statespacecheck 0.1.0__tar.gz

statespacecheck-0.1.0/.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

statespacecheck-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  quality:
+    name: Code Quality
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Install dependencies
+        run: uv pip install --system -e .[dev]
+
+      - name: Run ruff format check
+        run: ruff format --check .
+
+      - name: Run ruff linting
+        run: ruff check . --output-format=github
+
+      - name: Run mypy type checking
+        run: mypy src/
+
+  test:
+    name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Install dependencies
+        run: uv pip install --system -e .[dev]
+
+      - name: Run tests with coverage
+        run: pytest --cov=statespacecheck --cov-report=xml --cov-report=term-missing
+
+      - name: Upload coverage to Codecov
+        if: matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
+        uses: codecov/codecov-action@v4
+        continue-on-error: true
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          file: ./coverage.xml
+          flags: unittests
+          name: codecov-python-${{ matrix.python-version }}
+
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+    needs: [quality, test]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Required for hatch-vcs to get version from git tags
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v4
+
+      - name: Install build dependencies
+        run: uv pip install --system build twine
+
+      - name: Build sdist and wheel
+        run: python -m build
+
+      - name: Check distribution metadata
+        run: twine check dist/*
+
+      - name: List distribution contents
+        run: |
+          echo "=== Built distributions ==="
+          ls -lh dist/
+          echo ""
+          echo "=== Wheel contents ==="
+          unzip -l dist/*.whl || true
+          echo ""
+          echo "=== SDist contents ==="
+          tar -tzf dist/*.tar.gz | head -20 || true
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist-${{ github.sha }}
+          path: dist/
+          retention-days: 7
+
+  test-install:
+    name: Test install from ${{ matrix.package }}
+    runs-on: ubuntu-latest
+    needs: [build]
+    strategy:
+      fail-fast: false
+      matrix:
+        package: ['wheel', 'sdist']
+        python-version: ["3.10", "3.13"]
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-${{ github.sha }}
+          path: dist/
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install from wheel
+        if: matrix.package == 'wheel'
+        run: pip install dist/*.whl
+
+      - name: Install from sdist
+        if: matrix.package == 'sdist'
+        run: pip install dist/*.tar.gz
+
+      - name: Verify installation
+        run: |
+          python -c "import statespacecheck; print('Package:', statespacecheck.__name__)"
+          python -c "import statespacecheck; print('Version:', statespacecheck.__version__)"
+          python -c "from statespacecheck import kl_divergence, hpd_overlap, highest_density_region; print('Imports successful')"
+
+      - name: Check public API
+        run: |
+          python -c "
+          import statespacecheck as ssc
+          expected = {'kl_divergence', 'hpd_overlap', 'highest_density_region',
+                      'predictive_density', 'log_predictive_density',
+                      'aggregate_over_period', 'predictive_pvalue',
+                      'DEFAULT_COVERAGE', 'DistributionArray'}
+          actual = set(ssc.__all__)
+          missing = expected - actual
+          extra = actual - expected
+          if missing:
+              raise ValueError(f'Missing from __all__: {missing}')
+          if extra:
+              print(f'Extra in __all__: {extra}')
+          print(f'✓ All {len(expected)} expected exports present')
+          "
+
+  publish-testpypi:
+    name: Publish to TestPyPI
+    runs-on: ubuntu-latest
+    needs: [test-install]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/project/statespacecheck/
+    permissions:
+      id-token: write
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-${{ github.sha }}
+          path: dist/
+
+      - name: Publish to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  publish-pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    needs: [publish-testpypi]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    environment:
+      name: pypi
+      url: https://pypi.org/project/statespacecheck/
+    permissions:
+      id-token: write
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-${{ github.sha }}
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  create-release:
+    name: Create GitHub Release
+    runs-on: ubuntu-latest
+    needs: [publish-pypi]
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist-${{ github.sha }}
+          path: dist/
+
+      - name: Extract version from tag
+        id: get_version
+        run: echo "VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
+
+      - name: Generate release notes
+        id: release_notes
+        run: |
+          cat > release_notes.md << 'EOF'
+          ## statespacecheck v${{ steps.get_version.outputs.VERSION }}
+
+          Goodness-of-fit diagnostics for state space models in neuroscience.
+
+          ### Installation
+
+          ```bash
+          pip install statespacecheck==${{ steps.get_version.outputs.VERSION }}
+          ```
+
+          ### Documentation
+
+          See [README](https://github.com/edeno/statespacecheck#readme) for usage examples.
+
+          ### Changes
+
+          See [commit history](https://github.com/edeno/statespacecheck/commits/v${{ steps.get_version.outputs.VERSION }}) for detailed changes.
+          EOF
+
+      - name: Create GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          body_path: release_notes.md
+          files: dist/*
+          draft: false
+          prerelease: false
+          generate_release_notes: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

