From b952d850a4a20ed62954db0cb802d05a1bc8d381 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fran=C3=A7ois=20Michonneau?= Date: Fri, 10 Sep 2021 17:13:21 +0200 Subject: [PATCH] 20210909 styles upgrade (#569) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * 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 https://github.com/swcarpentry/git-novice/pull/662#issuecomment-499555724 * 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 * [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 * 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 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 * 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 * 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 Co-authored-by: François Michonneau * 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 * 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 2c6b97e57dce86830bdbde8d9f8a871c0b46a035, reversing changes made to 53e991355f617c108912a21eae00cfe46823aca4. * 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 * pin ubuntu version to 20.04 (#540) Co-authored-by: Zhian N. Kamvar * 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 https://github.com/carpentries/styles/issues/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 https://github.com/carpentries/styles/issues/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: https://github.com/swcarpentry/r-novice-gapminder/pull/696#issuecomment-796265728 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 https://github.com/carpentries/styles/issues/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 * 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 * 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@f488d248d55637f05bea3f9592451f887a3a7c83 Co-authored-by: François Michonneau Co-authored-by: François Michonneau * Navigation bar: allow excluding extras (#617) Port of carpentries/instructor-training@dc1b52ab11fa7d247db32df0523e0656faf74dc5 Co-authored-by: maneesha sane Co-authored-by: maneesha sane * add styling for lesson in The Carpentries Lab Co-authored-by: Toby Hodges * remove contractions * remove contraction * remove contraction * remove funding file to use organization's Co-authored-by: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com> Co-authored-by: Maxim Belkin Co-authored-by: maneesha sane Co-authored-by: Rayna M Harris Co-authored-by: Allen Lee Co-authored-by: K.E. Koziar Co-authored-by: stamper Co-authored-by: Michael Joseph Co-authored-by: Joao Rodrigues Co-authored-by: Sarah Brown Co-authored-by: Anthony Gitter Co-authored-by: Zhian N. Kamvar Co-authored-by: Thomas Green Co-authored-by: ocaisa Co-authored-by: Joseph Stachelek Co-authored-by: Renato Alves Co-authored-by: Henry Schreiner Co-authored-by: Christina K Co-authored-by: Kilian Co-authored-by: Trevor Keller Co-authored-by: Andrew Reid Co-authored-by: Bailey Harrington Co-authored-by: Alan O'Callaghan Co-authored-by: Benson Muite --- .editorconfig | 1 + .github/ISSUE_TEMPLATE.md | 20 ++- .github/PULL_REQUEST_TEMPLATE.md | 20 ++- .github/workflows/template.yml | 184 ++++++++++++++++++++ .github/workflows/website.yml | 122 ++++++++++++++ .gitignore | 10 +- 404.md | 25 +++ CODE_OF_CONDUCT.md | 3 +- Gemfile | 14 ++ Makefile | 178 +++++++++++++------- _includes/aio-script.md | 51 +++--- _includes/all_keypoints.html | 8 +- _includes/base_path.html | 54 +++--- _includes/episode_keypoints.html | 9 +- _includes/episode_navbar.html | 14 +- _includes/episode_overview.html | 50 +++++- _includes/javascript.html | 28 ++++ _includes/lesson_footer.html | 2 +- _includes/life_cycle.html | 14 +- _includes/links.md | 5 +- _includes/main_title.html | 7 + _includes/manual_episode_order.html | 116 +++++++++++++ _includes/navbar.html | 25 ++- _includes/syllabus.html | 36 +++- _layouts/base.html | 6 +- aio.md | 4 +- assets/css/bootstrap.css | 4 +- assets/css/katex.min.css | 1 + assets/css/lesson.scss | 88 ++++++++-- assets/img/carpentrieslab.svg | 249 ++++++++++++++++++++++++++++ assets/js/anchor.min.js | 9 + assets/js/jquery.min.js | 8 +- assets/js/jquery.min.map | 2 +- assets/js/katex-auto-render.min.js | 1 + assets/js/katex.min.js | 1 + assets/js/lesson.js | 4 +- bin/boilerplate/.travis.yml | 64 +++++-- bin/boilerplate/CONTRIBUTING.md | 16 +- bin/boilerplate/README.md | 2 +- bin/boilerplate/_config.yml | 22 +-- bin/boilerplate/_extras/figures.md | 21 ++- bin/chunk-options.R | 26 ++- bin/dependencies.R | 107 ++++++++++++ bin/generate_md_episodes.R | 72 ++++---- bin/install_r_deps.sh | 1 + bin/lesson_check.py | 163 ++++++++++++------ bin/lesson_initialize.py | 14 +- bin/markdown_ast.rb | 10 +- bin/repo_check.py | 9 +- bin/reporter.py | 75 +++++++++ bin/run-make-docker-serve.sh | 10 ++ bin/test_lesson_check.py | 10 +- bin/util.py | 117 +++---------- bin/workshop_check.py | 9 +- 54 files changed, 1688 insertions(+), 433 deletions(-) create mode 100644 .github/workflows/template.yml create mode 100644 .github/workflows/website.yml create mode 100644 404.md create mode 100644 Gemfile create mode 100644 _includes/manual_episode_order.html create mode 100644 assets/css/katex.min.css create mode 100644 assets/img/carpentrieslab.svg create mode 100644 assets/js/anchor.min.js create mode 100644 assets/js/katex-auto-render.min.js create mode 100644 assets/js/katex.min.js create mode 100644 bin/dependencies.R create mode 100755 bin/install_r_deps.sh mode change 100755 => 100644 bin/lesson_check.py mode change 100755 => 100644 bin/lesson_initialize.py mode change 100755 => 100644 bin/repo_check.py create mode 100644 bin/reporter.py create mode 100755 bin/run-make-docker-serve.sh mode change 100755 => 100644 bin/test_lesson_check.py mode change 100755 => 100644 bin/workshop_check.py diff --git a/.editorconfig b/.editorconfig index 1d7d564d5..5bf4860b1 100644 --- a/.editorconfig +++ b/.editorconfig @@ -9,6 +9,7 @@ trim_trailing_whitespace = true indent_size = 2 indent_style = space max_line_length = 100 # Please keep this in sync with bin/lesson_check.py! +trim_trailing_whitespace = false # keep trailing spaces in markdown - 2+ spaces are translated to a hard break (
