rhiza 0.8.2__tar.gz → 0.8.4__tar.gz

rhiza-0.8.4/.github/ISSUE_TEMPLATE/assign_ui_implementation.md

@@ -0,0 +1 @@
+- [ ] Assign implementation to GitHub Copilot

{rhiza-0.8.2 → rhiza-0.8.4}/.github/workflows/rhiza_book.yml

@@ -40,18 +40,17 @@ jobs:
         with:
           lfs: true
 
-      # Determine the Python version to use
-      - name: Get Python version
-        id: get-python
-        run: |
-          echo "python-version=$(python ./.rhiza/utils/version_max.py)" >> "$GITHUB_OUTPUT"
-
-      # Use the composite action to set up the project
-      - name: Setup the project
-        uses: ./.github/rhiza/actions/setup-project
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: ${{ steps.get-python.outputs.python-version }}
-          uv-extra-index-url: ${{ secrets.UV_EXTRA_INDEX_URL }}
+          version: "0.9.21"
+
+      - name: "Sync the virtual environment for ${{ github.repository }}"
+        shell: bash
+        run: |
+          export UV_EXTRA_INDEX_URL="${{ secrets.uv-extra-index-url }}"
+          # will just use .python-version?
+          uv sync --all-extras --frozen
 
       - name: "Make the book"
         run: |

{rhiza-0.8.2 → rhiza-0.8.4}/.github/workflows/rhiza_ci.yml

@@ -14,8 +14,9 @@ permissions:
 
 on:
   push:
+    branches: [ main, master ]
   pull_request:
-    branches: [main, master]
+    branches: [ main, master ]
 
 jobs:
   generate-matrix:
@@ -49,11 +50,17 @@ jobs:
         with:
           lfs: true
 
-      - name: Setup the project
-        uses: ./.github/rhiza/actions/setup-project
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: ${{ matrix.python-version }}
-          uv-extra-index-url: ${{ secrets.UV_EXTRA_INDEX_URL }}
+          version: "0.9.21"
+
+      - name: "Sync the virtual environment for ${{ github.repository }}"
+        shell: bash
+        run: |
+          export UV_EXTRA_INDEX_URL="${{ secrets.uv-extra-index-url }}"
+          uv venv --python ${{ matrix.python-version }}
+          uv sync --all-extras --frozen
 
       - name: Install dependencies
         run: |

rhiza-0.8.4/.github/workflows/rhiza_codeql.yml

@@ -0,0 +1,102 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL Advanced"
+
+on:
+  push:
+    branches: [ "main", "master" ]
+  pull_request:
+    branches: [ "main", "master" ]
+  schedule:
+    - cron: '27 1 * * 1'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    if: ${{ !github.event.repository.private }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: actions
+          build-mode: none
+        - language: python
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v6
+
+    # Add any setup steps before running the `github/codeql-action/init` action.
+    # This includes steps like installing compilers or runtimes (`actions/setup-node`
+    # or others). This is typically only required for manual builds.
+    # - name: Setup runtime (example)
+    #   uses: actions/setup-example@v1
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v4
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - name: Run manual build steps
+      if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v4
+      with:
+        category: "/language:${{matrix.language}}"

{rhiza-0.8.2 → rhiza-0.8.4}/.github/workflows/rhiza_deptry.yml

@@ -18,6 +18,7 @@ permissions:
 
 on:
   push:
+    branches: [ main, master ]
   pull_request:
     branches: [ main, master ]
 
@@ -26,7 +27,7 @@ jobs:
     name: Check dependencies with deptry
     runs-on: ubuntu-latest
     container:
-      image: ghcr.io/astral-sh/uv:0.9.18-python3.12-trixie
+      image: ghcr.io/astral-sh/uv:0.9.21-python3.12-trixie
 
     steps:
       - uses: actions/checkout@v6

{rhiza-0.8.2 → rhiza-0.8.4}/.github/workflows/rhiza_marimo.yml

@@ -22,6 +22,7 @@ permissions:
 
 on:
   push:
+    branches: [ main, master ]
   pull_request:
     branches: [ main, master ]
 
@@ -79,7 +80,7 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v7
         with:
-          version: "0.9.18"
+          version: "0.9.21"
 
       # Execute the notebook with the appropriate runner based on its content
       - name: Run notebook

{rhiza-0.8.2 → rhiza-0.8.4}/.github/workflows/rhiza_pre-commit.yml

@@ -20,6 +20,7 @@ permissions:
 
 on:
   push:
+    branches: [ main, master ]
   pull_request:
     branches: [ main, master ]
 