statespacecheck-0.1.0/.github/workflows/docs.yml

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+name: docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+    paths:
+      - 'docs/**'
+      - 'mkdocs.yml'
+      - 'examples/**'
+      - '.github/workflows/docs.yml'
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+
+      - name: Install dependencies
+        run: |
+          uv pip install --system -e ".[docs]"
+
+      - name: Build docs
+        run: mkdocs build --strict
+
+      - name: Upload artifact
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: ./site
+
+  deploy:
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

statespacecheck-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$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
+
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+docs/.cache/
+.mkdocs_cache/
+
+# 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/
+
+# 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
+*.DS_Store
+# VCS version file (auto-generated by hatch-vcs)
+src/statespacecheck/_version.py

statespacecheck-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+        exclude: '^mkdocs\.yml$'
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+        exclude: '^(docs/examples/.*\.ipynb|scripts/.*\.(pdf|png))$'
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: mixed-line-ending
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.14.3
+    hooks:
+      - id: ruff
+        args: [--fix]
+        exclude: '^docs/examples/.*\.(ipynb|py)$'
+      - id: ruff-format
+        exclude: '^docs/examples/.*\.(ipynb|py)$'
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.13.0
+    hooks:
+      - id: mypy
+        files: ^src/
+        additional_dependencies:
+          - numpy>=1.26.0
+          - scipy>=1.11.0
+
+  - repo: local
+    hooks:
+      - id: pytest
+        name: pytest
+        entry: uv run pytest
+        language: system
+        pass_filenames: false
+        always_run: true
+        stages: [pre-commit]

statespacecheck-0.1.0/.python-version

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+3.13

statespacecheck-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2025-11-11
+
+### Added
+
+#### Core Diagnostics
+- `kl_divergence()`: Measure information divergence between state distributions and likelihood
+- `hpd_overlap()`: Compute spatial overlap between highest posterior density regions
+- `highest_density_region()`: Compute boolean masks for highest density regions
+
+#### Predictive Checks
+- `predictive_density()`: Compute predictive density from state distribution and likelihood
+- `log_predictive_density()`: Numerically stable log-space computation of predictive density
+- `predictive_pvalue()`: Monte Carlo p-values for goodness-of-fit testing
+
+#### Period Detection
+- `flag_low_overlap()`: Identify time periods with poor posterior-likelihood agreement
+- `flag_extreme_kl()`: Detect anomalous KL divergence using robust z-scores
+- `flag_extreme_pvalues()`: Flag extreme predictive p-values
+- `combine_flags()`: Aggregate multiple diagnostic flags with majority voting
+- `find_low_overlap_intervals()`: Extract contiguous intervals of poor model fit
+- `aggregate_over_period()`: Summarize metrics over time periods with flexible aggregation
+
+#### Visualization
+- `plot_diagnostics()`: Three-panel diagnostic visualization with time-resolved metrics
+- Support for flagging problematic time periods in plots
+
+#### Documentation
+- Comprehensive README with neuroscience examples
+- Four tutorial notebooks covering core concepts and workflows
+- API reference documentation with mkdocs-material
+- CONTRIBUTING.md with development guidelines
+
+#### Infrastructure
+- Full test suite with 230 tests and 100% code coverage
+- Property-based testing with Hypothesis
+- Type hints with strict mypy compliance
+- Code quality enforcement with ruff (formatting and linting)
+- Pre-commit hooks for automated checks
+- CI/CD with GitHub Actions
+- Automated documentation deployment
+
+### Features
+
+- **Flexible Dimensionality**: Supports 1D `(n_time, n_position)` and 2D `(n_time, n_x, n_y)` spatial arrays
+- **Robust Edge Cases**: Proper handling of NaN values, zero sums, and empty distributions
+- **Automatic Normalization**: All functions normalize inputs automatically
+- **Time-Resolved Analysis**: All metrics return time series for local model evaluation
+- **Vectorized Operations**: Efficient NumPy-based implementation with no Python loops
+- **Scientific Python Standards**: Follows SPEC 0 for version support and best practices
+
+[0.1.0]: https://github.com/edeno/statespacecheck/releases/tag/v0.1.0