Development

.github/workflows/test-macosx.yml

@@ -5,9 +5,9 @@ on:
   pull_request:
 
 jobs:
-  build:
+  build_virus_macrophage:
 
-    runs-on: macos-latest
+    runs-on: macos-11
 
     steps:
     - uses: actions/checkout@v2
@@ -23,13 +23,23 @@ jobs:
     - name: Run Virus Macrophage cell lines project
       run: |
         ./virus-sample
-
+
+
+  build_physiboss_cell_lines:
+
+    runs-on: macos-11
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Install dependencies
+      run : brew install gcc@11
+
     - name: Build PhysiBoSS cell lines project
       run: |
-        make reset
         make physiboss-cell-lines-sample
         make clean
-        make PHYSICELL_CPP=g++-10
+        make PHYSICELL_CPP=g++-11
 
     - name: Run PhysiBoSS cell lines project
       run: |

.gitignore

@@ -1,6 +1,14 @@
-
 *.o
-unit-test-conservation.exe
-Makefile-backup
 *.exe
-cancer_immune_3D
+.DS_Store
+Makefile-backup
+config/PhysiCell_settings-backup.xml
+documentation/.DS_Store
+unit_tests/.DS_Store
+sample_projects/.DS_Store
+sample_projects/biorobots/.DS_Store
+sample_projects/cancer_biorobots/.DS_Store
+sample_projects/cancer_immune/.DS_Store
+sample_projects/celltypes3/.DS_Store
+sample_projects/heterogeneity/.DS_Store
+sample_projects/template/.DS_Store

BioFVM/BioFVM_microenvironment.cpp

@@ -269,7 +269,7 @@ void Microenvironment::apply_dirichlet_conditions( void )
 	{ density_vector( dirichlet_indices[i] ) = dirichlet_value_vectors[i]; }
 	*/
 
-	#pragma omp parallel for 
+	// #pragma omp parallel for 
 	for( unsigned int i=0 ; i < mesh.voxels.size() ;i++ )
 	{
 		/*

BioFVM/BioFVM_vector.cpp

@@ -185,6 +185,20 @@ std::ostream& operator<<(std::ostream& os, const std::vector<double>& v )
  return os; 
 }
 
+std::ostream& operator<<(std::ostream& os, const std::vector<int>& v )
+{
+ for( unsigned int i=0; i < v.size(); i++ )
+ { os << v[i] << " " ; }
+ return os; 
+}
+
+std::ostream& operator<<(std::ostream& os, const std::vector<std::string>& v )
+{
+ for( unsigned int i=0; i < v.size(); i++ )
+ { os << v[i] << " " ; }
+ return os; 
+}
+
 // this one returns a new vector that has been normalized
 std::vector<double> normalize( std::vector<double>& v )
 {

BioFVM/BioFVM_vector.h

@@ -80,6 +80,8 @@ void operator/=( std::vector<double>& v1, const double& a );
 /* other commonly needed operations on vectors */ 
 
 std::ostream& operator<<(std::ostream& os, const std::vector<double>& v ); 
+std::ostream& operator<<(std::ostream& os, const std::vector<int>& v );
+std::ostream& operator<<(std::ostream& os, const std::vector<std::string>& v );
 
 // this one returns a new vector that has been normalized
 std::vector<double> normalize( std::vector<double>& v );

CITATION.txt

@@ -1,7 +1,7 @@
 If you use PhysiCell in your project, please cite PhysiCell and the version 
 number, such as below:                                                      
 
-We implemented and solved the model using PhysiCell (Version 1.9.1) [1].    
+We implemented and solved the model using PhysiCell (Version 1.10.4) [1].    
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
     PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellu-  
@@ -11,7 +11,7 @@ We implemented and solved the model using PhysiCell (Version 1.9.1) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.9.1) [1],    
+We implemented and solved the model using PhysiCell (Version 1.10.4) [1],    
 with BioFVM [2] to solve the transport equations.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 

Makefile

@@ -41,7 +41,8 @@ BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
 
 PhysiCell_core_OBJECTS := PhysiCell_phenotype.o PhysiCell_cell_container.o PhysiCell_standard_models.o \
-PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o
+PhysiCell_cell.o PhysiCell_custom.o PhysiCell_utilities.o PhysiCell_constants.o PhysiCell_basic_signaling.o \
+PhysiCell_signal_behavior.o 
 
