@ workflows update PYTHONPATH

.github/workflows/apple.yml

@@ -21,7 +21,7 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     env:
-      PYTHONPATH: /Users/runner/work/physicelldataloader/physicelldataloader
+      PYTHONPATH: /Users/runner/work/physicelldataloader/physicelldataloader:/Users/runner/work/python-loader/python-loader
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/linux.yml

@@ -21,7 +21,7 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     env:
-      PYTHONPATH: /home/runner/work/physicelldataloader/physicelldataloader
+      PYTHONPATH: /home/runner/work/physicelldataloader/physicelldataloader:/home/runner/work/python-loader/python-loader
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/windows.yml

@@ -21,7 +21,7 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     env:
-      PYTHONPATH: D:\a\physicelldataloader\physicelldataloader
+      PYTHONPATH: D:\a\physicelldataloader\physicelldataloader:D:\a\python-loader\python-loader
 
     steps:
     - uses: actions/checkout@v4

man/docstring/mcds.__init__.md

@@ -23,8 +23,9 @@
                 processing, similar to the original pyMCDS_cells.py script.
 
             graph: boole; default True
-                should neighbor garph and attached graph be loaded?
-                setting graph to False will use less memory and speed up processing.
+                should neighbor garph, attached graph, and spring attached graph
+                be loaded? setting graph to False will use less memory and
+                speed up processing.
 
             physiboss: boole; default True
                 should physiboss state data be loaded, if found?

man/docstring/mcds.make_conc_vtk.md

@@ -3,13 +3,15 @@
 
 ## input:
 ```
+            visualize: boolean; default is True
+                additionally, visualize cells using vtk renderer.
 
 ```
 
 ## output:
 ```
             s_vtkpathfile: vtk rectilinear grid file that contains
-            3D distributions of all substrates over the microenvironment.
+                3D distributions of all substrates over the microenvironment.
 
 ```
 

man/docstring/mcds.make_graph_gml.md

@@ -7,6 +7,7 @@
                 to specify which physicell output data should be processed.
                 neighbor, touch: processes mcds.get_neighbor_graph_dict dictionary.
                 attached: processes mcds.get_attached_graph_dict dictionary.
+                spring: processes mcds.get_spring_graph_dict dictionary.
 
             edge_attribute: boolean; default True
                 specifies if the spatial Euclidean distance is used for

man/docstring/mcdsts.__init__.md

@@ -23,8 +23,9 @@
                 processing, similar to the original pyMCDS_cells.py script.
 
             graph: boole; default True
-                should neighbor graph and attached graph be loaded?
-                setting graph to False will use less memory and speed up processing.
+                should neighbor garph, attached graph, and spring attached graph
+                be loaded? setting graph to False will use less memory and
+                speed up processing.
 
             physiboss: boole; default True
                 should physiboss state data be loaded, if found?

man/docstring/mcdsts.make_conc_vtk.md

@@ -3,6 +3,8 @@
 
 ## input:
 ```
+            visualize: boolean; default is False
+                additionally, visualize cells using vtk renderer.
 
 ```
 

man/docstring/mcdsts.make_graph_gml.md

@@ -5,10 +5,11 @@
 ```
             self: pyMCDS class instance.
 
-            graph_type: string; default is neighbor
+            graph_type: string
                 to specify which physicell output data should be processed.
-                attached: processes mcds.get_attached_graph_dict dictionary.
+                attached, touch: processes mcds.get_attached_graph_dict dictionary.
                 neighbor: processes mcds.get_neighbor_graph_dict dictionary.
+                spring: processes mcds.get_spring_graph_dict dictionary.
 
             edge_attribute: boolean; default True
                 specifies if the spatial Euclidean distance is used for

man/docstring/pcdl_get_anndata.md

@@ -31,8 +31,9 @@ options:
                         will use less memory and speed up processing, similar
                         to the original pyMCDS_cells.py script. default is
                         True.
-  --graph GRAPH         should neighbor graph and attach graph be extracted
-                        and loaded into the anndata object? default is True.
+  --graph GRAPH         should neighbor graph, attach graph, and attached
+                        spring graph be extracted and loaded into the anndata
+                        object? default is True.
   --physiboss PHYSIBOSS
                         if found, should physiboss state data be extracted and
                         loaded into the anndata object? default is True.

man/docstring/pcdl_make_graph_gml.md

@@ -19,7 +19,9 @@ positional arguments:
   graph_type            to specify which physicell output data should be
                         processed. attached: processes
                         mcds.get_attached_graph_dict dictionary. neighbor:
-                        processes mcds.get_neighbor_graph_dict dictionary.
+                        processes mcds.get_neighbor_graph_dict dictionary
+                        spring: processes mcds.get_spring_graph_dict
+                        dictionary.
 
 options:
   -h, --help            show this help message and exit

man/scarab.py

@@ -91,6 +91,11 @@ def docstring_md(s_function, ls_doc, s_header=None, s_opath='man/docstring/'):
     f.close()
 
 
+# download test dataset
+if not os.path.exists('pcdl/output_2d/') or not os.path.exists('pcdl/output_3d/'):
+    pcdl.install_data()
+
+
 # load data
 mcds = pcdl.TimeStep(
     'pcdl/output_2d/output00000000.xml',

pcdl/VERSION.py

@@ -1 +1 @@
-__version__ = '3.3.2'
+__version__ = '3.3.3'