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Attempt to update to latest styles (#9)
* 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 swcarpentry/r-novice-gapminder-es#53 * translate 'cite' to 'cita' as per swcarpentry/r-novice-gapminder-es#54 * Update navbar.html fix typo, as suggested in swcarpentry/r-novice-gapminder-es#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 <tbyhdgs@gmail.com> * [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 <allen.lee@asu.edu> * 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 <dan.mccloy@gmail.com>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 <sarah_m_brown@brown.edu> * 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 <tomgreen66@hotmail.com> * 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 <maxim.belkin@gmail.com> Co-authored-by: François Michonneau <francois.michonneau@gmail.com> * 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 <maxim.belkin@gmail.com> * GitHub Actions: website (#488) * GitHub Actions: better workflow and job names (#500) * GitHub Action: website.yml: don't run in forks (#501) * GH Website action: rename + don't use lesson directory (#504) When 'Website' action tests a lesson, it checks out repositories into the current working directory: 'lesson' directory doesn't exist. As a result, steps that use "lesson" as the working directory fail. * lesson.scss: styling for DIVs for embedding Youtube videos (#503) * update link to discuss mailing list (#507) * add default repository to install_required_packages() (#509) * add warning blockquote * Revert "Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages" This reverts commit 2c6b97e, reversing changes made to 53e9913. * add warning code block * update expected reference filename (#508) * lesson.scss: no borders around unrecognized code (#510) * bump ruby version (as specified in github-pages v209) * drop patch version, fix at v1 * removing contractions from CONTRIBUTING (#512) * add image-with-shadow class * _config.yml: mention Carpentries Incubator * Matlab -> MATLAB * set CRAN url if default is "@cran@" This will fix #526 * Fix Ruby style * accept any base filename for Rmd episodes * run R-based lessons in forks This is a modification for #501 * add control structure * 404 page for better learner experience * lesson.scss: wildcard selectors for code blocks * Ignore .jekyll-metatada * Speed up builds of R-based lessons R-based lessons might take a while to build because packages need to be compiled from source. RStudio Package Manager has compiled versions of packages for ubuntu distros starting with 16.04: https://packagemanager.rstudio.com/client/#/repos/1/overview I've added the necessary magic in the actions yaml to make it work. * No need for User Agent string * permissive checks for pre-alpha lessons This will fix #533 * bin/lesson_check.py: allow 'language-*' code blocks (#532) * bin/lesson_check.py: allow 'caution' blockquote * avoid ansi color characters from being printed * deploy from "website" action * deploy R-based lessons without using another action * also delete _site * include @zkamvar suggestions Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> * pin ubuntu version to 20.04 (#540) Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> * GitHub Actions: cache required R packages (#534) * add missing parenthesis * Add incubator option for carpentry field. (#542) Closes #541 * .editorconfig: don't trim trailing spaces in markdown * lesson.scss: HTML block carpentries/styles#519 * add patch to clean gh-pages before committing (#545) This will address #544 * Fix Kramdown parser crash ... by using GFM (GitHub-flavored Markdown) parser (`kramdown-parser-gfm`) instead of the default one (`kramdown`). The default one fails to produce an AST (Abstract Syntax Tree) when there is no blank line before the line with the opening code fence. Related: - gettalong/kramdown#530 - Python-Markdown/markdown#807 Fixes: carpentries/styles#543 * bin/util.py: Change ruby executable to "bundle exec ruby" Closes: carpentries/styles#547 * Change link colours (#549) ...to make them distinguishable from regular text. And for accessibility! * bin/workshop_check.py: update default contact email address * Gemfile: add 'webrick' dependency for Ruby 3.0.0 and above Fixes carpentries/styles#552 * lesson_check.py allow for missing life_cycle This will fix carpentries/styles#556 * update with Maxim's suggestion * Add catch for None type code block in lesson_check There are times when the AST is malformed and does not emit a class for the code element. We do not want the parser