From 4352fbc3cdaf38cb211fe2dc727aa235263fdb59 Mon Sep 17 00:00:00 2001 From: Sarah Brown Date: Fri, 1 Jun 2018 02:52:21 -0700 Subject: [PATCH 001/185] fix typos and add clarifying text to boilerplate --- bin/boilerplate/_episodes/01-introduction.md | 6 +++--- bin/boilerplate/index.md | 8 ++++++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/bin/boilerplate/_episodes/01-introduction.md b/bin/boilerplate/_episodes/01-introduction.md index 17e25138..528cd072 100644 --- a/bin/boilerplate/_episodes/01-introduction.md +++ b/bin/boilerplate/_episodes/01-introduction.md @@ -5,7 +5,7 @@ exercises: 0 questions: - "Key question" objectives: -- "First objective." +- "First learning objective." keypoints: -- "First key point." ---- \ No newline at end of file +- "First key point. Brief Answer to questions." +--- diff --git a/bin/boilerplate/index.md b/bin/boilerplate/index.md index 2809a1bf..81522f4d 100644 --- a/bin/boilerplate/index.md +++ b/bin/boilerplate/index.md @@ -1,10 +1,14 @@ --- layout: lesson -root: . # Is the only page that don't follow the partner /:path/index.html -permalink: index.html # Is the only page that don't follow the partner /:path/index.html +root: . # Is the only page that doesn't follow the pattern /:path/index.html +permalink: index.html # Is the only page that doesn't follow the pattern /:path/index.html --- FIXME: home page introduction + + +{% comment %} This is a comment in Liquid {% endcomment %} + > ## Prerequisites > > FIXME From e8b4a1c542e08a44427199a72d6dcc0f30bbd7b6 Mon Sep 17 00:00:00 2001 From: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com> Date: Wed, 20 Jun 2018 07:26:48 +0200 Subject: [PATCH 002/185] Link to lessons (closes swcarpentry/r-novice-inflammation/#371) --- _includes/links.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/_includes/links.md b/_includes/links.md index e18ce632..1b283414 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -9,6 +9,7 @@ [cran-checkpoint]: https://cran.r-project.org/package=checkpoint [cran-knitr]: https://cran.r-project.org/package=knitr [cran-stringr]: https://cran.r-project.org/package=stringr +[dc-lessons]: http://www.datacarpentry.org/lessons/ [email]: mailto:team@carpentries.org [github-importer]: https://import.github.com/ [importer]: https://github.com/new/import @@ -18,6 +19,7 @@ [jekyll]: https://jekyllrb.com/ [jupyter]: https://jupyter.org/ [lesson-example]: https://carpentries.github.io/lesson-example/ +[lc-lessons]: https://librarycarpentry.org/#portfolio [mit-license]: https://opensource.org/licenses/mit-license.html [morea]: https://morea-framework.github.io/ [numfocus]: https://numfocus.org/ @@ -33,5 +35,6 @@ [rubygems]: https://rubygems.org/pages/download/ [styles]: https://github.com/carpentries/styles/ [swc-releases]: https://github.com/swcarpentry/swc-releases +[swc-lessons]: https://software-carpentry.org/lessons/ [workshop-repo]: {{ site.workshop_repo }} [yaml]: http://yaml.org/ From 05ee737be5982c18397e9184840c594487fab3d4 Mon Sep 17 00:00:00 2001 From: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com> Date: Wed, 20 Jun 2018 07:57:03 +0200 Subject: [PATCH 003/185] Sort alphabetically --- _includes/links.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_includes/links.md b/_includes/links.md index 1b283414..b5db6ab5 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -18,8 +18,8 @@ [jekyll-windows]: http://jekyll-windows.juthilo.com/ [jekyll]: https://jekyllrb.com/ [jupyter]: https://jupyter.org/ -[lesson-example]: https://carpentries.github.io/lesson-example/ [lc-lessons]: https://librarycarpentry.org/#portfolio +[lesson-example]: https://carpentries.github.io/lesson-example/ [mit-license]: https://opensource.org/licenses/mit-license.html [morea]: https://morea-framework.github.io/ [numfocus]: https://numfocus.org/ @@ -34,7 +34,7 @@ [ruby-installer]: https://rubyinstaller.org/ [rubygems]: https://rubygems.org/pages/download/ [styles]: https://github.com/carpentries/styles/ -[swc-releases]: https://github.com/swcarpentry/swc-releases [swc-lessons]: https://software-carpentry.org/lessons/ +[swc-releases]: https://github.com/swcarpentry/swc-releases [workshop-repo]: {{ site.workshop_repo }} [yaml]: http://yaml.org/ From d2b83c815a32c3e7eba006f579dc4ba37bc4dfcc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Wed, 20 Jun 2018 13:22:51 -0400 Subject: [PATCH 004/185] lesson_check.py: check YAML headers in Rmd episodes Check that Rmd episode files include `source: Rmd` Fixes carpentries/styles#273 --- bin/lesson_check.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/bin/lesson_check.py b/bin/lesson_check.py index 8ed1bf89..b728dcb9 100755 --- a/bin/lesson_check.py +++ b/bin/lesson_check.py @@ -18,6 +18,9 @@ # Where to look for source Markdown files. SOURCE_DIRS = ['', '_episodes', '_extras'] +# Where to look for source Rmd files. +SOURCE_RMD_DIRS = ['_episodes_rmd'] + # Required files: each entry is ('path': YAML_required). # FIXME: We do not yet validate whether any files have the required # YAML headers, but should in the future. @@ -108,6 +111,7 @@ def main(): args = parse_args() args.reporter = Reporter() check_config(args.reporter, args.source_dir) + check_source_rmd(args.reporter, args.source_dir, args.parser) args.references = read_references(args.reporter, args.reference_path) docs = read_all_markdown(args.source_dir, args.parser) @@ -184,6 +188,19 @@ def check_config(reporter, source_dir): 'configuration', '"root" not set to "." in configuration') +def check_source_rmd(reporter, source_dir, parser): + """Check that Rmd episode files include `source: Rmd`""" + + episode_rmd_dir = [os.path.join(source_dir, d) for d in SOURCE_RMD_DIRS] + episode_rmd_files = [os.path.join(d, '*.Rmd') for d in episode_rmd_dir] + results = {} + for pat in episode_rmd_files: + for f in glob.glob(pat): + data = read_markdown(parser, f) + dy = data['metadata'] + if dy: + reporter.check_field(f, 'episode_rmd', + dy, 'source', 'Rmd') def read_references(reporter, ref_path): """Read shared file of reference links, returning dictionary of valid references From d39ad8017a7c173c36906de96f2ddb2763e2a6da Mon Sep 17 00:00:00 2001 From: trk Date: Sat, 23 Jun 2018 13:54:36 +0000 Subject: [PATCH 005/185] Update Library Carpentry link, resolve #304 --- bin/boilerplate/_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/boilerplate/_config.yml b/bin/boilerplate/_config.yml index a62f808b..c98cb184 100644 --- a/bin/boilerplate/_config.yml +++ b/bin/boilerplate/_config.yml @@ -35,7 +35,7 @@ carpentries_site: "https://carpentries.org/" dc_site: "http://datacarpentry.org" example_repo: "https://github.com/carpentries/lesson-example" example_site: "https://carpentries.github.io/lesson-example" -lc_site: "https://librarycarpentry.github.io/" +lc_site: "https://librarycarpentry.org/" swc_github: "https://github.com/swcarpentry" swc_pages: "https://swcarpentry.github.io" swc_site: "https://software-carpentry.org" From 95f65b89624418e85ab17c5158625ac36e5cec35 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Wed, 27 Jun 2018 15:40:40 -0400 Subject: [PATCH 006/185] [fix carpentries/styles#311] update descriptions of the carpentries --- _includes/carpentries.html | 58 ++++++++++++++++++++++++++------------ 1 file changed, 40 insertions(+), 18 deletions(-) diff --git a/_includes/carpentries.html b/_includes/carpentries.html index 4d5c9060..d51504b1 100644 --- a/_includes/carpentries.html +++ b/_includes/carpentries.html @@ -1,17 +1,38 @@ {% comment %} General description of Software and Data Carpentry. {% endcomment %} +
+
+ The Carpentries logo +
+
+

