diff --git a/Makefile b/Makefile index 02b313890..455aae566 100644 --- a/Makefile +++ b/Makefile @@ -387,17 +387,16 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp # cleanup reset: - rm -f *.cpp PhysiCell_cell.o - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -410,7 +409,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -491,17 +490,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/Makefile-default b/sample_projects/Makefile-default index 02b313890..455aae566 100644 --- a/sample_projects/Makefile-default +++ b/sample_projects/Makefile-default @@ -387,17 +387,16 @@ PhysiCell_geometry.o: ./modules/PhysiCell_geometry.cpp # cleanup reset: - rm -f *.cpp PhysiCell_cell.o - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -410,7 +409,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -491,17 +490,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 " " diff --git a/sample_projects/PhysiCell_settings.xml-default b/sample_projects/PhysiCell_settings.xml-default new file mode 100644 index 000000000..d35c44fc7 --- /dev/null +++ b/sample_projects/PhysiCell_settings.xml-default @@ -0,0 +1,271 @@ + + + + -500 + 500 + -500 + 500 + -10 + 10 + 20 + 20 + 20 + true + + + + 14400 + min + micron + 0.01 + 0.1 + 6 + + + + 6 + + + + output + + 60 + true + + + 60 + true + + + false + + + + + false + true + + + + + + 100000.0 + 0.1 + + 38 + 0 + + 38 + 10 + 10 + 38 + 0 + 0 + + + + + 10 + .1 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + + 10 + 0.1 + + 0 + 0 + + 0 + 0 + 0 + 0 + 0 + 0 + + + + true + true + + ./config/initial.mat + + + ./config/dirichlet.mat + + + + + + + + + + 0.000 + + + + + 5.31667e-05 + + 516 + + + 0.05 + 0 + 1.66667e-02 + 5.83333e-03 + 0 + 2.0 + + + + 2.80E-03 + + 0 + 86400 + + + 1.11667e-2 + 8.33333e-4 + 5.33333e-5 + 2.16667e-3 + 0 + 2.0 + + + + + 2494 + 0.75 + 540 + 0.05 + 0.0045 + 0.0055 + 0 + 0 + 2.0 + + + 0.4 + 10.0 + 1.25 + + 1 + + + 1.8 + 15.12 + + 4.0 + 10.0 + 0.01 + 0.0 + 0.0 + + + 1 + 1 + .5 + + false + true + + false + oxygen + 1 + + + false + false + + 0.0 + 0.0 + 0.0 + + + + + + + 0 + 1 + 10 + 0 + + + 0.0 + 1 + 0.0 + 0.0 + + + 0.0 + 1 + 0.0 + 0.0 + + + + 0 + + 0 + 0 + + + 0 + 0 + + 1 + + 0 + 0 + + + + + 0 + 0 + + + + + 1.0 + + + + + + + ./config + cells.csv + + + + + + + ./config + cell_rules_v2.csv + + + + + + + + 0 + 0 + + \ No newline at end of file diff --git a/sample_projects/biorobots/Makefile b/sample_projects/biorobots/Makefile index 26314225c..ac4c97235 100644 --- a/sample_projects/biorobots/Makefile +++ b/sample_projects/biorobots/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/cancer_biorobots/Makefile b/sample_projects/cancer_biorobots/Makefile index b74f8837a..be43706c3 100644 --- a/sample_projects/cancer_biorobots/Makefile +++ b/sample_projects/cancer_biorobots/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 " " diff --git a/sample_projects/cancer_immune/Makefile b/sample_projects/cancer_immune/Makefile index 5cbb2ca8f..7c60292da 100644 --- a/sample_projects/cancer_immune/Makefile +++ b/sample_projects/cancer_immune/Makefile @@ -172,15 +172,16 @@ cancer_immune_3D.o: ./custom_modules/cancer_immune_3D.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -193,7 +194,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -279,17 +280,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/celltypes3/Makefile b/sample_projects/celltypes3/Makefile index 29732af20..a0862534f 100644 --- a/sample_projects/celltypes3/Makefile +++ b/sample_projects/celltypes3/Makefile @@ -171,17 +171,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 " " diff --git a/sample_projects/heterogeneity/Makefile b/sample_projects/heterogeneity/Makefile index 93d055ea9..12c6117b7 100644 --- a/sample_projects/heterogeneity/Makefile +++ b/sample_projects/heterogeneity/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/interactions/Makefile b/sample_projects/interactions/Makefile index c42fc9666..84160b2e1 100644 --- a/sample_projects/interactions/Makefile +++ b/sample_projects/interactions/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 " " diff --git a/sample_projects/mechano/Makefile b/sample_projects/mechano/Makefile index e90a9966f..b4e1dff70 100644 --- a/sample_projects/mechano/Makefile +++ b/sample_projects/mechano/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -279,16 +278,17 @@ save: mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) cp Makefile ./user_projects/$(PROJ) + sed -i "0,/PROJ := /{s/PROJ := .