create_output_directory in load xml fn

this avoids having it in every main.cpp also, merged recent dev changes allow beta/test_run_samples.py to set a different output directory if provided edit tests.yml to use this^ feature set a boolean to decide which ones will check svg output
MathCancer · Oct 1, 2024 · cfe30a3 · cfe30a3
2 parents 1e3dec4 + 80016c1
commit cfe30a3
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diff --git a/.github/workflows/build_binaries.yml b/.github/workflows/build_binaries.yml
@@ -130,15 +130,15 @@ jobs:
     - uses: actions/checkout@v4
 
     - name: Install dependencies
-      run : brew install gcc@11
+      run : brew install gcc@13
 
     - name: Build ${{ matrix.projects.name }} project
       run: |
         export MACOSX_DEPLOYMENT_TARGET=12
         make ${{ matrix.projects.project }}
         make clean
         ${{ matrix.projects.extra_run }}
-        make PHYSICELL_CPP=g++-11 static
+        make PHYSICELL_CPP=g++-13 static
         cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macos12
 
     - name: Caching produced project binary 
@@ -173,19 +173,16 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Downgrade XCODE to 14.3.1
-      run: sudo xcode-select -switch /Applications/Xcode_14.3.1.app   
-
     - name: Install dependencies
-      run : brew install gcc@11
+      run : brew install gcc@13
 
     - name: Build ${{ matrix.projects.name }} project
       run: |
         export MACOSX_DEPLOYMENT_TARGET=12
         make ${{ matrix.projects.project }}
         make clean
         ${{ matrix.projects.extra_run }}
-        make PHYSICELL_CPP=g++-11 static
+        make PHYSICELL_CPP=g++-13 static
         cp ${{ matrix.projects.binary }} ${{ matrix.projects.binary }}_macosm1
    
     - name: Caching produced project binary 

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -9,6 +9,7 @@ jobs:
 
   tests:
     strategy:
+      fail-fast: false
       matrix:
         os: [
           {name: "Ubuntu", os: "ubuntu-latest", shell: "bash", compiler: "g++"},
@@ -17,18 +18,21 @@ jobs:
           {name: "Windows", os: "windows-latest", shell: "msys2", compiler: "g++"},
         ]
         projects: [
-          {project: "template", name: "PhysiCell Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
-          {project: "heterogeneity-sample", name: "PhysiCell Heterogeneity", binary: "heterogeneity", max_time: 99, config: "config/PhysiCell_settings.xml", output_folder: "output"},
-          {project: "template_BM", name: "PhysiBoSS Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
-          {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", max_time: 120, config: "config/PhysiCell_settings.xml", output_folder: "output"},
-          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, output_folder: "output"},
-          {project: "interaction-sample", name: "PhysiCell Interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 99, output_folder: "output"},
-          {project: "physiboss-tutorial", name: "PhysiBoSS Tutorial", binary: "project", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 600, output_folder: "output"},
-          {project: "worm-sample", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "rules-sample", name: "PhysiCell Rules", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, output_folder: "output"},
-          {project: "physiboss-tutorial-invasion", name: "PhysiBoSS Cancer Invasion", binary: "invasion_model", config: "config/PhysiCell_settings_2D.xml", max_time: 120, output_folder: "output"},
+          {project: "template", name: "PhysiCell Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
+          {project: "template_BM", name: "PhysiBoSS Template", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
+          {project: "physiboss-cell-lines-sample", name: "PhysiBoSS Cell Lines", binary: "PhysiBoSS_Cell_Lines", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: true, output_folder: "output"},
+          {project: "physimess-sample", name: "PhysiMeSS Sample", binary: "project", config: "config/Fibre_Degradation/mymodel_matrix_degradation.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "physiboss-tutorial", name: "PhysiBoSS Tutorial", binary: "project", config: "config/cell_cycle/PhysiCell_settings.xml", max_time: 300, compare_svgs: true, output_folder: "output"},
+          {project: "worm-sample", name: "PhysiCell worm", binary: "worm", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
+          {project: "virus-macrophage-sample", name: "Virus Macrophage", binary: "virus-sample", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
+          {project: "mechano-sample", name: "PhysiCell Mechano", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: true, output_folder: "output"},
+          {project: "cancer-biorobots-sample", name: "PhysiCell Cancer Biorobots", binary: "cancer_biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "biorobots-sample", name: "PhysiCell Biorobots", binary: "biorobots", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "celltypes3-sample", name: "PhysiCell Celltypes3", binary: "celltypes3", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "custom-division-sample", name: "PhysiCell custom division", binary: "project", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "interaction-sample", name: "PhysiCell interactions", binary: "interaction_demo", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "pred-prey-farmer", name: "PhysiCell prey predator", binary: "pred_prey", config: "config/PhysiCell_settings.xml", max_time: 120, compare_svgs: false, output_folder: "output"},
+          {project: "template", name: "PhysiCell Template - make output folder", binary: "project", max_time: 120, config: "config/PhysiCell_settings.xml", compare_svgs: false, "output_folder": "test/create/output/folder"}
         ]
 
     name: Testing ${{ matrix.projects.name }} on ${{ matrix.os.name }}
@@ -54,8 +58,9 @@ jobs:
         
