neurospatial 0.1.0__tar.gz

neurospatial-0.1.0/.claude/commands/freshstart.md

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+I'm working on the neurospatial project.
+
+Start now by reading the files and telling me which task you'll work on first.
+
+Your workflow MUST be:
+
+    First, read these files IN ORDER:
+        CLAUDE.md (implementation guide)
+        docs/SCRATCHPAD.md (notes and current status)
+        docs/TASKS.md (current tasks)
+
+    THEN if you need more detail:
+        docs/UX_IMPLEMENTATION_PLAN.md (overall project plan)
+
+    Find the FIRST unchecked [ ] task in TASKS.md
+
+    For EVERY feature, follow TDD:
+      a. Create the TEST file first
+      b. Run the test and verify it FAILS
+      c. Only then create the implementation
+      d. Run test until it PASSES
+      e. Apply review agents (code-reviewer, other relevant agents)
+      f. Refactor for clarity and efficiency based on feedback
+      g. Add/Update docstrings and types.
+
+    Update TASKS.md checkboxes as you complete items.
+
+    Update SCRATCHPAD.md with notes
+
+    Commit frequently with messages like "feat(F24): implement error handling"
+
+Do not change tests or skip tests to match broken code. Ask permission to change requirements if needed.
+
+## Remember
+
+- **Read before you code** - Use Read tool to understand context
+- **Test before you implement** - TDD is mandatory
+- **Verify before you claim completion** - Use verification-before-completion skill
+- **Ask when uncertain** - Better to ask than assume
+- **Document as you go** - Update SCRATCHPAD.md with decisions/blockers
+
+---
+
+## When Blocked
+
+If you encounter any of these, STOP and document in SCRATCHPAD.md:
+
+1. **Unclear requirements** - Ask for clarification
+2. **Unexpected test failures** - Use systematic-debugging skill
+3. **Conflicting requirements** - Ask for guidance
+4. **Need to change baselines** - Request approval
+5. **Missing dependencies** - Document and ask for help
+
+**Never proceed with assumptions** - this is critical scientific infrastructure.
+
+You MUST investigate any test failures using the systematic debugging skill. Flaky tests are not an acceptable reason to skip or ignore tests.
+
+---
+
+Now tell me: **What task are you working on next?**

neurospatial-0.1.0/.gitattributes

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

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

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+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment
+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: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies
+        run: |
+          uv sync --extra docs
+
+      - name: Sync example notebooks
+        run: |
+          uv run python docs/sync_notebooks.py
+
+      - name: Build documentation
+        run: |
+          uv 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'
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

neurospatial-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies
+        run: |
+          uv sync --extra dev
+
+      - name: Build package
+        run: |
+          uv build
+
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: [build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/neurospatial
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  publish-to-testpypi:
+    name: Publish to TestPyPI (for testing)
+    needs: [build]
+    runs-on: ubuntu-latest
+    if: github.event.release.prerelease
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/neurospatial
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish distribution to TestPyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

neurospatial-0.1.0/.github/workflows/release.yml

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+name: Create Release
+
+on:
+  push:
+    tags:
+      - 'v*.*.*'
+
+permissions:
+  contents: write
+
+jobs:
+  release:
+    name: Create GitHub Release
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch all history for changelog generation
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Get version from tag
+        id: get_version
+        run: echo "VERSION=${GITHUB_REF#refs/tags/v}" >> $GITHUB_OUTPUT
+
+      - name: Generate changelog
+        id: changelog
+        run: |
+          # Get the previous tag
+          PREVIOUS_TAG=$(git tag --sort=-version:refname | grep -A1 "${{ github.ref_name }}" | tail -1)
+
+          # If no previous tag, use initial commit
+          if [ -z "$PREVIOUS_TAG" ]; then
+            PREVIOUS_TAG=$(git rev-list --max-parents=0 HEAD)
+          fi
+
+          # Generate changelog
+          echo "## What's Changed" > CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+
+          # Get commits between tags, group by type
+          echo "### Features" >> CHANGELOG.txt
+          git log $PREVIOUS_TAG..${{ github.ref_name }} --pretty=format:"- %s (%h)" --grep="^feat" >> CHANGELOG.txt || echo "No new features" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+
+          echo "### Bug Fixes" >> CHANGELOG.txt
+          git log $PREVIOUS_TAG..${{ github.ref_name }} --pretty=format:"- %s (%h)" --grep="^fix" >> CHANGELOG.txt || echo "No bug fixes" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+
+          echo "### Documentation" >> CHANGELOG.txt
+          git log $PREVIOUS_TAG..${{ github.ref_name }} --pretty=format:"- %s (%h)" --grep="^docs" >> CHANGELOG.txt || echo "No documentation changes" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+
+          echo "### Other Changes" >> CHANGELOG.txt
+          git log $PREVIOUS_TAG..${{ github.ref_name }} --pretty=format:"- %s (%h)" --grep="^chore\|^test\|^refactor" >> CHANGELOG.txt || echo "No other changes" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+          echo "" >> CHANGELOG.txt
+
+          echo "**Full Changelog**: https://github.com/${{ github.repository }}/compare/${PREVIOUS_TAG}...${{ github.ref_name }}" >> CHANGELOG.txt
+
+      - name: Create Release
+        uses: softprops/action-gh-release@v2
+        with:
+          name: Release v${{ steps.get_version.outputs.VERSION }}
+          body_path: CHANGELOG.txt
+          draft: false
+          prerelease: ${{ contains(github.ref_name, 'rc') || contains(github.ref_name, 'beta') || contains(github.ref_name, 'alpha') }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Update CHANGELOG.md
+        run: |
+          # Prepend the new changes to CHANGELOG.md
+          if [ -f CHANGELOG.md ]; then
+            # Add new release to existing changelog
+            echo "# Changelog" > CHANGELOG.new.md
+            echo "" >> CHANGELOG.new.md
+            echo "## [v${{ steps.get_version.outputs.VERSION }}] - $(date +%Y-%m-%d)" >> CHANGELOG.new.md
+            echo "" >> CHANGELOG.new.md
+            cat CHANGELOG.txt >> CHANGELOG.new.md
+            echo "" >> CHANGELOG.new.md
+            tail -n +2 CHANGELOG.md >> CHANGELOG.new.md
+            mv CHANGELOG.new.md CHANGELOG.md
+          else
+            # Create new changelog
+            echo "# Changelog" > CHANGELOG.md
+            echo "" >> CHANGELOG.md
+            echo "All notable changes to this project will be documented in this file." >> CHANGELOG.md
+            echo "" >> CHANGELOG.md
+            echo "The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)," >> CHANGELOG.md
+            echo "and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html)." >> CHANGELOG.md
+            echo "" >> CHANGELOG.md
+            echo "## [v${{ steps.get_version.outputs.VERSION }}] - $(date +%Y-%m-%d)" >> CHANGELOG.md
+            echo "" >> CHANGELOG.md
+            cat CHANGELOG.txt >> CHANGELOG.md
+          fi
+
+      - name: Commit updated CHANGELOG.md
+        run: |
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git add CHANGELOG.md
+          git commit -m "docs: update CHANGELOG.md for v${{ steps.get_version.outputs.VERSION }}" || echo "No changes to commit"
+          git push origin HEAD:main || echo "Failed to push changelog update"

