itasc 0.2.0.dev0__tar.gz

itasc-0.2.0.dev0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  checks:
+    name: ${{ matrix.os }} · Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Linux carries the full supported-Python sweep; Windows and macOS
+        # each run one job on 3.12 (the version most scientific users are on,
+        # and the least likely to be missing native wheels for torch/numba/
+        # pymaxflow) so JOSS reviewers' `pip install` path is covered on every
+        # OS without a 3x CI-minute bill.
+        include:
+          - os: ubuntu-latest
+            python-version: "3.10"
+          - os: ubuntu-latest
+            python-version: "3.13"
+          - os: windows-latest
+            python-version: "3.12"
+          - os: macos-latest
+            python-version: "3.12"
+
+    env:
+      QT_QPA_PLATFORM: offscreen
+
+    # Git Bash ships on the Windows runner, so a single shell keeps the
+    # heredocs and line-continuations below identical across all three OSes.
+    defaults:
+      run:
+        shell: bash
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Install Qt/OpenGL system libraries
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libegl1 libopengl0 libgl1 libglib2.0-0 libdbus-1-3 \
+            libxkbcommon0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 \
+            libxcb-randr0 libxcb-render-util0 libxcb-shape0 libxcb-xinerama0 \
+            libxcb-cursor0
+
+      - name: Install package and tooling
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[dev]
+          python -m pip install build
+
+      - name: Lint
+        run: python -m ruff check .
+
+      - name: Test
+        # napari's Viewer canvas needs an OpenGL context. The Linux runner has
+        # software GL (Mesa/llvmpipe via the Qt libs above), so the full suite
+        # runs there; GitHub's Windows and macOS runners have no GL fallback and
+        # segfault on canvas creation, so the GUI tests are deselected on them.
+        # Every non-GUI test — the actual install-correctness surface — still
+        # runs on all three OSes. GUI coverage on Windows/macOS is by manual VM.
+        run: |
+          if [ "$RUNNER_OS" = "Linux" ]; then
+            python -m pytest
+          else
+            python -m pytest --ignore=tests/napari
+          fi
+
+      - name: Build package
+        run: python -m build --sdist --wheel --outdir dist
+
+      - name: Build extracted distributions
+        run: |
+          python -m build --wheel packages/itasc-core --outdir dist
+          python -m build --wheel packages/itasc-aggregate --outdir dist
+          python -m build --wheel packages/itasc-tracking --outdir dist
+          python -m build --wheel packages/itasc-cellpose --outdir dist
+
+      - name: Verify isolated install (PEP 420 namespace + headless core)
+        run: |
+          python -m venv cf-verify
+          # venv puts its scripts in bin/ on Linux+macOS, Scripts/ on Windows.
+          VENV_BIN=cf-verify/bin
+          [ -d "$VENV_BIN" ] || VENV_BIN=cf-verify/Scripts
+          . "$VENV_BIN/activate"
+          # Use `python -m pip` throughout: on Windows `pip install --upgrade pip`
+          # can't replace its own running pip.exe and errors out.
+          python -m pip install --upgrade pip
+          python -m pip install h5py numpy scipy scikit-image tifffile sqlalchemy pydantic pandas "tomli>=2.0; python_version < '3.11'"
+          python -m pip install --no-deps dist/itasc_core-*.whl dist/itasc_aggregate-*.whl dist/itasc_tracking-*.whl dist/itasc_cellpose-*.whl
+          python - <<'PY'
+          import os, tempfile, numpy as np, tifffile, h5py
+          import itasc            # PEP 420 namespace, no orchestrator present
+          import itasc.core.tiff
+          from itasc.contact_analysis import build_contacts
+          d = tempfile.mkdtemp()
+          labels = np.zeros((2, 5, 6), dtype=np.uint16)
+          labels[:, :, :3] = 1
+          labels[:, :, 3:] = 2
+          cp = os.path.join(d, "cells.tif")
+          tifffile.imwrite(cp, labels)
+          out = build_contacts(cell_labels_path=cp, output_path=os.path.join(d, "ca.h5"))
+          with h5py.File(out) as h5:
+              assert h5["cells/table/cell_id"][:].tolist() == [1, 2, 1, 2]
+          print("isolated itasc-aggregate install OK")
+
+          # itasc-tracking composes into the same namespace without the
+          # orchestrator or the contact piece, and its headless backend imports.
+          import itasc.tracking_ultrack.db_build  # noqa: F401
+          import itasc.tracking_ultrack.validation_state as v
+          import itasc.correction.labels  # noqa: F401
+          from itasc.core.lineage import build_lineage
+          from itasc.core.cancellation import CancelledError  # noqa: F401
+          from itasc.tracking_ultrack.corrections import Correction
+          nd = tempfile.mkdtemp()
+          v.add_correction(nd, Correction(cell_id=7, t=0, kind="validated", y=1.0, x=2.0))
+          assert v.read_validated_tracks(nd) == {7: {0}}
+          assert os.path.exists(os.path.join(nd, "corrections.json"))
+          lanes = build_lineage(labels)
+          assert {lane.cell_id for lane in lanes.lanes} == {1, 2}
+          print("isolated itasc-tracking backend OK")
+
+          # itasc-cellpose composes into the same namespace on itasc-core
+          # alone. The Cellpose model lib is an optional extra (lazy import), so
+          # the runner module imports without it, and the divergence-map builder
+          # runs headlessly on synthetic prob/dp stacks.
+          import itasc.cellpose.cellpose_runner  # noqa: F401  (no cellpose lib needed to import)
+          from itasc.cellpose import build_divergence_maps
+          cp_dir = tempfile.mkdtemp()
+          prob = np.zeros((2, 2, 10, 10), dtype="float32")          # (T, Z, Y, X)
+          dp = np.zeros((2, 2, 2, 10, 10), dtype="float32")         # (T, Z, 2, Y, X)
+          prob_p = os.path.join(cp_dir, "nucleus_prob.tif")
+          dp_p = os.path.join(cp_dir, "nucleus_dp.tif")
+          tifffile.imwrite(prob_p, prob)
+          tifffile.imwrite(dp_p, dp)
+          report = build_divergence_maps(
+              prob_p, dp_p,
+              os.path.join(cp_dir, "nucleus_contours.tif"),
+              os.path.join(cp_dir, "nucleus_foreground.tif"),
+              foreground_z_reduction="mean",
+              contour_z_reduction="mean",
+              smoothing_sigma=0.0,
+              median_radius=0,
+          )
+          assert report.frames == 2
+          assert os.path.exists(os.path.join(cp_dir, "nucleus_foreground.tif"))
+          print("isolated itasc-cellpose backend OK")
+          PY
+
+      - name: Verify napari manifests validate
+        run: |
+          python -m pip install npe2
+          python - <<'PY'
+          from npe2 import PluginManifest
+          for path, name in [
+              ("src/itasc/napari.yaml", "itasc"),
+              ("src/itasc/contact_analysis/napari.yaml", "itasc-aggregate"),
+              ("src/itasc/tracking_ultrack/napari.yaml", "itasc-tracking"),
+              ("src/itasc/cellpose/napari.yaml", "itasc-cellpose"),
+          ]:
+              m = PluginManifest.from_file(path)
+              assert m.name == name, (m.name, name)
+              print("manifest OK:", m.name)
+
+          # The full install folds each extracted piece's widget factory into the
+          # single itasc manifest; assert it mirrors the standalone factories.
+          def factories(path):
+              m = PluginManifest.from_file(path)
+              return {c.python_name for c in m.contributions.commands}
+
+          folded = factories("src/itasc/napari.yaml")
+          for path in (
+              "src/itasc/contact_analysis/napari.yaml",
+              "src/itasc/tracking_ultrack/napari.yaml",
+              "src/itasc/cellpose/napari.yaml",
+          ):
+              assert factories(path) <= folded, path
+          print("folded manifest mirrors standalone factories OK")
+          PY

