Feature/biwt package#3
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Pull request overview
Introduces a new standalone biwt Python package (core + PyQt5 GUI walkthrough) and wires PhysiCell Studio to prefer the packaged BIWT implementation (with legacy fallback), along with unit tests, fixtures, and CI.
Changes:
- Add a pure-Python BIWT core (data loading, domain logic, positioning utilities) plus a PyQt5 walkthrough UI and step windows.
- Add session-level unit tests and CSV fixtures for spatial, non-spatial, and spot-deconvolution flows.
- Add Studio integration bridge + a GitHub Actions workflow to run BIWT tests.
Reviewed changes
Copilot reviewed 35 out of 39 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| biwt/tests/test_session.py | New end-to-end session/unit tests for loader, domain logic, step predicates, and pipeline outputs |
| biwt/tests/fixtures/spot_deconv.csv | Spot-deconvolution CSV fixture with probability columns |
| biwt/tests/fixtures/spatial.csv | Spatial CSV fixture with x/y/type |
| biwt/tests/fixtures/nonspatial.csv | Non-spatial CSV fixture with type only |
| biwt/tests/init.py | Marks BIWT tests package |
| biwt/src/biwt/types.py | Defines public API dataclasses: DomainSpec, BiwtInput, BiwtResult |
| biwt/src/biwt/gui/windows/write_positions.py | Adds (deprecated-style) output writer window for CSV/XML |
| biwt/src/biwt/gui/windows/spot_deconvolution.py | Adds spot-deconvolution query step window |
| biwt/src/biwt/gui/windows/spatial_query.py | Adds spatial-data usage query step window |
| biwt/src/biwt/gui/windows/rename_cell_types.py | Adds rename step window with duplicate blocking and suggestions |
| biwt/src/biwt/gui/windows/load_cell_parameters.py | Adds cell-parameter template assignment step window |
| biwt/src/biwt/gui/windows/edit_cell_types.py | Adds keep/merge/delete UI with optional scatter plot + legend |
| biwt/src/biwt/gui/windows/cluster_column.py | Adds cluster/label column selection step window |
| biwt/src/biwt/gui/windows/cell_counts.py | Adds non-spatial cell-counts configuration step window |
| biwt/src/biwt/gui/windows/base.py | Adds common walkthrough window base class + navigation helpers |
| biwt/src/biwt/gui/windows/init.py | Exports step windows in a single module |
| biwt/src/biwt/gui/widgets.py | Adds shared Qt widgets (buttons, line edits, filtered combo, legend dialog, etc.) |
| biwt/src/biwt/gui/walkthrough.py | Implements session dataclass, step predicate table, walkthrough controller, and result assembly |
| biwt/src/biwt/gui/init.py | Guards GUI import on PyQt5 availability and exports create_biwt_widget |
| biwt/src/biwt/core/positioning.py | Adds coordinate scaling, IC dataframe creation, and spot-expansion helper |
| biwt/src/biwt/core/parameters/xml_defaults.py | Adds default PhysiCell XML section snippets |
| biwt/src/biwt/core/parameters/init.py | Documents the parameters subpackage purpose |
| biwt/src/biwt/core/domain.py | Adds domain inference and mismatch classification logic |
| biwt/src/biwt/core/data_loader.py | Adds unified loader for .h5ad, R formats, and .csv into BiwtData |
| biwt/src/biwt/core/cell_types.py | Adds cell-type action/config model and name suggestion heuristics |
| biwt/src/biwt/core/init.py | Core package marker/docstring |
| biwt/src/biwt/init.py | Package exports and version |
| biwt/pyproject.toml | Packaging metadata + optional dependency extras + pytest config |
| biwt/progress.md | Development decisions log for BIWT |
| biwt/README.md | BIWT package documentation, usage, and status |
| biwt/PRD.md | BIWT requirements/specification document |
| biwt/.gitignore | BIWT-specific ignore rules |
| bin/ics_tab.py | Studio integration: prefer biwt package widget when installed; host writes output via callback |
| README.md | Top-level repo README now references BIWT package and usage |
| CLAUDE.md | Repo architecture guide updated to include BIWT package and integration |
| .gitignore | Adds venv/editor ignores at repo root |
| .github/workflows/ci.yml | Adds CI job to install BIWT and run tests |
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| - name: Install BIWT with dev dependencies | ||
| # TODO (standalone repo): change to: pip install -e ".[dev]" | ||
| run: pip install -e "biwt/[dev]" | ||
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| - name: Run tests | ||
| # TODO (standalone repo): remove "cd biwt &&" | ||
| run: cd biwt && PYTHONPATH=src python -m pytest tests/ -v |
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| all = ["biwt[anndata,seurat,gui]"] | ||