*/PROJ := $(PROJ)/}" ./user_projects/$(PROJ)/Makefile 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 " " diff --git a/sample_projects/physimess/Makefile b/sample_projects/physimess/Makefile index 0dcd2449c..7adfd6924 100644 --- a/sample_projects/physimess/Makefile +++ b/sample_projects/physimess/Makefile @@ -189,18 +189,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/mymodel.xml *.csv - rm -fr ./config/Cell_Fibre_Mechanics ./config/Fibre_Crosslinks ./config/Fibre_Initialisation ./config/Neighbours_in_voxels ./config/Fibre_Degradation - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -213,7 +211,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -294,6 +292,7 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config @@ -303,8 +302,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/pred_prey_farmer/Makefile b/sample_projects/pred_prey_farmer/Makefile index 06ec2705e..425fca742 100644 --- a/sample_projects/pred_prey_farmer/Makefile +++ b/sample_projects/pred_prey_farmer/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -279,17 +278,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 " " diff --git a/sample_projects/rules_sample/Makefile b/sample_projects/rules_sample/Makefile index 6682b5c46..ccb6bd44b 100644 --- a/sample_projects/rules_sample/Makefile +++ b/sample_projects/rules_sample/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/template/Makefile b/sample_projects/template/Makefile index 6682b5c46..ccb6bd44b 100644 --- a/sample_projects/template/Makefile +++ b/sample_projects/template/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 " " diff --git a/sample_projects/virus_macrophage/Makefile b/sample_projects/virus_macrophage/Makefile index d8c8ad4e8..99febe95f 100644 --- a/sample_projects/virus_macrophage/Makefile +++ b/sample_projects/virus_macrophage/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects/worm/Makefile b/sample_projects/worm/Makefile index e953e28ad..dce60c267 100644 --- a/sample_projects/worm/Makefile +++ b/sample_projects/worm/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -278,17 +277,18 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 " " diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile index 34e9ccba1..8c5b97cbe 100644 --- a/sample_projects_intracellular/boolean/cancer_invasion/Makefile +++ b/sample_projects_intracellular/boolean/cancer_invasion/Makefile @@ -220,24 +220,25 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - rm ALL_CITATIONS.txt - rm ./config/PhysiCell_settings_*.xml - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -rf ./config/boolean_network/ ./config/cells.csv ./config/rules.csv ./config/init.tsv + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -f *.mat rm -f *.xml @@ -245,11 +246,11 @@ data-cleanup: rm -rf ./output mkdir ./output touch ./output/empty.txt - + # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -314,6 +315,7 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config @@ -323,8 +325,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile index 383e0051e..4f032ed35 100644 --- a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile +++ b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile @@ -217,35 +217,36 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -rf ./config/model_*.bnd ./config/model.cfg ./config/cells.csv + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -f *.mat rm -f *.xml rm -f *.svg rm -f ./output/* touch ./output/empty.txt - + # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -310,6 +311,7 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config @@ -319,8 +321,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./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 " " diff --git a/sample_projects_intracellular/boolean/template_BM/Makefile b/sample_projects_intracellular/boolean/template_BM/Makefile index 989398e41..f3ef2118c 100644 --- a/sample_projects_intracellular/boolean/template_BM/Makefile +++ b/sample_projects_intracellular/boolean/template_BM/Makefile @@ -217,40 +217,41 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -fr ./config/cells.csv ./config/cell_rules.csv + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -rf ./output mkdir ./output touch ./output/empty.txt - + # archival - + checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* - + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* + zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* cp latest.zip $$(date +%b_%d_%Y_%H%M).zip cp latest.zip VERSION_$(VERSION).zip mv *.zip archives/ - + tar: tar --ignore-failed-read -czf latest.tar Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* cp latest.tar $$(date +%b_%d_%Y_%H%M).tar @@ -260,7 +261,7 @@ tar: unzip: cp ./archives/latest.zip . unzip latest.zip - + untar: cp ./archives/latest.tar . tar -xzf latest.tar @@ -324,6 +325,7 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config @@ -333,8 +335,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ pack: @echo " " diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile index 193ee09cb..9ad2ec01a 100644 --- a/sample_projects_intracellular/boolean/tutorial/Makefile +++ b/sample_projects_intracellular/boolean/tutorial/Makefile @@ -220,25 +220,25 @@ custom.o: ./custom_modules/custom.cpp $(MaBoSS) # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - rm -rf ./config/simple_tnf/ - rm -fr ./config/cell_cycle/ - rm -fr ./config/differentiation/ + make MaBoSS-clean + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml rm -rf ./scripts MaBoSS-clean: rm -fr addons/PhysiBoSS/MaBoSS-env-2.0 - + clean: rm -f *.o rm -f $(PROGRAM_NAME)* - + data-cleanup: rm -f *.mat rm -f *.xml @@ -246,11 +246,11 @@ data-cleanup: rm -rf ./output mkdir ./output touch ./output/empty.txt - + # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -315,6 +315,7 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) cp -r ./config/* ./user_projects/$(PROJ)/config @@ -324,8 +325,8 @@ load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp -r ./user_projects/$(PROJ)/config/* ./config/ - cp -r ./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 " " diff --git a/sample_projects_intracellular/fba/cancer_metabolism/Make-windows b/sample_projects_intracellular/fba/cancer_metabolism/Make-windows index 245bbe2a2..1854f4aa6 100644 --- a/sample_projects_intracellular/fba/cancer_metabolism/Make-windows +++ b/sample_projects_intracellular/fba/cancer_metabolism/Make-windows @@ -198,14 +198,15 @@ cancer_metabolism.o: ./custom_modules/cancer_metabolism.cpp # cleanup reset: + make clean rm -f *.cpp cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* + rm -fr ./custom_modules/* touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings_default.xml ./config/PhysiCell_settings.xml - touch ./config/empty.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/fba/cancer_metabolism/Makefile b/sample_projects_intracellular/fba/cancer_metabolism/Makefile index 1ed8367ee..8a4fb6582 100755 --- a/sample_projects_intracellular/fba/cancer_metabolism/Makefile +++ b/sample_projects_intracellular/fba/cancer_metabolism/Makefile @@ -203,16 +203,15 @@ cancer_metabolism.o: ./custom_modules/cancer_metabolism.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm ./config/*.csv + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o diff --git a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile index 0e85b19ef..61e0ca3a8 100644 --- a/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile +++ b/sample_projects_intracellular/fba/ecoli_acetic_switch/Makefile @@ -251,15 +251,15 @@ ecoli_acetic_switch.o: ./custom_modules/ecoli_acetic_switch.cpp # cleanup reset: + make clean rm -f *.cpp cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* + rm -fr ./custom_modules/* touch ./custom_modules/empty.txt touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml clean: rm -f *.o @@ -275,7 +275,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/sample_projects_intracellular/ode/ode_energy/Makefile b/sample_projects_intracellular/ode/ode_energy/Makefile index 42168464c..a541abc02 