diff --git a/.github/actions/setup-poetry-env/action.yml b/.github/actions/setup-poetry-env/action.yml deleted file mode 100644 index d1aafa7..0000000 --- a/.github/actions/setup-poetry-env/action.yml +++ /dev/null @@ -1,43 +0,0 @@ -name: "setup-poetry-env" -description: "Composite action to setup the Python and poetry environment." - -inputs: - python-version: - required: false - description: "The python version to use" - default: "3.11" - -runs: - using: "composite" - steps: - - name: Set up python - uses: actions/setup-python@v5 - with: - python-version: ${{ inputs.python-version }} - - - name: Install Poetry - env: - POETRY_VERSION: "1.8.5" - run: curl -sSL https://install.python-poetry.org | python - -y - shell: bash - - - name: Add Poetry to Path - run: echo "$HOME/.local/bin" >> $GITHUB_PATH - shell: bash - - - name: Configure Poetry virtual environment in project - run: poetry config virtualenvs.in-project true - shell: bash - - - name: Load cached venv - id: cached-poetry-dependencies - uses: actions/cache@v4 - if: github.run_attempt == 1 - with: - path: .venv - key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('poetry.lock') }} - - - name: Install dependencies - if: github.run_attempt > 1 || steps.cached-poetry-dependencies.outputs.cache-hit != 'true' - run: poetry install --no-interaction - shell: bash diff --git a/.github/actions/setup-uv-env/action.yml b/.github/actions/setup-uv-env/action.yml new file mode 100644 index 0000000..e8c5470 --- /dev/null +++ b/.github/actions/setup-uv-env/action.yml @@ -0,0 +1,33 @@ +name: "setup-uv-env" +description: "Composite action to setup the Python and uv environment." + +inputs: + python-version: + required: false + description: "The python version to use" + default: "3.11" + +runs: + using: "composite" + steps: + - name: Set up python + uses: actions/setup-python@v6 + with: + python-version: ${{ inputs.python-version }} + + - name: Install UV + run: curl -LsSf https://astral.sh/uv/install.sh | sh + shell: bash + + - name: Load cached venv + id: cached-uv-dependencies + uses: actions/cache@v4 + if: github.run_attempt == 1 + with: + path: .venv + key: venv-${{ runner.os }}-${{ inputs.python-version }}-${{ hashFiles('uv.lock') }} + + - name: Install dependencies + if: github.run_attempt > 1 || steps.cached-uv-dependencies.outputs.cache-hit != 'true' + run: uv sync --all-groups + shell: bash diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 08ed261..14e1c1a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -20,7 +20,7 @@ jobs: key: pre-commit-${{ hashFiles('.pre-commit-config.yaml') }} - name: Set up the environment - uses: ./.github/actions/setup-poetry-env + uses: ./.github/actions/setup-uv-env - name: Run checks run: make check @@ -29,7 +29,7 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"] fail-fast: false defaults: run: @@ -39,18 +39,21 @@ jobs: uses: actions/checkout@v4 - name: Set up the environment - uses: ./.github/actions/setup-poetry-env + uses: ./.github/actions/setup-uv-env with: python-version: ${{ matrix.python-version }} - name: Install xvfb run: sudo apt-get update && sudo apt-get install -y xvfb + - name: Sync uv project + run: uv sync --all-groups + - name: Run tests - run: xvfb-run poetry run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml + run: xvfb-run uv run pytest tests --cov --cov-config=pyproject.toml --cov-report=xml - name: Check typing - run: poetry run mypy + run: uv run mypy - name: Upload coverage reports to Codecov with GitHub Action on Python 3.11 uses: codecov/codecov-action@v4 @@ -63,7 +66,7 @@ jobs: uses: actions/checkout@v4 - name: Set up the environment - uses: ./.github/actions/setup-poetry-env + uses: ./.github/actions/setup-uv-env - name: Check if documentation can be built - run: poetry run mkdocs build -s + run: uv run mkdocs build -s diff --git a/.github/workflows/on-release-main.yml