histoweave-spatial 0.1.0__tar.gz

histoweave_spatial-0.1.0/.dockerignore

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+# Git
+.git
+.gitattributes
+.gitignore
+
+# Python cache & build
+__pycache__
+*.pyc
+*.pyo
+*.egg-info
+dist/
+build/
+
+# Tests, benchmarks, and generated results
+.pytest_cache/
+.pytest_tmp/
+.tox/
+htmlcov/
+.coverage
+5x10_dlpfc_benchmark/
+figure3_results/
+study_grouped_5slice_results/
+study_grouped_phaseb_results/
+study_grouped_results/
+work/
+tmp/
+
+# Documentation output
+docs/_build/
+docs/site/
+site/
+
+# IDE and local tools
+.vscode/
+.idea/
+.claude/
+.playwright-cli/
+output/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Environment
+.venv/
+venv/
+.env

histoweave_spatial-0.1.0/.gitattributes

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+* text=auto
+*.svg text eol=lf
+7x15_cross_platform/dataset_features.csv text eol=lf
+7x15_cross_platform/performance_matrix_mean.csv text eol=lf
+7x15_cross_platform/platform_topography.csv text eol=lf
+7x15_cross_platform/platform_topography.json text eol=lf
+7x15_cross_platform/topography_manifest.json text eol=lf

histoweave_spatial-0.1.0/.github/CODEOWNERS

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+# HistoWeave code owners — automatically assign reviewers via GitHub.
+# Last match wins; global catch-all at the bottom.
+
+* @histoweave-spatial/core

histoweave_spatial-0.1.0/.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: weekly
+    groups:
+      python-dependencies:
+        patterns:
+          - "*"
+
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: weekly
+
+  - package-ecosystem: docker
+    directory: "/workflows/containers"
+    schedule:
+      interval: weekly

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

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  quality_build:
+    name: quality and build gate
+    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 quality and build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[dev,docs]"
+          python -m pip install pip-audit
+
+      - name: Audit Python dependencies
+        run: python -m pip_audit
+
+      - name: Build documentation
+        run: mkdocs build --strict
+
+      - name: Lint
+        run: ruff check .
+
+      - name: Type-check
+        run: mypy src
+
+      - name: Quality inventory (mypy strength + test/src ratio)
+        run: pytest tests/test_quality_inventory.py -q
+
+      - name: Method docs cover every registered method
+        run: |
+          python scripts/generate_method_docs.py
+          pytest tests/test_method_docs_coverage.py tests/test_method_coverage_expansion.py -q
+
+      - name: Build distributions
+        run: python -m build
+
+      - name: Validate built wheel dependencies
+        run: |
+          python -m pip install --force-reinstall dist/*.whl
+          python -m pip check
+
+  test:
+    needs: quality_build
+    name: test (py${{ matrix.python-version }} on ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: ["3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Clean stale pytest temp dirs (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $toRemove = Get-ChildItem -Path "$env:USERPROFILE\AppData\Local\Temp" -Filter "pytest-*" -Directory -ErrorAction SilentlyContinue
+          if ($toRemove) {
+            $toRemove | ForEach-Object { Remove-Item -Recurse -Force $_.FullName -ErrorAction SilentlyContinue }
+            Write-Host "Cleaned $($toRemove.Count) stale pytest temp dir(s)"
+          } else {
+            Write-Host "No stale pytest temp dirs found"
+          }
+
+      - name: Install
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[dev]"
+
+      - name: Test
+        run: pytest -m "not property and not perf" --cov=histoweave --cov-report=term-missing --cov-fail-under=79
+
+      - name: Property-based tests
+        run: pytest -m property -q
+
+
+  federation:
+    name: federated evidence network gate
+    runs-on: ubuntu-latest
+    needs: test
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install federation + dev dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[federation,dev]"
+
+      # 1. Federation unit + integration + property tests (isolated view).
+      - name: Federation test suite
+        run: pytest tests/test_federation_*.py -q
+
+      # 2. Every committed node registry entry must parse + validate, and the
+      #    generated index must build. (Skeleton/index files are auto-skipped.)
+      - name: Validate node registry
+        run: |
+          python - <<'PY'
+          from histoweave.federation import load_registry, build_index
+          entries = load_registry("federation/nodes")
+          print(f"validated {len(entries)} node(s): {[e.node_id for e in entries]}")
+          for e in entries:
+              e.validate()
+          build_index(entries)
+          PY
+
+      # 3. Every committed evidence bundle must offline-verify against the registry.
+      - name: Verify committed evidence bundles
+        run: |
+          shopt -s nullglob
+          bundles=(federation/bundles/*.json)
+          if [ ${#bundles[@]} -eq 0 ]; then
+            echo "no committed bundles to verify"; exit 0
+          fi
+          for b in "${bundles[@]}"; do
+            echo "::group::verify $b"
+            histoweave fed verify "$b" --nodes-dir federation/nodes
+            echo "::endgroup::"
+          done
+
+      # 4. End-to-end dogfood: pull committed bundles -> consensus -> landscape check.
+      - name: Pull + consensus dry run
+        run: |
+          histoweave fed pull \
+            --nodes-dir federation/nodes \
+            --store "$RUNNER_TEMP/evidence_store.jsonl"
+          histoweave fed consensus \
+            --store "$RUNNER_TEMP/evidence_store.jsonl" \
+            --out "$RUNNER_TEMP/consensus.json" \
+            --check-landscape
+          histoweave fed status \
+            --store "$RUNNER_TEMP/evidence_store.jsonl" \
+            --nodes-dir federation/nodes
+
+  benchmark:
+    name: scientific + performance regression gates
+    runs-on: ubuntu-latest
+    needs: test
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install benchmark dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[dev]"
+      # Scientific accuracy gate (ARI / leaderboard).
+      # Oracle-K is explicit here: this gate checks method capacity when K is known.
+      # The default scientific protocol uses k_policy=estimate (non-oracle).
+      - name: Domain-detection leaderboard (oracle-K capacity gate)
+        run: >
+          histoweave benchmark --min-score 0.90 --fail-on-error
+          --k-policy oracle --allow-oracle-k
+          --out benchmark.json
+      - name: Non-oracle K + statistical review smoke
+        run: >
+          histoweave benchmark --k-policy estimate --stats --n-boot 50
+          --out benchmark_estimate_stats.json
+      - name: Stats review + K-selection unit tests
+        run: pytest tests/test_stats_review.py tests/test_k_selection.py tests/test_harness_stats_and_k.py -q
+      # Computational performance gate (kNN / zscore / PCA / features).
+      - name: Micro-benchmark performance ceilings
+        run: pytest -m perf -q --tb=line
+
+      - name: Freeze phenomenology capability plan
+        run: |
+          histoweave benchmark --suite phenomenology --dry-run \
+            --out-dir phenomenology_plan
+
+      - name: Run dependency-light phenomenology smoke
+        run: |
+          histoweave benchmark --suite phenomenology --tiny \
+            --phenomena compartment --conditions clean \
+            --methods basic_qc,log1p_cp10k,kmeans \
+            --fail-on-error --out-dir phenomenology_smoke
+
+      - name: Upload benchmark artifacts
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: benchmark-regression-artifacts
+          path: |
+            benchmark.json
+            benchmark_estimate_stats.json
+            phenomenology_plan/
+            phenomenology_smoke/
+          if-no-files-found: warn

