From 3455c4ff25189b10dd7559087e8d4bf0dee46c1c Mon Sep 17 00:00:00 2001 From: Sarah Stevens Date: Fri, 30 Apr 2021 14:55:56 -0500 Subject: [PATCH] Attempt to update to latest styles (#9) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * translate CONDUCT.md * translate LICENSE.md * translate files * translate files * translate files * translate files * translate files * translate files * don't translate organization names * Update CONDUCT.md * updated license following this https://creativecommons.org/licenses/by/4.0/deed.es insead of usted tu * fix link referrence * r reproducible * r reproducible * r reproducible * translate overview and teaching * change finish for Final * Update schedule.html Traducido * translate 'finish' to 'final as per https://github.com/swcarpentry/r-novice-gapminder-es/issues/53 * translate 'cite' to 'cita' as per https://github.com/swcarpentry/r-novice-gapminder-es/issues/54 * Update navbar.html fix typo, as suggested in https://github.com/swcarpentry/r-novice-gapminder-es/issues/92 * mejore -> mejora * 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: 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. Co-authored-by: Erin Becker Co-authored-by: Paula Andrea Co-authored-by: François Michonneau Co-authored-by: raynamharris Co-authored-by: Paola Prieto <31372246+PaoPrieto@users.noreply.github.com> Co-authored-by: Rayna M Harris Co-authored-by: Raniere Silva Co-authored-by: K.E. Koziar Co-authored-by: Maxim Belkin Co-authored-by: stamper Co-authored-by: Michael Joseph Co-authored-by: Joao Rodrigues Co-authored-by: Sarah Brown Co-authored-by: Allen Lee Co-authored-by: Anthony Gitter Co-authored-by: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com> 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/FUNDING.yml | 2 + .github/ISSUE_TEMPLATE.md | 20 ++- .github/PULL_REQUEST_TEMPLATE.md | 20 ++- .github/workflows/template.yml | 182 ++++++++++++++++++++++++++++ .github/workflows/website.yml | 121 ++++++++++++++++++ .gitignore | 7 ++ 404.md | 25 ++++ CODE_OF_CONDUCT.md | 3 +- Gemfile | 14 +++ Makefile | 157 ++++++++++++++++-------- _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 | 16 +++ _includes/lesson_footer.html | 2 +- _includes/links.md | 4 +- _includes/main_title.html | 7 ++ _includes/manual_episode_order.html | 116 ++++++++++++++++++ _includes/navbar.html | 17 ++- _includes/syllabus.html | 17 ++- _layouts/base.html | 4 + assets/css/bootstrap.css | 2 +- assets/css/katex.min.css | 1 + assets/css/lesson.scss | 177 +++++++++++++++++++++------ 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 | 14 +-- bin/boilerplate/README.md | 2 +- bin/boilerplate/_config.yml | 20 +-- bin/boilerplate/_extras/figures.md | 21 +++- bin/chunk-options.R | 19 ++- bin/dependencies.R | 62 ++++++++++ bin/generate_md_episodes.R | 71 +++++------ bin/install_r_deps.sh | 1 + bin/lesson_check.py | 72 ++++++----- bin/lesson_initialize.py | 14 +-- bin/markdown_ast.rb | 10 +- bin/repo_check.py | 6 +- bin/run-make-docker-serve.sh | 10 ++ bin/test_lesson_check.py | 6 +- bin/util.py | 20 +-- bin/workshop_check.py | 6 +- 50 files changed, 1199 insertions(+), 336 deletions(-) create mode 100644 .github/FUNDING.yml 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/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 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 1d7d564d..5bf4860b 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/FUNDING.yml b/.github/FUNDING.yml new file mode 100644 index 00000000..2ee9d0ee --- /dev/null +++ b/.github/FUNDING.yml @@ -0,0 +1,2 @@ +github: [carpentries, swcarpentry, datacarpentry, librarycarpentry] +custom: ["https://carpentries.wedid.it"] diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md index ec2d4fe1..077de4cf 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 