The Carpentries comprises + Software Carpentry and Data Carpentry, communities of Instructors, Trainers, + Maintainers, helpers, and supporters who share a mission to teach + foundational coding and data science skills to researchers. In January, + 2018, The Carpentries was formed by the merger of Software Carpentry and + Data Carpentry.

+ +

While individual lessons and workshops continue to be run under each + lesson project, The Carpentries provide overall staffing and governance, as + well as support for assessment, instructor training and mentoring. + Memberships are joint, and the Carpentries project maintains a shared Code + of Conduct. The Carpentries is a fiscally sponsored project of Community + Initiatives, a registered 501(c)3 non-profit based in California, USA.

+
+
Software Carpentry logo
- Since 1998, - Software Carpentry - has been teaching researchers in science, engineering, medicine, and related disciplines - the computing skills they need to get more done in less time and with less pain. - Its volunteer instructors have run hundreds of events - for thousands of learners in the past two and a half years. +

Since 1998, Software Carpentry has + been teaching researchers across all disciplines the foundational coding + skills they need to get more done in less time and with less pain. Its + volunteer instructors have run hundreds of events for thousands of learners + around the world. Now that all research involves some degree of + computational work, whether with big data, cloud computing, or simple task + automation, these skills are needed more than ever.


@@ -20,10 +41,13 @@ Data Carpentry logo
- Data Carpentry develops and teaches workshops on the fundamental data skills needed to conduct research. - Its target audience is researchers who have little to no prior computational experience, - and its lessons are domain specific, - building on learners' existing knowledge to enable them to quickly apply skills learned to their own research. +

Data Carpentry develops and teaches + workshops on the fundamental data skills needed to conduct research. Its + target audience is researchers who have little to no prior computational + experience, and its lessons are domain specific, building on learners' + existing knowledge to enable them to quickly apply skills learned to their + own research. Data Carpentry workshops take researchers through the entire + data life cycle.


@@ -32,13 +56,11 @@ Library Carpentry logo
- Library Carpentry is made by librarians to help librarians - automate repetitive, boring, error-prone tasks; - create, maintain and analyse sustainable and reusable data; - work effectively with IT and systems colleagues; - better understand the use of software in research; - and much more. - Library Carpentry was the winner of the 2016 - British Library Labs Teaching and Learning Award. +

Library Carpentry develops lessons and + teaches workshops for and with people working in library- and + information-related roles. Its goal is to create an on-ramp to empower this + community to use software and data in their own work, as well as be + advocates for and train others in efficient, effective and reproducible data + and software practices.

