diff --git a/.github/workflows/apple.yml b/.github/workflows/apple.yml index 17fff68..f97a713 100644 --- a/.github/workflows/apple.yml +++ b/.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 diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml index 933d075..0fbcd1d 100644 --- a/.github/workflows/linux.yml +++ b/.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 diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml index e2fbe83..c4250b5 100644 --- a/.github/workflows/windows.yml +++ b/.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 diff --git a/man/docstring/mcds.__init__.md b/man/docstring/mcds.__init__.md index 25ff0fb..7fdb6ec 100644 --- a/man/docstring/mcds.__init__.md +++ b/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? diff --git a/man/docstring/mcds.make_conc_vtk.md b/man/docstring/mcds.make_conc_vtk.md index b8fbf88..660500b 100644 --- a/man/docstring/mcds.make_conc_vtk.md +++ b/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. ``` diff --git a/man/docstring/mcds.make_graph_gml.md b/man/docstring/mcds.make_graph_gml.md index 809d1c9..d3dd4f1 100644 --- a/man/docstring/mcds.make_graph_gml.md +++ b/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 diff --git a/man/docstring/mcdsts.__init__.md b/man/docstring/mcdsts.__init__.md index fae06c7..1581c00 100644 --- a/man/docstring/mcdsts.__init__.md +++ b/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? diff --git a/man/docstring/mcdsts.make_conc_vtk.md b/man/docstring/mcdsts.make_conc_vtk.md index 23a854c..753e1e7 100644 --- a/man/docstring/mcdsts.make_conc_vtk.md +++ b/man/docstring/mcdsts.make_conc_vtk.md @@ -3,6 +3,8 @@ ## input: ``` + visualize: boolean; default is False + additionally, visualize cells using vtk renderer. ``` diff --git a/man/docstring/mcdsts.make_graph_gml.md b/man/docstring/mcdsts.make_graph_gml.md index 1ca43d9..c28b163 100644 --- a/man/docstring/mcdsts.make_graph_gml.md +++ b/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 diff --git a/man/docstring/pcdl_get_anndata.md b/man/docstring/pcdl_get_anndata.md index 4bdaa78..54e4763 100644 --- a/man/docstring/pcdl_get_anndata.md +++ b/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. diff --git a/man/docstring/pcdl_make_graph_gml.md b/man/docstring/pcdl_make_graph_gml.md index 0f2050b..20dfbd0 100644 --- a/man/docstring/pcdl_make_graph_gml.md +++ b/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 diff --git a/man/scarab.py b/man/scarab.py index f17908f..6d38dc3 100644 --- a/man/scarab.py +++ b/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', diff --git a/pcdl/VERSION.py b/pcdl/VERSION.py index 6093f83..bbeb48b 100644 --- a/pcdl/VERSION.py +++ b/pcdl/VERSION.py @@ -1 +1 @@ -__version__ = '3.3.2' +__version__ = '3.3.3'