pyvcell 0.2.0__tar.gz → 0.2.2__tar.gz

{pyvcell-0.2.0 → pyvcell-0.2.2}/PKG-INFO

@@ -1,45 +1,38 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pyvcell
-Version: 0.2.0
+Version: 0.2.2
 Summary: This is the python wrapper for vcell modeling and simulation
-Home-page: https://github.com/virtualcell/pyvcell
-Author: Jim Schaff
-Author-email: schaff@uchc.edu
-Requires-Python: >=3.11,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: antimony (>=2.15.0,<3.0.0)
-Requires-Dist: h5py (>=3.11.0,<4.0.0)
-Requires-Dist: imageio (>=2.37.0,<3.0.0)
-Requires-Dist: libvcell (>=0.0.15,<0.0.16)
-Requires-Dist: lxml (>=5.3.1,<6.0.0)
-Requires-Dist: matplotlib (>=3.10.0,<4.0.0)
-Requires-Dist: numexpr (>=2.10.0,<3.0.0)
-Requires-Dist: numpy (>=1.26.4,<3.0)
-Requires-Dist: orjson (>=3.10.3,<4.0.0)
-Requires-Dist: overrides (>=7.7.0,<8.0.0)
-Requires-Dist: pydantic (>=2.10.5,<3.0.0)
-Requires-Dist: python-dateutil (>=2.8.2,<3.0.0)
-Requires-Dist: python-libsbml (>=5.20.4,<6.0.0)
-Requires-Dist: pyvcell-fvsolver (>=0.1.1,<0.2.0)
-Requires-Dist: pyvista (>=0.44.2,<0.45.0)
-Requires-Dist: requests (>=2.32.3,<3.0.0)
-Requires-Dist: requests-oauth2client (>=1.6.0,<2.0.0)
-Requires-Dist: sympy (>=1.13.1,<2.0.0)
-Requires-Dist: tensorstore (>=0.1.72,<0.2.0)
-Requires-Dist: trame (>=3.8.1,<4.0.0)
-Requires-Dist: trame-server (>=3.4.0,<4.0.0)
-Requires-Dist: trame-vtk (>=2.8.15,<3.0.0)
-Requires-Dist: trame-vuetify (>=2.8.1,<3.0.0)
-Requires-Dist: typer (>=0.12.3,<1.0.0)
-Requires-Dist: typing-extensions (>=4.12.2,<5.0.0)
-Requires-Dist: urllib3 (>=2.3.0,<3.0.0)
-Requires-Dist: vtk (>=9.3.1,<10.0.0)
-Requires-Dist: zarr (>=2.17.2,<3.0.0)
-Project-URL: Documentation, https://virtualcell.github.io/pyvcell/
-Project-URL: Repository, https://github.com/virtualcell/pyvcell
+Author: Jim Schaff, Logan Drescher
+Author-email: Jim Schaff <schaff@uchc.edu>, Logan Drescher <drescher@uchc.edu>
+Requires-Dist: antimony>=3.1.3
+Requires-Dist: h5py>=3.11.0,<4
+Requires-Dist: imageio>=2.37.0,<3
+Requires-Dist: libvcell>=0.0.15.3
+Requires-Dist: lxml>=6.1.0,<7
+Requires-Dist: matplotlib>=3.10.0,<4
+Requires-Dist: numexpr>=2.10,<3
+Requires-Dist: numpy>=1.26.4,<3.0
+Requires-Dist: orjson>=3.10.3,<4
+Requires-Dist: overrides>=7.7.0,<8
+Requires-Dist: pydantic>=2.10.5,<3
+Requires-Dist: python-dateutil>=2.8.2,<3
+Requires-Dist: python-libsbml>=5.20.4,<6
+Requires-Dist: pyvcell-fvsolver>=0.2.1
+Requires-Dist: pyvista>=0.44.2,<1
+Requires-Dist: requests>=2.32.3,<3
+Requires-Dist: requests-oauth2client>=1.6.0,<2
+Requires-Dist: sympy>=1.13.1,<2
+Requires-Dist: tensorstore>=0.1.72,<1
+Requires-Dist: trame>=3.8.1,<4
+Requires-Dist: trame-server>=3.4.0,<4
+Requires-Dist: trame-vtk>=2.8.15,<3
+Requires-Dist: trame-vuetify>=3.2.2,<4
+Requires-Dist: typer>=0.12.3,<1.0.0
+Requires-Dist: typing-extensions>=4.12.2,<5
+Requires-Dist: urllib3>=2.3.0,<3
+Requires-Dist: vtk>=9.3.1,<10
+Requires-Dist: zarr>=2.17.2,<3
+Requires-Python: >=3.11, <4.0
 Description-Content-Type: text/markdown
 