From cb60e6bcbec203f47f88f2cc493663fd6a575f78 Mon Sep 17 00:00:00 2001 From: Tracy Teal Date: Wed, 27 Jun 2018 14:36:30 -0700 Subject: [PATCH 007/185] added about the discussion stage to the LC description --- _includes/carpentries.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/carpentries.html b/_includes/carpentries.html index 4d5c9060..1aeccb37 100644 --- a/_includes/carpentries.html +++ b/_includes/carpentries.html @@ -32,7 +32,7 @@ Library Carpentry logo
- Library Carpentry is made by librarians to help librarians + Library Carpentry is in discussions with The Carpentries to be a Lesson Project, like Software Carpentry and Data Carpentry. It is made by librarians to help librarians automate repetitive, boring, error-prone tasks; create, maintain and analyse sustainable and reusable data; work effectively with IT and systems colleagues; From bcc090d57fda379f68dff8bf1231b6e6f83f2f5a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Tue, 3 Jul 2018 16:21:46 -0400 Subject: [PATCH 008/185] center images --- assets/css/lesson.scss | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index 8a7b2954..ea69097a 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -138,7 +138,10 @@ code { } img { - max-width: 100%; + display: block; + margin-left: auto; + margin-right: auto; + max-width: 100%; } //---------------------------------------- From cb2346ee3d382434dfe9c66735981379aa82a6ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Tue, 3 Jul 2018 16:30:31 -0400 Subject: [PATCH 009/185] use 20px margin --- assets/css/lesson.scss | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index ea69097a..499c4d0c 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -139,8 +139,7 @@ code { img { display: block; - margin-left: auto; - margin-right: auto; + margin: 20px auto; max-width: 100%; } From 09d9cce4be20f0185de8e0ecc7b9e6a5a095284f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Tue, 3 Jul 2018 16:44:33 -0400 Subject: [PATCH 010/185] restrict to article --- assets/css/lesson.scss | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index 499c4d0c..c32d7743 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -137,7 +137,7 @@ code { background-color: #e7e7e7; } -img { +article img { display: block; margin: 20px auto; max-width: 100%; From 80d6638a0c94abdd20c1e020d5ec5609c28210de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Tue, 3 Jul 2018 17:45:43 -0400 Subject: [PATCH 011/185] space out callout elements better --- assets/css/lesson.scss | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index 8a7b2954..0a2ecc6b 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -29,10 +29,10 @@ $color-testimonial: #fc8dc1 !default; //---------------------------------------- @mixin cdSetup($color) { - color: $color; - border-left: solid 5px $color; - margin-bottom: 0px; - border-radius: 4px 0 0 4px; + color: $color; + border-left: solid 5px $color; + margin: 15px; + border-radius: 4px 0 0 4px; } .error { @include cdSetup($color-error); } @@ -81,8 +81,11 @@ $codeblock-padding: 5px !default; padding-right: 0; border: 1px solid; border-color: $color; + border-radius: 4px; padding-bottom: $codeblock-padding; + margin: 15px; + h2 { padding-top: $codeblock-padding; padding-bottom: $codeblock-padding; @@ -126,6 +129,10 @@ $codeblock-padding: 5px !default; font-size: 18px; } +blockquote p { + margin: 5px; +} + //---------------------------------------- // Override Bootstrap settings. //---------------------------------------- From 4aa8830594683ac51433d5eb74988f6b5e5bd8dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Thu, 12 Jul 2018 15:02:15 +1000 Subject: [PATCH 012/185] fix survey link variables --- bin/boilerplate/_config.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/bin/boilerplate/_config.yml b/bin/boilerplate/_config.yml index c98cb184..d1b4c02f 100644 --- a/bin/boilerplate/_config.yml +++ b/bin/boilerplate/_config.yml @@ -45,9 +45,12 @@ workshop_repo: "https://github.com/carpentries/workshop-template" workshop_site: "https://carpentries.github.io/workshop-template" # Surveys. -pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id=" -post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id=" +swc_pre_survey: "https://www.surveymonkey.com/r/swc_pre_workshop_v1?workshop_id=" +swc_post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_id=" training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training" +dc_pre_survey: "https://www.surveymonkey.com/r/dcpreworkshopassessment?workshop_id=" +dc_post_survey: "https://www.surveymonkey.com/r/dcpostworkshopassessment?workshop_id=" + # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am). start_time: 0 From b01dd227c382b6e136db7a92c0f014d549e87d02 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Tue, 17 Jul 2018 16:53:56 -0500 Subject: [PATCH 013/185] Makefile: fix typo in clean-rmd rule --- Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Makefile b/Makefile index f0b73e60..5ee09806 100644 --- a/Makefile +++ b/Makefile @@ -43,7 +43,7 @@ clean : @find . -name '*.pyc' -exec rm {} \; ## clean-rmd : clean intermediate R files (that need to be committed to the repo). -clear-rmd : +clean-rmd : @rm -rf ${RMD_DST} @rm -rf fig/rmd-* From 4248451ccbf6a7d59ba8d908cabe76a7744b1918 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Fri, 20 Jul 2018 09:09:25 -0400 Subject: [PATCH 014/185] add LC survey links --- bin/boilerplate/_config.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bin/boilerplate/_config.yml b/bin/boilerplate/_config.yml index d1b4c02f..963b72de 100644 --- a/bin/boilerplate/_config.yml +++ b/bin/boilerplate/_config.yml @@ -50,6 +50,8 @@ swc_post_survey: "https://www.surveymonkey.com/r/swc_post_workshop_v1?workshop_i training_post_survey: "https://www.surveymonkey.com/r/post-instructor-training" dc_pre_survey: "https://www.surveymonkey.com/r/dcpreworkshopassessment?workshop_id=" dc_post_survey: "https://www.surveymonkey.com/r/dcpostworkshopassessment?workshop_id=" +lc_pre_survey: "https://www.surveymonkey.com/r/lcpreworkshopsurvey?workshop_id=" +lc_post_survey: "https://www.surveymonkey.com/r/lcpostworkshopsurvey?workshop_id=" # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am). From e23c81661539319851ed8680a44824cca599042d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Fri, 20 Jul 2018 09:13:00 -0400 Subject: [PATCH 015/185] [fix #332] add instructor training survey links --- bin/boilerplate/_config.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/bin/boilerplate/_config.yml b/bin/boilerplate/_config.yml index 963b72de..795a35c3 100644 --- a/bin/boilerplate/_config.yml +++ b/bin/boilerplate/_config.yml @@ -52,6 +52,8 @@ dc_pre_survey: "https://www.surveymonkey.com/r/dcpreworkshopassessment?workshop_ dc_post_survey: "https://www.surveymonkey.com/r/dcpostworkshopassessment?workshop_id=" lc_pre_survey: "https://www.surveymonkey.com/r/lcpreworkshopsurvey?workshop_id=" lc_post_survey: "https://www.surveymonkey.com/r/lcpostworkshopsurvey?workshop_id=" +instructor_pre_survey: "https://www.surveymonkey.com/r/instructor_training_pre_survey?workshop_id=" +instructor_post_survey: "https://www.surveymonkey.com/r/instructor_training_post_survey?workshop_id=" # Start time in minutes (0 to be clock-independent, 540 to show a start at 09:00 am). From c6b61291e98f4921d7379813ab51324fbdf4886f Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Fri, 3 Aug 2018 08:32:39 +0100 Subject: [PATCH 016/185] Fix lesson_initialize.py to initialize new lessons CODE_OF_CONDUCT.md is already at the root of the repository. --- bin/boilerplate/CODE_OF_CONDUCT.md | 11 ----------- bin/lesson_initialize.py | 1 - 2 files changed, 12 deletions(-) delete mode 100644 bin/boilerplate/CODE_OF_CONDUCT.md diff --git a/bin/boilerplate/CODE_OF_CONDUCT.md b/bin/boilerplate/CODE_OF_CONDUCT.md deleted file mode 100644 index c3b96690..00000000 --- a/bin/boilerplate/CODE_OF_CONDUCT.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -layout: page -title: "Contributor Code of Conduct" ---- -As contributors and maintainers of this project, -we pledge to follow the [Carpentry Code of Conduct][coc]. - -Instances of abusive, harassing, or otherwise unacceptable behavior -may be reported by following our [reporting guidelines][coc-reporting]. - -{% include links.md %} diff --git a/bin/lesson_initialize.py b/bin/lesson_initialize.py index a96ba383..a5eb6d05 100755 --- a/bin/lesson_initialize.py +++ b/bin/lesson_initialize.py @@ -11,7 +11,6 @@ '.travis.yml', 'AUTHORS', 'CITATION', - 'CODE_OF_CONDUCT.md', 'CONTRIBUTING.md', 'README.md', '_config.yml', From 56c504729f0bfb3208f1c75912ecf500c540003e Mon Sep 17 00:00:00 2001 From: Tracy Teal Date: Mon, 6 Aug 2018 09:33:35 -0400 Subject: [PATCH 017/185] added workshop calendar --- _includes/workshop_calendar.html | 1 + 1 file changed, 1 insertion(+) create mode 100644 _includes/workshop_calendar.html diff --git a/_includes/workshop_calendar.html b/_includes/workshop_calendar.html new file mode 100644 index 00000000..53a0eac8 --- /dev/null +++ b/_includes/workshop_calendar.html @@ -0,0 +1 @@ +Add to your Google Calendar. From 7e86166e4de20ed225f35d9c6b8d5f885bb922c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Tue, 14 Aug 2018 10:58:33 -0400 Subject: [PATCH 018/185] avoid warnings and errors around github metadata for local rendering --- bin/boilerplate/_config.