) [*.r] max_line_length = 80 diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md index ec2d4fe13..077de4cf3 100644 --- a/.github/ISSUE_TEMPLATE.md +++ b/.github/ISSUE_TEMPLATE.md @@ -1,11 +1,21 @@ -Please delete this line and the text below before submitting your contribution. +
+Instructions ---- +Thanks for contributing! :heart: -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 contribution is for instructor training, please email the link to this contribution to +checkout@carpentries.org so we can record your progress. You've completed your contribution +step for instructor checkout 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 The Carpentries Team at team@carpentries.org. +Keep in mind that **lesson maintainers are volunteers** and it may take them some time to +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 The Carpentries Team at team@carpentries.org. ---- +You may delete these instructions from your comment. + +\- The Carpentries +
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index d9eb8c50a..07aadca2c 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,9 +1,19 @@ -Please delete this line and the text below before submitting your contribution. +
+Instructions ---- +Thanks for contributing! :heart: -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 contribution is for instructor training, please email the link to this contribution to +checkout@carpentries.org so we can record your progress. You've completed your contribution +step for instructor checkout by submitting this contribution! -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 The Carpentries Team at team@carpentries.org. +Keep in mind that **lesson maintainers are volunteers** and it may take them some time to +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 The Carpentries Team at team@carpentries.org. ---- +You may delete these instructions from your comment. + +\- The Carpentries +
diff --git a/.github/workflows/template.yml b/.github/workflows/template.yml new file mode 100644 index 000000000..9ff0d6628 --- /dev/null +++ b/.github/workflows/template.yml @@ -0,0 +1,184 @@ +name: Test template +on: + push: + branches: gh-pages + pull_request: +jobs: + check-template: + name: ${{ matrix.lesson-name }} (${{ matrix.os-name }}) + if: github.repository == 'carpentries/styles' + runs-on: ${{ matrix.os }} + continue-on-error: ${{ matrix.experimental }} + strategy: + fail-fast: false + matrix: + lesson: [swcarpentry/shell-novice, datacarpentry/r-intro-geospatial, librarycarpentry/lc-git] + os: [ubuntu-20.04, macos-latest, windows-latest] + experimental: [false] + include: + - os: ubuntu-20.04 + os-name: Linux + - os: macos-latest + os-name: macOS + - os: windows-latest + os-name: Windows + - lesson: swcarpentry/shell-novice + lesson-name: (SWC) Shell novice + - lesson: datacarpentry/r-intro-geospatial + lesson-name: (DC) R Intro Geospatial + - lesson: librarycarpentry/lc-git + lesson-name: (LC) Intro to Git + - lesson: datacarpentry/astronomy-python + lesson-name: (DC) Foundations of Astronomical Data Science + experimental: true + os: ubuntu-20.04 + os-name: Linux + - lesson: carpentries/lesson-example + lesson-name: (CP) Lesson Example + experimental: false + os: ubuntu-20.04 + os-name: Linux + defaults: + run: + shell: bash # forces 'Git for Windows' on Windows + env: + RSPM: 'https://packagemanager.rstudio.com/cran/__linux__/focal/latest' + steps: + - name: Set up Ruby + uses: ruby/setup-ruby@v1 + with: + ruby-version: '2.7' + bundler-cache: true + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: '3.x' + + - name: Install GitHub Pages, Bundler, and kramdown gems + run: | + gem install github-pages bundler kramdown kramdown-parser-gfm + + - name: Install Python modules + run: | + if [[ $RUNNER_OS == macOS || $RUNNER_OS == Linux ]]; then + python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests + elif [[ $RUNNER_OS == Windows ]]; then + python -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests + fi + + - name: Checkout the ${{ matrix.lesson }} lesson + uses: actions/checkout@master + with: + repository: ${{ matrix.lesson }} + path: lesson + fetch-depth: 0 + + - name: Sync lesson with carpentries/styles + working-directory: lesson + run: | + echo "::group::Fetch Styles" + if [[ -n "${{ github.event.pull_request.number }}" ]] + then + ref="refs/pull/${{ github.event.pull_request.number }}/head" + else + ref="gh-pages" + fi + + git config --global user.email "team@carpentries.org" + git config --global user.name "The Carpentries Bot" + + git