 # pyvcell
@@ -122,4 +115,3 @@ Full documentation is available at **https://virtualcell.github.io/pyvcell/**
 ### Geometry import example
 
 [![Open in Colab ](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/14L3WaV42PEu7NvAQdil7i8mEL4WTPF9h?usp=sharing)
-

{pyvcell-0.2.0 → pyvcell-0.2.2}/pyproject.toml

@@ -1,70 +1,80 @@
-[tool.poetry]
+[project]
 name = "pyvcell"
-version = "0.2.0"
+version = "0.2.2"
+requires-python = ">=3.11,<4.0"
 description = "This is the python wrapper for vcell modeling and simulation"
-authors = ["Jim Schaff <schaff@uchc.edu>"]
 repository = "https://github.com/virtualcell/pyvcell"
 documentation = "https://virtualcell.github.io/pyvcell/"
 readme = "README.md"
+authors = [
+    {name = "Jim Schaff",       email = "schaff@uchc.edu"},
+    {name = "Logan Drescher",   email = "drescher@uchc.edu"}
+]
+
 packages = [
-    {include = "pyvcell"},
+    {include="pyvcell"},
+]
+dependencies = [
+    "antimony (>=3.1.3)",
+    "h5py>=3.11.0,<4",
+    "imageio>=2.37.0,<3",
+    "libvcell (>=0.0.15.3)",
+    "lxml>=6.1.0,<7",
+    "matplotlib>=3.10.0,<4",
+    "numexpr>=2.10,<3",
+    "numpy>=1.26.4,<3.0",
+    "orjson>=3.10.3,<4",
+    "overrides>=7.7.0,<8",
+    "pydantic>=2.10.5,<3",
+    "python-dateutil>=2.8.2,<3",
+    "python-libsbml>=5.20.4,<6",
+    "pyvcell-fvsolver (>=0.2.1)",
+    "pyvista>=0.44.2,<1",
+    "requests>=2.32.3,<3",
+    "requests-oauth2client>=1.6.0,<2",
+    "sympy>=1.13.1,<2",
+    "tensorstore>=0.1.72,<1",
+    "trame>=3.8.1,<4",
+    "trame-server>=3.4.0,<4",
+    "trame-vtk>=2.8.15,<3",
+    "trame-vuetify>=3.2.2,<4",
+    "typer>=0.12.3,<1.0.0",
+    "typing-extensions>=4.12.2,<5",
+    "urllib3>=2.3.0,<3",
+    "vtk>=9.3.1,<10",
+    "zarr>=2.17.2,<3", # major upgrade will take some work!
 ]
 
-[tool.poetry.dependencies]
-python = ">=3.11,<4.0"
-numexpr = "^2.10.0"
-zarr = "^2.17.2"
-h5py = "^3.11.0"
-numpy = ">=1.26.4,<3.0"
-orjson = "^3.10.3"
-vtk = "^9.3.1"
-pyvcell-fvsolver = "^0.1.1"
-typer = ">=0.12.3,<1.0.0"
-pydantic = "^2.10.5"
-requests-oauth2client = "^1.6.0"
-overrides = "^7.7.0"
-typing-extensions = "^4.12.2"
-urllib3 = "^2.3.0"
-requests = "^2.32.3"
-python-dateutil = "^2.8.2"
-python-libsbml = "^5.20.4"
-matplotlib = "^3.10.0"
-lxml = "^5.3.1"
-imageio = "^2.37.0"
-tensorstore = "^0.1.72"
-libvcell = "^0.0.15"
-trame = "^3.8.1"
-trame-vtk = "^2.8.15"
-trame-vuetify = "^2.8.1"
-pyvista = "^0.44.2"
-trame-server = "^3.4.0"
-sympy = "^1.13.1"
-antimony = "^2.15.0"
-
-[tool.poetry.group.dev.dependencies]
-pytest = "^7.2.0"
-pytest-cov = "^4.0.0"
-deptry = "^0.16.2"
-mypy = "^1.5.1"
-pre-commit = "^3.8.0"
-tox = "^4.11.1"
-types-requests = "^2.32.0.20241016"
-notebook = "^7.3.2"
-lxml-stubs = "^0.5.1"
-trame-jupyter-extension = "^2.1.4"
-ipywidgets = "^8.1.5"
-copasi-basico = ">=0.65"
-
-[tool.poetry.group.docs.dependencies]
-mkdocs = "^1.6.1"
-mkdocs-material = "^9.5.50"
-mkdocstrings = {extras = ["python"], version = "^0.27.0"}
-griffe = "^1.5.5"
-mkdocs-jupyter = "^0.25.1"
+[dependency-groups]
+dev = [
+    "pytest>=7.2.0,<8",
+    "pytest-cov>=4.0.0,<5",
+    "deptry>=0.16.2,<1",
+    "mypy>=1.5.1,<2",
+    "pre-commit>=3.8.0,<4",
+    "tox>=4.11.1,<5",
+    "types-requests>=2.32.0.20241016,<3",
+    "notebook>=7.3.2,<8",
+    "lxml-stubs>=0.5.1,<1",
+    "trame-jupyter-extension>=2.1.4,<3",
+    "ipywidgets>=8.1.5,<9",
+    "copasi-basico>=0.65,<1",
+]
+docs = [
+    "mkdocs>=1.6.1,<2",
+    "mkdocs-material>=9.5.50,<10",
+    "mkdocstrings[python]>=0.27.0,<1",
+    "griffe>=1.5.5,<2",
+    "mkdocs-jupyter>=0.25.1,<1",
+]
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["uv_build >= 0.11.7, <0.12.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "pyvcell"
+module-root = ""
 