b/.github/workflows/on-release-main.yml index 6a13b1c..cbfc408 100644 --- a/.github/workflows/on-release-main.yml +++ b/.github/workflows/on-release-main.yml @@ -13,7 +13,7 @@ jobs: uses: actions/checkout@v4 - name: Set up the environment - uses: ./.github/actions/setup-poetry-env + uses: ./.github/actions/setup-uv-env - name: Export tag id: vars @@ -22,7 +22,7 @@ jobs: - name: Build and publish run: | source .venv/bin/activate - poetry version $RELEASE_VERSION + uv version $RELEASE_VERSION make build-and-publish env: PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }} @@ -36,7 +36,7 @@ jobs: uses: actions/checkout@v4 - name: Set up the environment - uses: ./.github/actions/setup-poetry-env + uses: ./.github/actions/setup-uv-env - name: Deploy documentation - run: poetry run mkdocs gh-deploy --force + run: uv run mkdocs gh-deploy --force diff --git a/Makefile b/Makefile index 746e810..d3ba520 100644 --- a/Makefile +++ b/Makefile @@ -1,30 +1,29 @@ .PHONY: install -install: ## Install the poetry environment and install the pre-commit hooks - @echo "🚀 Creating virtual environment using pyenv and poetry" - @poetry install - @ poetry run pre-commit install - @poetry shell +install: ## Install the uv environment and install the pre-commit hooks + @echo "🚀 Creating virtual environment using uv" + @uv sync + @uv run pre-commit install .PHONY: check check: ## Run code quality tools. - @echo "🚀 Checking Poetry lock file consistency with 'pyproject.toml': Running poetry check --lock" - @poetry check --lock + @echo "🚀 Checking UV lock file consistency with 'pyproject.toml': Running uv lock --check" + @uv lock --check @echo "🚀 Linting code: Running pre-commit" - @poetry run pre-commit run -a + @uv run pre-commit run -a @echo "🚀 Static type checking: Running mypy" - @poetry run mypy + @uv run mypy @echo "🚀 Checking for obsolete dependencies: Running deptry" - @poetry run deptry --exclude=.venv --exclude=.venv_jupyter --exclude=examples --exclude=tests . + @uv run deptry --exclude=.venv --exclude=.venv_jupyter --exclude=examples --exclude=tests . .PHONY: test test: ## Test the code with pytest @echo "🚀 Testing code: Running pytest" - @poetry run pytest --cov --cov-config=pyproject.toml --cov-report=xml + @uv run pytest --cov --cov-config=pyproject.toml --cov-report=xml .PHONY: build -build: clean-build ## Build wheel file using poetry +build: clean-build ## Build wheel file using uv @echo "🚀 Creating wheel file" - @poetry build + @uv build .PHONY: clean-build clean-build: ## clean build artifacts @@ -33,10 +32,9 @@ clean-build: ## clean build artifacts .PHONY: publish publish: ## publish a release to pypi. @echo "🚀 Publishing: Dry run." - @poetry config pypi-token.pypi $(PYPI_TOKEN) - @poetry publish --dry-run + @uv publish --dry-run --token $(PYPI_TOKEN) @echo "🚀 Publishing." - @poetry publish + @uv publish --token $(PYPI_TOKEN) .PHONY: build-and-publish build-and-publish: build publish ## Build and publish. @@ -44,15 +42,15 @@ build-and-publish: build publish ## Build and publish. .PHONY: docs-execute-notebooks docs-execute-notebooks: ## Execute guide notebooks and save outputs @echo "🚀 Executing guide notebooks" - @poetry run jupyter nbconvert --to notebook --execute --inplace $(filter-out docs/guides/notebooks/remote-simulations.ipynb,$(wildcard docs/guides/notebooks/*.ipynb)) + @uv run jupyter nbconvert --to notebook --execute --inplace $(filter-out docs/guides/notebooks/remote-simulations.ipynb,$(wildcard docs/guides/notebooks/*.ipynb)) .PHONY: docs-test docs-test: ## Test if documentation can be built without warnings or errors - @poetry run mkdocs build -s + @uv run mkdocs build -s .PHONY: docs docs: ## Build and serve the documentation - @poetry run mkdocs serve + @uv run mkdocs serve .PHONY: help help: diff --git a/docs/guides/images/building-concentrations.png b/docs/guides/images/building-concentrations.png