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/bin/boilerplate/_config.yml b/bin/boilerplate/_config.yml index 795a35c3..35e2cf1c 100644 --- a/bin/boilerplate/_config.yml +++ b/bin/boilerplate/_config.yml @@ -94,3 +94,7 @@ exclude: # Turn on built-in syntax highlighting. highlighter: rouge + +# Allow local rendering around github metadata +# from: https://github.com/github/pages-gem/issues/399#issuecomment-301827749 +github: [metadata] From b84e6ac5b787b831c496780d14bcc73242d8e172 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Tue, 14 Aug 2018 17:58:44 -0400 Subject: [PATCH 019/185] use site.github.url only in production --- _layouts/base.html | 18 +++++++++++++++++- bin/boilerplate/_config.yml | 4 ---- 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/_layouts/base.html b/_layouts/base.html index 99d65674..8a2e4b51 100644 --- a/_layouts/base.html +++ b/_layouts/base.html @@ -1,5 +1,21 @@ --- --- + +{% comment %} +When rendering websites locally, `site.github.url` doesn't get resolved +properly unless GitHub PAT are set up and available in the environment. +This leads to warnings and errors when trying to serve the site locally. +To work around this, we use the `jekyll.environment` variable which is set to +`development` when rendering the site locally, and set to `production` on +GitHub where `site.github.url` will be defined. +{% endcomment %} + +{% if jekyll.environment == "development" %} +{% assign search_domain_url = "" %} +{% elsif jekyll.environment == "production" %} +{% assign search_domain_url = site.github.url %} +{% endif %} + @@ -8,7 +24,7 @@ - + diff --git a/bin/boilerplate/_config.yml b/bin/boilerplate/_config.yml index 35e2cf1c..795a35c3 100644 --- a/bin/boilerplate/_config.yml +++ b/bin/boilerplate/_config.yml @@ -94,7 +94,3 @@ exclude: # Turn on built-in syntax highlighting. highlighter: rouge - -# Allow local rendering around github metadata -# from: https://github.com/github/pages-gem/issues/399#issuecomment-301827749 -github: [metadata] From 887f484d746c0547478f8da8ae53de4774c7bbea Mon Sep 17 00:00:00 2001 From: Raniere Silva Date: Wed, 15 Aug 2018 16:51:58 +0100 Subject: [PATCH 020/185] Fix footer and copyright notice Close carpentries/styles#325 --- _includes/lesson_footer.html | 24 ++++++++++++------------ assets/css/lesson.scss | 2 +- bin/boilerplate/_config.yml | 1 + 3 files changed, 14 insertions(+), 13 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 7df84da7..9be14181 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -5,23 +5,23 @@
From f40a94757aa8379c1c4bad47ad729229bbdb5e68 Mon Sep 17 00:00:00 2001 From: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com> Date: Wed, 14 Nov 2018 10:08:23 +0100 Subject: [PATCH 048/185] Nudge contributors to specify episodes unambigously See https://github.com/swcarpentry/r-novice-inflammation/issues/401 > 3. --- .github/ISSUE_TEMPLATE.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md index 6cc9e527..9dafd7fb 100644 --- a/.github/ISSUE_TEMPLATE.md +++ b/.github/ISSUE_TEMPLATE.md @@ -4,6 +4,8 @@ Please delete the text below before submitting your contribution. Thanks for contributing! If this contribution is for instructor training, please send an email to checkout@carpentries.org with a link to this contribution so we can record your progress. You’ve completed your contribution step for instructor checkout just by submitting this contribution. +If this issue is about a specific episode within a lesson, please provide its link or filename. + Please keep in mind that lesson maintainers are volunteers and it may be some time before they can respond to your contribution. Although not all contributions can be incorporated into the lesson materials, we appreciate your time and effort to improve the curriculum. If you have any questions about the lesson maintenance process or would like to volunteer your time as a contribution reviewer, please contact Kate Hertweck (k8hertweck@gmail.com). --- From c40e5523b88ce751edfc9ffb86e27c32f3bb9e16 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Thu, 29 Nov 2018 14:38:59 -0600 Subject: [PATCH 049/185] aio.md: fix indentation and variable declaration --- bin/boilerplate/aio.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/bin/boilerplate/aio.md b/bin/boilerplate/aio.md index 1900d884..523e7dd2 100644 --- a/bin/boilerplate/aio.md +++ b/bin/boilerplate/aio.md @@ -15,22 +15,22 @@ xmlHttp[i] = new XMLHttpRequest(); xmlHttp[i].episode = lesson_episodes[i]; /* To enable use this later. */ xmlHttp[i].onreadystatechange = function() { - if (this.readyState == 4 && this.status == 200) { - var article_here = document.getElementById(this.episode); - var parser = new DOMParser(); - var htmlDoc = parser.parseFromString(this.responseText,"text/html"); - var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0]; - article_here.innerHTML = htmlDocArticle.innerHTML; + if (this.readyState == 4 && this.status == 200) { + var article_here = document.getElementById(this.episode); + var parser = new DOMParser(); + var htmlDoc = parser.parseFromString(this.responseText,"text/html"); + var htmlDocArticle = htmlDoc.getElementsByTagName("article")[0]; + article_here.innerHTML = htmlDocArticle.innerHTML; } } - episode_url = "{{ relative_root_path }}" + lesson_episodes[i]; + var episode_url = "{{ relative_root_path }}" + lesson_episodes[i]; xmlHttp[i].open("GET", episode_url); xmlHttp[i].send(null); } } {% comment %} -Create anchor for each one of the episodes. +Create an anchor for every episode. {% endcomment %} {% for episode in site.episodes %}
From e67e9abcc395cb93292ffcedd9c7ed4dd65e1be9 Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 13:06:22 -0800 Subject: [PATCH 050/185] links.md: Update link to Library Carpentry lessons Pull Request: carpentries/styles#374 --- _includes/links.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/links.md b/_includes/links.md index bdf88671..94fc15f3 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -18,7 +18,7 @@ [jekyll-windows]: http://jekyll-windows.juthilo.com/ [jekyll]: https://jekyllrb.com/ [jupyter]: https://jupyter.org/ -[lc-lessons]: https://librarycarpentry.org/#portfolio +[lc-lessons]: https://librarycarpentry.org/lessons/ [lesson-example]: https://carpentries.github.io/lesson-example/ [mit-license]: https://opensource.org/licenses/mit-license.html [morea]: https://morea-framework.github.io/ From 55c136ca83729a27ff80d3ea332b33ce813ae417 Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 04:13:44 -0800 Subject: [PATCH 051/185] Add LC to instruction material section --- LICENSE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE.md b/LICENSE.md index 8fe99449..e6a3398d 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -5,7 +5,7 @@ root: . --- ## Instructional Material -All Software Carpentry and Data Carpentry instructional material is +All Software Carpentry, Data Carpentry, and Library Carpentry instructional material is made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 From 8871a8e5974cfb3bbd27e311bcde90c7c2ceea33 Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 04:35:19 -0800 Subject: [PATCH 052/185] Add lc to conditions, comments, text --- bin/workshop_check.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/workshop_check.py b/bin/workshop_check.py index bd15210a..e5e651ec 100755 --- a/bin/workshop_check.py +++ b/bin/workshop_check.py @@ -18,7 +18,7 @@ URL_PATTERN = r'https?://.+' # Defaults. -CARPENTRIES = ("dc", "swc") +CARPENTRIES = ("dc", "swc", "lc") DEFAULT_CONTACT_EMAIL = 'admin@software-carpentry.org' USAGE = 'Usage: "workshop_check.py path/to/root/directory"' @@ -91,7 +91,7 @@ def check_layout(layout): @look_for_fixme def check_carpentry(layout): - '''"carpentry" in YAML header must be "dc" or "swc".''' + '''"carpentry" in YAML header must be "dc", "swc", or "lc".''' return layout in CARPENTRIES @@ -117,7 +117,7 @@ def check_humandate(date): and 4-digit year. Examples include 'Feb 18-20, 2025' and 'Feb 18 and 20, 2025'. It may be in languages other than English, but the month name should be kept short to aid formatting of the main - Software Carpentry web site. + Carpentries web site. """ if ',' not in date: @@ -390,7 +390,7 @@ def check_config(reporter, filename): kind) carpentry = config.get('carpentry', None) - reporter.check(carpentry in ('swc', 'dc'), + reporter.check(carpentry in ('swc', 'dc', 'lc'), filename, 'Missing or unknown carpentry: {0}', carpentry) From cb4e249808ec5a2ecdaddbce2aaffc315747f4f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Mon, 3 Dec 2018 09:14:52 -0500 Subject: [PATCH 053/185] add cp as template option --- bin/workshop_check.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bin/workshop_check.py b/bin/workshop_check.py index e5e651ec..0523d0c2 100755 --- a/bin/workshop_check.py +++ b/bin/workshop_check.py @@ -18,7 +18,7 @@ URL_PATTERN = r'https?://.+' # Defaults. -CARPENTRIES = ("dc", "swc", "lc") +CARPENTRIES = ("dc", "swc", "lc", "cp") DEFAULT_CONTACT_EMAIL = 'admin@software-carpentry.org' USAGE = 'Usage: "workshop_check.py path/to/root/directory"' @@ -91,7 +91,7 @@ def check_layout(layout): @look_for_fixme def check_carpentry(layout): - '''"carpentry" in YAML header must be "dc", "swc", or "lc".''' + '''"carpentry" in YAML header must be "dc", "swc", "lc", or "cp".''' return layout in CARPENTRIES @@ -390,7 +390,7 @@ def check_config(reporter, filename): kind) carpentry = config.get('carpentry', None) - reporter.check(carpentry in ('swc', 'dc', 'lc'), + reporter.check(carpentry in ('swc', 'dc', 'lc', 'cp'), filename, 'Missing or unknown carpentry: {0}', carpentry) From 72c72b278656a9f389961d819dce012823a5b703 Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 04:38:30 -0800 Subject: [PATCH 054/185] Update to LC inclusive language --- _includes/lc/who.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/lc/who.html b/_includes/lc/who.html index fd9b38c4..ecbf7066 100644 --- a/_includes/lc/who.html +++ b/_includes/lc/who.html @@ -1,6 +1,6 @@

