

7 years agoAlways checking upstream
Greg Wilson [Fri, 15 Jul 2016 14:44:29 +0000 (10:44 -0400)]
Always checking upstream

7 years agoUsing 00:00 as a start time
Greg Wilson [Fri, 15 Jul 2016 14:12:27 +0000 (10:12 -0400)]
Using 00:00 as a start time

7 years agoCleaning up prev/next logic
Greg Wilson [Thu, 14 Jul 2016 17:40:18 +0000 (13:40 -0400)]
Cleaning up prev/next logic

7 years agoSynchronizing lesson checker with late changes
Greg Wilson [Thu, 14 Jul 2016 14:43:35 +0000 (10:43 -0400)]
Synchronizing lesson checker with late changes

7 years agoLesson initializer
Greg Wilson [Thu, 14 Jul 2016 14:38:48 +0000 (10:38 -0400)]
Lesson initializer

7 years agoSwitching to GitHub-defined variables
Greg Wilson [Thu, 14 Jul 2016 14:28:36 +0000 (10:28 -0400)]
Switching to GitHub-defined variables

7 years agoMaking the code a little more robust
Greg Wilson [Wed, 13 Jul 2016 11:19:05 +0000 (07:19 -0400)]
Making the code a little more robust

7 years agoAdding support for MATLAB
Greg Wilson [Fri, 8 Jul 2016 21:04:05 +0000 (17:04 -0400)]
Adding support for MATLAB

7 years agoHandling anchors by ignoring them
Greg Wilson [Fri, 8 Jul 2016 11:07:18 +0000 (07:07 -0400)]
Handling anchors by ignoring them

7 years agoTighter checks for figures
Greg Wilson [Thu, 7 Jul 2016 20:46:22 +0000 (16:46 -0400)]
Tighter checks for figures

7 years agoChecking for links to figures
Greg Wilson [Thu, 7 Jul 2016 19:35:33 +0000 (15:35 -0400)]
Checking for links to figures

7 years agoStarting on tool to check repository settings.
Greg Wilson [Thu, 7 Jul 2016 14:59:38 +0000 (10:59 -0400)]
Starting on tool to check repository settings.

1.  Created `bin/repo_check.py`.
2.  Moved `require()` to `util.py`.
3.  Updated `Makefile` with new target.

7 years agoChecking more configuration values
Greg Wilson [Wed, 6 Jul 2016 00:48:45 +0000 (20:48 -0400)]
Checking more configuration values

7 years agoMust provide permalinks in pages, not layouts
Greg Wilson [Sun, 3 Jul 2016 21:51:10 +0000 (17:51 -0400)]
Must provide permalinks in pages, not layouts

7 years agoChecking for .nojekyll file
Greg Wilson [Sun, 3 Jul 2016 21:43:08 +0000 (17:43 -0400)]
Checking for .nojekyll file

7 years agoImages cannot be wider than the page
Greg Wilson [Sun, 3 Jul 2016 18:52:02 +0000 (14:52 -0400)]
Images cannot be wider than the page

7 years agoMerge branch '2016-06' of github.com:swcarpentry/styles into 2016-06
Greg Wilson [Sat, 2 Jul 2016 21:34:09 +0000 (17:34 -0400)]
Merge branch '2016-06' of github.com:swcarpentry/styles into 2016-06

7 years agoLooking for missing or superfluous images
Greg Wilson [Sat, 2 Jul 2016 21:30:22 +0000 (17:30 -0400)]
Looking for missing or superfluous images

7 years agoMerge pull request #73 from fmichonneau/knitr_fig_path
Greg Wilson [Sat, 2 Jul 2016 13:05:56 +0000 (09:05 -0400)]
Merge pull request #73 from fmichonneau/knitr_fig_path

add function knitr_fig_path

7 years agoLesson checking parameter handling
Greg Wilson [Fri, 1 Jul 2016 18:10:07 +0000 (14:10 -0400)]
Lesson checking parameter handling

7 years agoadd function knitr_fig_path
Francois Michonneau [Fri, 1 Jul 2016 18:08:58 +0000 (14:08 -0400)]
add function knitr_fig_path

