eopf-geozarr 0.6.1__tar.gz

eopf_geozarr-0.6.1/.github/CI.md

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+# CI/CD Documentation
+
+This directory contains the GitHub Actions workflows and configuration for the eopf-geozarr project.
+
+## Workflows
+
+### 1. CI Workflow (`ci.yml`)
+**Triggers:** Push to main, Pull requests to main
+
+**Jobs:**
+- **pre-commit**: Runs pre-commit hooks for code quality
+- **test**: Runs tests on Python 3.11 and 3.12 on Ubuntu
+- **test-network**: Runs network-dependent tests (only on main branch pushes)
+- **docs**: Builds documentation
+- **security**: Runs security scans with bandit and safety
+
+**Features:**
+- Code coverage reporting with Codecov
+- Artifact uploads for documentation and security reports
+- Separate network tests to avoid CI failures from external dependencies
+
+### 2. Code Quality Workflow (`code-quality.yml`)
+**Triggers:** Pull requests to main
+
+**Jobs:**
+- **lint**: Runs black, isort, flake8, and mypy
+- **test-coverage**: Runs tests with coverage requirements (80% minimum)
+- **security-scan**: Runs bandit and safety security checks
+
+**Purpose:** Ensures code quality standards before merging PRs
+
+### 3. Release Workflow (`release.yml`)
+**Triggers:** GitHub releases
+
+**Jobs:**
+- **build**: Builds the Python package and validates it
+- **publish**: Publishes to PyPI using trusted publishing
+
+**Features:**
+- Automated PyPI publishing on releases
+- Package validation before publishing
+- Uses GitHub's trusted publishing for secure PyPI uploads
+
+### 4. Documentation Workflow (`docs.yml`)
+**Triggers:** Push to main, Pull requests to main
+
+**Jobs:**
+- **build-docs**: Builds Sphinx documentation
+- **deploy**: Deploys to GitHub Pages (main branch only)
+
+**Features:**
+- Automatic documentation deployment
+- Documentation artifacts for PR previews
+
+## Configuration Files
+
+### Pre-commit Configuration (`.pre-commit-config.yaml`)
+Defines hooks for:
+- Code formatting (black, isort)
+- Linting (flake8, mypy)
+- Security scanning (bandit)
+- General file checks (trailing whitespace, YAML validation, etc.)
+
+### Dependabot Configuration (`dependabot.yml`)
+Automated dependency updates for:
+- Python packages (weekly)
+- GitHub Actions (weekly)
+- Assigned to `developmentseed/data-model-developers` team
+
+## Setup Instructions
+
+### For Developers
+
+1. **Install pre-commit hooks:**
+   ```bash
+   pip install -e ".[dev]"
+   pre-commit install
+   ```
+
+2. **Run code quality checks locally:**
+   ```bash
+   black --check eopf_geozarr/
+   isort --check-only eopf_geozarr/
+   flake8 eopf_geozarr/
+   mypy eopf_geozarr/
+   ```
+
+3. **Run tests:**
+   ```bash
+   pytest eopf_geozarr/tests/ -v --tb=short -m "not network"
+   ```
+
+### For Repository Maintainers
+
+1. **Enable GitHub Pages:**
+   - Go to repository Settings > Pages
+   - Set source to "GitHub Actions"
+
+2. **Configure PyPI Publishing:**
+   - Set up trusted publishing on PyPI
+   - No secrets needed with trusted publishing
+
+3. **Configure Codecov:**
+   - Add repository to Codecov
+   - No additional configuration needed
+
+## Code Quality Standards
+
+- **Code Coverage:** Minimum 80% required
+- **Code Style:** Black formatting with 100 character line length
+- **Import Sorting:** isort with black profile
+- **Type Checking:** mypy with strict settings
+- **Security:** bandit security scanning
+- **Documentation:** All public APIs must be documented
+
+## Testing Strategy
+
+- **Unit Tests:** Fast tests without external dependencies
+- **Integration Tests:** Tests with real data processing
+- **Network Tests:** Tests requiring internet access (marked with `@pytest.mark.network`)
+- **End-to-End Tests:** CLI testing with real workflows
+
+## Release Process
+
+1. Update version in `pyproject.toml`
+2. Update `CHANGELOG.md`
+3. Create a GitHub release with tag
+4. Package is automatically built and published to PyPI
+
+## Troubleshooting
+
+### Common Issues
+
+1. **Pre-commit failures:** Run `pre-commit run --all-files` to fix issues
+2. **Test failures:** Check if network tests are failing due to external dependencies
+3. **Coverage failures:** Add tests or exclude lines with `# pragma: no cover`
+4. **Security scan failures:** Review bandit reports and add exclusions if needed
+
+### Getting Help
+
+- Check workflow logs in the Actions tab
+- Review the specific job that failed
+- Common fixes are usually code formatting or missing tests