index 67db458..992f5d9 100644 Binary files a/docs/guides/images/building-concentrations.png and b/docs/guides/images/building-concentrations.png differ diff --git a/docs/guides/images/building-geometry.png b/docs/guides/images/building-geometry.png index d6feca1..936cda5 100644 Binary files a/docs/guides/images/building-geometry.png and b/docs/guides/images/building-geometry.png differ diff --git a/docs/guides/images/building-slice3d-A.png b/docs/guides/images/building-slice3d-A.png index ba7590f..2871d27 100644 Binary files a/docs/guides/images/building-slice3d-A.png and b/docs/guides/images/building-slice3d-A.png differ diff --git a/docs/guides/images/complex-analytic-geometry.png b/docs/guides/images/complex-analytic-geometry.png index d6feca1..936cda5 100644 Binary files a/docs/guides/images/complex-analytic-geometry.png and b/docs/guides/images/complex-analytic-geometry.png differ diff --git a/docs/guides/images/complex-concentrations.png b/docs/guides/images/complex-concentrations.png index 2e83fd7..bb180dc 100644 Binary files a/docs/guides/images/complex-concentrations.png and b/docs/guides/images/complex-concentrations.png differ diff --git a/docs/guides/images/complex-geometry.png b/docs/guides/images/complex-geometry.png index 921d8de..74e3a6a 100644 Binary files a/docs/guides/images/complex-geometry.png and b/docs/guides/images/complex-geometry.png differ diff --git a/docs/guides/images/complex-slice3d-A.png b/docs/guides/images/complex-slice3d-A.png index 53312bd..55a226b 100644 Binary files a/docs/guides/images/complex-slice3d-A.png and b/docs/guides/images/complex-slice3d-A.png differ diff --git a/docs/guides/images/viz-concentrations.png b/docs/guides/images/viz-concentrations.png index 7b9c15d..7fefa59 100644 Binary files a/docs/guides/images/viz-concentrations.png and b/docs/guides/images/viz-concentrations.png differ diff --git a/docs/guides/images/viz-slice2d.png b/docs/guides/images/viz-slice2d.png index b4d5d60..ca118bd 100644 Binary files a/docs/guides/images/viz-slice2d.png and b/docs/guides/images/viz-slice2d.png differ diff --git a/docs/guides/images/viz-slice3d.png b/docs/guides/images/viz-slice3d.png index 82e4f73..b8c7f4f 100644 Binary files a/docs/guides/images/viz-slice3d.png and b/docs/guides/images/viz-slice3d.png differ diff --git a/examples/scripts/fielddata_from_image_workflow.py b/examples/scripts/fielddata_from_image_workflow.py index 856a033..3d2a4e2 100644 --- a/examples/scripts/fielddata_from_image_workflow.py +++ b/examples/scripts/fielddata_from_image_workflow.py @@ -19,7 +19,8 @@ def create_sinusoid( return sinusoid.astype(dtype=np.float64) -with tempfile.TemporaryDirectory() as temp_dir_name, Path(temp_dir_name) as temp_dir: +with tempfile.TemporaryDirectory() as temp_dir_name: + temp_dir = Path(temp_dir_name) print(f"temp_dir: {temp_dir}, exists={temp_dir.exists()}") # ----- make a workspace workspace_dir = temp_dir / "workspace" diff --git a/examples/scripts/fielddata_from_sim_workflow.py b/examples/scripts/fielddata_from_sim_workflow.py index e35f9bd..93ba6ab 100644 --- a/examples/scripts/fielddata_from_sim_workflow.py +++ b/examples/scripts/fielddata_from_sim_workflow.py @@ -5,7 +5,8 @@ import pyvcell.vcml as vc -with tempfile.TemporaryDirectory() as temp_dir_name, Path(temp_dir_name) as temp_dir: +with tempfile.TemporaryDirectory() as temp_dir_name: + temp_dir: Path = Path(temp_dir_name) # ----- make a workspace workspace_dir = temp_dir / "workspace" sim1_dir = workspace_dir / "sim1_dir" diff --git a/poetry.lock b/poetry.lock index 9e48221..8c8c3e5 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand. 