Merge branch 'main' into add-blog-rispy

Author: xmnlab

.editorconfig

@@ -0,0 +1,32 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.{py,rst,ini}]
+indent_style = space
+indent_size = 4
+
+[*.{html,css,scss,json,yml,yaml,xml,toml}]
+indent_style = space
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false
+indent_style = space
+indent_size = 2
+
+[default.conf]
+indent_style = space
+indent_size = 2
+
+["Makefile"]
+indent_style = tab
+
+[*.{diff,patch}]
+trim_trailing_whitespace = false

.github/workflows/main.yaml

@@ -1,43 +1,72 @@
-
 name: main
 
 on:
   push:
-    branches: [ main ]
+    branches: [main]
   pull_request:
-    branches: [ main ]
+    branches: [main]
 
 jobs:
+  check-branch:
+    if: ${{ github.event_name == 'pull_request' }}
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    concurrency:
+      group: check-pr-${{ github.ref }}
+      cancel-in-progress: true
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Check if the PR's branch is updated
+        uses: osl-incubator/gh-check-pr-is-updated@1.0.0
+        with:
+          remote_branch: origin/main
+          pr_sha: ${{ github.event.pull_request.head.sha }}
+
   build:
     runs-on: ubuntu-latest
     concurrency:
-      group: ci-${{ github.ref }}
+      group: ci-${{ github.event_name }}-${{ github.ref }}
       cancel-in-progress: true
     defaults:
       run:
         shell: bash -l {0}
     steps:
-    - uses: actions/checkout@v2
-
-    - uses: conda-incubator/setup-miniconda@v2
-      with:
-        miniconda-version: "latest"
-        mamba-version: "*"
-        environment-file: conda/dev.yaml
-        channels: conda-forge,nodefaults
-        activate-environment: osl-web
-        use-mamba: true
-        miniforge-variant: Mambaforge
-
-    - name: Build the book
-      run: |
-        makim pages.build
-        echo "opensciencelabs.org" > build/CNAME
-
-    # Push the book's HTML to github-pages
-    - name: GitHub Pages action
-      uses: peaceiris/actions-gh-pages@v3.5.9
-      if: ${{ github.event_name == 'push' }}
-      with:
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-        publish_dir: ./build
+      - uses: actions/checkout@v3
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          environment-file: conda/dev.yaml
+          channels: conda-forge,nodefaults
+          activate-environment: osl-web
+          auto-update-conda: true
+          conda-solver: libmamba
+
+      - name: Install dependencies
+        run: |
+          poetry check
+          poetry install
+          python -m nltk.downloader punkt
+
+      - name: Linter
+        if: ${{ github.event_name == 'pull_request' }}
+        run: |
+          pre-commit install
+          pre-commit run --all-file --verbose
+
+      - name: Build the book
+        run: |
+          makim pages.build
+          echo "opensciencelabs.org" > build/CNAME
+
+      # Push the book's HTML to github-pages
+      - name: GitHub Pages action
+        uses: peaceiris/actions-gh-pages@v3.5.9
+        if: ${{ github.event_name == 'push' }}
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./build

.makim.yaml

@@ -1,10 +1,9 @@
-version: 1.0
 groups:
   pages:
-    targets:
+    tasks:
       pre-build:
         help: pre-build step
-        shell: bash
+        backend: bash
         run: |
           mkdir -p build
           # Directory to search for .ipynb files
@@ -16,14 +15,29 @@ groups:
             "*.ipynb" -exec sh -c \
             'jupyter nbconvert --to markdown --template=theme/custom-markdown.tpl --output-dir "$(dirname "$0")" --output "index" "$0"' {} \;
 
+          # remove console colors from md files
+          find "$SEARCH_DIR" -name \
+            "index.md" -exec sh -c \
+            'cat "$(dirname "$0")/index.md" | python scripts/clean-output.py > "$(dirname "$0")/temp_index.md" && mv "$(dirname "$0")/temp_index.md" "$(dirname "$0")/index.md"' {} \;
+
       build:
         help: build the static page
-        dependencies:
-          - target: pages.pre-build
-        run: mkdocs build --verbose --clean
+        hooks:
+          pre-run:
+            - task: pages.pre-build
+        run: |
+          rm -rf build/*
+          mkdocs build --verbose --clean --strict
 
       preview:
         help: preview the web page dynamically
-        dependencies:
-          - target: pages.pre-build
+        args:
+          run-pre-build:
+            help: Run pre-build task
+            type: bool
+            action: store_true
+        hooks:
+          pre-run:
+            - task: pages.pre-build
+              if: ${{ args.run_pre_build }}
         run: mkdocs serve --watch pages --watch theme