Who: - The course is for librarians, archivists, and other information workers. + The course is for people working in library- and information-related roles. You don't need to have any previous knowledge of the tools that will be presented at the workshop. From 3018b07c82957cf0937fa495bfefb01daa24f3f1 Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 04:23:17 -0800 Subject: [PATCH 055/185] Include LC, Lesson Program date, update language --- _includes/carpentries.html | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/_includes/carpentries.html b/_includes/carpentries.html index 5691223f..c032bd54 100644 --- a/_includes/carpentries.html +++ b/_includes/carpentries.html @@ -1,5 +1,5 @@ {% comment %} - General description of Software and Data Carpentry. + General description of Software, Data, and Library Carpentry. {% endcomment %} {% include base_path.html %} @@ -10,11 +10,12 @@

The Carpentries comprises - Software Carpentry and Data Carpentry, communities of Instructors, Trainers, + Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach - foundational coding and data science skills to researchers. In January, + foundational coding and data science skills to researchers and people + working in library- and information-related roles. In January, 2018, The Carpentries was formed by the merger of Software Carpentry and - Data Carpentry.

+ Data Carpentry. Library Carpentry became an official Carpentries Lesson Program in November 2018.

While individual lessons and workshops continue to be run under each lesson project, The Carpentries provide overall staffing and governance, as @@ -59,9 +60,7 @@ Library Carpentry logo

-

Library Carpentry is in discussions with - The Carpentries to be a Lesson Project, like Software Carpentry* - and Data Carpentry. Library Carpentry develops lessons and +

Library Carpentry develops lessons and teaches workshops for and with people working in library- and information-related roles. Its goal is to create an on-ramp to empower this community to use software and data in their own work, as well as be From 28599aee6679189edfd291822bc8fcad25a58f4c Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 04:27:15 -0800 Subject: [PATCH 056/185] Add LC condition --- _includes/workshop_calendar.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/workshop_calendar.html b/_includes/workshop_calendar.html index 53a0eac8..f88327dc 100644 --- a/_includes/workshop_calendar.html +++ b/_includes/workshop_calendar.html @@ -1 +1 @@ -Add to your Google Calendar. +Add to your Google Calendar. From 348a4024bdf6fd62a093894830d45336c57c4797 Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 04:08:12 -0800 Subject: [PATCH 057/185] Add Carpentries, LC site, issues --- bin/boilerplate/CONTRIBUTING.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/bin/boilerplate/CONTRIBUTING.md b/bin/boilerplate/CONTRIBUTING.md index 5a6b02a7..96e81582 100644 --- a/bin/boilerplate/CONTRIBUTING.md +++ b/bin/boilerplate/CONTRIBUTING.md @@ -1,6 +1,6 @@ # Contributing -[Software Carpentry][swc-site] and [Data Carpentry][dc-site] are open source projects, +[The Carpentries][c-site]([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source projects, and we welcome contributions of all kinds: new lessons, fixes to existing material, @@ -14,7 +14,7 @@ you agree that we may redistribute your work under [our license](LICENSE.md). In exchange, we will address your issues and/or assess your change proposal as promptly as we can, and help you become a member of our community. -Everyone involved in [Software Carpentry][swc-site] and [Data Carpentry][dc-site] +Everyone involved in [The Carpentries][c-site]([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) agrees to abide by our [code of conduct](CODE_OF_CONDUCT.md). ## How to Contribute @@ -73,8 +73,8 @@ and submitting [bug reports][issues] about things that don't work, aren't clear, or are missing. If you are looking for ideas, please see the 'Issues' tab for a list of issues associated with this repository, -or you may also look at the issues for [Data Carpentry][dc-issues] -and [Software Carpentry][swc-issues] projects. +or you may also look at the issues for [Data Carpentry][dc-issues], +[Software Carpentry][swc-issues], and [Library Carpentry][lc-issues] projects. Comments on issues and reviews of pull requests are just as welcome: we are smarter together than we are on our own. @@ -146,3 +146,7 @@ You can also [reach us by email][email]. [swc-issues]: https://github.com/issues?q=user%3Aswcarpentry [swc-lessons]: https://software-carpentry.org/lessons/ [swc-site]: https://software-carpentry.org/ +[c-site]: https://carpentries.org/ +[lc-site]: https://librarycarpentry.org/ +[lc-issues]: https://github.com/issues?q=user%3Alibrarycarpentry + From 93a8400ccd1b66875e1d5bab167c3385d78cd4d1 Mon Sep 17 00:00:00 2001 From: Chris Erdmann Date: Sun, 2 Dec 2018 03:56:25 -0800 Subject: [PATCH 058/185] Update to inclusive language - roles --- _includes/lc/intro.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/lc/intro.html b/_includes/lc/intro.html index 7f8609a5..b218f2ba 100644 --- a/_includes/lc/intro.html +++ b/_includes/lc/intro.html @@ -1,6 +1,6 @@

Library Carpentry - is made by librarians, for librarians to help you: + is made by people working in library- and information-related roles to help you:

