Merge pull request #2 from VisLab/repo_setup

Initial refactoring and setup

Author: VisLab

.coveragerc

@@ -0,0 +1,15 @@
+[run]
+branch = True
+omit =
+        */__init__.py
+        */venv/*
+        */tests/*
+        **/tests/
+        **/test/
+        */test*
+        **/__init__.py
+        **/_version.py
+
+
+[report]
+skip_empty = true

.gitattributes

@@ -0,0 +1,44 @@
+hed/_version.py export-subst
+
+# Set default behavior to automatically normalize line endings to LF
+* text=auto eol=lf
+
+# Explicitly declare text files you want to always be normalized and converted to LF on checkout
+*.xml text eol=lf
+*.mediawiki text eol=lf
+*.tsv text eol=lf
+*.md text eol=lf
+*.rst text eol=lf
+*.txt text eol=lf
+*.py text eol=lf
+*.sh text eol=lf
+*.yml text eol=lf
+*.yaml text eol=lf
+*.json text eol=lf
+*.toml text eol=lf
+*.svg text eol=lf
+*.css text eol=lf
+*.js text eol=lf
+*.html text eol=lf
+
+# Denote all files that are truly binary and should not be modified
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.gif binary
+*.ico binary
+*.pdf binary
+*.zip binary
+*.gz binary
+*.tar binary
+*.mp3 binary
+*.mp4 binary
+*.mov binary
+*.avi binary
+*.exe binary
+*.dll binary
+*.so binary
+*.dylib binary
+*.class binary
+*.jar binary
+*.war binary

.github/dependabot.yml

@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "main"
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    target-branch: "main"
+    schedule:
+      interval: "weekly"

.github/workflows/black.yaml

@@ -0,0 +1,30 @@
+name: Black Code Formatter Check
+
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+permissions:
+  contents: read
+
+jobs:
+  black:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install Black
+        run: |
+          python -m pip install --upgrade pip
+          pip install black>=24.0.0
+
+      - name: Check code formatting with Black
+        run: |
+          black --check --diff --workers 1 .

.github/workflows/ci.yaml

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+name: CI
+
+on:
+  push:
+    branches: ["*"]
+  pull_request:
+    branches: ["*"]
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  determine_version:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - id: set-matrix
+        run: |
+          if [[ "${{ github.event_name }}" == 'push' && "${{ github.ref }}" == 'refs/heads/main' ]]; then
+            # Push to main branch
+            echo 'matrix=["3.10", "3.11", "3.12", "3.13", "3.14"]' >> $GITHUB_OUTPUT
+          elif [[ "${{ github.event_name }}" == 'pull_request' && "${{ github.event.pull_request.base.ref }}" == 'main' ]]; then
+            # PR to main branch
+            echo 'matrix=[ "3.10", "3.11", "3.12", "3.13", "3.14"]' >> $GITHUB_OUTPUT
+          else
+            echo 'matrix=["3.10", "3.13"]' >> $GITHUB_OUTPUT
+          fi
+
+  build:
+    needs: determine_version
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: ${{fromJson(needs.determine_version.outputs.matrix)}}
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -r docs/requirements.txt
+          pip install -e .[test]
+
+      # Run spec tests without coverage for non Python 3.10
+      - name: Run spec_test
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        continue-on-error: true
+        run: |  
+           python -m unittest discover spec_tests
+
+      # Run unittest without coverage
+      - name: Test with unittest
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          python -m unittest discover tests

.github/workflows/ci_cov.yaml

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+name: CI_COV
+
+on:
+  push:
+    branches: [main]
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+
+  build:
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: [ "3.10" ]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff -r requirements.txt -r docs/requirements.txt
+          pip install -e .[test]
+
+      # Run ruff
+      - name: Lint with ruff
+        run: |
+          ruff check . --output-format=github 
+
+      # Run unittest with coverage
+      - name: Test with unittest and coverage
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |  
+          coverage run -m unittest discover tests
+
+      # Run spec tests with coverage
+      - name: Run spec_test coverage
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |  
+          coverage run --append -m unittest discover spec_tests
+          coverage xml
+
+      # Upload coverage to qlty
+      - name: Upload coverage to qlty
+        uses: qltysh/qlty-action/coverage@v2
+        with:
+          oidc: true
+          files: coverage.xml

.github/workflows/ci_windows.yaml

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+name: CI Windows
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["main"]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        platform: [windows-latest]
+        python-version: ["3.10", "3.11", "3.12"]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: false
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - uses: actions/cache@v4
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('docs/requirements.txt') }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -e .[test]
+
+      - name: Test with unittest
+        env:
+          HED_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          python -m unittest discover tests

.github/workflows/codespell.yaml

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+---
+name: Codespell
+
+on:
+  push:
+    branches: [develop]
+  pull_request:
+    branches: [develop]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2