d9eb8c50..07aadca2 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 00000000..3e91db6b --- /dev/null +++ b/.github/workflows/template.yml @@ -0,0 +1,182 @@ +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 ${#files[@]})" + + - name: Set up R + if: steps.check-rmd.outputs.count != 0 + uses: r-lib/actions/setup-r@master + with: + r-version: 'release' + + - name: Install needed packages + if: steps.check-rmd.outputs.count != 0 + run: | + packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages())) + install.packages(packages, repo="https://cran.rstudio.com/") + shell: Rscript {0} + + - name: Query dependencies + if: steps.check-rmd.outputs.count != 0 + working-directory: lesson + run: | + source('bin/dependencies.R') + deps <- identify_dependencies() + create_description(deps) + saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) + writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") + shell: Rscript {0} + + - name: Cache R packages + if: runner.os != 'Windows' && steps.check-rmd.outputs.count != 0 + uses: actions/cache@v1 + 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 + 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 00000000..246d4c70 --- /dev/null +++ b/.github/workflows/website.yml @@ -0,0 +1,121 @@ +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: Cache R packages + if: steps.check-rmd.outputs.count != 0 + uses: actions/cache@v1 + 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: | + packages = setdiff(c('remotes', 'rprojroot', 'renv', 'desc', 'rmarkdown', 'knitr'), rownames(installed.packages())) + install.packages(packages, repo="https://cran.rstudio.com/") + shell: Rscript {0} + + - name: Query dependencies + if: steps.check-rmd.outputs.count != 0 + run: | + source('bin/dependencies.R') + deps <- identify_dependencies() + create_description(deps) + 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 + 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 6dca581d..81439802 100644 --- a/.gitignore +++ b/.gitignore @@ -4,9 +4,16 @@ .ipynb_checkpoints .sass-cache .jekyll-cache/ +.jekyll-metadata __pycache__ _site .Rproj.user .Rhistory .RData +.bundle/ +.vendor/ +vendor/ +.docker-vendor/ +Gemfile.lock +.*history *.Rproj diff --git a/404.md b/404.md new file mode 100644 index 00000000..2038a508 --- /dev/null +++ b/404.md @@ -0,0 +1,25 @@ +--- +layout: base +root: . +permalink: 404.html +title: "Page not found" +--- + +# Oops! We can't find that page. +{: style="text-align: center;"} + +> ## Our apologies! +> +> We can't seem to find the page you're 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 c3b96690..2cf1133b 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 00000000..8d69492b --- /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 d291abe6..8b02ab11 100644 --- a/Makefile +++ b/Makefile @@ -3,66 +3,103 @@ # Settings MAKEFILES=Makefile $(wildcard *.mk) -JEKYLL=jekyll -JEKYLL_VERSION=3.8.5 +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 - -## serve : run a local server. +# 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 ${JEKYLL} serve -## site : build files but do not run a server. +## * site : build website but do not run a server site : lesson-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 : + @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 + +## * 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. @@ -81,41 +118,57 @@ 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 diff --git a/_includes/aio-script.md b/_includes/aio-script.md index 926e0a6e..d90e6d68 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 e4fd289f..f0abd251 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 %} + {% 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 %} diff --git a/_layouts/base.html b/_layouts/base.html