  • automate repetitive, boring, error-prone tasks
  • From 269bfb59cb0f27a345d89d82095f9aa954358412 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Tue, 4 Dec 2018 09:47:35 -0600 Subject: [PATCH 059/185] links.md: lesson-specific links --- _includes/links.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/_includes/links.md b/_includes/links.md index 94fc15f3..63cf6be9 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -19,7 +19,13 @@ [jekyll]: https://jekyllrb.com/ [jupyter]: https://jupyter.org/ [lc-lessons]: https://librarycarpentry.org/lessons/ +[lesson-aio]: {{ relative_root_path }}{% link aio.md %} +[lesson-coc]: {{ relative_root_path }}{% link CODE_OF_CONDUCT.md %} [lesson-example]: https://carpentries.github.io/lesson-example/ +[lesson-license]: {{ relative_root_path }}{% link LICENSE.md %} +[lesson-mainpage]: {{ relative_root_path }}{% link index.md %} +[lesson-reference]: {{ relative_root_path }}{% link reference.md %} +[lesson-setup]: {{ relative_page_root }}{% link setup.md %} [mit-license]: https://opensource.org/licenses/mit-license.html [morea]: https://morea-framework.github.io/ [numfocus]: https://numfocus.org/ From 8a4dfc8340be9884c27600cf810bee1b8082d5e7 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Mon, 3 Dec 2018 22:41:08 +0000 Subject: [PATCH 060/185] CONTRIBUTING.md: remove repetitive text --- bin/boilerplate/CONTRIBUTING.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/bin/boilerplate/CONTRIBUTING.md b/bin/boilerplate/CONTRIBUTING.md index 96e81582..7925ceff 100644 --- a/bin/boilerplate/CONTRIBUTING.md +++ b/bin/boilerplate/CONTRIBUTING.md @@ -1,6 +1,6 @@ # Contributing -[The Carpentries][c-site]([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source projects, +[The Carpentries][c-site] ([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) are open source projects, and we welcome contributions of all kinds: new lessons, fixes to existing material, @@ -14,7 +14,7 @@ you agree that we may redistribute your work under [our license](LICENSE.md). In exchange, we will address your issues and/or assess your change proposal as promptly as we can, and help you become a member of our community. -Everyone involved in [The Carpentries][c-site]([Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]) +Everyone involved in [The Carpentries][c-site] agrees to abide by our [code of conduct](CODE_OF_CONDUCT.md). ## How to Contribute @@ -149,4 +149,3 @@ You can also [reach us by email][email]. [c-site]: https://carpentries.org/ [lc-site]: https://librarycarpentry.org/ [lc-issues]: https://github.com/issues?q=user%3Alibrarycarpentry - From 487c4b82635d1225eb8ee8f4e4f1d7a32df40faa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Thu, 6 Dec 2018 11:38:26 -0500 Subject: [PATCH 061/185] add meta tag for carpentry type --- _layouts/workshop.html | 1 + 1 file changed, 1 insertion(+) diff --git a/_layouts/workshop.html b/_layouts/workshop.html index cf57cdf4..2d28a6f6 100644 --- a/_layouts/workshop.html +++ b/_layouts/workshop.html @@ -20,6 +20,7 @@ + {% endif %} From ee234199a72c40f7c2b1ce1e7e3e809a92d715aa Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Fri, 7 Dec 2018 16:54:49 -0600 Subject: [PATCH 062/185] .travis.yml: use Python 3.7 Signed-off-by: Maxim Belkin --- bin/boilerplate/.travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/boilerplate/.travis.yml b/bin/boilerplate/.travis.yml index d30f78a4..de304aca 100644 --- a/bin/boilerplate/.travis.yml +++ b/bin/boilerplate/.travis.yml @@ -1,6 +1,6 @@ # dist: trusty # Ubuntu 14.04 language: python -python: 3.6 +python: 3.7 branches: only: - gh-pages From 8b7eae1a432b77efe41d3f57bcfb84de3f4a8d93 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Fri, 7 Dec 2018 14:55:51 -0600 Subject: [PATCH 063/185] links.md: sync with downstream (lesson-example) --- _includes/links.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/_includes/links.md b/_includes/links.md index 94fc15f3..4e87b32a 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -18,6 +18,7 @@ [jekyll-windows]: http://jekyll-windows.juthilo.com/ [jekyll]: https://jekyllrb.com/ [jupyter]: https://jupyter.org/ +[kramdown]: https://kramdown.gettalong.org/ [lc-lessons]: https://librarycarpentry.org/lessons/ [lesson-example]: https://carpentries.github.io/lesson-example/ [mit-license]: https://opensource.org/licenses/mit-license.html @@ -36,5 +37,6 @@ [styles]: https://github.com/carpentries/styles/ [swc-lessons]: https://software-carpentry.org/lessons/ [swc-releases]: https://github.com/swcarpentry/swc-releases +[training]: https://carpentries.github.io/instructor-training/ [workshop-repo]: {{ site.workshop_repo }} [yaml]: http://yaml.org/ From cb4e1ddab6472c812eefb3231bf4deb614f0fd37 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Wed, 12 Dec 2018 02:14:08 -0600 Subject: [PATCH 064/185] lesson_check.py: require _config.yml too --- bin/lesson_check.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/lesson_check.py b/bin/lesson_check.py index 84c28f37..78d78b2d 100755 --- a/bin/lesson_check.py +++ b/bin/lesson_check.py @@ -35,6 +35,7 @@ '%/README.md': False, '%/_extras/discuss.md': True, '%/_extras/guide.md': True, + '%/_config.yml': True, '%/index.md': True, '%/reference.md': True, '%/setup.md': True, From e488057711624b339109f456228ac68df9a0771a Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Wed, 12 Dec 2018 02:13:23 -0600 Subject: [PATCH 065/185] knit_lessons.sh: require 2 inputs exactly --- bin/knit_lessons.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/knit_lessons.sh b/bin/knit_lessons.sh index 194f1242..141c136a 100755 --- a/bin/knit_lessons.sh +++ b/bin/knit_lessons.sh @@ -3,6 +3,6 @@ # Only try running R to translate files if there are some files present. # The Makefile passes in the names of files. -if [ $# -ne 0 ] ; then +if [ $# -eq 2 ] ; then Rscript -e "source('bin/generate_md_episodes.R')" "$@" fi From 9abaca8cc52eb2f39be0d4a290a637e1906aaebf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Thu, 20 Dec 2018 13:12:29 -0500 Subject: [PATCH 066/185] update link for coc reporting --- _includes/links.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_includes/links.md b/_includes/links.md index 2e4b67a8..7ab32a9f 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -1,7 +1,7 @@ [cc-by-human]: https://creativecommons.org/licenses/by/4.0/ [cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode [ci]: http://communityin.org/ -[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#reporting-guidelines +[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#incident-reporting-guidelines [coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html [concept-maps]: https://carpentries.github.io/instructor-training/05-memory/ [contrib-covenant]: https://contributor-covenant.org/ From 98c4617f468c3023f87e1e36358f8df1c149e257 Mon Sep 17 00:00:00 2001 From: Gerard Capes Date: Wed, 23 Jan 2019 14:38:42 +0000 Subject: [PATCH 067/185] 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). --- .github/ISSUE_TEMPLATE.md | 2 +- .github/PULL_REQUEST_TEMPLATE.