Merge branch gh-pages of carpentries/styles

Author: maxim-belkin

.github/workflows/template.yml

@@ -8,14 +8,16 @@ jobs:
     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: Ubuntu
+            os-name: Linux
           - os: macos-latest
             os-name: macOS
           - os: windows-latest
@@ -26,6 +28,16 @@ jobs:
             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
@@ -62,25 +74,54 @@ jobs:
           path: lesson
           fetch-depth: 0
 
-      - name: Determine the proper reference to use
-        id: styles-ref
+      - name: Sync lesson with carpentries/styles
+        working-directory: lesson
         run: |
-          if [[ -n "${{ github.event.pull_request.number }}" ]]; then
-            echo "::set-output name=ref::refs/pull/${{ github.event.pull_request.number }}/head"
+          echo "::group::Fetch Styles"
+          if [[ -n "${{ github.event.pull_request.number }}" ]]
+          then
+            ref="refs/pull/${{ github.event.pull_request.number }}/head"
           else
-            echo "::set-output name=ref::gh-pages"
+            ref="gh-pages"
           fi
 
-      - name: Sync lesson with carpentries/styles
-        working-directory: lesson
-        run: |
           git config --global user.email "[email protected]"
           git config --global user.name "The Carpentries Bot"
+
           git remote add styles https://github.com/carpentries/styles.git
-          git config --local remote.styles.tagOpt --no-tags
-          git fetch styles ${{ steps.styles-ref.outputs.ref }}:styles-ref
-          git merge -s recursive -Xtheirs --no-commit styles-ref
-          git commit -m "Sync lesson with carpentries/styles"
+          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
@@ -136,3 +177,6 @@ jobs:
 
       - run: make site
         working-directory: lesson
+
+      - run: make lesson-check-all
+        working-directory: lesson

CODE_OF_CONDUCT.md

@@ -9,4 +9,5 @@ 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

_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 %}

_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:[email protected]
-[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/

assets/css/lesson.scss

@@ -64,16 +64,32 @@ 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-bash::before   { content: "Bash"; }
-div.language-c::before      { content: "C"; }
-div.language-cmake::before  { content: "CMake"; }
-div.language-cpp::before    { content: "C++"; }
-div.language-html::before   { content: "HTML"; }
-div.language-make::before   { content: "Make"; }
-div.language-matlab::before { content: "MATLAB"; }
-div.language-python::before { content: "Python"; }
-div.language-r::before      { content: "R"; }
-div.language-sql::before    { content: "SQL"; }
+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 {

bin/boilerplate/CONTRIBUTING.md

@@ -70,7 +70,7 @@ There are many ways to contribute,
 from writing new exercises and improving existing ones
 to updating or filling in the documentation
 and submitting [bug reports][issues]
-about things that do not work, aren not clear, or are missing.
+about things that do not work, are not clear, or are missing.
 If you are looking for ideas, please see the 'Issues' tab for
 a list of issues associated with this repository,
 or you may also look at the issues for [Data Carpentry][dc-issues], 
@@ -94,7 +94,7 @@ and (b) explain what you would take out to make room for it.
 The first encourages contributors to be honest about requirements;
 the second, to think hard about priorities.
 
-We are also not looking for exercises or other material that only run on one platform.
+We are also not looking for exercises or other material that will only run on one platform.
 Our workshops typically contain a mixture of Windows, macOS, and Linux users;
 in order to be usable,
 our lessons must run equally well on all three.
@@ -104,7 +104,7 @@ our lessons must run equally well on all three.
 If you choose to contribute via GitHub, you may want to look at
 [How to Contribute to an Open Source Project on GitHub][how-contribute].
 To manage changes, we follow [GitHub flow][github-flow].
-Each lesson has two maintainers who review issues and pull requests or encourage others to do so.
+Each lesson has at least two maintainers who review issues and pull requests or encourage others to do so.
 The maintainers are community volunteers and have final say over what gets merged into the lesson.
 To use the web interface for contributing to a lesson:
 
@@ -128,12 +128,12 @@ repository for reference while revising.
 
 ## Other Resources
 
-General discussion of [Software Carpentry][swc-site] and [Data Carpentry][dc-site]
+General discussion of [Software Carpentry][swc-site], [Data Carpentry][dc-site], and [Library Carpentry][lc-site]
 happens on the [discussion mailing list][discuss-list],
 which everyone is welcome to join.
 You can also [reach us by email][email].
 
-[email]: mailto:admin@software-carpentry.org
+[email]: mailto:team@carpentries.org
 [dc-issues]: https://github.com/issues?q=user%3Adatacarpentry
 [dc-lessons]: http://datacarpentry.org/lessons/
 [dc-site]: http://datacarpentry.org/

bin/dependencies.R

@@ -5,19 +5,20 @@ install_required_packages <- function(lib = NULL, repos = getOption("repos", def
   }
 
   message("lib paths: ", paste(lib, collapse = ", "))
-  missing_pkgs <- setdiff(
-    c("rprojroot", "desc", "remotes", "renv"),
-    rownames(installed.packages(lib.loc = lib))
-  )
+  required_pkgs <- c("rprojroot", "desc", "remotes", "renv")
+  installed_pkgs <- rownames(installed.packages(lib.loc = lib))
+  missing_pkgs <- setdiff(required_pkgs, installed_pkgs)
+
   # The default installation of R will have "@CRAN@" as the default repository, which directs contrib.url() to either
   # force the user to choose a mirror if interactive or fail if not. Since we are not interactve, we need to force the
   # mirror here.
   if ("@CRAN@" %in% repos) {
     repos <- c(CRAN = "https://cran.rstudio.com/")
   }
 
-  install.packages(missing_pkgs, lib = lib, repos = repos)
-
+  if (length(missing_pkgs) != 0) {
+    install.packages(missing_pkgs, lib = lib, repos = repos)
+  }
 }
 
 find_root <- function() {

bin/lesson_check.py

@@ -113,7 +113,10 @@ def main():
     if life_cycle == "pre-alpha":
         args.permissive = True
     check_source_rmd(args.reporter, args.source_dir, args.parser)
-    args.references = read_references(args.reporter, args.reference_path)
+
+    args.references = {}
+    if not using_remote_theme(args.source_dir):
+        args.references = read_references(args.reporter, args.reference_path)
 
     docs = read_all_markdown(args.source_dir, args.parser)
     check_fileset(args.source_dir, args.reporter, list(docs.keys()))
@@ -167,6 +170,10 @@ def parse_args():
 
     return args
 
+def using_remote_theme(source_dir):
+    config_file = os.path.join(source_dir, '_config.yml')
+    config = load_yaml(config_file)
+    return 'remote_theme' in config
 
 def check_config(reporter, source_dir):
     """Check configuration file."""
@@ -493,7 +500,8 @@ def check(self):
         """Run extra tests."""
 
         super().check()
-        self.check_reference_inclusion()
+        if not using_remote_theme(args.source_dir):
+            self.check_reference_inclusion()
 
     def check_metadata(self):
         super().check_metadata()