index 07a49727..27b116eb 100644 --- a/_layouts/base.html +++ b/_layouts/base.html @@ -16,6 +16,10 @@ + {% if page.math %} + + {% endif %} + {% include favicons.html %} diff --git a/assets/css/bootstrap.css b/assets/css/bootstrap.css index 7678046e..dacc1e5b 100644 --- a/assets/css/bootstrap.css +++ b/assets/css/bootstrap.css @@ -1476,7 +1476,7 @@ abbr[data-original-title] { blockquote { padding: 10px 20px; margin: 0 0 20px; - font-size: inherit; + font-size: 17.5px; border-left: 5px solid #eeeeee; } blockquote p:last-child, diff --git a/assets/css/katex.min.css b/assets/css/katex.min.css new file mode 100644 index 00000000..e1dfc046 --- /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) format("truetype")}@font-face{font-family:KaTeX_Caligraphic;font-style:normal;font-weight:700;src:url(fonts/KaTeX_Caligraphic-Bold.woff2) format("woff2"),url(fonts/KaTeX_Caligraphic-Bold.woff) format("woff"),url(fonts/KaTeX_Caligraphic-Bold.ttf) format("truetype")}@font-face{font-family:KaTeX_Caligraphic;font-style:normal;font-weight:400;src:url(fonts/KaTeX_Caligraphic-Regular.woff2) format("woff2"),url(fonts/KaTeX_Caligraphic-Regular.woff) format("woff"),url(fonts/KaTeX_Caligraphic-Regular.ttf) format("truetype")}@font-face{font-family:KaTeX_Fraktur;font-style:normal;font-weight:700;src:url(fonts/KaTeX_Fraktur-Bold.woff2) format("woff2"),url(fonts/KaTeX_Fraktur-Bold.woff) format("woff"),url(fonts/KaTeX_Fraktur-Bold.ttf) format("truetype")}@font-face{font-family:KaTeX_Fraktur;font-style:normal;font-weight:400;src:url(fonts/KaTeX_Fraktur-Regular.woff2) format("woff2"),url(fonts/KaTeX_Fraktur-Regular.woff) format("woff"),url(fonts/KaTeX_Fraktur-Regular.ttf) format("truetype")}@font-face{font-family:KaTeX_Main;font-style:normal;font-weight:700;src:url(fonts/KaTeX_Main-Bold.woff2) format("woff2"),url(fonts/KaTeX_Main-Bold.woff) format("woff"),url(fonts/KaTeX_Main-Bold.ttf) format("truetype")}@font-face{font-family:KaTeX_Main;font-style:italic;font-weight:700;src:url(fonts/KaTeX_Main-BoldItalic.woff2) format("woff2"),url(fonts/KaTeX_Main-BoldItalic.woff) format("woff"),url(fonts/KaTeX_Main-BoldItalic.ttf) format("truetype")}@font-face{font-family:KaTeX_Main;font-style:italic;font-weight:400;src:url(fonts/KaTeX_Main-Italic.woff2) format("woff2"),url(fonts/KaTeX_Main-Italic.woff) format("woff"),url(fonts/KaTeX_Main-Italic.ttf) format("truetype")}@font-face{font-family:KaTeX_Main;font-style:normal;font-weight:400;src:url(fonts/KaTeX_Main-Regular.woff2) format("woff2"),url(fonts/KaTeX_Main-Regular.woff) format("woff"),url(fonts/KaTeX_Main-Regular.ttf) format("truetype")}@font-face{font-family:KaTeX_Math;font-style:italic;font-weight:700;src:url(fonts/KaTeX_Math-BoldItalic.woff2) format("woff2"),url(fonts/KaTeX_Math-BoldItalic.woff) format("woff"),url(fonts/KaTeX_Math-BoldItalic.ttf) 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+$color-warning: #cda01d !default; $color-output: #303030 !default; $color-source: #360084 !default; // blockquotes $color-callout: #f4fd9c !default; +$color-caution: #cf000e !default; $color-challenge: #eec275 !default; $color-checklist: #dfd2a0 !default; $color-discussion: #eec275 !default; @@ -36,42 +38,103 @@ $color-testimonial: #fc8dc1 !default; border-radius: 4px 0 0 4px; } -.error { @include cdSetup($color-error); } -.output { @include cdSetup($color-output); } -.source { @include cdSetup($color-source); } - -.bash, .language-bash { @include cdSetup($color-source); } -.make, .language-make { @include cdSetup($color-source); } -.matlab, .language-matlab { @include cdSetup($color-source); } -.python, .language-python { @include cdSetup($color-source); } -.r, .language-r { @include cdSetup($color-source); } -.sql, .language-sql { @include cdSetup($color-source); } - -.