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md index 9dafd7fb..05fb019f 100644 --- a/.github/ISSUE_TEMPLATE.md +++ b/.github/ISSUE_TEMPLATE.md @@ -1,4 +1,4 @@ -Please delete the text below before submitting your contribution. +Please delete this line and the text below before submitting your contribution. --- diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 6cc9e527..f5a44c8c 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,4 +1,4 @@ -Please delete the text below before submitting your contribution. +Please delete this line and the text below before submitting your contribution. --- From ab8decae6cfafc87040ffec0d387cc9e403756dc Mon Sep 17 00:00:00 2001 From: Alex Whan Date: Wed, 6 Feb 2019 16:26:04 +1100 Subject: [PATCH 068/185] lesson_check.py: remove _config.yml from the list of required files Pull Request: carpentries/styles#388 --- bin/lesson_check.py | 1 - 1 file changed, 1 deletion(-) diff --git a/bin/lesson_check.py b/bin/lesson_check.py index 78d78b2d..84c28f37 100755 --- a/bin/lesson_check.py +++ b/bin/lesson_check.py @@ -35,7 +35,6 @@ '%/README.md': False, '%/_extras/discuss.md': True, '%/_extras/guide.md': True, - '%/_config.yml': True, '%/index.md': True, '%/reference.md': True, '%/setup.md': True, From b3e88ce20aa77f474e10fed622f07d114d3194a0 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Fri, 1 Mar 2019 13:03:05 -0600 Subject: [PATCH 069/185] Colorize all boxes Use the same colors but apply 12.5% opacity. Solution boxes use 30% opacity --- assets/css/lesson.scss | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index 6e9e81ea..e6627afb 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -129,6 +129,17 @@ $codeblock-padding: 5px !default; font-size: 18px; } +.challenge { background-color: #eec27520; } +.callout { background-color: #f4fd9c20; } +.challenge { background-color: #eec27520; } +.checklist { background-color: #dfd2a020; } +.discussion { background-color: #eec27520; } +.keypoints { background-color: #7ae78e20; } +.objectives { background-color: #daee8420; } +.prereq { background-color: #9cd6dc20; } +.solution { background-color: #ded4b94d; } +.testimonial { background-color: #fc8dc120; } + blockquote p { margin: 5px; } From 8bda280836c6cdf30d8b072124aa111d7a2bfe11 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Wed, 6 Mar 2019 13:56:33 -0600 Subject: [PATCH 070/185] Improve contrast of code elements --- assets/css/lesson.scss | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index e6627afb..f13beb8c 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -151,7 +151,7 @@ blockquote p { code { white-space: nowrap; padding: 2px 5px; - color: #3d90d9; + color: #006cad; background-color: #e7e7e7; } From 514fb469241fff95afaa44afe2c0551964879d92 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Mon, 11 Mar 2019 14:17:31 -0500 Subject: [PATCH 071/185] Prefix code blocks with language names Also, improve contrast of comments Signed-off-by: Maxim Belkin --- assets/css/bootstrap.css | 5 ++-- assets/css/lesson.scss | 51 ++++++++++++++++++++++------------------ assets/css/syntax.css | 12 +++++----- 3 files changed, 36 insertions(+), 32 deletions(-) diff --git a/assets/css/bootstrap.css b/assets/css/bootstrap.css index 6704f50c..688158a8 100644 --- a/assets/css/bootstrap.css +++ b/assets/css/bootstrap.css @@ -1562,15 +1562,14 @@ kbd kbd { pre { display: block; padding: 9.5px; - margin: 0 0 10px; + margin: 0; font-size: 13px; line-height: 1.42857143; color: inherit; /* #333; -- CHANGE -- */ word-break: break-all; word-wrap: break-word; background-color: #f5f5f5; - border: 1px solid #ccc; - border-radius: 4px; + border: none; } pre code { padding: 0; diff --git a/assets/css/lesson.scss b/assets/css/lesson.scss index f13beb8c..e0c34c99 100644 --- a/assets/css/lesson.scss +++ b/assets/css/lesson.scss @@ -30,8 +30,9 @@ $color-testimonial: #fc8dc1 !default; @mixin cdSetup($color) { color: $color; + border: solid 0.5px $color; border-left: solid 5px $color; - margin: 15px 0; + margin: 15px 5px 10px 0; border-radius: 4px 0 0 4px; } @@ -46,24 +47,32 @@ $color-testimonial: #fc8dc1 !default; .r, .language-r { @include cdSetup($color-source); } .sql, .language-sql { @include cdSetup($color-source); } -.error pre, -.output pre, -.source pre, -.bash pre, -.language-bash pre, -.make pre, -.language-make pre, -.matlab pre, -.language-matlab pre, -.python pre, -.language-python pre, -.r pre, -.language-r pre, -.sql pre , -.language-sql pre { - border-radius: 0 4px 4px 0; +.error::before, +.output::before, +.source::before, +.bash::before, .language-bash::before, +.make::before, .language-make::before, +.matlab::before, .language-matlab::before, +.python::before, .language-python::before, +.r::before, .language-r::before, +.sql::before, .language-sql::before { + background-color: #f2eff6; + display: block; + font-weight: bold; + padding: 5px 10px; } +.error::before { background-color: #ffebe6; content: "Error"; } +.output::before { background-color: #efefef; content: "Output"; } +.source::before { content: "Code"; } +.bash::before, .language-bash::before { content: "Bash"; } +.make::before, .language-make::before { content: "Make"; } +.matlab::before, .language-matlab::before { content: "Matlab"; } +.python::before, .language-python::before { content: "Python"; } +.r::before, .language-r::before { content: "R"; } +.sql::before, .language-sql::before { content: "SQL"; } + + //---------------------------------------- // Specialized blockquote environments for learning objectives, callouts, etc. //---------------------------------------- @@ -75,16 +84,12 @@ $codeblock-padding: 5px !default; $gradientcolor1: $color; $gradientcolor2: scale-color($color, $lightness: 10%); - padding-left: $codeblock-padding; - padding-top: 0; - padding-bottom: 0; - padding-right: 0; + padding: 0 0 $codeblock-padding $codeblock-padding; border: 1px solid; border-color: $color; border-radius: 4px; - padding-bottom: $codeblock-padding; - margin: 15px 0; + margin: 15px 5px 10px 0; h2 { padding-top: $codeblock-padding; diff --git a/assets/css/syntax.css b/assets/css/syntax.css index 572069c1..83a7e979 100644 --- a/assets/css/syntax.css +++ b/assets/css/syntax.css @@ -1,15 +1,15 @@ .highlight .hll { background-color: #ffffcc } .highlight { background: #f8f8f8; } -.highlight .c { color: #408080; font-style: italic } /* Comment */ +.highlight .c { color: #387d7d; font-style: italic } /* Comment */ .highlight .err { border: 1px solid #FF0000 } /* Error */ .highlight .k { color: #008000; font-weight: bold } /* Keyword */ .highlight .o { color: #666666 } /* Operator */ -.highlight .ch { color: #408080; font-style: italic } /* Comment.Hashbang */ -.highlight .cm { color: #408080; font-style: italic } /* Comment.Multiline */ +.highlight .ch { color: #387d7d; font-style: italic } /* Comment.Hashbang */ +.highlight .cm { color: #387d7d; font-style: italic } /* Comment.Multiline */ .highlight .cp { color: #BC7A00 } /* Comment.Preproc */ -.highlight .cpf { color: #408080; font-style: italic } /* Comment.PreprocFile */ -.highlight .c1 { color: #408080; font-style: italic } /* Comment.Single */ -.highlight .cs { color: #408080; font-style: italic } /* Comment.Special */ +.highlight .cpf { color: #387d7d; font-style: italic } /* Comment.PreprocFile */ +.highlight .c1 { color: #387d7d; font-style: italic } /* Comment.Single */ +.highlight .cs { color: #387d7d; font-style: italic } /* Comment.Special */ .highlight .gd { color: #A00000 } /* Generic.Deleted */ .highlight .ge { font-style: italic } /* Generic.Emph */ .highlight .gr { color: #FF0000 } /* Generic.Error */ From cd761b2951134d4a5311d002b5999a3a3f255605 Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Tue, 12 Mar 2019 12:30:44 -0500 Subject: [PATCH 072/185] Fix contrast of links in challenge blocks --- assets/css/bootstrap.