neurospatial-0.1.0/.github/workflows/test.yml

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+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ['3.10', '3.11', '3.12', '3.13']
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
+
+      - name: Install dependencies
+        run: |
+          uv sync --extra dev
+
+      - name: Run ruff check
+        run: |
+          uv run ruff check .
+
+      - name: Run ruff format check
+        run: |
+          uv run ruff format --check .
+
+      - name: Run mypy
+        run: |
+          uv run mypy src/neurospatial
+        continue-on-error: true  # Don't fail build on type errors (yet)
+
+      - name: Run tests with coverage
+        run: |
+          uv run pytest --cov=src/neurospatial --cov-report=xml --cov-report=term
+        env:
+          MPLBACKEND: Agg  # Use non-GUI backend for matplotlib
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13'
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

neurospatial-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
+
+# 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
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.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
+
+# 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

neurospatial-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$'
+      - id: check-added-large-files
+        args: ['--maxkb=1000']
+        exclude: '^examples/.*\.ipynb$'
+      - 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]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.13.0
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - numpy
+          - pandas
+          - matplotlib
+          - networkx
+          - scipy
+          - scikit-learn
+          - shapely
+        args: [--ignore-missing-imports, --warn-unused-ignores]

neurospatial-0.1.0/.python-version

@@ -0,0 +1 @@
+3.13

neurospatial-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to the neurospatial project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0] - 2025-11-03
+
+### Added
+- **CompositeEnvironment API parity**: Added `bins_in_region()`, `mask_for_region()`, `shortest_path()`, `info()`, `save()`, and `load()` methods to CompositeEnvironment for full API compatibility with Environment class
+- **KDTree-optimized spatial queries**: CompositeEnvironment.bin_at() now uses KDTree for O(M log N) performance instead of O(N×M) sequential queries (enabled by default via `use_kdtree_query=True`)
+- **Structured logging infrastructure**: New `_logging.py` module with NullHandler by default, enabling optional logging for debugging and workflow tracing
+- **Centralized numerical constants**: New `_constants.py` module consolidating all magic numbers (tolerances, KDTree parameters, epsilon values) for consistent behavior
+- **Comprehensive type validation**: CompositeEnvironment constructor now validates input types with actionable error messages
+- **Graph metadata validation**: Added `validate_connectivity_graph()` to enforce required node/edge attributes from layout engines
+- **Dimensionality support documentation**: New `docs/dimensionality_support.md` clarifying 1D/2D/3D feature support with compatibility matrix
+
+### Changed
+- **Updated alignment module**: Now uses centralized constants (`IDW_MIN_DISTANCE`, `KDTREE_LEAF_SIZE`)
+- **Updated regions module**: Uses `POINT_TOLERANCE` constant for consistent geometric comparisons
+- **Enhanced error messages**: CompositeEnvironment now provides detailed diagnostics for dimension mismatches and type errors
+- **Clarified 2D-only transforms**: Updated `transforms.py` docstring to explicitly state 2D-only status and suggest scipy for 3D
+
+### Fixed
+- Removed unused `type: ignore` comment in `regular_grid.py`
+- Fixed potential `KeyError` in logging by renaming `name` parameter to `env_name` (avoids conflict with LogRecord reserved field)
+
+### Documentation
+- Added comprehensive dimensionality support guide (1D/2D/3D feature matrix)
+- Updated CLAUDE.md with latest patterns and requirements
+- Added 18 new tests for CompositeEnvironment type validation
+- Added 23 new tests for Environment error path coverage
+- Added 28 new tests for graph validation
+
+### Internal
+- Consolidated duplicate dimension inference code (already done in earlier commits, verified)
+- All 614 tests passing
+- Ruff and mypy checks passing
+- Test coverage: 78%