@@ -30,14 +31,5 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - name: Get Python version
-        id: get-python
-        run: |
-          echo "python-version=$(python ./.rhiza/utils/version_max.py)" >> "$GITHUB_OUTPUT"
-
-      - uses: ./.github/rhiza/actions/setup-project
-        with:
-          python-version: ${{ steps.get-python.outputs.python-version }}
-          uv-extra-index-url: ${{ secrets.UV_EXTRA_INDEX_URL }}
-
       - uses: pre-commit/action@v3.0.1
+

{rhiza-0.8.2 → rhiza-0.8.4}/.github/workflows/rhiza_release.yml

@@ -7,7 +7,7 @@
 #
 # 📋 Pipeline Phases:
 #   1. 🔍 Validate Tag - Check tag format and ensure release doesn't already exist
-#   2. 🏗️  Build - Build Python package with Hatch (if [build-system] is defined in pyproject.toml
+#   2. 🏗️ Build - Build Python package with Hatch (if [build-system] is defined in pyproject.toml
 #   3. 📝 Draft Release - Create draft GitHub release with build artifacts
 #   4. 🚀 Publish to PyPI - Publish package using OIDC or custom feed
 #   5. 🐳 Publish Devcontainer - Build and publish devcontainer image (conditional)
@@ -107,14 +107,18 @@ jobs:
         uses: actions/checkout@v6
         with:
           fetch-depth: 0
-          ref: ${{ github.ref }}
 
-      # Use the composite action to set up the project
-      - name: Setup the project
-        uses: ./.github/rhiza/actions/setup-project
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
         with:
-          python-version: ${{ vars.PYTHON_DEFAULT_VERSION || '3.14' }}
-          uv-extra-index-url: ${{ secrets.UV_EXTRA_INDEX_URL }}
+          version: "0.9.21"
+
+      - name: "Sync the virtual environment for ${{ github.repository }}"
+        shell: bash
+        run: |
+          export UV_EXTRA_INDEX_URL="${{ secrets.uv-extra-index-url }}"
+          # will just use .python-version?
+          uv sync --all-extras --frozen
 
       - name: Verify version matches tag
         if: hashFiles('pyproject.toml') != ''
@@ -181,7 +185,6 @@ jobs:
         uses: actions/checkout@v6
         with:
           fetch-depth: 0
-          #ref: ${{ github.ref }}
 
       - name: Download dist artifact
         uses: actions/download-artifact@v7
@@ -230,7 +233,6 @@ jobs:
         uses: actions/checkout@v6
         with:
           fetch-depth: 0
-          ref: ${{ github.ref }}
 
       - name: Check if devcontainer should be published
         id: check_publish
@@ -316,17 +318,21 @@ jobs:
         uses: actions/checkout@v6
         with:
           fetch-depth: 0
-          ref: ${{ github.ref }}
 
-      - name: Get Python version
-        id: get-python
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.9.21"
+
+      - name: "Sync the virtual environment for ${{ github.repository }}"
+        shell: bash
         run: |
-          echo "python-version=$(python ./.rhiza/utils/version_max.py)" >> "$GITHUB_OUTPUT"
+          export UV_EXTRA_INDEX_URL="${{ secrets.uv-extra-index-url }}"
+          # will just use .python-version?
+          uv sync --all-extras --frozen
 
       - name: Set up Python
         uses: actions/setup-python@v6
-        with:
-          python-version: ${{ fromJSON(steps.get-python.outputs.python-version) }}
 
       - name: Generate Devcontainer Link
         id: devcontainer_link

{rhiza-0.8.2 → rhiza-0.8.4}/.github/workflows/rhiza_validate.yml

@@ -5,6 +5,7 @@ permissions:
 
 on:
   push:
+    branches: [ main, master ]
   pull_request:
     branches: [ main, master ]
 
@@ -14,13 +15,13 @@ jobs:
     # don't run this in rhiza itself. Rhiza has no template.yml file.
     if: ${{ github.repository != 'jebel-quant/rhiza' }}
     container:
-      image: ghcr.io/astral-sh/uv:0.9.18-python3.12-trixie
+      image: ghcr.io/astral-sh/uv:0.9.21-python3.12-trixie
 
     steps:
       - name: Checkout repository
         uses: actions/checkout@v6
 
-      #- name: Validate Rhiza config
-      #  shell: bash
-      #  run: |
-      #    uvx rhiza validate .
+      - name: Validate Rhiza config
+        shell: bash
+        run: |
+          uvx "rhiza>=0.8.0" validate .