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"; } +// Generic setup. Has to come before .error, .warning, and .output +div[class^='language-'] { @include cdSetup($color-source); } +div.source { @include cdSetup($color-source); } +div.error { @include cdSetup($color-error); } +div.warning { @include cdSetup($color-warning); } +div.output { @include cdSetup($color-output); } + +div.error::before, +div.warning:before, +div.output::before, +div.source::before, +div[class^='language-']::before { + background-color: #f2eff6; + display: block; + font-weight: bold; + padding: 5px 10px; +} + +div[class^='language-']::before, +div.source::before { content: "Code"; } + +div.error::before { background-color: #ffebe6; content: "Error"; } +div.warning:before { background-color: #f8f4e8; content:" Warning"; } +div.output::before { background-color: #efefef; content: "Output"; } + +div.language-basic::before { content: "Basic"; } +div.language-bash::before { content: "Bash"; } +div.language-c::before { content: "C"; } +div.language-chapel::before { content: "Chapel"; } +div.language-cmake::before { content: "CMake"; } +div.language-cpp::before { content: "C++"; } +div.language-cuda::before { content: "Cuda"; } +div.language-d::before { content: "D"; } +div.language-fortran::before { content: "Fortran"; } +div.language-go::before { content: "Go"; } +div.language-html::before { content: "HTML"; } +div.language-java::before { content: "Java"; } +div.language-julia::before { content: "Julia"; } +div.language-kotlin::before { content: "Kotlin"; } +div.language-lua::before { content: "Lua"; } +div.language-make::before { content: "Make"; } +div.language-matlab::before { content: "MATLAB"; } +div.language-opencl::before { content: "OpenCL"; } +div.language-perl::before { content: "Perl"; } +div.language-python::before { content: "Python"; } +div.language-r::before { content: "R"; } +div.language-ruby::before { content: "Ruby"; } +div.language-rust::before { content: "Rust"; } +div.language-scala::before { content: "Scala"; } +div.language-sql::before { content: "SQL"; } +div.language-vulkan::before { content: "Vulkan"; } + +// Tab panels are used on Setup pages to show instructions for different Operating Systems +.tab-pane { + border: solid 1px #ddd; // #ddd == @nav-tabs-active-link-hover-border-color + border-top: none; + padding: 20px 20px 10px 20px; + border-radius: 0 0 4px 4px; // 4px == @border-radius-base +} + +// Stripe above tab panels where OS tabs are shown +ul.nav.nav-tabs { + background: #E1E1E1; + border-radius: 4px 4px 0 0; // 4px == @border-radius-base +} + +// adjust line height of links so that clickable area (of OS tabs) is 44px high +ul.nav.nav-tabs li a { line-height: 24px; } // or 1.714285716 + +// This color provides better contrast ratio on most backgrounds used on Carpentries websites +// 9.24 on FFFFFF: https://webaim.org/resources/contrastchecker/?fcolor=204A6F&bcolor=FFFFFF&api (body) +// 8.78 on F9F9F9: https://webaim.org/resources/contrastchecker/?fcolor=204A6F&bcolor=F9F9F9&api (tables) +// 7.07 on E1E1E1: https://webaim.org/resources/contrastchecker/?fcolor=204A6F&bcolor=E1E1E1&api (tab panels) +a { color: #204A6F; } + +// .yt-wrapper2 can be used for limiting maximum width of YouTube iframes only +.yt-wrapper2 { max-width: 100%; margin: 0 auto; } + +// Use full width on small displays +@media only screen and (max-width: 600px) { .yt-wrapper2 { max-width: 100%; } } + +.yt-wrapper { + height: 0; + margin-top: 10px; + padding-bottom: 56.25%; + position: relative; + width: 100%; +} + +.yt-frame { + height: 100%; + left: 0; + position: absolute; + top: 0; + width: 100%; +} //---------------------------------------- // Specialized blockquote environments for learning objectives, callouts, etc. @@ -113,6 +176,7 @@ $codeblock-padding: 5px !default; } .callout{ @include bkSetup($color-callout, "\e146"); } +.caution{ @include bkSetup($color-caution, "\e107"); } .challenge{ @include bkSetup($color-challenge, "\270f"); } .checklist{ @include bkSetup($color-checklist, "\e067"); } .discussion{ @include bkSetup($color-discussion, "\e123"); } @@ -148,18 +212,46 @@ font-size: 18px; blockquote p { margin: 5px; } +blockquote :not(h2) + p { + padding-top: 1em; +} //---------------------------------------- // Override Bootstrap settings. //---------------------------------------- +blockquote { font-size: inherit; } + +a code { + color: #006cad; +} + +a:link { + color: #196EBD; +} + +a:active, +a:hover { + outline: 0; + text-decoration: underline; +} + +a:visited { + color: #1AA4DA; +} + code { white-space: nowrap; padding: 2px 5px; - color: #006cad; + color: #24292e; background-color: #e7e7e7; } +samp { hyphens: none; } + +dt { margin-top: 20px; } +dd { margin-left: 2em; } + article img { display: block; margin: 20px auto; @@ -194,7 +286,7 @@ article pre { text-align: center; } -footer .copyright, +footer .license, footer .help-links { font-size: inherit; @@ -225,6 +317,11 @@ span.fold-unfold { } +p.image-with-shadow img, +img.image-with-shadow { + box-shadow: 0 6px 24px 0 #888; +} + //---------------------------------------- // Life cycle box //---------------------------------------- @@ -255,6 +352,12 @@ div.life-cycle { background: #d9edf7; } +// Remove border around spans of text within code blocks +// that the highlighter (rouge) failed to recognize. +pre.highlight span.err { + border: none; +} + //---------------------------------------- // keyboard key style, from StackExchange. diff --git a/assets/js/jquery.min.js b/assets/js/jquery.min.js index f3644431..b0614034 100644 --- a/assets/js/jquery.min.js +++ b/assets/js/jquery.min.js @@ -1,6 +1,2 @@ -/*! jQuery v1.11.3 | (c) 2005, 2015 jQuery Foundation, Inc. | jquery.org/license */ -!function(a,b){"object"==typeof module&&"object"==typeof module.exports?module.exports=a.document?b(a,!0):function(a){if(!a.document)throw new Error("jQuery requires a window with a document");return b(a)}:b(a)}("undefined"!=typeof window?window:this,function(a,b){var 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diff --git a/_includes/base_path.html b/_includes/base_path.html index 7efb3570..41139587 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.url + 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.url | append: 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 2baa53ef..5c283ea8 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 ea368eba..5abf86f2 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 cb87e0f6..169ab26b 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 fcc74e6e..77080ae5 100644 --- a/_includes/javascript.html +++ b/_includes/javascript.html @@ -12,3 +12,19 @@ ga('create', 'UA-37305346-2', 'auto'); ga('send', 'pageview'); +{% if page.math %} + + + +{% endif %} + diff --git a/_includes/lesson_footer.html b/_includes/lesson_footer.html index 03091a7c..b0eb2991 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/links.md b/_includes/links.md index 4a85ed46..7f8e0026 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -12,7 +12,7 @@ [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/ @@ -35,7 +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 b08af4a7..7d17317f 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 00000000..79086271 --- /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 won't 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 cc9b884a..9db636a2 100644 --- a/_includes/navbar.html +++ b/_includes/navbar.html @@ -3,6 +3,7 @@ {% endcomment %} {% include gh_variables.html %} +{% include manual_episode_order.html %}

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