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* bin/lesson_check.py: avoid inconsistent grammar Pull Request: carpentries/styles#396 * util.py: hot fix for YAML loader * add data-checker-ignore attributes to links that only work on GitHub * add data-checker-ignore attributes to footer links * make title show episode title first * use ndash as separator display it only if both `page.title` and `site.title` are defined. * upgrade to bootstrap 3.4.1 * update coc incident reporting link * Update PULL_REQUEST_TEMPLATE.md * Update ISSUE_TEMPLATE.md * links.md: fix lesson-setup link * links.md: include base_path.html * aio.md: multiple improvements Pull Request: carpentries/styles#406 * change all-in-one file to have the same 'depth' as episode files * move the core script of aio.md into _includes/aio-script.md * include comment to inform maintainers to not edit the file * move aio.md to the root of styles repository * [fix #408] remove aio from files that need to be initialized * lesson-check: exclude aio.md, fix read_references * bump jekyll version to match github pages version https://pages.github.com/versions/ * Callout (and other) blocks: proper font size, margins * Use darker purple for code blocks * Use 1px borders: fix Google Chrome & Edge See swcarpentry/git-novice#662 (comment) * specify language based on engine - fix swcarpentry/r-novice-inflammation#436 * Ignore Jekyll 4's cache See https://jekyllrb.com/news/2019/08/20/jekyll-4-0-0-released/#cache-all-the-things- & https://github.com/jekyll/jekyll/releases/tag/v4.0.0 It appears during `make site` & `make serve`. * assets/css/lesson.scss: add proper padding to the top of paragraphs in blockquotes (#425) * restore lost CSS settings * Manual ordering of episodes and extras Co-authored-by: stamper <[email protected]> * [fix carpentries/workshop-template#513] remove site.title outside lessons * update survey links * Switch to Liquid comments HTML comments end up in the generated HTML pages: they're not displayed by the browsers but they're still present there. Liquid comments do not end up in the generated HTML pages * bin/boilerplate/README.md: fix typo carpentries/styles#441 * Use Jekyll to generate the 'all-in-one' page (carpentries/styles#438) * manual_episode_order.html: fix typo in a comment * Enable 'Sponsor' button on GitHub repos * remove Jekyll command markers from comment block fix carpentries/lesson-example#281 * Forced re-encoding of text to UTF-8, to avoid issues on Windows * Refactored paths to make use of OS agnostic methods * Modified shebang to use python, not python3. * Reverted change of permissiveness on lesson_check * Cleaned leftover debug code and old implementations. * Added PYTHON variable to define executable to run python scripts * Reverted variable names * Removed shebang lines from Python scripts to avoid cross-OS problems * Fixes encoding problem on Windows systems, with minimal changes to existing code. * Silenced output of PYTHON calls * Makefile: detect Python 3 * util.py: remove empty line * Undo optimizations to read_all_markdown These will be submitted in a separate PR * 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. * lesson_initialize: windows compatibility * lesson_check.py: Windows-compatible regular expression pattern * repo_check.py: enforce utf-8 encoding ... for compatibility with Windows * clarify comment on python check block * Makefile: Windows does not like single quotes * test_lesson_check.py: skip unnecessary steps * Makefile: suppress error message on Windows * fix typo in lesson_initialize.py * Makefile: suppress another error message on Windows These '2>/dev/null' are important on Windows because without them a mere `make` stalls. * Makefile: handle MS Store's Python 3 * Makefile: fix syntax in conditional * Makefile: fix two more syntax errors in conditionals * fix urls in _config.yml * use bundler to render lessons * install gems locally * refactor use of docker Co-authored-by: Allen Lee <[email protected]> * add @maxim-belkin suggestions * add .bundle to .gitignore * Makefile: Specify shell. Don't include commands.mk * Makefile: use Python to execute repo_check.py * Makefile: improve commands target and commands categories (#450) * Makefile: improve commands target and commands categories * replace 'files' with 'website' * 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 * specify YAML loader Co-authored-by: Daniel McCloy <[email protected]>c * add warning hook + CSS class for Rmd-based lessons (#455) * Update PyPI link * Use carpentries/lesson-docker for docker-serve make rule (#461) * Use renv (#462) * Improve issue template (#463) Co-authored-by: Sarah Brown <[email protected]> * lesson.scss: style tab panels on setup pages (#464) * Improve pull request template (#465) * OS stripe color (#468) * bump ruby version * 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 * 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 <[email protected]> * License is not a copyright. License info ID (#472) * fix AMY's URL * Deprecated