Merge pull request #35 from elmbeech/master

release v4.0.4

Author: elmbeech

.github/workflows/apple.yml

@@ -7,7 +7,9 @@ run-name: ${{ github.actor }}::pytest pcdl library on mac os x; the latest pytho
 
 on:
   push:
-    branches: ["utest"]  # ["master", "v3", "v4"]
+    branches: ["utest", "master"]  # ["v3", "v4"]
+  pull:
+    branches: ["master"]
 
 jobs:
   build-macosx:

.github/workflows/linux.yml

@@ -7,7 +7,9 @@ run-name: ${{ github.actor }}::pytest pcdl library on linux os; all python3 vers
 
 on:
   push:
-    branches: ["utest"]  # ["master", "v3", "v4"]
+    branches: ["utest","master"]  # ["v3", "v4"]
+  pull:
+    branches: ["master"]
 
 jobs:
   build-linux:

.github/workflows/windows.yml

@@ -7,7 +7,9 @@ run-name: ${{ github.actor }}::pytest pcdl library on windows os; the latest pyt
 
 on:
   push:
-    branches: ["utest"]  # ["master", "v3", "v4"]
+    branches: ["utest", "master"]  # ["v3", "v4"]
+  pull:
+    branches: ["master"] 
 
 jobs:
   build-windows:

README.md

@@ -91,7 +91,7 @@ Within the pcdl library, we tried to stick to the documentation policy laid out
 
 + original PhysiCell-Tools python-loader implementation: Patrick Wall, Randy Heiland, Paul Macklin
 + fork pcdl implementation: Elmar Bucher
-+ fork pcdl co-programmer: Furkan Kurtoglu, Jennifer Eng, Heber Rocha
++ fork pcdl co-programmer: Furkan Kurtoglu, Heber Rocha, Jennifer Eng
 + fork pcdl continuous testing and feedbacks: Aneequa Sundus, John Metzcar
 + student prj on pcdl:
   Benjamin Jacobs (make\_graph\_gml),
@@ -125,6 +125,9 @@ Developers, please make pull requests to the https://github.com/elmbeech/physice
 + evt generate lineage tree graph output files.
 
 ## Release Notes:
++ version 4.0.4 (2025-07-23): elmbeech/physicelldataloader
+    + command line commands now return **error code 0** if the command runs successfully.
+
 + version 4.0.3 (2025-07-20): elmbeech/physicelldataloader
     + timestep and timeseries **plot_contour**, **plot_scatter**, and **plot_timeseries** handle now **kwargs** arguments.
     + minor bugfixes.
@@ -152,6 +155,9 @@ Developers, please make pull requests to the https://github.com/elmbeech/physice
     + new **render_neuroglancer** function, to render ome tiff image into neuroglancer.
     + new **pcdl_render_neuroglancer** function, to render ome tiff images into neuroglancer.
 
++ version 3.3.8 (2025-07-23): elmbeech/physicelldataloader
+    + command line commands now return **error code 0** if the command runs successfully.
+
 + version 3.3.7 (2025-06-01): elmbeech/physicelldataloader
     + compatible with current (non end-of-life cycle) python versions.
     + minor bugfixes.

pcdl/VERSION.py

@@ -1 +1 @@
-__version__ = '4.0.3'
+__version__ = '4.0.4'

pcdl/commandline.py

@@ -98,7 +98,8 @@ def get_version():
     )
     s_version = f'version:\n{mcds.get_physicell_version()}\n{mcds.get_multicellds_version()}\npcdl_{pcdl.__version__}'
     # going home
-    return s_version
+    print(s_version)
+    return 0
 
 
 def get_unit_dict():
@@ -175,7 +176,8 @@ def get_unit_dict():
     se_unit.sort_index(inplace=True)
     se_unit.to_csv(s_opathfile)
     # going home
-    return s_opathfile
+    print(s_opathfile)
+    return 0
 
 
 ###########################################
@@ -240,7 +242,8 @@ def get_substrate_list():
         verbose = True if args.verbose.lower().startswith('t') else False
     )
     # going home
-    return mcds.get_substrate_list()
+    print(mcds.get_substrate_list())
+    return 0
 
 
 def get_conc_attribute():
@@ -342,7 +345,8 @@ def get_conc_attribute():
     s_opathfile = s_path + '/' + s_ofile
     json.dump(dl_variable, open(s_opathfile, 'w'), sort_keys=True)
     # going home
-    return s_opathfile
+    print(s_opathfile)
+    return 0
 
 
 def get_conc_df():
@@ -439,7 +443,7 @@ def get_conc_df():
         # going home
         s_opathfile = s_pathfile.replace('.xml','_conc.csv')
         df_conc.to_csv(s_opathfile)
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -464,12 +468,15 @@ def get_conc_df():
         if b_collapse:
             s_opathfile = f'{s_path}/timeseries_conc.csv'
             ldf_conc.to_csv(s_opathfile)
-            return s_opathfile
+            print(s_opathfile)
         else:
             ls_opathfile = [f"{s_path}/{s_xmlfile.replace('.xml','_conc.csv')}" for s_xmlfile in mcdsts.get_xmlfile_list()]
             for i, df_conc in enumerate(ldf_conc):
                 df_conc.to_csv(ls_opathfile[i])
-            return ls_opathfile
+            print(ls_opathfile)
+
+    # going home
+    return 0
 
 
 def plot_contour():
@@ -655,7 +662,7 @@ def plot_contour():
             figbgcolor = None if (args.figbgcolor.lower() == 'none') else args.figbgcolor,
         )
         # going home
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -687,7 +694,10 @@ def plot_contour():
         )
         # going home
         s_opath = '/'.join(ls_opathfile[0].split('/')[:-1])
-        return s_opath
+        print(s_opath)
+
+    # going home
+    return 0
 
 
 def make_conc_vtk():
@@ -750,7 +760,7 @@ def make_conc_vtk():
         )
         s_opathfile = mcds.make_conc_vtk()
         # going home
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -765,8 +775,10 @@ def make_conc_vtk():
         )
         ls_opathfile = mcdsts.make_conc_vtk()
         # going home
-        return ls_opathfile
+        print(ls_opathfile)
 