{rhiza-0.8.2 → rhiza-0.8.4}/.gitignore

@@ -3,6 +3,9 @@
 .venv
 .ruff_cache
 
+### Don't expose API keys, etc.
+.env
+
 __marimo__
 
 _tests
@@ -29,7 +32,7 @@ presentation.pdf
 # C extensions
 *.so
 
-# .DS_Store 
+# .DS_Store
 .DS_Store
 
 # Distribution / packaging
@@ -65,6 +68,7 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
+coverage.json
 *.cover
 *.py,cover
 .hypothesis/

{rhiza-0.8.2 → rhiza-0.8.4}/.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
         args: ["--verbose"]
 
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.9
+    rev: v1.7.10
     hooks:
       - id: actionlint
         args: [ -ignore, SC ]

rhiza-0.8.4/.python-version

@@ -0,0 +1 @@
+3.12

{rhiza-0.8.2 → rhiza-0.8.4}/.rhiza/history

@@ -6,9 +6,9 @@
 # Files under template control:
 .editorconfig
 .github/dependabot.yml
-.github/rhiza/actions/setup-project/action.yml
 .github/workflows/rhiza_book.yml
 .github/workflows/rhiza_ci.yml
+.github/workflows/rhiza_codeql.yml
 .github/workflows/rhiza_deptry.yml
 .github/workflows/rhiza_devcontainer.yml
 .github/workflows/rhiza_docker.yml
@@ -19,12 +19,13 @@
 .github/workflows/rhiza_validate.yml
 .gitignore
 .pre-commit-config.yaml
-.rhiza/CONFIG.md
-.rhiza/TOKEN_SETUP.md
+.rhiza/docs/CONFIG.md
+.rhiza/docs/TOKEN_SETUP.md
 .rhiza/scripts/book.sh
 .rhiza/scripts/bump.sh
 .rhiza/scripts/customisations/build-extras.sh
 .rhiza/scripts/customisations/post-release.sh
+.rhiza/scripts/generate-coverage-badge.sh
 .rhiza/scripts/marimushka.sh
 .rhiza/scripts/release.sh
 .rhiza/scripts/update-readme-help.sh
@@ -34,6 +35,7 @@ CODE_OF_CONDUCT.md
 CONTRIBUTING.md
 Makefile
 book/Makefile.book
+book/README.md
 book/marimo/README.md
 book/marimo/rhiza.py
 book/minibook-templates/custom.html.jinja2
@@ -50,10 +52,12 @@ tests/test_rhiza/benchmarks/README.md
 tests/test_rhiza/benchmarks/analyze_benchmarks.py
 tests/test_rhiza/conftest.py
 tests/test_rhiza/test_bump_script.py
+tests/test_rhiza/test_coverage_badge.py
 tests/test_rhiza/test_docstrings.py
 tests/test_rhiza/test_git_repo_fixture.py
 tests/test_rhiza/test_makefile.py
 tests/test_rhiza/test_marimushka_script.py
+tests/test_rhiza/test_notebooks.py
 tests/test_rhiza/test_readme.py
 tests/test_rhiza/test_release_script.py
 tests/test_rhiza/test_structure.py

{rhiza-0.8.2 → rhiza-0.8.4}/.rhiza/scripts/book.sh

@@ -8,6 +8,11 @@
 
 set -e
 
+# Determine SCRIPTS_FOLDER if not set
+if [ -z "${SCRIPTS_FOLDER}" ]; then
+  SCRIPTS_FOLDER="$(cd "$(dirname "$0")" && pwd)"
+fi
+
 BLUE="\033[36m"
 YELLOW="\033[33m"
 RESET="\033[0m"
@@ -43,6 +48,12 @@ if [ -f _tests/html-coverage/index.html ]; then
   else
     LINKS_ENTRIES='"Coverage": "./tests/html-coverage/index.html"'
   fi
+  
+  # Generate coverage badge JSON if coverage.json exists
+  if [ -f _tests/coverage.json ]; then
+    printf "%b[INFO] Generating coverage badge...%b\n" "$BLUE" "$RESET"
+    /bin/sh "${SCRIPTS_FOLDER}/generate-coverage-badge.sh"
+  fi
 else
   printf "%b[WARN] No coverage report found or directory is empty%b\n" "$YELLOW" "$RESET"
 fi

{rhiza-0.8.2 → rhiza-0.8.4}/.rhiza/scripts/bump.sh

@@ -131,8 +131,7 @@ do_bump() {
   if [ -n "$TYPE" ]; then
     # For bump types (patch/minor/major), calculate what the new version will be
     printf "%b[INFO] Bumping version using: %s%b\n" "$BLUE" "$TYPE" "$RESET"
-    NEW_VERSION=$("$UV_BIN" version --bump "$TYPE" --dry-run --short 2>/dev/null)
-    if [ $? -ne 0 ] || [ -z "$NEW_VERSION" ]; then
+    if ! NEW_VERSION=$("$UV_BIN" version --bump "$TYPE" --dry-run --short 2>/dev/null) || [ -z "$NEW_VERSION" ]; then
       printf "%b[ERROR] Failed to calculate new version with type: %s%b\n" "$RED" "$TYPE" "$RESET"
       exit 1
     fi