use of --path when installing bundle (#473) * add warning blockquote style, carpentries/styles#49 (#475) * Make links in code tags distinguishable (#478) * _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 * repo_check.py: allow URLs not ending with .git (#482) * 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`. * repo_check.py: match https repositories (#483) * Makefile: don't use /bin/bash shell (#484) * [fix carpentries/styles#477] rewrite travis script * add vendor folder to gitignore and _config.yml * OS stripe: adjust line height (#490) * 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. * 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. * only display Episodes drop-down if we have episodes to show (#491) * fix variable name * GitHub Actions: check lesson template (#489) Co-authored-by: Maxim Belkin <[email protected]> Co-authored-by: François Michonneau <[email protected]> * fix: tighten definitions of highlighter (#496) * add three more common languages (#497) * remove unused code highlight classes (#498) * Sync styles first (#494) Co-authored-by: Maxim Belkin <[email protected]> * GitHub Actions: website (#488) * GitHub Actions: better workflow and job names (#500) * GitHub Action: website.yml: don't run in forks (#501) * 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. * lesson.scss: styling for DIVs for embedding Youtube videos (#503) * update link to discuss mailing list (#507) * add default repository to install_required_packages() (#509) * add warning blockquote * Revert "Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages" This reverts commit 2c6b97e, reversing changes made to 53e9913. * add warning code block * update expected reference filename (#508) * lesson.scss: no borders around unrecognized code (#510) * bump ruby version (as specified in github-pages v209) * drop patch version, fix at v1 * removing contractions from CONTRIBUTING (#512) * add image-with-shadow class * _config.yml: mention Carpentries Incubator * Matlab -> MATLAB * set CRAN url if default is "@cran@" This will fix #526 * Fix Ruby style * accept any base filename for Rmd episodes * run R-based lessons in forks This is a modification for #501 * add control structure * 404 page for better learner experience * lesson.scss: wildcard selectors for code blocks * 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 * 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 <[email protected]> * pin ubuntu version to 20.04 (#540) Co-authored-by: Zhian N. Kamvar <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 * lesson-check.py: read `config.yml` only once 1. Read `config.yml` file only once and store the contents in a global variable `CONFIG`. We're currently reading this file twice. 2. Detect lesson life cycle in `main` instead of making `check_config` return it. 3. Replace `using_remote_theme` function with a single test that checks that `remote_theme` keyword is present in `_config.yml` 4. CheckEpisode class: `check` method: move "remote theme test" inside the `check_reference_inclusion`. 5. main: mvoe "remote theme test" inside the `read_references` * 404.md: expand contractions (#620) * Syllabus: add conditional intructor training pre-/post- surveys (#618) Port of carpentries/instructor-training@f488d24 Co-authored-by: François Michonneau <[email protected]> Co-authored-by: François Michonneau <[email protected]> * Navigation bar: allow excluding extras (#617) Port of carpentries/instructor-training@dc1b52a Co-authored-by: maneesha sane <[email protected]> Co-authored-by: maneesha sane <[email protected]> * add styling for lesson in The Carpentries Lab Co-authored-by: Toby Hodges <[email protected]> * remove contractions * remove contraction * remove contraction * remove funding file to use organization's Co-authored-by: Katrin Leinweber <[email protected]> Co-authored-by: Maxim Belkin <[email protected]> Co-authored-by: maneesha sane <[email protected]> Co-authored-by: Rayna M Harris <[email protected]> Co-authored-by: Allen Lee <[email protected]> Co-authored-by: K.E. Koziar <[email protected]> Co-authored-by: stamper <[email protected]> Co-authored-by: Michael Joseph <[email protected]> Co-authored-by: Joao Rodrigues <[email protected]> Co-authored-by: Sarah Brown <[email protected]> Co-authored-by: Anthony Gitter <[email protected]> Co-authored-by: Zhian N. Kamvar <[email protected]> Co-authored-by: Thomas Green <[email protected]> Co-authored-by: ocaisa <[email protected]> Co-authored-by: Joseph Stachelek <[email protected]> Co-authored-by: Renato Alves <[email protected]> Co-authored-by: Henry Schreiner <[email protected]> Co-authored-by: Christina K <[email protected]> Co-authored-by: Kilian <[email protected]> Co-authored-by: Trevor Keller <[email protected]> Co-authored-by: Andrew Reid <[email protected]> Co-authored-by: Bailey Harrington <[email protected]> Co-authored-by: Alan O'Callaghan <[email protected]> Co-authored-by: Benson Muite <[email protected]>
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