+    # going home
+    return 0
 
 ############################################
 # cell agent relatd command line functions #
@@ -835,7 +847,8 @@ def get_celltype_list():
         verbose = True if args.verbose.lower().startswith('t') else False
     )
     # going home
-    return mcds.get_celltype_list()
+    print(mcds.get_celltype_list())
+    return 0
 
 
 def get_cell_attribute_list():
@@ -912,7 +925,7 @@ def get_cell_attribute_list():
     )
 
     # going home
-    return mcds.get_cell_attribute_list()
+    print(mcds.get_cell_attribute_list())
 
 
 def get_cell_attribute():
@@ -1068,7 +1081,8 @@ def get_cell_attribute():
         allvalues = b_allvalues,
     )
     json.dump(dl_variable, open(s_opathfile, 'w'), sort_keys=True)
-    return s_opathfile
+    print(s_opathfile)
+    return 0
 
 
 def get_cell_df():
@@ -1180,7 +1194,7 @@ def get_cell_df():
         # going home
         s_opathfile = s_pathfile.replace('.xml','_cell.csv')
         df_cell.to_csv(s_opathfile)
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -1205,12 +1219,15 @@ def get_cell_df():
         if b_collapse:
             s_opathfile = f'{s_path}/timeseries_cell.csv'
             ldf_cell.to_csv(s_opathfile)
-            return s_opathfile
+            print(s_opathfile)
         else:
             ls_opathfile = [f"{s_path}/{s_xmlfile.replace('.xml','_cell.csv')}" for s_xmlfile in mcdsts.get_xmlfile_list()]
             for i, df_cell in enumerate(ldf_cell):
                 df_cell.to_csv(ls_opathfile[i])
-            return ls_opathfile
+            print(ls_opathfile)
+
+    # going home
+    return 0
 
 
 def get_anndata():
@@ -1352,7 +1369,7 @@ def get_anndata():
         # going home
         s_opathfile = s_pathfile.replace('.xml', f'_cell_{args.scale}.h5ad')
         ann_mcds.write_h5ad(s_opathfile)
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -1378,12 +1395,15 @@ def get_anndata():
         if b_collapse :
             s_opathfile = f'{s_path}/timeseries_cell_{args.scale}.h5ad'
             ann_mcdsts.write_h5ad(s_opathfile)
-            return s_opathfile
+            print(s_opathfile)
         else:
             ls_opathfile = [f"{s_path}/{s_xmlfile.replace('.xml', '_cell_{}.h5ad'.format(args.scale))}" for s_xmlfile in mcdsts.get_xmlfile_list()]
             for i, ann_mcds in enumerate(ann_mcdsts):
                 ann_mcds.write_h5ad(ls_opathfile[i])
-            return ls_opathfile
+            print(ls_opathfile)
+
+    # going home
+    return 0
 
 
 def make_graph_gml():
@@ -1502,7 +1522,7 @@ def make_graph_gml():
             node_attribute = args.node_attribute,
         )
         # going home
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -1521,7 +1541,10 @@ def make_graph_gml():
             node_attribute = args.node_attribute,
         )
         # going home
-        return ls_opathfile
+        print(ls_opathfile)
+
+    # going home
+    return 0
 
 
 def plot_scatter():
@@ -1734,7 +1757,7 @@ def plot_scatter():
             figbgcolor = None if (args.figbgcolor.lower() == 'none') else args.figbgcolor,
         )
         # going home
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -1767,7 +1790,10 @@ def plot_scatter():
         )
         # going home
         s_opath = '/'.join(ls_opathfile[0].split('/')[:-1])
-        return s_opath
+        print(s_opath)
+
+    # going home
+    return 0
 
 
 def make_cell_vtk():
@@ -1872,7 +1898,7 @@ def make_cell_vtk():
             attribute = args.attribute,
         )
         # going home
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -1889,7 +1915,10 @@ def make_cell_vtk():
             attribute = args.attribute,
         )
         # going home
-        return ls_opathfile
+        print(ls_opathfile)
+
+    # going home
+    return 0
 
 
 ###################################################
@@ -2174,7 +2203,8 @@ def plot_timeseries():
         figbgcolor = None if (args.figbgcolor.lower() == 'none') else args.figbgcolor,
     )
     # going home
-    return s_pathfile
+    print(s_pathfile)
+    return 0
 
 
 def make_ome_tiff():
@@ -2301,7 +2331,7 @@ def make_ome_tiff():
             file = True,
         )
         # going home
-        return s_opathfile
+        print(s_opathfile)
 
     else:
         mcdsts = pcdl.TimeSeries(
@@ -2322,7 +2352,10 @@ def make_ome_tiff():
             collapse = False if args.collapse.lower().startswith('f') else True,
         )
         # going home
-        return o_opathfile
+        print(o_opathfile)
+
+    # going home
+    return 0
 
 
 #######################
@@ -2416,7 +2449,8 @@ def make_gif():
         interface = args.interface,
     )
     # going home
-    return s_opathfile
+    print(s_opathfile)
+    return 0
 
 
 def make_movie():
@@ -2468,4 +2502,5 @@ def make_movie():
         framerate = args.framerate,
     )
     # going home
-    return s_opathfile
+    print(s_opathfile)
+    return 0