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/css/bootstrap.css b/assets/css/bootstrap.css index 688158a8..58a33dde 100644 --- a/assets/css/bootstrap.css +++ b/assets/css/bootstrap.css @@ -1098,7 +1098,7 @@ textarea { line-height: inherit; } a { - color: #337ab7; + color: #2876b5; text-decoration: none; } a:hover, From 124dea1b44cab5e00ba3ca60e916b43a717e6e12 Mon Sep 17 00:00:00 2001 From: Ana Costa <29195893+anacost@users.noreply.github.com> Date: Wed, 20 Mar 2019 19:43:23 +0000 Subject: [PATCH 073/185] 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. --- bin/boilerplate/README.md | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/bin/boilerplate/README.md b/bin/boilerplate/README.md index 43a6b722..22a3f79a 100644 --- a/bin/boilerplate/README.md +++ b/bin/boilerplate/README.md @@ -2,7 +2,7 @@ [![Create a Slack Account with us](https://img.shields.io/badge/Create_Slack_Account-The_Carpentries-071159.svg)](https://swc-slack-invite.herokuapp.com/) -FIXME +This repository generates the corresponding lesson website from [The Carpentries](https://carpentries.org/) repertoire of lessons. ## Contributing @@ -13,9 +13,21 @@ We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTR the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even how to write new episodes. +Please see the current list of [issues][] for ideas for contributing to this +repository. For making your contribution, we use the GitHub flow, which is +nicely explained in the chapter [Contributing to a Project](http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git +by Scott Chacon. +Look for the tag ![good_first_issue](https://img.shields.io/badge/-good%20first%20issue-yellowgreen.svg). This indicates that the mantainers will welcome a pull request fixing this issue. + + ## Maintainer(s) -* FIXME +Current maintainers of this lesson are + +* +* +* + ## Authors From 5fc0f39109587631c41aae6ca10dfc42d2655b31 Mon Sep 17 00:00:00 2001 From: Ana Costa <29195893+anacost@users.noreply.github.com> Date: Thu, 21 Mar 2019 09:28:22 +0000 Subject: [PATCH 074/185] gold colour to badge gold looks more like the yellow from the original badge --- bin/boilerplate/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/boilerplate/README.md b/bin/boilerplate/README.md index 22a3f79a..2554ac8f 100644 --- a/bin/boilerplate/README.md +++ b/bin/boilerplate/README.md @@ -17,7 +17,7 @@ Please see the current list of [issues][] for ideas for contributing to this repository. For making your contribution, we use the GitHub flow, which is nicely explained in the chapter [Contributing to a Project](http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git by Scott Chacon. -Look for the tag ![good_first_issue](https://img.shields.io/badge/-good%20first%20issue-yellowgreen.svg). This indicates that the mantainers will welcome a pull request fixing this issue. +Look for the tag ![good_first_issue](https://img.shields.io/badge/-good%20first%20issue-gold.svg). This indicates that the mantainers will welcome a pull request fixing this issue. ## Maintainer(s) From 962e3d9cd0ef8b4a7629880bc894f4940a1fe303 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Thu, 21 Mar 2019 11:54:01 +0100 Subject: [PATCH 075/185] add 'FIXME' so they will be picked up by checks --- bin/boilerplate/README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/bin/boilerplate/README.md b/bin/boilerplate/README.md index 2554ac8f..ed47f43c 100644 --- a/bin/boilerplate/README.md +++ b/bin/boilerplate/README.md @@ -13,7 +13,7 @@ We'd like to ask you to familiarize yourself with our [Contribution Guide](CONTR the [more detailed guidelines][lesson-example] on proper formatting, ways to render the lesson locally, and even how to write new episodes. -Please see the current list of [issues][] for ideas for contributing to this +Please see the current list of [issues][FIXME] for ideas for contributing to this repository. For making your contribution, we use the GitHub flow, which is nicely explained in the chapter [Contributing to a Project](http://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project) in Pro Git by Scott Chacon. @@ -24,9 +24,9 @@ Look for the tag ![good_first_issue](https://img.shields.io/badge/-good%20first% Current maintainers of this lesson are -* -* -* +* FIXME +* FIXME +* FIXME ## Authors From 853155cd12ad88c42b5a4d1f25b5a8b4054b644e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Wed, 27 Mar 2019 17:13:57 +0100 Subject: [PATCH 076/185] use xenial on travis --- bin/boilerplate/.travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/boilerplate/.travis.yml b/bin/boilerplate/.travis.yml index de304aca..4f23be8c 100644 --- a/bin/boilerplate/.travis.yml +++ b/bin/boilerplate/.travis.yml @@ -1,4 +1,4 @@ -# dist: trusty # Ubuntu 14.04 +dist: xenial # Ubuntu 16.04 (required for python 3.7) language: python python: 3.7 branches: From 51d615d0f9fc12535adf932b3abf1cb94bd757ec Mon Sep 17 00:00:00 2001 From: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com> Date: Thu, 18 Apr 2019 16:41:19 +0200 Subject: [PATCH 077/185] bin/lesson_check.py: avoid inconsistent grammar Pull Request: carpentries/styles#396 --- bin/lesson_check.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/lesson_check.py b/bin/lesson_check.py index 84c28f37..b0b5581a 100755 --- a/bin/lesson_check.py +++ b/bin/lesson_check.py @@ -342,7 +342,7 @@ def check_line_lengths(self): n > MAX_LINE_LEN) and (not l.startswith('!'))] self.reporter.check(not over, self.filename, - 'Line(s) are too long: {0}', + 'Line(s) too long: {0}', ', '.join([str(i) for i in over])) def check_trailing_whitespace(self): From 19885f709c30028a447e4bc03aa3d0b5a3acccbb Mon Sep 17 00:00:00 2001 From: Maxim Belkin Date: Thu, 18 Apr 2019 14:26:28 -0500 Subject: [PATCH 078/185] util.py: hot fix for YAML loader --- bin/util.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/util.py b/bin/util.py index 522f5dfc..f9dc12f3 100644 --- a/bin/util.py +++ b/bin/util.py @@ -144,7 +144,7 @@ def split_metadata(path, text): metadata_raw = pieces[1] text = pieces[2] try: - metadata_yaml = yaml.load(metadata_raw) + metadata_yaml = yaml.load(metadata_raw, Loader=yaml.FullLoader) except yaml.YAMLError as e: print('Unable to parse YAML header in {0}:\n{1}'.format( path, e), file=sys.stderr) @@ -161,7 +161,7 @@ def load_yaml(filename): try: with open(filename, 'r') as reader: - return yaml.load(reader) + return yaml.load(reader, Loader=yaml.FullLoader) except (yaml.YAMLError, IOError) as e: print('Unable to load YAML file {0}:\n{1}'.format( filename, e), file=sys.stderr) From 29dc6c4785278ecbf7dd67988c83d58a49dd7b44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Fri, 26 Apr 2019 14:51:30 -0400 Subject: [PATCH 079/185] add data-checker-ignore attributes to links that only work on GitHub --- _includes/lesson_footer.html | 4 ++-- _includes/navbar.html | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 621243df..9f669db1 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -36,11 +36,11 @@ Edit on GitHub {% endif %} / - Contributing + Contributing / Source / - Cite + Cite / Contact
diff --git a/_includes/navbar.html b/_includes/navbar.html index 40939226..cc9b884a 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -77,10 +77,10 @@
  • License
  • {% if page.source %} {% if page.source == "Rmd" %} -
  • Improve this page
  • +
  • Improve this page
  • {% endif %} {% else %} -
  • Improve this page
  • +
  • Improve this page
  • {% endif %} From 766155a9b5fe0140648fc63665478c7c2d3316c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Fri, 26 Apr 2019 14:57:59 -0400 Subject: [PATCH 080/185] add data-checker-ignore attributes to footer links --- _includes/lesson_footer.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 9f669db1..03091a7c 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -30,10 +30,10 @@