 PhysiCell_module_OBJECTS := PhysiCell_SVG.o PhysiCell_pathology.o PhysiCell_MultiCellDS.o PhysiCell_various_outputs.o \
 PhysiCell_pugixml.o PhysiCell_settings.o PhysiCell_geometry.o
@@ -63,10 +64,16 @@ all:
 	make heterogeneity-sample
 	make 
 
+name:
+	@echo ""
+	@echo "Executable name is" $(PROGRAM_NAME)
+	@echo ""
+
 # sample projects 	
 list-projects:
 	@echo "Sample projects: template biorobots-sample cancer-biorobots-sample cancer-immune-sample"
-	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample worm-sample"
+	@echo "                 celltypes3-sample heterogeneity-sample pred-prey-farmer virus-macrophage-sample"
+	@echo "                 worm-sample interaction-sample"
 	@echo ""
 	@echo "Sample intracellular projects: ode-energy-sample physiboss-cell-lines-sample cancer-metabolism-sample"
 	@echo ""
@@ -153,7 +160,16 @@ worm-sample:
 	cp Makefile Makefile-backup
 	cp ./sample_projects/worm/Makefile .
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/worm/config/* ./config/	
+	cp ./sample_projects/worm/config/* ./config/
+
+interaction-sample:
+	cp ./sample_projects/interactions/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/interactions/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/interactions/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/interactions/config/* ./config/
 
 # ---- intracellular projects 
 ode-energy-sample:
@@ -192,6 +208,7 @@ cancer-metabolism-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml
 	cp ./sample_projects_intracellular/fba/cancer_metabolism/config/* ./config/
 
+
 # early examples for convergence testing 
 
 physicell_test_mech1: $(PhysiCell_OBJECTS) ./examples/PhysiCell_test_mechanics_1.cpp 
@@ -246,6 +263,9 @@ PhysiCell_custom.o: ./core/PhysiCell_custom.cpp
 PhysiCell_constants.o: ./core/PhysiCell_constants.cpp
 	$(COMPILE_COMMAND) -c ./core/PhysiCell_constants.cpp 
 
+PhysiCell_signal_behavior.o: ./core/PhysiCell_signal_behavior.cpp
+	$(COMPILE_COMMAND) -c ./core/PhysiCell_signal_behavior.cpp 
+
 # BioFVM core components (needed by PhysiCell)
 
 BioFVM_vector.o: ./BioFVM/BioFVM_vector.cpp
@@ -360,11 +380,11 @@ FRAMERATE := 24
 OUTPUT := output
 
 jpeg: 
-	@magick identify -format "%h" $(OUTPUT)/initial.svg >> __H.txt 
-	@magick identify -format "%w" $(OUTPUT)/initial.svg >> __W.txt 
-	@expr 2 \* \( $$(grep . __H.txt) / 2 \) >> __H1.txt 
-	@expr 2 \* \( $$(grep . __W.txt) / 2 \) >> __W1.txt 
-	@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" >> __resize.txt 
+	@magick identify -format "%h" $(OUTPUT)/initial.svg > __H.txt 
+	@magick identify -format "%w" $(OUTPUT)/initial.svg > __W.txt 
+	@expr 2 \* \( $$(grep . __H.txt) / 2 \) > __H1.txt 
+	@expr 2 \* \( $$(grep . __W.txt) / 2 \) > __W1.txt 
+	@echo "$$(grep . __W1.txt)!x$$(grep . __H1.txt)!" > __resize.txt 
 	@magick mogrify -format jpg -resize $$(grep . __resize.txt) $(OUTPUT)/s*.svg
 	rm -f __H*.txt __W*.txt __resize.txt 
 
@@ -378,8 +398,8 @@ movie:
 
 SOURCE := PhysiCell_upgrade.zip 
 get-upgrade: 
-	@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) >> VER.txt 
-	@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip >> DL_FILE.txt 
+	@echo $$(curl https://raw.githubusercontent.com/MathCancer/PhysiCell/master/VERSION.txt) > VER.txt 
+	@echo https://github.com/MathCancer/PhysiCell/releases/download/$$(grep . VER.txt)/PhysiCell_V.$$(grep . VER.txt).zip > DL_FILE.txt 
 	rm -f VER.txt
 	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
 	rm -f DL_FILE.txt