remote add styles https://github.com/carpentries/styles.git + git fetch styles $ref:styles-ref + echo "::endgroup::" + echo "::group::Synchronize Styles" + # Sync up only if necessary + if [[ $(git rev-list --count HEAD..styles-ref) != 0 ]] + then + + # The merge command below might fail for lessons that use remote theme + # https://github.com/carpentries/carpentries-theme + echo "Testing merge using recursive strategy, accepting upstream changes without committing" + if ! git merge -s recursive -Xtheirs --no-commit styles-ref + then + + # Remove "deleted by us, unmerged" files from the staging area. + # these are the files that were removed from the lesson + # but are still present in the carpentries/styles repo + echo "Removing previously deleted files" + git rm $(git diff --name-only --diff-filter=DU) + + # If there are still "unmerged" files, + # let's raise an error and look into this more closely + if [[ -n $(git diff --name-only --diff-filter=U) ]] + then + echo "There were unmerged files in ${{ matrix.lesson-name }}:" + echo "$(git diff --compact-summary --diff-filter=U)" + exit 1 + fi + fi + + echo "Committing changes" + git commit -m "Sync lesson with carpentries/styles" + fi + echo "::endgroup::" + + - name: Look for R-markdown files + id: check-rmd + working-directory: lesson + run: | + echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" + + - name: Set up R + if: steps.check-rmd.outputs.count != 0 + uses: r-lib/actions/setup-r@master + with: + r-version: 'release' + + - name: Install needed packages + if: steps.check-rmd.outputs.count != 0 + working-directory: lesson + run: | + source('bin/dependencies.R') + install_required_packages(.libPaths()[1]) + shell: Rscript {0} + + - name: Query dependencies + if: steps.check-rmd.outputs.count != 0 + working-directory: lesson + run: | + source('bin/dependencies.R') + deps <- identify_dependencies() + create_description(deps) + use_bioc_repos() + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Restore Package Cache + if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0 + uses: actions/cache@v2 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + + - name: Install stringi from source + if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0 + run: install.packages('stringi', repos='https://cloud.r-project.org') + shell: Rscript {0} + + - name: Install system dependencies for R packages + if: runner.os == 'Linux' && steps.check-rmd.outputs.count != 0 + working-directory: lesson + run: | + while read -r cmd + do + eval sudo $cmd || echo "Nothing to update" + done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")') + + - run: make site + working-directory: lesson + + - run: make lesson-check-all + working-directory: lesson diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml new file mode 100644 index 000000000..9d47e3008 --- /dev/null +++ b/.github/workflows/website.yml @@ -0,0 +1,122 @@ +name: Website +on: + push: + branches: + - gh-pages + - main + pull_request: [] +jobs: + build-website: + if: ${{ !endsWith(github.repository, '/styles') }} + runs-on: ubuntu-20.04 + env: + RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + defaults: + run: + shell: bash + steps: + - name: Set up Ruby + uses: ruby/setup-ruby@v1 + with: + ruby-version: '2.7' + bundler-cache: true + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: '3.x' + + - name: Install GitHub Pages, Bundler, and kramdown gems + run: | + gem install github-pages bundler kramdown kramdown-parser-gfm + + - name: Install Python modules + run: | + python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests + + - name: Checkout the lesson + uses: actions/checkout@master + with: + fetch-depth: 0 + ref: ${{ github.event.pull_request.head.sha }} + + - name: Look for R-markdown files + id: check-rmd + run: | + echo "::set-output name=count::$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" + + - name: Set up R + if: steps.check-rmd.outputs.count != 0 + uses: r-lib/actions/setup-r@master + with: + r-version: 'release' + + - name: Restore R Cache + if: steps.check-rmd.outputs.count != 0 + uses: actions/cache@v2 + with: + path: ${{ env.R_LIBS_USER }} + key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} + restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + + - name: Install needed packages + if: steps.check-rmd.outputs.count != 0 + run: | + source('bin/dependencies.R') + install_required_packages() + shell: Rscript {0} + + - name: Query dependencies + if: steps.check-rmd.outputs.count != 0 + run: | + source('bin/dependencies.R') + deps <- identify_dependencies() + create_description(deps) + use_bioc_repos() + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + + - name: Install system dependencies for R packages + if: steps.check-rmd.outputs.count != 0 + run: | + while read -r cmd + do + eval sudo $cmd || echo "Nothing to update" + done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")') + + - name: Render the markdown and confirm that the site can be built + run: make site + + - name: Checkout github pages + if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}} + uses: actions/checkout@master + with: + ref: gh-pages + path: gh-pages + + - name: Commit and Push + if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}} + run: | + # clean up gh-pages + cd gh-pages + git rm -rf . # remove all previous files + git restore --staged . # remove things from the stage + cd .. + # copy everything into gh-pages site + cp -r `ls -A | grep -v 'gh-pages' | grep -v '.git' | grep -v '.bundle/' | grep -v '_site'` gh-pages + # move into gh-pages, add, commit, and push + cd gh-pages + # setup git + git config --local user.email "actions@github.com" + git config --local user.name "GitHub Actions" + git add -A . + git commit --allow-empty -m "[Github Actions] render website (via ${{ github.sha }})" + git push origin gh-pages + # return + cd .. + + - run: make lesson-check-all + if: always() diff --git a/.gitignore b/.gitignore index 63552e192..e3ce3b79a 100644 --- a/.gitignore +++ b/.gitignore @@ -3,10 +3,16 @@ .DS_Store .ipynb_checkpoints .sass-cache +.jekyll-cache/ +.jekyll-metadata __pycache__ _site .Rproj.user .Rhistory .RData -.jekyll-cache - +.bundle/ +.vendor/ +vendor/ +.docker-vendor/ +Gemfile.lock +.*history diff --git a/404.md b/404.md new file mode 100644 index 000000000..c1cf9dd47 --- /dev/null +++ b/404.md @@ -0,0 +1,25 @@ +--- +layout: base +root: . +permalink: 404.html +title: "Page not found" +--- + +# Oops! We cannot find that page. +{: style="text-align: center;"} + +> ## Our apologies! +> +> We cannot seem to find the page you are looking for. +> Try going back to the previous page or +> navigate to any other page using the navigation bar above +> {%- if site.kind == "lesson" -%} or the schedule below {%- endif -%}. +> If you got here by clicking on a link in the +> {%- if site.kind == "lesson" -%} lesson {%- else -%} workshop {%- endif -%}, +> please report this link to the +> {%- if site.kind == "lesson" -%} lesson developers {%- else -%} workshop organizers {%- endif -%}. +{: .caution} + +{% if site.kind == "lesson" %} + {% include syllabus.html %} +{% endif%} diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index c3b966907..2cf1133bb 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -8,4 +8,5 @@ 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 %} +[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html +[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html diff --git a/Gemfile b/Gemfile new file mode 100644 index 000000000..8d69492bf --- /dev/null +++ b/Gemfile @@ -0,0 +1,14 @@ +# frozen_string_literal: true + +source 'https://rubygems.org' + +git_source(:github) { |repo_name| "https://github.com/#{repo_name}" } + +# Synchronize with https://pages.github.com/versions +ruby '>=2.7.1' + +gem 'github-pages', group: :jekyll_plugins + +if Gem::Version.new(RUBY_VERSION) >= Gem::Version.new('3.0.0') + gem 'webrick', '>= 1.6.1' +end \ No newline at end of file diff --git a/Makefile b/Makefile index 8569e7a4d..6bf02c6d5 100644 --- a/Makefile +++ b/Makefile @@ -3,69 +3,110 @@ # Settings MAKEFILES=Makefile $(wildcard *.mk) -JEKYLL=jekyll -JEKYLL_VERSION=3.7.3 +JEKYLL=bundle config set --local path .vendor/bundle && bundle install && bundle update && bundle exec jekyll PARSER=bin/markdown_ast.rb DST=_site -# Controls -.PHONY : commands clean files -.NOTPARALLEL: -all : commands - -## commands : show all commands. -commands : - @grep -h -E '^##' ${MAKEFILES} | sed -e 's/## //g' - -## docker-serve : use docker to build the site -docker-serve : - docker run --rm -it -v ${PWD}:/srv/jekyll -p 127.0.0.1:4000:4000 jekyll/jekyll:${JEKYLL_VERSION} make serve - -### jupyter : run JupyterHub and support a Python3 notebook with this data -jupyter : - docker run --rm -p 8888:8888 -e JUPYTER_ENABLE_LAB=yes -v ${PWD}:/home/jovyan/ jupyter/scipy-notebook:latest -## serve : run a local server. -serve : lesson-md +# Find Docker +DOCKER := $(shell which docker 2>/dev/null) + +# Check Python 3 is installed and determine if it's called via python3 or python +# (https://stackoverflow.com/a/4933395) +PYTHON3_EXE := $(shell which python3 2>/dev/null) +ifneq (, $(PYTHON3_EXE)) + ifeq (,$(findstring Microsoft/WindowsApps/python3,$(subst \,/,$(PYTHON3_EXE)))) + PYTHON := $(PYTHON3_EXE) + endif +endif + +ifeq (,$(PYTHON)) + PYTHON_EXE := $(shell which python 2>/dev/null) + ifneq (, $(PYTHON_EXE)) + PYTHON_VERSION_FULL := $(wordlist 2,4,$(subst ., ,$(shell python --version 2>&1))) + PYTHON_VERSION_MAJOR := $(word 1,${PYTHON_VERSION_FULL}) + ifeq (3, ${PYTHON_VERSION_MAJOR}) + PYTHON := $(PYTHON_EXE) + else + PYTHON_NOTE = "Your system does not appear to have Python 3 installed." + endif + else + PYTHON_NOTE = "Your system does not appear to have any Python installed." + endif +endif + + +# Default target +.DEFAULT_GOAL := commands + +## I. Commands for both workshop and lesson websites +## ================================================= + +.PHONY: site docker-serve repo-check clean clean-rmd + +## * serve : render website and run a local server +serve : lesson-md index.md ${JEKYLL} serve -## site : build files but do not run a server. -site : lesson-md +## * site : build website but do not run a server +site : lesson-md index.md ${JEKYLL} build -# repo-check : check repository settings. -repo-check : - @bin/repo_check.py -s . - -## clean : clean up junk files. +## * docker-serve : use Docker to serve the site +docker-serve : +ifeq (, $(DOCKER)) + $(error Your system does not appear to have Docker installed) +else + @$(DOCKER) pull carpentries/lesson-docker:latest + @$(DOCKER) run --rm -it \ + -v $${PWD}:/home/rstudio \ + -p 4000:4000 \ + -p 8787:8787 \ + -e USERID=$$(id -u) \ + -e GROUPID=$$(id -g) \ + carpentries/lesson-docker:latest +endif + +## * repo-check : check repository settings +repo-check : python + @${PYTHON} bin/repo_check.py -s . + +## * clean : clean up junk files clean : @rm -rf ${DST} @rm -rf .sass-cache @rm -rf bin/__pycache__ + @rm -rf .vendor + @rm -rf .bundle + @rm -f Gemfile.lock @find . -name .DS_Store -exec rm {} \; @find . -name '*~' -exec rm {} \; @find . -name '*.pyc' -exec rm {} \; -## clean-rmd : clean intermediate R files (that need to be committed to the repo). +## * clean-rmd : clean intermediate R files (that need to be committed to the repo) clean-rmd : @rm -rf ${RMD_DST} @rm -rf fig/rmd-* -## ---------------------------------------- -## Commands specific to workshop websites. + +## +## II. Commands specific to workshop websites +## ================================================= .PHONY : workshop-check -## workshop-check : check workshop homepage. -workshop-check : - @bin/workshop_check.py . +## * workshop-check : check workshop homepage +workshop-check : python + @${PYTHON} bin/workshop_check.py . + -## ---------------------------------------- -## Commands specific to lesson websites. +## +## III. Commands specific to lesson websites +## ================================================= -.PHONY : lesson-check lesson-md lesson-files lesson-fixme +.PHONY : lesson-check lesson-md lesson-files lesson-fixme install-rmd-deps # RMarkdown files -RMD_SRC = $(wildcard _episodes_rmd/??-*.Rmd) +RMD_SRC = $(wildcard _episodes_rmd/*.Rmd) RMD_DST = $(patsubst _episodes_rmd/%.Rmd,_episodes/%.md,$(RMD_SRC)) # Lesson source files in the order they appear in the navigation menu. @@ -84,41 +125,64 @@ HTML_DST = \ ${DST}/conduct/index.html \ ${DST}/setup/index.html \ $(patsubst _episodes/%.md,${DST}/%/index.html,$(sort $(wildcard _episodes/*.md))) \ - ${DST}/reference/index.html \ + ${DST}/reference.html \ $(patsubst _extras/%.md,${DST}/%/index.html,$(sort $(wildcard _extras/*.md))) \ ${DST}/license/index.html -## lesson-md : convert Rmarkdown files to markdown +## * install-rmd-deps : Install R packages dependencies to build the RMarkdown lesson +install-rmd-deps: + @${SHELL} bin/install_r_deps.sh + +## * lesson-md : convert Rmarkdown files to markdown lesson-md : ${RMD_DST} -_episodes/%.md: _episodes_rmd/%.Rmd - @bin/knit_lessons.sh $< $@ +_episodes/%.md: _episodes_rmd/%.Rmd install-rmd-deps + @mkdir -p _episodes + @$(SHELL) bin/knit_lessons.sh $< $@ -## lesson-check : validate lesson Markdown. -lesson-check : lesson-fixme - @bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md +## * lesson-check : validate lesson Markdown +lesson-check : python lesson-fixme + @${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -## lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace. -lesson-check-all : - @bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive +## * lesson-check-all : validate lesson Markdown, checking line lengths and trailing whitespace +lesson-check-all : python + @${PYTHON} bin/lesson_check.py -s . -p ${PARSER} -r _includes/links.md -l -w --permissive -## unittest : run unit tests on checking tools. -unittest : - @bin/test_lesson_check.py +## * unittest : run unit tests on checking tools +unittest : python + @${PYTHON} bin/test_lesson_check.py -## lesson-files : show expected names of generated files for debugging. +## * lesson-files : show expected names of generated files for debugging lesson-files : @echo 'RMD_SRC:' ${RMD_SRC} @echo 'RMD_DST:' ${RMD_DST} @echo 'MARKDOWN_SRC:' ${MARKDOWN_SRC} @echo 'HTML_DST:' ${HTML_DST} -## lesson-fixme : show FIXME markers embedded in source files. +## * lesson-fixme : show FIXME markers embedded in source files lesson-fixme : - @fgrep -i -n FIXME ${MARKDOWN_SRC} || true + @grep --fixed-strings --word-regexp --line-number --no-messages FIXME ${MARKDOWN_SRC} || true + +## +## IV. Auxililary (plumbing) commands +## ================================================= -#------------------------------------------------------------------------------- -# Include extra commands if available. -#------------------------------------------------------------------------------- +.PHONY : commands python --include commands.mk +## * commands : show all commands. +commands : + @sed -n -e '/^##/s|^##[[:space:]]*||p' $(MAKEFILE_LIST) + +python : +ifeq (, $(PYTHON)) + $(error $(PYTHON_NOTE)) +else + @: +endif + +index.md : +ifeq (, $(wildcard index.md)) + $(error index.md not found) +else + @: +endif diff --git a/_includes/aio-script.md b/_includes/aio-script.md index 926e0a6ea..d90e6d684 100644 --- a/_includes/aio-script.md +++ b/_includes/aio-script.md @@ -1,38 +1,25 @@ {% comment %} As a maintainer, you don't need to edit this file. -If you notice that something doesn't work, please +If you notice that something doesn't work, please open an issue: https://github.com/carpentries/styles/issues/new {% endcomment %} - -{% comment %} -Create an anchor for every episode. -{% endcomment %} -{% for episode in site.episodes %} -
+{% include manual_episode_order.html %} + +{% for lesson_episode in lesson_episodes %} + +{% if site.episode_order %} + {% assign e = site.episodes | where: "slug", lesson_episode | first %} +{% else %} + {% assign e = lesson_episode %} +{% endif %} + +

