Merge pull request #27 from virtualcell/sysbio-course-7

notebook for importing geometry

Author: jcschaff

README.md

@@ -5,7 +5,8 @@
 [![codecov](https://codecov.io/gh/virtualcell/pyvcell/branch/main/graph/badge.svg)](https://codecov.io/gh/virtualcell/pyvcell)
 [![Commit activity](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)](https://img.shields.io/github/commit-activity/m/virtualcell/pyvcell)
 [![License](https://img.shields.io/github/license/virtualcell/pyvcell)](https://img.shields.io/github/license/virtualcell/pyvcell)
-[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/101BPDYqu4_PupqmunT6Qhextks_VT-8X?usp=sharing)
+
+[//]: # "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/101BPDYqu4_PupqmunT6Qhextks_VT-8X?usp=sharing)"
 
 This is the python wrapper for vcell modeling and simulation for
 
@@ -63,3 +64,13 @@ results.plotter.plot_concentrations()
 # Documentation
 
 coming soon.
+
+# Examples:
+
+### Antimony example
+
+[![Open in Colab ](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1aGttld4SKxuC7Vh-h1A7gsPIJT8u00fN?usp=sharing)
+
+### Parameters example
+
+[![Open in Colab ](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/drive/1nNlMvXuZdn7Ay8la0KOKmSwi6dSurkte?usp=sharing)

examples/notebooks/sysbio-3-geometry.ipynb

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyvcell"
-version = "0.1.17"
+version = "0.1.18"
 description = "This is the python wrapper for vcell modeling and simulation"
 authors = ["Jim Schaff <[email protected]>"]
 repository = "https://github.com/virtualcell/pyvcell"

pyproject.toml

@@ -291,6 +291,14 @@ def add_surface(self, name: str, sub_volume_1: SubVolume | str, sub_volume_2: Su
         self.surface_classes.append(surface_class)
         return surface_class
 
+    @property
+    def subvolume_names(self) -> list[str]:
+        return [subvolume.name for subvolume in self.subvolumes]
+
+    @property
+    def surface_class_names(self) -> list[str]:
+        return [surface_class.name for surface_class in self.surface_classes]
+
 
 class StructureMapping(VcmlNode):
     structure_name: str