itasc-0.2.0.dev0/.github/workflows/docs.yml

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+name: docs
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    paths:
+      - "docs/**"
+      - "src/itasc/**"
+      - "pyproject.toml"
+      - ".github/workflows/docs.yml"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install package + docs dependencies
+        run: |
+          python -m pip install --upgrade pip
+          # Heavy/GUI deps are mocked in conf.py, so the bare package is enough.
+          python -m pip install -e .[docs]
+
+      - name: Build documentation
+        # -W turns documentation drift (broken refs, deleted symbols, malformed
+        # docstrings) into a failing check. The baseline build is warning-clean.
+        run: |
+          sphinx-build -b html -W --keep-going docs docs/_build/html
+
+      - name: Upload built docs
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-html
+          path: docs/_build/html

itasc-0.2.0.dev0/.gitignore

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+__pycache__/
+*.py[cod]
+*.egg-info/
+*.egg
+dist/
+build/
+packages/_wheels/
+.eggs/
+*.tif
+*.tiff
+.pytest_cache/
+.mypy_cache/
+.ipynb_checkpoints/
+*.so
+.env
+
+# Local sample/test datasets (image + segmentation data, not code)
+sample_data/
+sample_data_dimensionality_test/
+.venv
+.envrc
+.claude/
+.worktrees/
+.deepseek/
+.qwen/
+.superpowers/
+.devcontainer/
+scripts/experiment_*.py
+notes/itasc_source_concatenated.md
+docs/staging/segmentation_ui_redesign/all_source.py
+test_dupes.py
+AGENTS.md
+TODO.md
+
+# Serena tool workspace
+.serena/

itasc-0.2.0.dev0/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use ITASC, please cite this software using the metadata from this file."
+title: "ITASC"
+version: "0.2.0"
+abstract: "A napari-based research software project for time-lapse cell microscopy, Cellpose-derived segmentation inputs, Ultrack-based tracking, interactive correction, and contact analysis."
+authors:
+  - family-names: "Ruppel"
+    given-names: "Artur"
+    email: artur@ruppel.pro
+repository-code: https://github.com/ArturRuppel/ITASC
+url: https://github.com/ArturRuppel/ITASC
+license: AGPL-3.0-only
+keywords:
+  - cell-tracking
+  - microscopy
+  - napari
+  - segmentation