100644 --- a/sample_projects_intracellular/ode/ode_energy/Makefile +++ b/sample_projects_intracellular/ode/ode_energy/Makefile @@ -227,20 +227,15 @@ data-cleanup: touch ./output/empty.txt reset: - rm -f *.cpp PhysiCell_cell.o - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm ./config/*.csv - rm ./config/*.m - rm ./config/*.cps - rm ./config/Toy_Metabolic_Model.xml - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml FOLDER := output FRAMERATE := 24 @@ -252,7 +247,7 @@ movie: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* diff --git a/unit_tests/custom_DCs_2substrates/Makefile b/unit_tests/custom_DCs_2substrates/Makefile index faa887869..e1494f866 100644 --- a/unit_tests/custom_DCs_2substrates/Makefile +++ b/unit_tests/custom_DCs_2substrates/Makefile @@ -174,17 +174,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -197,7 +196,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -279,18 +278,19 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile cp Makefile ./user_projects/$(PROJ) cp VERSION.txt ./user_projects/$(PROJ) - cp ./config/* ./user_projects/$(PROJ)/config - cp ./custom_modules/* ./user_projects/$(PROJ)/custom_modules + cp -r ./config/* ./user_projects/$(PROJ)/config + cp -r ./custom_modules/* ./user_projects/$(PROJ)/custom_modules # useage: make load PROJ=your_project_name load: echo "Loading project from $(PROJ) ... " cp ./user_projects/$(PROJ)/main.cpp . cp ./user_projects/$(PROJ)/Makefile . - cp ./user_projects/$(PROJ)/config/* ./config/ - cp ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ + cp -r ./user_projects/$(PROJ)/config/* ./config/ + cp -r ./user_projects/$(PROJ)/custom_modules/* ./custom_modules/ # useage: make share PROJ=your_project_name share: diff --git a/unit_tests/custom_voxel_values/Makefile b/unit_tests/custom_voxel_values/Makefile index e27362f79..d68adc2fb 100644 --- a/unit_tests/custom_voxel_values/Makefile +++ b/unit_tests/custom_voxel_values/Makefile @@ -171,17 +171,16 @@ custom.o: ./custom_modules/custom.cpp # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - touch ./core/PhysiCell_cell.cpp - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings-backup.xml ./config/PhysiCell_settings.xml - touch ./config/empty.csv - rm -f ./config/*.csv - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)* @@ -194,7 +193,7 @@ data-cleanup: # archival checkpoint: - zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/*.xml custom_modules/* + zip -r $$(date +%b_%d_%Y_%H%M).zip Makefile *.cpp *.h config/* custom_modules/* zip: zip -r latest.zip Makefile* *.cpp *.h BioFVM/* config/* core/* custom_modules/* matlab/* modules/* sample_projects/* @@ -276,18 +275,19 @@ save: mkdir -p ./user_projects/$(PROJ)/custom_modules mkdir -p ./user_projects/$(PROJ)/config cp main.cpp ./user_projects/$(PROJ) + awk -i inplace '{gsub("^PROJ :=.*$$", "PROJ := $(PROJ)", $$0); print $$0}' Makefile 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 # useage: make load PROJ=your_project_name 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/ # useage: make share PROJ=your_project_name share: diff --git a/unit_tests/substrate_internalization/Makefile-unit-test-conservation b/unit_tests/substrate_internalization/Makefile-unit-test-conservation index d5c82fae8..87cac2f63 100644 --- a/unit_tests/substrate_internalization/Makefile-unit-test-conservation +++ b/unit_tests/substrate_internalization/Makefile-unit-test-conservation @@ -140,15 +140,16 @@ custom-unit-substrate-conservation.o: ./custom_modules/custom-unit-substrate-con # cleanup reset: - rm -f *.cpp - cp ./sample_projects/Makefile-default Makefile - rm -f ./custom_modules/* - touch ./custom_modules/empty.txt - touch ALL_CITATIONS.txt - rm ALL_CITATIONS.txt - cp ./config/PhysiCell_settings_default.xml ./config/PhysiCell_settings.xml - touch ./config/empty.txt - + make clean + rm -f *.cpp + cp ./sample_projects/Makefile-default Makefile + rm -fr ./custom_modules/* + touch ./custom_modules/empty.txt + touch ALL_CITATIONS.txt + rm ALL_CITATIONS.txt + rm -fr ./config/* + cp ./sample_projects/PhysiCell_settings.xml-default ./config/PhysiCell_settings.xml + clean: rm -f *.o rm -f $(PROGRAM_NAME)*