{{ e.title }}

+ +{% include episode_overview.html teaching_time=e.teaching exercise_time=e.exercises episode_questions=e.questions episode_objectives=e.objectives %} + +{{ e.content }} + +{% include episode_keypoints.html episode_keypoints=e.keypoints %} +
{% endfor %} diff --git a/_includes/all_keypoints.html b/_includes/all_keypoints.html index e4fd289ff..f0abd251c 100644 --- a/_includes/all_keypoints.html +++ b/_includes/all_keypoints.html @@ -3,10 +3,16 @@ {% endcomment %} {% include base_path.html %} +{% include manual_episode_order.html %}

Key Points

-{% for episode in site.episodes %} +{% for lesson_episode in lesson_episodes %} + {% if site.episode_order %} + {% assign episode = site.episodes | where: "slug", lesson_episode | first %} + {% else %} + {% assign episode = lesson_episode %} + {% endif %} {% unless episode.break %} - {% for episode in site.episodes %} + {% if site.instructor_training %} + + {% if multiday %}{% endif %} + + + + + {% endif %} + {% for lesson_episode in lesson_episodes %} + {% if site.episode_order %} + {% assign episode = site.episodes | where: "slug", lesson_episode | first %} + {% else %} + {% assign episode = lesson_episode %} + {% endif %} {% if episode.start %} {% comment %} Starting a new day? {% endcomment %} {% assign day = day | plus: 1 %} {% if day > 1 %} {% comment %} If about to start day 2 or later, show finishing time for previous day {% endcomment %} @@ -65,6 +86,17 @@

Schedule

{% endfor %} {% assign hours = current | divided_by: 60 %} {% assign minutes = current | modulo: 60 %} + {% if site.instructor_training %} + + {% if multiday %}{% endif %} + + + + + {% assign current = current | plus: 15 %} + {% assign hours = current | divided_by: 60 %} + {% assign minutes = current | modulo: 60 %} + {% endif %} {% if multiday %}{% endif %} diff --git a/_layouts/base.html b/_layouts/base.html index 07a497272..67b6d7af4 100644 --- a/_layouts/base.html +++ b/_layouts/base.html @@ -16,6 +16,10 @@ + {% if page.math %} + + {% endif %} + {% include favicons.html %} @@ -28,7 +32,7 @@ {% if page.title %}{{ page.title }}{% endif %}{% if page.title and site.title %} – {% endif %}{% if site.title %}{{ site.title }}{% endif %} - + diff --git a/aio.md b/aio.md index 0ab72ea55..8d1806d29 100644 --- a/aio.md +++ b/aio.md @@ -3,8 +3,8 @@ permalink: /aio/index.html --- {% comment %} -As a maintainer, you don't need to edit this file. -If you notice that something doesn't work, please +As a maintainer, you do not need to edit this file. +If you notice that something does not work, please open an issue: https://github.com/carpentries/styles/issues/new {% endcomment %} diff --git a/assets/css/bootstrap.css b/assets/css/bootstrap.css index fcab41554..2be255914 100644 --- a/assets/css/bootstrap.css +++ b/assets/css/bootstrap.css @@ -1608,8 +1608,8 @@ pre code { margin-left: auto; } .row { - margin-right: -15px; - margin-left: -15px; + margin-right: -10px; + margin-left: -10px; } .row-no-gutters { margin-right: 0; diff --git a/assets/css/katex.min.css b/assets/css/katex.min.css new file mode 100644 index 000000000..e1dfc046a --- /dev/null +++ b/assets/css/katex.min.css @@ -0,0 +1 @@ +@font-face{font-family:KaTeX_AMS;font-style:normal;font-weight:400;src:url(fonts/KaTeX_AMS-Regular.woff2) format("woff2"),url(fonts/KaTeX_AMS-Regular.woff) format("woff"),url(fonts/KaTeX_AMS-Regular.ttf) 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diff --git a/_includes/base_path.html b/_includes/base_path.html index 7efb3570a..4f343afa8 100644 --- a/_includes/base_path.html +++ b/_includes/base_path.html @@ -1,27 +1,41 @@ -{% comment %} -This is adapted from: https://ricostacruz.com/til/relative-paths-in-jekyll +{%- comment -%} +When the website is built by GitHub Pages, +'site.url' is set to 'https://username.github.io' +'site.baseurl' is set to '/lesson-name' -`page.url` gives the URL of the current page with a leading /: +When we start a local server using `jekyll serve`, +'site.url' is set to 'http://localhost:4000' and +'site.baseurl' is empty. -- when the URL ends with the extension (e.g., /foo/bar.html) then we can get - the depth by counting the number of / and remove - 1 -- when the URL ends with a / (e.g. /foo/bar/) then the number / gives the depth - directly -{% endcomment %} +In both of the above cases we set 'relative_root_path' to 'site.baseurl'. -{% assign relative_root_path = '' %} +When we build a website locally with `jekyll build`, +both 'site.url' and 'site.baseurl' are empty. +This case is handled by the last 'else' in the code below. +The logic there follows the (adapted) instructions found at: + https://ricostacruz.com/til/relative-paths-in-jekyll -{% assign last_char = page.url | slice: -1 %} + `page.url` gives the URL of the current page with a leading /: -{% if last_char == "/"} -{% assign offset = 0 %} -{% else %} -{% assign offset = 1 %} -{% endif %} + - when the URL ends with an extension (e.g., /foo/bar.html), + we can get the 'depth' of the page by counting the number of + forward slashes ('/') and subtracting 1 + - when the URL ends with a forward slash (e.g. /foo/bar/), + we can get the depth of the page by counting the number of / +{%- endcomment -%} -{% assign depth = page.url | split: '/' | size | minus: offset %} -{% if depth <= 1 %}{% assign relative_root_path = '.' %} -{% elsif depth == 2 %}{% assign relative_root_path = '..' %} -{% elsif depth == 3 %}{% assign relative_root_path = '../..' %} -{% elsif depth == 4 %}{% assign relative_root_path = '../../..' %} +{% if site.url %} + {% assign relative_root_path = site.baseurl %} +{% else %} + {% assign last_char = page.url | slice: -1 %} + {% if last_char == "/" %} + {% assign offset = 0 %} + {% else %} + {% assign offset = 1 %} + {% endif %} + {% assign depth = page.url | split: '/' | size | minus: offset %} + {% if depth <= 1 %}{% assign relative_root_path = '.' %} + {% elsif depth == 2 %}{% assign relative_root_path = '..' %} + {% else %}{% capture relative_root_path %}..{% for i in (3..depth) %}/..{% endfor %}{% endcapture %} + {% endif %} {% endif %} diff --git a/_includes/episode_keypoints.html b/_includes/episode_keypoints.html index 2baa53ef0..5c283ea82 100644 --- a/_includes/episode_keypoints.html +++ b/_includes/episode_keypoints.html @@ -1,10 +1,17 @@ {% comment %} Display key points for an episode. {% endcomment %} + +{% if page.keypoints == nil %} +{% assign episode_keypoints = include.episode_keypoints %} +{% else %} +{% assign episode_keypoints = page.keypoints %} +{% endif %} +