7 years agoChecking ends of lines
Greg Wilson [Thu, 30 Jun 2016 03:16:39 +0000 (23:16 -0400)]
Checking ends of lines

7 years agoMerge branch 'move-data' of https://github.com/fmichonneau/styles into fmichonneau...
Greg Wilson [Tue, 28 Jun 2016 16:01:44 +0000 (12:01 -0400)]
Merge branch 'move-data' of https://github.com/fmichonneau/styles into fmichonneau-move-data

7 years agore-add ./data folder
Francois Michonneau [Tue, 28 Jun 2016 15:35:08 +0000 (11:35 -0400)]
re-add ./data folder

7 years agosimplify to single _episodes_rmd/data folder
Francois Michonneau [Tue, 28 Jun 2016 15:27:31 +0000 (11:27 -0400)]
simplify to single _episodes_rmd/data folder

7 years agoMerge branch 'styling-workshops' into 2016-06
Greg Wilson [Mon, 27 Jun 2016 01:39:12 +0000 (21:39 -0400)]
Merge branch 'styling-workshops' into 2016-06

7 years agoMerge branch 'markdownify' into 2016-06
Greg Wilson [Mon, 27 Jun 2016 01:39:01 +0000 (21:39 -0400)]
Merge branch 'markdownify' into 2016-06

7 years agoMerge branch 'converting-to-reporter' into 2016-06
Greg Wilson [Mon, 27 Jun 2016 01:38:50 +0000 (21:38 -0400)]
Merge branch 'converting-to-reporter' into 2016-06

7 years agoMerge branch '2016-06' of github.com:swcarpentry/styles into 2016-06
Greg Wilson [Mon, 27 Jun 2016 00:46:42 +0000 (20:46 -0400)]
Merge branch '2016-06' of github.com:swcarpentry/styles into 2016-06

7 years agoUpdating contribution guidelines in boilerplate
Greg Wilson [Mon, 27 Jun 2016 00:45:43 +0000 (20:45 -0400)]
Updating contribution guidelines in boilerplate

7 years agoMerge pull request #67 from gvwilson/clean-rmd
Francois Michonneau [Mon, 27 Jun 2016 00:28:24 +0000 (20:28 -0400)]
Merge pull request #67 from gvwilson/clean-rmd

Only cleaning intermediate R files on demand.

7 years agoMaking pages work for workshops as well as lessons
Greg Wilson [Sun, 26 Jun 2016 23:14:01 +0000 (19:14 -0400)]
Making pages work for workshops as well as lessons

7 years agoStyling workshops correctly.
Greg Wilson [Sun, 26 Jun 2016 22:54:18 +0000 (18:54 -0400)]
Styling workshops correctly.

1.  Use site.root for root path if set, otherwise use site.github.url.
2.  Display extra files for workshop-template repo as well as for lessons.

7 years agoMarkdownifying questions, keypoints, etc.
Greg Wilson [Sun, 26 Jun 2016 04:25:00 +0000 (00:25 -0400)]
Markdownifying questions, keypoints, etc.

7 years agoAdding error handling for YAML import.
Greg Wilson [Sun, 26 Jun 2016 02:23:19 +0000 (22:23 -0400)]
Adding error handling for YAML import.

1.  Moving all YAML library usage into 'util.py' via utility function.
2.  Wrapping 'import yaml' in error handling to report what library to install.

7 years agoChecking CONTRIBUTING.md (without YAML)
Greg Wilson [Sun, 26 Jun 2016 00:56:47 +0000 (20:56 -0400)]
Checking CONTRIBUTING.md (without YAML)

7 years agoConverting workshop checker to use Reporter class.
Greg Wilson [Sun, 26 Jun 2016 00:52:47 +0000 (20:52 -0400)]
Converting workshop checker to use Reporter class.

1.  Converting error reporting.
2.  Simplifying checking logic.
3.  Refactoring metadata loading.
4.  Modifying lesson checker to reflect refactoring.

Closes #47.

7 years agoChecking for non-Markdown files.
Greg Wilson [Sat, 25 Jun 2016 23:55:00 +0000 (19:55 -0400)]
Checking for non-Markdown files.

Closes #55.