     - name: Run ${{ matrix.projects.name }} project
       run: |
-        python beta/test_run_sample.py ${{ matrix.projects.binary }} ${{ matrix.projects.config }} ${{ matrix.projects.max_time }}
+        python beta/test_run_sample.py ${{ matrix.projects.binary }} ${{ matrix.projects.config }} ${{ matrix.projects.max_time }} ${{ matrix.projects.output_folder }}
     
     - name: Check ${{ matrix.projects.name }} project simulation results
+      if: matrix.projects.compare_svgs
       run: |
-        python beta/test_diff_svg.py ${{ matrix.projects.output_folder }} tests/cases/output_${{ matrix.projects.project }}
+        python beta/test_diff_svg.py output tests/cases/output_${{ matrix.projects.project }}
diff --git a/.gitignore b/.gitignore
@@ -1,30 +1,21 @@
-*.o
-*.exe
+*.asv
+._.DS_Store
 .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
-pmb_debug.log
-heterogeneity
-**/.DS_Store
-**/._.DS_Store
-cancer_immune_3D
-biorobots
-project
-initial.svg
-initial.svg
-interaction_demo
+*.exe
+*.o
 addons/libRoadrunner/roadrunner/
 addons/libRoadrunner/roadrunner-win64-vs14-cp35m.zip
 addons/PhysiBoSS/MaBoSS/
 addons/PhysiBoSS/libMaBoSS-*.tar.gz
+biorobots
+cancer_immune_3D
+config/PhysiCell_settings-backup.xml
+heterogeneity
+initial.svg
+interaction_demo
+Makefile-backup
+pmb_debug.log
+project
+studio_debug.log
 user_projects/*
-!user_projects/empty.txt
+!user_projects/empty.txt
diff --git a/.travis.yml b/.travis.yml
diff --git a/BioFVM/BioFVM_MultiCellDS.cpp b/BioFVM/BioFVM_MultiCellDS.cpp
@@ -515,15 +515,21 @@ void set_save_biofvm_cell_data_as_custom_matlab( bool newvalue )
 
 /* writing parts of BioFVM to a MultiCellDS file */ 
 
+static bool BioFVM_substrates_initialized_in_dom = false;
+
+void reset_BioFVM_substrates_initialized_in_dom( void )
+{
+	BioFVM_substrates_initialized_in_dom = false;
+}
+
+
 void add_BioFVM_substrates_to_open_xml_pugi( pugi::xml_document& xml_dom , std::string filename_base, Microenvironment& M )
 {
 	add_MultiCellDS_main_structure_to_open_xml_pugi( xml_dom ); 
 
 	pugi::xml_node root = biofvm_doc.child( "MultiCellDS" );
 	pugi::xml_node node = root.child( "microenvironment" ); 
 
-	static bool BioFVM_substrates_initialized_in_dom = false; 
-
 	// if the TME has not yet been initialized in the DOM, create all the 
 	// right data elements, and populate the meshes. 
 	if( !BioFVM_substrates_initialized_in_dom )

diff --git a/BioFVM/BioFVM_MultiCellDS.h b/BioFVM/BioFVM_MultiCellDS.h
@@ -181,6 +181,7 @@ void set_save_biofvm_cell_data_as_custom_matlab( bool newvalue ); // default: tr
 
 /* writing parts of BioFVM to a MultiCellDS file */ 
 
+void reset_BioFVM_substrates_initialized_in_dom( void );
 void add_BioFVM_substrates_to_open_xml_pugi( pugi::xml_document& xml_dom , std::string filename_base , Microenvironment& M ); 
 void add_BioFVM_basic_agent_to_open_xml_pugi(  pugi::xml_document& xml_dom, Basic_Agent& BA ); // not implemented -- future edition 
 void add_BioFVM_agents_to_open_xml_pugi( pugi::xml_document& xml_dom, std::string filename_base, Microenvironment& M  ); 

diff --git a/BioFVM/BioFVM_basic_agent.cpp b/BioFVM/BioFVM_basic_agent.cpp
@@ -54,10 +54,16 @@ namespace BioFVM{
 
 std::vector<Basic_Agent*> all_basic_agents(0); 
 
+static int max_basic_agent_ID = 0;
+
+void reset_max_basic_agent_ID( void )
+{
+	max_basic_agent_ID = 0;
+}
+
 Basic_Agent::Basic_Agent()
 {
 	//give the agent a unique ID  
-	static int max_basic_agent_ID = 0; 
 	ID = max_basic_agent_ID; // 
 	max_basic_agent_ID++; 
 	// initialize position and velocity
@@ -341,4 +347,4 @@ void Basic_Agent::simulate_secretion_and_uptake( Microenvironment* pS, double dt
 	return; 
 }
 