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| # pip install biwt[dev] — development / testing extras | ||
| dev = ["pytest>=7", "pytest-qt", "biwt[all]"] |
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| def __init__(self, walkthrough): | ||
| super().__init__(walkthrough) | ||
| s = walkthrough.session | ||
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| csv_path = s.biwt_input.output_csv_path or "./config/cells.csv" | ||
| self._full_fname: str | None = None | ||
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| vbox = QVBoxLayout() | ||
| vbox.addWidget(QLabel( | ||
| "Confirm output file, then choose to overwrite or append." | ||
| )) | ||
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| self._csv_path_edit = QLineEdit(csv_path) | ||
| browse_btn = QPushButton("Browse…") |
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| def test_data_at_exactly_50pct_each_axis_returns_none(self): | ||
| # width=500 (50%), height=500 (50%), area=25% → small (area check) | ||
| data = DomainSpec(xmin=-250, xmax=250, ymin=-250, ymax=250) | ||
| assert classify_domain_mismatch(data, self.PREFERRED) == "small" | ||
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| def test_data_covers_more_than_50pct_returns_none(self): | ||
| # width=700 (70%), height=700 (70%), area=49% — below 50% area threshold | ||
| data = DomainSpec(xmin=-350, xmax=350, ymin=-350, ymax=350) | ||
| assert classify_domain_mismatch(data, self.PREFERRED) == "small" | ||
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| coords_df = build_ic_dataframe(self.session.coords_by_type) | ||
| mapping = self.session.cell_type_config.resolve() | ||
| s = self.session | ||
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| # Build cell-definitions XML if the parameters step populated the registry. | ||
| if s.cell_definitions_registry: | ||
| root = ET.Element("PhysiCell_settings", version="devel-version") | ||
| for key, xml_str in xml_defaults.items(): | ||
| wrapped = f"<{key}>{xml_str.strip()}</{key}>" | ||
| root.append(ET.fromstring(wrapped)) | ||
| cell_defs = ET.SubElement(root, "cell_definitions") | ||
| for template_elem in s.cell_definitions_registry.values(): | ||
| cell_defs.append(copy.deepcopy(template_elem)) | ||
| s.cell_definitions_xml = ET.tostring( | ||
| root, encoding="unicode", xml_declaration=False | ||
| ) | ||
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| result = BiwtResult( | ||
| coordinates=coords_df, | ||
| cell_type_map=mapping, | ||
| domain_used=s.effective_domain, | ||
| cell_definitions_xml=s.cell_definitions_xml, | ||
| ) |
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| # Normalize to [0, 1] | ||
| normalized = (coords - src_min) / src_range | ||
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| domain_widths = np.array([domain.width, domain.height, domain.depth]) | ||
| domain_origins = np.array([domain.xmin, domain.ymin, domain.zmin]) | ||
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| out = np.zeros((len(coords), 3)) | ||
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| if preserve_aspect: | ||
| # Scale by the smallest ratio so data fits within domain without distortion, | ||
| # then center the result. | ||
| n_spatial = min(n_dims, 2) # only x/y for 2-D data | ||
| scale = min(domain_widths[i] for i in range(n_spatial)) | ||
| for i in range(n_dims): | ||
| center = domain_origins[i] + 0.5 * domain_widths[i] | ||
| data_width = scale if i < 2 else domain_widths[2] | ||
| out[:, i] = (normalized[:, i] - 0.5) * data_width + center | ||
| else: |
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- add the new src-layout biwt package with pyproject metadata, public host/package contracts, core loaders/domain/cell-type/positioning modules, parameter templates, icons, and a modular PyQt walkthrough under gui/windows/ - refactor the walkthrough around explicit session state and step predicates, with better navigation, plotting/layout cleanup, domain mismatch editing, cell count and rename validation, template loading from TOML, and improved out-of-bounds handling - make Studio consume the package behind --biwt via bin/ics_tab.py while keeping the legacy fallback tab; BIWT now returns an in-memory BiwtResult and Studio owns CSV/XML save, append, browse, and reload flows - document the package split and install path in the repo README and BIWT docs, add PRD/progress/CLAUDE guidance, and add package CI plus session tests and CSV fixtures
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