7 years agoOnly cleaning intermediate R files on demand.
Greg Wilson [Sat, 25 Jun 2016 14:24:34 +0000 (10:24 -0400)]
Only cleaning intermediate R files on demand.

1.  Splitting commands to clean intermediate R files into separate target.  These files must be committed to the repo, so they shouldn't be deleted under normal circumstances.
2.  Modifying intermediate file generation to create fig/rmd-* rather than fig/swc-rmd-*, since this template is used by other carpentries (not just SWC).

7 years agomove data/ into _episodes/ and _episodes_rmd/
Francois Michonneau [Fri, 24 Jun 2016 17:13:26 +0000 (13:13 -0400)]
move data/ into _episodes/ and _episodes_rmd/

`generate_md_episodes()` is modified such that datasets storred into
_episodes_rmd/data/ needed to knit the episodes, are copied into
_episodes/data/, and are made available at the root of the site.

7 years agoMerge pull request #64 from gvwilson/building-r
Greg Wilson [Fri, 24 Jun 2016 16:37:47 +0000 (12:37 -0400)]
Merge pull request #64 from gvwilson/building-r

Only try building R files if there are some

7 years agoChanging text of auto-generated file
Greg Wilson [Thu, 23 Jun 2016 21:07:18 +0000 (17:07 -0400)]
Changing text of auto-generated file

7 years agoMerge branch '2016-06' into building-r
Greg Wilson [Thu, 23 Jun 2016 21:03:27 +0000 (17:03 -0400)]
Merge branch '2016-06' into building-r

7 years agoUpdating _config_dev.yml to match changes to root and repo vars
Greg Wilson [Thu, 23 Jun 2016 21:01:00 +0000 (17:01 -0400)]
Updating _config_dev.yml to match changes to root and repo vars

7 years agoSwitching to site.root and site.repo
Greg Wilson [Thu, 23 Jun 2016 20:50:38 +0000 (16:50 -0400)]
Switching to site.root and site.repo

7 years agoOnly try building R files if there are some
Greg Wilson [Thu, 23 Jun 2016 19:43:47 +0000 (15:43 -0400)]
Only try building R files if there are some

7 years agoBetter display of file groups in Makefile
Greg Wilson [Thu, 23 Jun 2016 14:54:58 +0000 (10:54 -0400)]
Better display of file groups in Makefile

7 years agoMerge pull request #62 from fmichonneau/fix-knitr-env
Francois Michonneau [Wed, 22 Jun 2016 21:13:02 +0000 (17:13 -0400)]
Merge pull request #62 from fmichonneau/fix-knitr-env

use anonymous function to generate markdown files

7 years agouse anonymous function to generate markdown files
Francois Michonneau [Wed, 22 Jun 2016 21:08:51 +0000 (17:08 -0400)]
use anonymous function to generate markdown files

7 years agoChecking metadata fields more carefully
Greg Wilson [Wed, 22 Jun 2016 19:09:02 +0000 (15:09 -0400)]
Checking metadata fields more carefully

7 years agoPrinting error messages in sorted order
Greg Wilson [Wed, 22 Jun 2016 18:53:32 +0000 (14:53 -0400)]
Printing error messages in sorted order

7 years agoChecking that episodes are numbered consecutively
Greg Wilson [Wed, 22 Jun 2016 18:10:31 +0000 (14:10 -0400)]
Checking that episodes are numbered consecutively

7 years agoMaking line-length checking optional for lessons.
Greg Wilson [Wed, 22 Jun 2016 17:57:22 +0000 (13:57 -0400)]
Making line-length checking optional for lessons.

1.  Modify `read_markdown` to return list of (index, line, line_length).
2.  Modify `lesson_check.py` to make line-length checking optional.

7 years agoRaising exception instead of printing error on bad YAML
Greg Wilson [Wed, 22 Jun 2016 17:17:02 +0000 (13:17 -0400)]
Raising exception instead of printing error on bad YAML

7 years agoMerge pull request #61 from fmichonneau/fix-rmd-formatting
Greg Wilson [Wed, 22 Jun 2016 14:59:22 +0000 (10:59 -0400)]
Merge pull request #61 from fmichonneau/fix-rmd-formatting

Fix Rmd formatting