-};
+};
diff --git a/BioFVM/BioFVM_basic_agent.h b/BioFVM/BioFVM_basic_agent.h
@@ -55,7 +55,9 @@
 #include "BioFVM_vector.h"
 
 namespace BioFVM{
-
+
+void reset_max_basic_agent_ID( void );
+
 class Basic_Agent
 {
  private:

diff --git a/CITATION.txt b/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 1.13.1) [1].    
+We implemented and solved the model using PhysiCell (Version 1.14.0) [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 1.13.1) [1].
 Because PhysiCell extensively uses BioFVM, we suggest you also cite BioFVM  
     as below:                                                               
 
-We implemented and solved the model using PhysiCell (Version 1.13.1) [1],    
+We implemented and solved the model using PhysiCell (Version 1.14.0) [1],    
 with BioFVM [2] to solve the transport equations.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
@@ -25,7 +25,7 @@ with BioFVM [2] to solve the transport equations.
 
 If you use PhysiBoSS, please cite as below:
 
-We implemented and solved the model using PhysiCell (Version 1.11.0) [1],    
+We implemented and solved the model using PhysiCell (Version 1.14.0) [1],    
 with PhysiBoSS[2,3] to simulate the intracellular mechanisms.                           
 
 [1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin, 
@@ -50,3 +50,9 @@ If you use libRoadrunner, please cite:
     König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro, libRoadRunner: 
     a high performance SBML simulation and analysis library, 
     Bioinformatics 31(20): 3315–21, 2015: DOI: 10.1093/bioinformatics/btv363
+
+If you use PhysiMeSS, please cite: 
+
+    V. Noël, M. Ruscone, R. Shuttle-worth, and C.K. Macnamara. PhysiMeSS--
+    A New PhysiCell Addon for Extracellular Matrix Modelling, bioRxiv [preprint] 
+    2023.10.27.564365, 2023. DOI: 10.1101/2023.10.27.564365. 
diff --git a/Makefile b/Makefile
@@ -73,20 +73,19 @@ name:
 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"
-	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample"
+	@echo "                 worm-sample interaction-sample mechano-sample rules-sample physimess-sample custom-division-sample"
 	@echo ""
 	@echo "Sample intracellular projects: template_BM ode-energy-sample physiboss-cell-lines-sample"
 	@echo "                 cancer-metabolism-sample physiboss-tutorial physiboss-tutorial-invasion"
 	@echo ""
 
 template:
-	cp ./sample_projects/template/custom_modules/* ./custom_modules/
+	cp -r ./sample_projects/template/custom_modules/* ./custom_modules/
 	touch main.cpp && cp main.cpp main-backup.cpp
 	cp ./sample_projects/template/main.cpp ./main.cpp 
 	cp Makefile Makefile-backup
 	cp ./sample_projects/template/Makefile .
-	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
-	cp ./sample_projects/template/config/* ./config/
+	cp -r ./sample_projects/template/config/* ./config 
 
 # sample projects 
 
@@ -198,6 +197,16 @@ physimess-sample:
 	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
 	cp -r ./sample_projects/physimess/config/* ./config/
 
+
+custom-division-sample:
+	cp ./sample_projects/custom_division/custom_modules/* ./custom_modules/
+	touch main.cpp && cp main.cpp main-backup.cpp
+	cp ./sample_projects/custom_division/main.cpp ./main.cpp 
+	cp Makefile Makefile-backup
+	cp ./sample_projects/custom_division/Makefile .
+	cp ./config/PhysiCell_settings.xml ./config/PhysiCell_settings-backup.xml 
+	cp ./sample_projects/custom_division/config/* ./config/
+
 # ---- intracellular projects 
 ode-energy-sample:
 	cp ./sample_projects_intracellular/ode/ode_energy/custom_modules/* ./custom_modules/
@@ -389,7 +398,7 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp
 reset:
 	rm -f *.cpp PhysiCell_cell.o
 	cp ./sample_projects/Makefile-default Makefile 
-	rm -f ./custom_modules/*
+	rm -rf ./custom_modules/*
 	touch ./custom_modules/empty.txt 
 	touch ALL_CITATIONS.txt 
 	touch ./core/PhysiCell_cell.cpp
@@ -493,15 +502,15 @@ save:
 	cp main.cpp ./user_projects/$(PROJ)
 	cp Makefile ./user_projects/$(PROJ)
 	cp VERSION.txt ./user_projects/$(PROJ)
-	cp ./config/* ./user_projects/$(PROJ)/config
-	cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
+	cp -r ./config/* ./user_projects/$(PROJ)/config
+	cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules
 
 load: 
 	echo "Loading project from $(PROJ) ... "
 	cp ./user_projects/$(PROJ)/main.cpp .
 	cp ./user_projects/$(PROJ)/Makefile .
-	cp ./user_projects/$(PROJ)/config/* ./config/ 
-	cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
+	cp -r ./user_projects/$(PROJ)/config/* ./config/ 
+	cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ 
 
 pack:
 	@echo " "