.pre-commit-config.yaml

@@ -0,0 +1,62 @@
+default_stages:
+  - pre-commit
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: "pages/blog"
+      - id: end-of-file-fixer
+        exclude: "pages/blog"
+      - id: check-json
+      - id: check-toml
+      - id: check-xml
+        exclude: ".*.svg"
+      - id: check-builtin-literals
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: detect-private-key
+        exclude: "theme"
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.2"
+    hooks:
+      - id: prettier
+        exclude: "pages/blog|theme"
+
+  - repo: local
+    hooks:
+      - id: mkdocs-build
+        name: mkdocs-build
+        entry: makim pages.build
+        files: pages
+        language: system
+        pass_filenames: false
+
+      - id: linkcheckmd
+        name: linkcheckmd
+        entry: python scripts/check-broken-links-md.py
+        language: system
+        pass_filenames: false
+
+      - id: check-internal-links
+        name: check-internal-links
+        entry: python scripts/check-broken-links-internal.py
+        language: system
+        pass_filenames: false
+
+      - id: ruff-format
+        name: ruff-format
+        entry: ruff format
+        language: system
+        pass_filenames: true
+        types:
+          - python
+
+      - id: ruff-linter
+        name: ruff-linter
+        entry: ruff check
+        language: system
+        pass_filenames: true
+        types:
+          - python

.prettierignore

@@ -0,0 +1 @@
+docs/changelog.md

.prettierrc.yaml

@@ -0,0 +1,6 @@
+overrides:
+  - files: "*.md"
+    options:
+      parser: remark
+      proseWrap: always
+      printWidth: 80

.wellKnown/funding-manifest-urls

@@ -0,0 +1 @@
+Find the OSL funding.json file at: www.opensciencelabs.org/funding.json

CODE_OF_CONDUCT.md

@@ -6,8 +6,8 @@ We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
 identity and expression, level of experience, education, socio-economic status,
-nationality, personal appearance, race, religion, or sexual identity
-and orientation.
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
 
 We pledge to act and interact in ways that contribute to an open, welcoming,
 diverse, inclusive, and healthy community.
@@ -17,23 +17,23 @@ diverse, inclusive, and healthy community.
 Examples of behavior that contributes to a positive environment for our
 community include:
 
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
   and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the
-  overall community
+- Focusing on what is best not just for us as individuals, but for the overall
+  community
 
 Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery, and sexual attention or
-  advances of any kind
-* Trolling, insulting or derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email
-  address, without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+- The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+- Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ## Enforcement Responsibilities
@@ -60,8 +60,8 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-opensciencelabs@gmail.com.
-All complaints will be reviewed and investigated promptly and fairly.
+team@opensciencelabs.org. All complaints will be reviewed and investigated
+promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
 reporter of any incident.
@@ -82,15 +82,15 @@ behavior was inappropriate. A public apology may be requested.
 
 ### 2. Warning
 
-**Community Impact**: A violation through a single incident or series
-of actions.
+**Community Impact**: A violation through a single incident or series of
+actions.
 
 **Consequence**: A warning with consequences for continued behavior. No
 interaction with the people involved, including unsolicited interaction with
 those enforcing the Code of Conduct, for a specified period of time. This
 includes avoiding interactions in community spaces as well as external channels
-like social media. Violating these terms may lead to a temporary or
-permanent ban.
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
 
 ### 3. Temporary Ban
 
@@ -106,20 +106,20 @@ Violating these terms may lead to a permanent ban.
 ### 4. Permanent Ban
 
 **Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior,  harassment of an
+standards, including sustained inappropriate behavior, harassment of an
 individual, or aggression toward or disparagement of classes of individuals.
 
-**Consequence**: A permanent ban from any sort of public interaction within
-the community.
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
 
 ## Attribution
 
 This Code of Conduct is adapted from the [Contributor Covenant][homepage],
 version 2.0, available at
 https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
 
-Community Impact Guidelines were inspired by [Mozilla's code of conduct
-enforcement ladder](https://github.com/mozilla/diversity).
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder](https://github.com/mozilla/diversity).
 
 [homepage]: https://www.contributor-covenant.org