 [tool.mypy]
 files = ["pyvcell", "tests", "examples"]

{pyvcell-0.2.0 → pyvcell-0.2.2}/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 @@ class BiomodelRef(BaseModel):
             "ownerName": obj.get("ownerName"),
             "ownerKey": obj.get("ownerKey"),
             "versionFlag": obj.get("versionFlag"),
+            "privacy": obj.get("privacy"),
         })
         return _obj

{pyvcell-0.2.0 → pyvcell-0.2.2}/pyvcell/_internal/geometry/segmented_image_geometry.py

@@ -91,14 +91,16 @@ class SegmentedImageGeometry:
         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))

{pyvcell-0.2.0 → pyvcell-0.2.2}/pyvcell/_internal/simdata/zarr_writer.py

@@ -144,21 +144,29 @@ def write_zarr(pde_dataset: PdeDataSet, data_functions: DataFunctions, mesh: Car
 
         # add volumetric functions
         for f in volume_functions:
-            func_data = f.evaluate(variable_bindings=bindings).reshape((num_z, num_y, num_x))
+            evaluated_data = f.evaluate(variable_bindings=bindings)
+            is_pre_sized: bool = evaluated_data.shape == (num_z, num_y, num_x)
+            if evaluated_data.shape == ():  # scalar value
+                func_data = np.zeros((num_z, num_y, num_x), dtype=evaluated_data.dtype)
+                func_data.fill(evaluated_data.min())  # min of a scalar value is the value itself.
+            else:
+                func_data = evaluated_data if is_pre_sized else evaluated_data.reshape((num_z, num_y, num_x))
             z1[t, c, :, :, :] = func_data
-            domain_name = f.name.split("::")[0]
-            function_name = f.name.split("::")[1]
+            name_parts = f.name.split("::")
+            if len(name_parts) > 2:
+                raise ValueError(f"Volume function name `{f.name}` is not in the expected format")
+            domain_half: str = f.name.split("::")[0] if len(name_parts) == 2 else ""
+            name_half: str = f.name.split("::")[-1]
             if t == 0:
                 channel_metadata.append({
                     "index": c,
-                    "label": function_name,
-                    "domain_name": domain_name,
+                    "label": name_half,
+                    "domain_name": domain_half,
                     "min_values": [],
                     "max_values": [],
                     "mean_values": [],
                 })
-            domain_mask = _get_domain_mask(domain_name)
-            masked = func_data[domain_mask]
+            masked = func_data if len(domain_half) == 0 else func_data[_get_domain_mask(domain_half)]
             channel_metadata[c]["min_values"].append(float(np.min(masked)))
             channel_metadata[c]["max_values"].append(float(np.max(masked)))
             channel_metadata[c]["mean_values"].append(float(np.mean(masked)))

{pyvcell-0.2.0 → pyvcell-0.2.2}/pyvcell/sim_results/widget.py

@@ -127,9 +127,9 @@ class App:
         # 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()
 

pyvcell-0.2.0/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2024, Jim Schaff
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.