eopf_geozarr-0.6.1/.github/dependabot.yml

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+version: 2
+updates:
+  # Enable version updates for Python dependencies
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "09:00"
+    open-pull-requests-limit: 10
+    reviewers:
+      - "developmentseed/data-model-developers"
+    assignees:
+      - "developmentseed/data-model-developers"
+    commit-message:
+      prefix: "deps"
+      include: "scope"
+
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+      time: "09:00"
+    open-pull-requests-limit: 5
+    reviewers:
+      - "developmentseed/data-model-developers"
+    assignees:
+      - "developmentseed/data-model-developers"
+    commit-message:
+      prefix: "ci"
+      include: "scope"

eopf_geozarr-0.6.1/.github/workflows/build_uv_cache.yml

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+name: Build uv cache
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "uv.lock"
+      - "pyproject.toml"
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 */5 * *"  # Every 5 days, before cache expiry
+
+jobs:
+  build-cache:
+    runs-on: ubuntu-latest
+    
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          version: "0.8.4"
+          python-version: "3.13"
+          enable-cache: false
+
+      - name: Install dependencies and populate cache
+        run: |
+          echo "Building global UV cache..."
+          uv sync --group dev --group test
+          echo "Cache populated successfully"
+
+      - name: Save uv caches
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.cache/uv
+            ~/.local/share/uv
+            .venv
+          key: uv-main-${{ hashFiles('uv.lock') }}

eopf_geozarr-0.6.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v5
+    - uses: actions/setup-python@v6
+      with:
+        python-version: '3.11'
+    - uses: pre-commit/action@v3.0.1
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.11', '3.12']
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Restore global uv cache
+      id: cache-restore
+      uses: actions/cache/restore@v4
+      with:
+        path: |
+          ~/.cache/uv
+          ~/.local/share/uv
+          .venv
+        key: uv-main-${{ hashFiles('uv.lock') }}
+        restore-keys: |
+          uv-main-
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+      with:
+        version: "0.8.4"
+        python-version: "3.13"
+        enable-cache: false
+
+    - name: Install dependencies
+      run: uv sync --group dev --group test
+
+    - name: Run tests
+      run: |
+        uv run pytest tests/ -v --tb=short -m "not network" --cov=eopf_geozarr --cov-report=xml --cov-report=term-missing
+
+    - name: Upload coverage to Codecov
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+      uses: codecov/codecov-action@v5
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+
+    - name: Save uv caches
+      if: steps.cache-restore.outputs.cache-hit != 'true'
+      uses: actions/cache/save@v4
+      with:
+        path: |
+          ~/.cache/uv
+          ~/.local/share/uv
+          .venv
+        key: uv-main-${{ hashFiles('uv.lock') }}
+
+  security:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.11'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install bandit safety
+
+    - name: Run security checks
+      run: |
+        bandit -r eopf_geozarr/ -f json -o bandit-report.json || true
+        safety check --json --output safety-report.json || true
+
+    - name: Upload security reports
+      uses: actions/upload-artifact@v5
+      with:
+        name: security-reports
+        path: |
+          bandit-report.json
+          safety-report.json

eopf_geozarr-0.6.1/.github/workflows/docs.yml

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+name: Documentation
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+    paths:
+      - "docs/**"
+
+jobs:
+  build-docs:
+    permissions:
+      contents: write
+      pages: write   
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.11'
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+      with:
+        version: "0.8.4"
+        python-version: "3.13"
+        enable-cache: false
+
+    - name: Install dependencies
+      run: uv sync --group docs
+
+    - name: Build docs
+      if: github.event_name == 'pull_request'
+      run: uv run -- mkdocs build
+
+    - name: Deploy docs
+      if: github.event_name == 'push'
+      run: uv run -- mkdocs gh-deploy --force

eopf_geozarr-0.6.1/.github/workflows/release.yml

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+name: Release
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.11'
+
+    - name: Install build dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build twine
+
+    - name: Build package
+      run: python -m build
+
+    - name: Check package
+      run: twine check dist/*
+
+    - name: Upload build artifacts
+      uses: actions/upload-artifact@v5
+      with:
+        name: dist
+        path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+    - name: Download build artifacts
+      uses: actions/download-artifact@v6
+      with:
+        name: dist
+        path: dist/
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages-dir: dist/

eopf_geozarr-0.6.1/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
+#  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+tests-output/
+
+# uv
+uv.lock
+.vscode/settings.json
+
+# VCS versioning
+src/eopf_geozarr/_version.py

eopf_geozarr-0.6.1/.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.24.1
+    hooks:
+      - id: validate-pyproject
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.3
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.11.2
+    hooks:
+      - id: mypy
+        language_version: python
+        exclude: tests/.*
+        additional_dependencies:
+        - types-attrs
+        - typing-extensions>=4.15.0
+        - pydantic>=2.12