Key Points

    - {% for keypoint in page.keypoints %} + {% for keypoint in episode_keypoints %}
  • {{ keypoint|markdownify }}
    • {% endfor %}
diff --git a/_includes/episode_navbar.html b/_includes/episode_navbar.html index ea368eba2..5abf86f2c 100644 --- a/_includes/episode_navbar.html +++ b/_includes/episode_navbar.html @@ -9,11 +9,17 @@ Navigation bar for an episode. {% endcomment %} +{% include manual_episode_order.html %} +{% comment %} + 'previous_episode' and 'next_episodes' are defined in 'manual_episode_order.html'. + These replace 'page.previous' and 'page.next' objects, correspondingly. +{% endcomment %} +

- {% if page.previous.url %} - previous episode + {% if previous_episode %} + previous episode {% else %} lesson home {% endif %} @@ -26,8 +32,8 @@

{{ site.title }}

- {% if page.next.url %} - next episode + {% if next_episode %} + next episode {% else %} lesson home {% endif %} diff --git a/_includes/episode_overview.html b/_includes/episode_overview.html index cb87e0f66..169ab26b6 100644 --- a/_includes/episode_overview.html +++ b/_includes/episode_overview.html @@ -1,19 +1,59 @@ {% comment %} - Display an episode's timings and learning objectives. + Display episode's timings and learning objectives. + + Regarding the `if page.*** == nil` below: + all-in-one page combines all episodes into one. + It, therefore, does not define its own objectives, exercises, + and questions, which 'normal' episodes define in the front matter. + + To display episodes' teaching and exercise times, as well as episode + questions and objectives, we pass them as parameters to the Liquid's + `include` statement when we generate the page: + + include episode_overview.html teaching_time=e.teaching ... + + Here we obtain the information we need either from the episode itself or + from the parameters passed in. {% endcomment %} + +{% if page.teaching == nil %} +{% assign teaching_time = include.teaching_time %} +{% else %} +{% assign teaching_time = page.teaching %} +{% endif %} + +{% if page.exercises == nil %} +{% assign exercise_time = include.exercise_time %} +{% else %} +{% assign exercise_time = page.exercises %} +{% endif %} + +{% if page.questions == nil %} +{% assign episode_questions = include.episode_questions %} +{% else %} +{% assign episode_questions = page.questions %} +{% endif %} + +{% if page.objectives == nil %} +{% assign episode_objectives = include.episode_objectives %} +{% else %} +{% assign episode_objectives = page.objectives %} +{% endif %} + +

Overview

- Teaching: {{ page.teaching }} min + Teaching: {{ teaching_time }} min
- Exercises: {{ page.exercises }} min + Exercises: {{ exercise_time }} min
Questions
    - {% for question in page.questions %} + {% for question in episode_questions %}
  • {{ question|markdownify }}
    • {% endfor %}
@@ -26,7 +66,7 @@

Overview

Objectives
    - {% for objective in page.objectives %} + {% for objective in episode_objectives %}
  • {{ objective|markdownify }}
    • {% endfor %}
diff --git a/_includes/javascript.html b/_includes/javascript.html index fcc74e6ec..1c4877a6c 100644 --- a/_includes/javascript.html +++ b/_includes/javascript.html @@ -4,6 +4,7 @@ + + +{% if page.math %} + + + +{% endif %} + +{%- comment -%} +AnchorJS: A JavaScript utility for adding deep anchor links +https://github.com/bryanbraun/anchorjs +https://cdn.jsdelivr.net/npm/anchor-js/anchor.min.js +{%- endcomment -%} + + + diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 03091a7cd..b0eb29912 100644 --- a/_includes/lesson_footer.html +++ b/_includes/lesson_footer.html @@ -6,7 +6,7 @@
-
+
{% if site.carpentry == "swc" %} Licensed under CC-BY 4.0 2018–{{ 'now' | date: "%Y" }} by The Carpentries diff --git a/_includes/life_cycle.html b/_includes/life_cycle.html index efc5b6d99..37a1259c4 100644 --- a/_includes/life_cycle.html +++ b/_includes/life_cycle.html @@ -28,7 +28,19 @@ {% elsif site.life_cycle == "stable" %} {% comment %} -We don't do anything special for now +We do not do anything special unless this is a Carpentries Lab lesson {% endcomment %} +{% if site.carpentry == "lab" %} +{% if site.doi contains "zenodo" %}{% assign listing=" on Zenodo" %} +{% elsif site.doi contains "jose" %}{% assign listing=" in JOSE" %} +{% else %}{% assign listing="none" %} +{% endif %} + +
+
+ This lesson has passed peer-review! {% if site.doi != "" %}See the publication{{ listing }}.{% endif %} +
+
+{% endif %} {% endif %} diff --git a/_includes/links.md b/_includes/links.md index 620a68c0e..7f8e00268 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -12,14 +12,13 @@ [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/ +[github-importer]: https://import2.github.com/ [importer]: https://github.com/new/import [jekyll-collection]: https://jekyllrb.com/docs/collections/ [jekyll-install]: https://jekyllrb.com/docs/installation/ [jekyll-windows]: http://jekyll-windows.juthilo.com/ [jekyll]: https://jekyllrb.com/ [jupyter]: https://jupyter.org/ -[jupyterlab]: https://jupyterlab.readthedocs.io/en/stable/ [kramdown]: https://kramdown.gettalong.org/ [lc-lessons]: https://librarycarpentry.org/lessons/ [lesson-aio]: {{ relative_root_path }}{% link aio.md %} @@ -36,7 +35,7 @@ [pandoc]: https://pandoc.org/ [paper-now]: https://github.com/PeerJ/paper-now [python-gapminder]: https://swcarpentry.github.io/python-novice-gapminder/ -[pyyaml]: https://pypi.python.org/pypi/PyYAML +[pyyaml]: https://pypi.org/project/PyYAML/ [r-markdown]: https://rmarkdown.rstudio.com/ [rstudio]: https://www.rstudio.com/ [ruby-install-guide]: https://www.ruby-lang.org/en/downloads/ diff --git a/_includes/main_title.html b/_includes/main_title.html index b08af4a78..7d17317f1 100644 --- a/_includes/main_title.html +++ b/_includes/main_title.html @@ -4,4 +4,11 @@ {% include base_path.html %} +{% if site.kind == "lesson" %}