histoweave_spatial-0.1.0/.github/workflows/containers.yml

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+name: Publish containers
+
+on:
+  push:
+    branches: [main]
+    tags: ["v*"]
+    paths:
+      - "src/**"
+      - "pyproject.toml"
+      - "workflows/containers/**"
+      - ".github/workflows/containers.yml"
+  pull_request:
+    paths:
+      - "src/**"
+      - "pyproject.toml"
+      - "workflows/containers/**"
+      - ".github/workflows/containers.yml"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  build-and-push:
+    name: Build and push ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: histoweave-python
+            context: .
+            dockerfile: workflows/containers/histoweave-python/Dockerfile
+          - name: histoweave-r
+            context: .
+            dockerfile: workflows/containers/histoweave-r/Dockerfile
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GHCR
+        if: github.event_name != 'pull_request'
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract image metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository_owner }}/${{ matrix.name }}
+          tags: |
+            type=raw,value=latest,enable={{is_default_branch}}
+            type=ref,event=branch
+            type=ref,event=tag
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=sha,prefix=sha-
+          labels: |
+            org.opencontainers.image.title=${{ matrix.name }}
+            org.opencontainers.image.description=HistoWeave spatial transcriptomics ${{ matrix.name }} container
+
+      - name: Build and push
+        uses: docker/build-push-action@v6
+        with:
+          context: ${{ matrix.context }}
+          file: ${{ matrix.dockerfile }}
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          build-args: |
+            VERSION=${{ steps.meta.outputs.version }}
+            REVISION=${{ github.sha }}
+          cache-from: type=gha,scope=${{ matrix.name }}
+          cache-to: type=gha,mode=max,scope=${{ matrix.name }}
+          provenance: mode=max
+          sbom: true