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1022840..56ef7f4 100644 --- a/pyvcell/_internal/api/vcell_client/models/biomodel_ref.py +++ b/pyvcell/_internal/api/vcell_client/models/biomodel_ref.py @@ -33,7 +33,8 @@ class BiomodelRef(BaseModel): owner_name: Optional[StrictStr] = Field(default=None, alias="ownerName") owner_key: Optional[StrictInt] = Field(default=None, alias="ownerKey") version_flag: Optional[StrictInt] = Field(default=None, alias="versionFlag") - __properties: ClassVar[List[str]] = ["bmKey", "name", "ownerName", "ownerKey", "versionFlag"] + privacy: Optional[StrictInt] = Field(default=None, alias="privacy") + __properties: ClassVar[List[str]] = ["bmKey", "name", "ownerName", "ownerKey", "versionFlag", "privacy"] model_config = ConfigDict( populate_by_name=True, @@ -94,5 +95,6 @@ def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]: "ownerName": obj.get("ownerName"), "ownerKey": obj.get("ownerKey"), "versionFlag": obj.get("versionFlag"), + "privacy": obj.get("privacy"), }) return _obj diff --git a/pyvcell/_internal/geometry/segmented_image_geometry.py b/pyvcell/_internal/geometry/segmented_image_geometry.py index 2de8b6f..952333f 100644 --- a/pyvcell/_internal/geometry/segmented_image_geometry.py +++ b/pyvcell/_internal/geometry/segmented_image_geometry.py @@ -91,14 +91,16 @@ def plot(self, save_path: str | Path | None = None) -> None: cmap = plt.colormaps["tab10"] label_to_pos = {label: i for i, label in enumerate(unique_labels)} - plotter = pv.Plotter(off_screen=True, window_size=(800, 600)) + plotter = pv.Plotter(off_screen=True, window_size=[800, 600]) for label in unique_labels: thresh = grid.threshold(value=[label - 0.5, label + 0.5], scalars="subvolume") color = cmap(label_to_pos[label] / max(n_labels - 1, 1))[:3] name = self.label_names.get(int(label), f"region_{label}") plotter.add_mesh(thresh, color=color, label=name, opacity=0.6) - plotter.add_legend() + plotter.add_legend() # type: ignore[call-arg] img = plotter.screenshot(return_img=True) + if img is None: + raise RuntimeError("Could not render image") plotter.close() fig, ax = plt.subplots(figsize=(8, 6)) diff --git a/pyvcell/sim_results/widget.py b/pyvcell/sim_results/widget.py index 4e2b947..6802fd9 100644 --- a/pyvcell/sim_results/widget.py +++ b/pyvcell/sim_results/widget.py @@ -127,9 +127,9 @@ def _render(self, variable: str, time_index: int, clip_level: float) -> None: # Render self.pl.clear() self.pl.add_mesh(clipped, name=variable, show_scalar_bar=True) - self.pl.show_bounds() - self.pl.show_grid() - self.pl.reset_camera() + self.pl.show_bounds() # type: ignore[call-arg] + self.pl.show_grid() # type: ignore[call-arg] + self.pl.reset_camera() # type: ignore[call-arg] self.pl.render() self.ctrl.view_update() diff --git a/tests/_internal/api/vcell_client/test_publication_api.py b/tests/_internal/api/vcell_client/test_publication_api.py index 13ee240..ab5faac 100644 --- a/tests/_internal/api/vcell_client/test_publication_api.py +++ b/tests/_internal/api/vcell_client/test_publication_api.py @@ -45,6 +45,7 @@ def test_get_publications() -> None: owner_name="Dolgitzer", owner_key=259537152, version_flag=3, + privacy=0, ) ], mathmodel_refs=[], diff --git a/tests/_internal/geometry/test_segmented_image_geometry.py b/tests/_internal/geometry/test_segmented_image_geometry.py index fb8b45b..bcc9722 100644 --- a/tests/_internal/geometry/test_segmented_image_geometry.py +++ b/tests/_internal/geometry/test_segmented_image_geometry.py @@ -74,7 +74,8 @@ def test_to_pyvista(self, simple_seg: SegmentedImageGeometry) -> None: grid = simple_seg.to_pyvista() assert grid.dimensions == (11, 11, 11) assert grid.spacing == (1.0, 1.0, 1.0) - assert grid.origin == (0.0, 0.0, 0.0) + # seems to be mistyped in pyvista, documentation backs up this next origin assignment + assert grid.origin == (0.0, 0.0, 0.0) # type: ignore[comparison-overlap] assert "subvolume" in grid.cell_data assert grid.cell_data["subvolume"].shape == (1000,) @@ -89,7 +90,8 @@ def test_to_pyvista_nonunit_spacing(self) -> None: 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