to crash when this happens, but we also want to notify ourselves that the AST is malformed. This should not result in an error because as we saw in carpentries/styles#543, the parser itself can cause these malformations when the lesson itself renders well. Even though we fixed the previous issue with an updated parser, problems still persist: swcarpentry/r-novice-gapminder#696 (comment) I fully admit that this is a kludge. * fix syntax I've removed the print condition, because it will just result in an error no matter what (sigh) * Makefile: fix 'bundle config' command flags * Makefile: clean target: remove .vendor, .bundle, Gemfile.lock Clean up: 1. `.vendor` directory where Bundler installs all the gems. 2. `.bundle` directory where Bundler stores its settings. 3. `Gemfile.lock` file generated by the Bundler. * Makefile: silence Docker commands * use Ruby's official GH Actions * Makefile: use SHELL to call bin/knit_lesson.sh * Makefile: fix up PHONY targets * Fix GitHub actions for lessons in Rmarkdown Specifically, set CRAN repository to https://cran.rstudio.com * apply single shadow to image class * use grey shadow instead of transparent black * expand image-with-shadow selection * Makefile: don't fail when Python isn't found * bin/dependencies.R: handle 'no packages were specified' error Fixes the following issue: ``` $ make site lib paths: /Library/Frameworks/R.framework/Versions/3.5/Resources/library Error in install.packages(missing_pkgs, lib = lib, repos = repos) : no packages were specified Calls: install_required_packages -> install.packages Execution halted make: *** [install-rmd-deps] Error 1 ``` * Don't check links.md in lessons that use remote theme Fixes carpentries/styles#570 * add link references to code_of_conduct.md (#572) * Update links.md * add source_dir argument This will fix carpentries/styles#576 * Improved relative_root_path * update contributing guide * add further languages for box titles (#580) Will be useful for HPC-Carpentry lessons, GPU programming lesson as well as Julia lessons which are currently in the incubator. * bin/lesson_check.py: one more fix for using_remote_theme() * Template workflow: add two more lessons * add make lesson-check-all step * Set working directory for the 'make site' step * Template workflow: smarter syncing with the styles repo Current syncing procedure that used in the Template workflow fails for: 1. Lessons that are, in fact, nsync with the styles repo. 2. For lessons that use The Carpentries' remote theme and have deleted some of the files. This PR makes this step a little bit more intelligent and takes into account the above two scenarios. * Apply Zhian's suggestions Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> * add math support with katex (#573) * bin/util.py: remove unused 'IMAGE_FILE_SUFFIX' var (#590) It should've been removed in 7e835fd. Co-authored-by: Erin Becker <erinstellabecker@gmail.com> Co-authored-by: Paula Andrea <orchid00@users.noreply.github.com> Co-authored-by: François Michonneau <francois.michonneau@gmail.com> Co-authored-by: raynamharris <rayna.harris@utexas.edu> Co-authored-by: Paola Prieto <31372246+PaoPrieto@users.noreply.github.com> Co-authored-by: Rayna M Harris <raynamharris@users.noreply.github.com> Co-authored-by: Raniere Silva <raniere@rgaiacs.com> Co-authored-by: K.E. Koziar <katherine.koziar@ucr.edu> Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com> Co-authored-by: stamper <tbyhdgs@gmail.com> Co-authored-by: Michael Joseph <josephmje.22@gmail.com> Co-authored-by: Joao Rodrigues <j.p.g.l.m.rodrigues@gmail.com> Co-authored-by: Sarah Brown <sarah_m_brown@brown.edu> Co-authored-by: Allen Lee <allen.lee@asu.edu> Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com> Co-authored-by: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com> Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com> Co-authored-by: Thomas Green <tomgreen66@hotmail.com> Co-authored-by: ocaisa <a.ocais@fz-juelich.de> Co-authored-by: Joseph Stachelek <jsta@users.noreply.github.com> Co-authored-by: Renato Alves <alves.rjc@gmail.com> Co-authored-by: Henry Schreiner <HenrySchreinerIII@gmail.com> Co-authored-by: Christina K <christinakconnect@gmail.com> Co-authored-by: Kilian <kilian.lieret@posteo.de> Co-authored-by: Trevor Keller <trevor.keller@gmail.com> Co-authored-by: Andrew Reid <andrew.reid@nist.gov> Co-authored-by: Bailey Harrington <baileythegreen@gmail.com> Co-authored-by: Alan O'Callaghan <alan.ocallaghan@outlook.com> Co-authored-by: Benson Muite <bkmgit@users.noreply.github.com>
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