histoweave_spatial-0.1.0/.github/workflows/nextflow-smoke.yml

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+name: Nextflow smoke test
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - "src/**"
+      - "workflows/nextflow/**"
+      - "pyproject.toml"
+      - ".github/workflows/nextflow-smoke.yml"
+  pull_request:
+    paths:
+      - "src/**"
+      - "workflows/nextflow/**"
+      - "pyproject.toml"
+      - ".github/workflows/nextflow-smoke.yml"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  smoke:
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install HistoWeave
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ".[dev]"
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v3
+        with:
+          version: "26.04.4"
+
+      - name: Run demo pipeline
+        run: |
+          nextflow run workflows/nextflow/main.nf -profile local,test --outdir nf-smoke
+          test -s nf-smoke/pipeline_trace.tsv
+          grep -q "COMPLETED" nf-smoke/pipeline_trace.tsv
+          find nf-smoke -maxdepth 1 -name "*_report.html" -size +0 | grep -q .
+
+      - name: Upload smoke-test diagnostics
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: nextflow-smoke-diagnostics
+          path: |
+            .nextflow.log*
+            nf-smoke/
+          if-no-files-found: warn

histoweave_spatial-0.1.0/.github/workflows/pages.yml

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+name: Deploy leaderboard to GitHub Pages
+
+on:
+  # Rebuild whenever anything the site depends on changes.
+  push:
+    branches: [main]
+    paths:
+      - "leaderboard/**"
+      - "5x15_spatial_aware/benchmark_long.csv"
+      - "5x10_dlpfc_benchmark/benchmark_long.csv"
+      - "benchmark_crossplatform/benchmark_long.csv"
+      - "benchmark_crossplatform/dataset_manifest.json"
+      # Federated evidence: refresh the site when nodes or their signed bundles change.
+      - "federation/nodes/**"
+      - "federation/bundles/**"
+      - "federation/consensus.json"
+      - ".github/workflows/pages.yml"
+  # Manual trigger from the Actions tab.
+  workflow_dispatch:
+
+# GH Pages: one deployment in flight at a time; skip queued duplicates.
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      # generate.py has no external dependencies beyond the stdlib + optional
+      # h5py; we don't install h5py here because CI has no h5ad files anyway
+      # and the script gracefully degrades.
+
+      # Rebuild the derived consensus view from the committed, signed evidence
+      # bundles so the site shows current federation status. consensus.json is
+      # not committed (derived, regenerable); if there are no nodes/bundles this
+      # is a no-op and generate.py emits the plain v2 feed.
+      - name: Rebuild federation consensus (if any evidence is registered)
+        run: |
+          if compgen -G "federation/bundles/*.json" > /dev/null && \
+             compgen -G "federation/nodes/*.json" > /dev/null; then
+            python -m pip install --upgrade pip
+            python -m pip install -e ".[federation]"
+            histoweave fed pull \
+              --nodes-dir federation/nodes \
+              --store "$RUNNER_TEMP/evidence_store.jsonl"
+            histoweave fed consensus \
+              --store "$RUNNER_TEMP/evidence_store.jsonl" \
+              --out federation/consensus.json
+          else
+            echo "no registered evidence; skipping consensus rebuild"
+          fi
+
+      - name: Regenerate data.json
+        run: python leaderboard/generate.py
+
+      - name: Prepare pages artifact
+        run: |
+          required_files=(
+            leaderboard/index.html
+            leaderboard/styles.css
+            leaderboard/main.js
+            leaderboard/data.json
+            leaderboard/README.md
+          )
+          for file in "${required_files[@]}"; do
+            if [[ ! -f "$file" ]]; then
+              echo "::error file=$file::Required GitHub Pages asset is missing"
+              exit 1
+            fi
+          done
+
+          install -d _site
+          cp "${required_files[@]}" _site/
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: _site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

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

@@ -0,0 +1,61 @@
+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Verify release tag matches package version
+        shell: bash
+        run: |
+          package_version="$(python -c 'from pathlib import Path; import re; text=Path("src/histoweave/__init__.py").read_text(); print(re.search(r"__version__\s*=\s*\"([^\"]+)\"", text).group(1))')"
+          release_version="${GITHUB_REF_NAME#v}"
+          if [[ "$package_version" != "$release_version" ]]; then
+            echo "::error::Release tag $GITHUB_REF_NAME does not match package version $package_version"
+            exit 1
+          fi
+
+      - name: Build and validate distributions
+        run: |
+          python -m pip install --upgrade build twine
+          python -m build
+          python -m twine check dist/*
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+          if-no-files-found: error
+
+  publish:
+    name: Publish distributions to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/histoweave-spatial
+    permissions:
+      id-token: write
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+      - name: Publish with Trusted Publishing
+        uses: pypa/gh-action-pypi-publish@release/v1