Merge branch 'development' of https://github.com/MathCancer/PhysiCell …

…into development

beta/get_studio.py

@@ -0,0 +1,43 @@
+# Python script to download the latest release of PhysiCell Studio. It will create a /studio directory 
+# from wherever this script is run. Sample commands to run the Studio will be printed.
+
+import requests
+import os
+import zipfile
+import shutil
+
+response = requests.get("https://api.github.com/repos/PhysiCell-Tools/PhysiCell-Studio/releases/latest")
+release_name_str = response.json()["name"]
+print(release_name_str)
+print(release_name_str.split())
+vnum = release_name_str.split()[0]
+print("vnum=",vnum)  # e.g., vnum= v2.26.7
+
+
+try:
+    os.system('rm -rf studio')
+except:
+    pass
+
+# PhysiCell-Studio-2.26.7
+remote_url = 'https://github.com/PhysiCell-Tools/PhysiCell-Studio/archive/refs/tags/' + vnum + '.zip'
+print("remote_url=",remote_url)
+local_file = 'Studio.zip'
+data = requests.get(remote_url)
+with open(local_file, 'wb')as file:
+   file.write(data.content)
+print("downloaded version ",vnum," to ",local_file)
+
+print("unzip-ing ",local_file)
+with zipfile.ZipFile(local_file, 'r') as zip_ref:
+    zip_ref.extractall(".")
+
+latest_studio_dir = "PhysiCell-Studio-" + vnum[1:]  # need to drop the 'v' as first character
+shutil.move(latest_studio_dir,"studio")
+print(f"renamed '{latest_studio_dir}' to 'studio'")
+
+print("\n-- Sample commands to run the Studio:")
+print("python studio/bin/studio.py     # attempts to load config/PhysiCell_settings.xml")
+print("python studio/bin/studio.py -c <config_file.xml> -e <executable_program>")
+print("python studio/bin/studio.py --help")
+print()

sample_projects/asymmetric_division/main.cpp

@@ -181,7 +181,7 @@ int main( int argc, char* argv[] )
 		while( PhysiCell_globals.current_time < PhysiCell_settings.max_time + 0.1*diffusion_dt )
 		{
 			// save data if it's time. 
-			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_full_save_time ) < 0.01 * diffusion_dt )
+			if( PhysiCell_globals.current_time > PhysiCell_globals.next_full_save_time - 0.5 * diffusion_dt )
 			{
 				display_simulation_status( std::cout ); 
 				if( PhysiCell_settings.enable_legacy_saves == true )
@@ -201,7 +201,7 @@ int main( int argc, char* argv[] )
 			}
 
 			// save SVG plot if it's time
-			if( fabs( PhysiCell_globals.current_time - PhysiCell_globals.next_SVG_save_time  ) < 0.01 * diffusion_dt )
+			if( PhysiCell_globals.current_time > PhysiCell_globals.next_SVG_save_time - 0.5 * diffusion_dt )
 			{
 				if( PhysiCell_settings.enable_SVG_saves == true )
 				{	

sample_projects/template/config/PhysiCell_settings.xml

@@ -88,10 +88,10 @@
             <phenotype>
                 <cycle code="6" name="Flow cytometry model (separated)">
                     <phase_durations units="min">
-                        <duration index="0" fixed_duration="false">300.030003</duration>
-                        <duration index="1" fixed_duration="true">480.076812</duration>
-                        <duration index="2" fixed_duration="true">239.980802</duration>
-                        <duration index="3" fixed_duration="true">59.998800</duration>
+                        <duration index="0" fixed_duration="false">300.0</duration>
+                        <duration index="1" fixed_duration="true">480.0</duration>
+                        <duration index="2" fixed_duration="true">240.0</duration>
+                        <duration index="3" fixed_duration="true">60.0</duration>
                     </phase_durations>
                 </cycle>
                 <death>