rhiza-0.8.4/.rhiza/scripts/generate-coverage-badge.sh

@@ -0,0 +1,79 @@
+#!/bin/sh
+# Generate a coverage badge endpoint JSON for shields.io
+# This script reads _tests/coverage.json and creates a shields.io endpoint JSON file
+
+set -e
+
+BLUE="\033[36m"
+YELLOW="\033[33m"
+RESET="\033[0m"
+
+COVERAGE_JSON="_tests/coverage.json"
+OUTPUT_DIR="_book/tests"
+BADGE_JSON="${OUTPUT_DIR}/coverage-badge.json"
+
+if [ ! -f "${COVERAGE_JSON}" ]; then
+  printf "%b[WARN] Coverage JSON file not found at ${COVERAGE_JSON}, skipping badge generation%b\n" "$YELLOW" "$RESET"
+  exit 0
+fi
+
+printf "%b[INFO] Generating coverage badge from ${COVERAGE_JSON}...%b\n" "$BLUE" "$RESET"
+
+# Extract coverage percentage and round it
+if ! COVERAGE=$(COVERAGE_JSON="${COVERAGE_JSON}" python3 << 'PYTHON_SCRIPT'
+import json
+import sys
+import os
+
+coverage_json = os.environ['COVERAGE_JSON']
+
+try:
+    with open(coverage_json, 'r') as f:
+        data = json.load(f)
+    percent = data['totals']['percent_covered']
+    print(f'{percent:.0f}')
+except Exception as e:
+    print(f'Error extracting coverage: {e}', file=sys.stderr)
+    sys.exit(1)
+PYTHON_SCRIPT
+); then
+  printf "%b[ERROR] Failed to extract coverage percentage%b\n" "$YELLOW" "$RESET"
+  exit 1
+fi
+
+if [ -z "${COVERAGE}" ]; then
+  printf "%b[ERROR] Coverage percentage is empty%b\n" "$YELLOW" "$RESET"
+  exit 1
+fi
+
+printf "%b[INFO] Coverage: ${COVERAGE}%%%b\n" "$BLUE" "$RESET"
+
+# Determine badge color based on coverage percentage
+if [ "${COVERAGE}" -ge 90 ]; then
+  COLOR="brightgreen"
+elif [ "${COVERAGE}" -ge 80 ]; then
+  COLOR="green"
+elif [ "${COVERAGE}" -ge 70 ]; then
+  COLOR="yellowgreen"
+elif [ "${COVERAGE}" -ge 60 ]; then
+  COLOR="yellow"
+elif [ "${COVERAGE}" -ge 50 ]; then
+  COLOR="orange"
+else
+  COLOR="red"
+fi
+
+# Create output directory if it doesn't exist
+mkdir -p "${OUTPUT_DIR}"
+
+# Generate shields.io endpoint JSON
+cat > "${BADGE_JSON}" << EOF
+{
+  "schemaVersion": 1,
+  "label": "coverage",
+  "message": "${COVERAGE}%",
+  "color": "${COLOR}"
+}
+EOF
+
+printf "%b[INFO] Coverage badge JSON generated at ${BADGE_JSON}%b\n" "$BLUE" "$RESET"

{rhiza-0.8.2 → rhiza-0.8.4}/.rhiza/scripts/marimushka.sh

@@ -74,4 +74,4 @@ cd "$MARIMO_FOLDER"
 # Ensure GitHub Pages does not process with Jekyll
 # The : command is a no-op that creates an empty file
 # .nojekyll tells GitHub Pages to serve files as-is without Jekyll processing
-: > "$OUTPUT_DIR/.nojekyll"
+: > "$OUTPUT_DIR/.nojekyll"

{rhiza-0.8.2 → rhiza-0.8.4}/.rhiza/template.yml

@@ -1,7 +1,7 @@
 template-repository: "jebel-quant/rhiza"
 template-branch: "main"
 include:
-    - .github
+    - .github/workflows
     - .rhiza
     - tests
     - .editorconfig
@@ -16,5 +16,5 @@ include:
     - book
     - renovate.json
 exclude:
-    - .github/workflows/docker.yml
-    - .github/workflows/devcontainer.yml
+    - .github/workflows/rhiza_docker.yml
+    - .github/workflows/rhiza_devcontainer.yml

rhiza-0.8.4/.rhiza.env

@@ -0,0 +1,11 @@
+MARIMO_FOLDER=book/marimo
+SOURCE_FOLDER=src
+SCRIPTS_FOLDER=.rhiza/scripts
+CUSTOM_SCRIPTS_FOLDER=.rhiza/scripts/customisations
+
+# Book-specific variables
+BOOK_TITLE=RHIZA
+BOOK_SUBTITLE=Generated by minibook
+PDOC_TEMPLATE_DIR=book/pdoc-templates
+BOOK_TEMPLATE=book/minibook-templates/custom.html.jinja2
+DOCFORMAT=google