{{ site.title }}{% if page.title %}: {{ page.title }}{% endif %}

+ +{% else %} + +

{{ page.title }}

+ +{% endif %} diff --git a/_includes/manual_episode_order.html b/_includes/manual_episode_order.html new file mode 100644 index 000000000..9729ac504 --- /dev/null +++ b/_includes/manual_episode_order.html @@ -0,0 +1,116 @@ +{% comment %} + This file enables manual episode ordering until + GitHub Pages switches to Jekyll that supports it + without any major hackery. Note, some logic will + be required even when this transition happens + but it will not be as involved as what we have to do + in this file. + + To order lesson episodes or extras manually + (instead of the default alpha-numerical order), + create array variables 'episode_order' and + 'extras_order' in `_config.yml` like so: + + episode_order: + - episodeA + - episodeB + + extras_order: + - extraA + - extraB + + Note that "Reference" page is currently always + added to "Extras" as the first item. + + The main outcomes of the code in this file are: + - 'lesson_episodes' variable that replaces + 'site.episodes' variable when manual episode + order is defined. + - 'lesson_extras' variable that replaces + 'site.extras' variable when manual ordering of + files in '_extras' is used + - 'previous_episode' and 'next_episode' objects + that replace 'page.previous' and 'page.next' variables, + correspondingly, and that have such properties + as 'url' and 'title' and that are used in + 'episode_navbar.html'. + + When episode order is specified manually, the 'lesson_episodes' + variable contains a list of episode names ("slugs", to be precise; + "slug" is the episode name without '.md'). Therefore, when we + iterate over 'lesson_episodes' (in syllabus.html and navbar.html) , + we have to check whether we use manual episode ordering and, if so, + find the corresponding episode object. This is what we do with the + following code in every loop over 'lesson_episodes': + + {% if site.episode_order %} + {% assign episode = site.episodes | where: "slug", lesson_episode | first %} + {% else %} + {% assign episode = lesson_episode %} + {% endif %} +{% endcomment %} + +{% comment %} +Manual ordering of Episodes begins here +{% endcomment %} + +{% if site.episode_order %} + {% assign lesson_episodes = site.episode_order %} +{% else %} + {% assign lesson_episodes = site.episodes %} +{% endif %} + + +{% comment %} + If 'episode_order' is defined, we need to determine + - previous episode object ('previous_episode') + - and next episode object ('next_episode') +{% endcomment %} + + +{% if site.episode_order %} + {% for lesson_episode in lesson_episodes %} + + {% comment %} + We iterate over the specified lesson episodes using + a 'for' loop because we can use + 'forloop.first', 'forloop.last', and 'forloop.index0'. + {% endcomment %} + + {% unless lesson_episode == page.slug %} {% continue %} {% endunless %} + + {% if forloop.first %} + {% assign previous_episode = nil %} + {% else %} + {% assign p_idx = forloop.index0 | minus: 1 %} + {% assign p_name = lesson_episodes[p_idx] %} + {% assign previous_episode = site.episodes | where: "slug", p_name | first %} + {% endif %} + + {% if forloop.last == true %} + {% assign next_episode = nil %} + {% else %} + {% assign n_idx = forloop.index0 | plus: 1 %} + {% assign n_name = lesson_episodes[n_idx] %} + {% assign next_episode = site.episodes | where: "slug", n_name | first %} + {% endif %} + {% endfor %} +{% else %} + {% assign previous_episode = page.previous %} + {% assign next_episode = page.next %} +{% endif %} + + +{% comment %} +Manual ordering of Extras begins here +{% endcomment %} + +{% if site.extras_order %} + {% assign lesson_extras = site.extras_order %} +{% else %} + {% assign lesson_extras = site.extras %} +{% endif %} + +{% comment %} + We do not need to determine "previous" or "next" extra. +{% endcomment %} diff --git a/_includes/navbar.html b/_includes/navbar.html index cc9b884a7..a8e3d596c 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -3,6 +3,7 @@ {% endcomment %} {% include gh_variables.html %} +{% include manual_episode_order.html %}

Setup Download files required for the lesson
Pre-training surveyPlease fill out our pre-training survey before the start of the course.
{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif +++ %}{{ minutes }}Post-training surveyPlease fill out our post-training survey after the course.
{% if hours < 10 %}0{% endif %}{{ hours }}:{% if minutes < 10 %}0{% endif %}{{ minutes }}
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