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* add image-with-shadow class * Ignore .jekyll-metatada * Speed up builds of R-based lessons R-based lessons might take a while to build because packages need to be compiled from source. RStudio Package Manager has compiled versions of packages for ubuntu distros starting with 16.04: https://packagemanager.rstudio.com/client/#/repos/1/overview I've added the necessary magic in the actions yaml to make it work. * No need for User Agent string * Update repo names * permissive checks for pre-alpha lessons This will fix #533 * bin/lesson_check.py: allow 'language-*' code blocks (#532) * bin/lesson_check.py: allow 'caution' blockquote * avoid ansi color characters from being printed * deploy from "website" action * deploy R-based lessons without using another action * also delete _site * include @zkamvar suggestions Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> * pin ubuntu version to 20.04 (#540) Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> * GitHub Actions: cache required R packages (#534) * add missing parenthesis * Add incubator option for carpentry field. (#542) Closes #541 * .editorconfig: don't trim trailing spaces in markdown * lesson.scss: HTML block carpentries/styles#519 * add patch to clean gh-pages before committing (#545) This will address #544 * Fix Kramdown parser crash ... by using GFM (GitHub-flavored Markdown) parser (`kramdown-parser-gfm`) instead of the default one (`kramdown`). The default one fails to produce an AST (Abstract Syntax Tree) when there is no blank line before the line with the opening code fence. Related: - gettalong/kramdown#530 - Python-Markdown/markdown#807 Fixes: carpentries/styles#543 * bin/util.py: Change ruby executable to "bundle exec ruby" Closes: carpentries/styles#547 * Change link colours (#549) ...to make them distinguishable from regular text. And for accessibility! * bin/workshop_check.py: update default contact email address * Gemfile: add 'webrick' dependency for Ruby 3.0.0 and above Fixes carpentries/styles#552 * lesson_check.py allow for missing life_cycle This will fix carpentries/styles#556 * update with Maxim's suggestion * Add catch for None type code block in lesson_check There are times when the AST is malformed and does not emit a class for the code element. We do not want the parser to crash when this happens, but we also want to notify ourselves that the AST is malformed. This should not result in an error because as we saw in carpentries/styles#543, the parser itself can cause these malformations when the lesson itself renders well. Even though we fixed the previous issue with an updated parser, problems still persist: swcarpentry/r-novice-gapminder#696 (comment) I fully admit that this is a kludge. * fix syntax I've removed the print condition, because it will just result in an error no matter what (sigh) * Makefile: fix 'bundle config' command flags * Makefile: clean target: remove .vendor, .bundle, Gemfile.lock Clean up: 1. `.vendor` directory where Bundler installs all the gems. 2. `.bundle` directory where Bundler stores its settings. 3. `Gemfile.lock` file generated by the Bundler. * Makefile: silence Docker commands * use Ruby's official GH Actions * Makefile: use SHELL to call bin/knit_lesson.sh * Makefile: fix up PHONY targets * Fix GitHub actions for lessons in Rmarkdown Specifically, set CRAN repository to https://cran.rstudio.com * apply single shadow to image class * use grey shadow instead of transparent black * expand image-with-shadow selection * Makefile: don't fail when Python isn't found * bin/dependencies.R: handle 'no packages were specified' error Fixes the following issue: ``` $ make site lib paths: /Library/Frameworks/R.framework/Versions/3.5/Resources/library Error in install.packages(missing_pkgs, lib = lib, repos = repos) : no packages were specified Calls: install_required_packages -> install.packages Execution halted make: *** [install-rmd-deps] Error 1 ``` * Don't check links.md in lessons that use remote theme Fixes carpentries/styles#570 * add link references to code_of_conduct.md (#572) * Update links.md * add source_dir argument This will fix carpentries/styles#576 * Improved relative_root_path * update contributing guide * add further languages for box titles (#580) Will be useful for HPC-Carpentry lessons, GPU programming lesson as well as Julia lessons which are currently in the incubator. * bin/lesson_check.py: allow comments and empty lines in links.md * bin/lesson_check.py: one more fix for using_remote_theme() * Template workflow: add two more lessons * add make lesson-check-all step * Set working directory for the 'make site' step * Template workflow: smarter syncing with the styles repo Current syncing procedure that used in the Template workflow fails for: 1. Lessons that are, in fact, nsync with the styles repo. 2. For lessons that use The Carpentries' remote theme and have deleted some of the files. This PR makes this step a little bit more intelligent and takes into account the above two scenarios. * Apply Zhian's suggestions Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> * add math support with katex (#573) * bin/util.py: remove unused 'IMAGE_FILE_SUFFIX' var (#590) It should've been removed in 7e835fd. * bin/lesson_check.py: use proper function * bin/lesson_check.py: allow exceptions to line length limit Allow lines that contain a single image or a single link to go over the suggested line length limit. * lesson_check.py: harden single-line image/link pattern This change hardens the pattern that matches single-line image or link: 1. It extends the pattern to be matched in a heading 2. It allows the line to contain {: ...} customizations 3. It allows the line to end with \ * lesson_check.py: relax P_LINK_IMAGE_LINE pattern This PR allows up to 3 non-word (`\W` in Python's `re`-speak) characters in the beginning and end of the pattern that matches links and images. This is to allow lesson developers place punctuation marks, parentheses, or other symbols before or after the link or image on the same line in Markdown. * bin/util.py: Factor out reporter class. Define __all__ * Don't force hostname into relative_root_path * lesson_check.py: add a comment about importing * from a package Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> * lesson.scss: define 'inline' class for images Define `inline` class for images that should not be displayed as block elements. By appending `{:class="inline"}` or `{: .inline}` to the image definition in Markdown, one can create an inline image that doesn't break the current line and is embedded in the paragraph. Useful for showing special symbols and hieroglyphs that we can't display by other means. * Fix Reporter class imports * update R dependency search; Allow Bioconductor packages (#600) * Automatically add deep anchor links using AnchorJS * Makefile: require index.md (#607) * Makefile: docker-serve target: ensure Docker is installed (#608) * Fix broken "How to contribute" link * lesson_check.py: report check status at the end * util.py: load_yaml: Don't fail when it's not necessary Also, make 'require()' function not fail by default. The only case where we really need to fail is when 'kramdown' parser is not specified. This is a highly unlikely scenario, tbh (because arguments to `lesson_check.py` are set in the Makefile), but we can think about reworking/optimizing this part later. * lesson_check.py: fix error message for the 'defaults' check * lesson_check.py: use proper regex for matching episode files Co-authored-by: Toby Hodges <tbyhdgs@gmail.com> Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com> Co-authored-by: François Michonneau <francois.michonneau@gmail.com> Co-authored-by: Trevor Keller <trevor.keller@gmail.com> Co-authored-by: Renato Alves <alves.rjc@gmail.com> Co-authored-by: Andrew Reid <andrew.reid@nist.gov> Co-authored-by: Bailey Harrington <baileythegreen@gmail.com> Co-authored-by: Michael Joseph <josephmje.22@gmail.com> Co-authored-by: Alan O'Callaghan <alan.ocallaghan@outlook.com> Co-authored-by: Benson Muite <bkmgit@users.noreply.github.com> Co-authored-by: K.E. Koziar <katherine.koziar@ucr.edu>
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