Added save, load, pack, unpack, list-user-projects instructions in Ph…

…ysiBoSS projects Makefile
sysbio-curie · Jun 4, 2024 · 0371cde · 0371cde
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diff --git a/sample_projects_intracellular/boolean/cancer_invasion/Makefile b/sample_projects_intracellular/boolean/cancer_invasion/Makefile
@@ -273,4 +273,78 @@ untar:
 
 movie:
 	ffmpeg -r 25 -i output/snapshot%08d.svg -pix_fmt yuv420p output.mp4
-	vlc output.mp4
+	vlc output.mp4
+
+# upgrade rules 
+
+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.$$(grep . VER.txt).zip > DL_FILE.txt 
+	rm -f VER.txt
+	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
+	rm -f DL_FILE.txt 
+
+PhysiCell_upgrade.zip: 
+	make get-upgrade 
+
+upgrade: $(SOURCE)
+	unzip $(SOURCE) PhysiCell/VERSION.txt
+	mv -f PhysiCell/VERSION.txt . 
+	unzip $(SOURCE) PhysiCell/core/* 
+	cp -r PhysiCell/core/* core 
+	unzip $(SOURCE) PhysiCell/modules/* 
+	cp -r PhysiCell/modules/* modules 
+	unzip $(SOURCE) PhysiCell/sample_projects/* 
+	cp -r PhysiCell/sample_projects/* sample_projects 
+	unzip $(SOURCE) PhysiCell/BioFVM/* 
+	cp -r PhysiCell/BioFVM/* BioFVM
+	unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
+	mv -f PhysiCell/documentation/User_Guide.pdf documentation
+	rm -f -r PhysiCell
+	rm -f $(SOURCE) 
+
+# use: make save PROJ=your_project_name
+PROJ := my_project
+
+save: 
+	echo "Saving project as $(PROJ) ... "
+	mkdir -p ./user_projects
+	mkdir -p ./user_projects/$(PROJ)
+	mkdir -p ./user_projects/$(PROJ)/custom_modules
+	mkdir -p ./user_projects/$(PROJ)/config 
+	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
+
+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/ 
+
+pack:
+	@echo " "
+	@echo "Preparing project $(PROJ) for sharing ... "
+	@echo " " 
+	cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
+	@echo " "
+	@echo "Share ./user_projects/$(PROJ).zip ... "
+	@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
+	@echo " " 
+
+unpack:
+	@echo " "
+	@echo "Preparing shared project $(PROJ).zip for use ... "
+	@echo " " 
+	cd ./user_projects && unzip $(PROJ).zip 
+	@echo " "
+	@echo "Load this project via make load PROJ=$(PROJ) ... "
+	@echo " " 	
+
+list-user-projects:
+	@echo "user projects::"
+	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
diff --git a/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile b/sample_projects_intracellular/boolean/physiboss_cell_lines/Makefile
@@ -266,3 +266,81 @@ unzip:
 untar: 
 	cp ./archives/latest.tar .
 	tar -xzf latest.tar
+
+movie:
+	ffmpeg -r 25 -i output/snapshot%08d.svg -pix_fmt yuv420p output.mp4
+	vlc output.mp4
+
+# upgrade rules 
+
+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 
+	rm -f VER.txt
+	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
+	rm -f DL_FILE.txt 
+
+PhysiCell_upgrade.zip: 
+	make get-upgrade 
+
+upgrade: $(SOURCE)
+	unzip $(SOURCE) PhysiCell/VERSION.txt
+	mv -f PhysiCell/VERSION.txt . 
+	unzip $(SOURCE) PhysiCell/core/* 
+	cp -r PhysiCell/core/* core 
+	unzip $(SOURCE) PhysiCell/modules/* 
+	cp -r PhysiCell/modules/* modules 
+	unzip $(SOURCE) PhysiCell/sample_projects/* 
+	cp -r PhysiCell/sample_projects/* sample_projects 
+	unzip $(SOURCE) PhysiCell/BioFVM/* 
+	cp -r PhysiCell/BioFVM/* BioFVM
+	unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
+	mv -f PhysiCell/documentation/User_Guide.pdf documentation
+	rm -f -r PhysiCell
+	rm -f $(SOURCE) 
+
+# use: make save PROJ=your_project_name
+PROJ := my_project
+
+save: 
+	echo "Saving project as $(PROJ) ... "
+	mkdir -p ./user_projects
+	mkdir -p ./user_projects/$(PROJ)
+	mkdir -p ./user_projects/$(PROJ)/custom_modules
+	mkdir -p ./user_projects/$(PROJ)/config 
+	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
+
+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/ 
+
+pack:
+	@echo " "
+	@echo "Preparing project $(PROJ) for sharing ... "
+	@echo " " 
+	cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
+	@echo " "
+	@echo "Share ./user_projects/$(PROJ).zip ... "
+	@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
+	@echo " " 
+
+unpack:
+	@echo " "
+	@echo "Preparing shared project $(PROJ).zip for use ... "
+	@echo " " 
+	cd ./user_projects && unzip $(PROJ).zip 
+	@echo " "
+	@echo "Load this project via make load PROJ=$(PROJ) ... "
+	@echo " " 	
+
+list-user-projects:
+	@echo "user projects::"
+	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
diff --git a/sample_projects_intracellular/boolean/tutorial/Makefile b/sample_projects_intracellular/boolean/tutorial/Makefile
@@ -274,4 +274,78 @@ untar:
 
 movie:
 	ffmpeg -r 25 -i output/snapshot%08d.svg -pix_fmt yuv420p output.mp4
-	vlc output.mp4
+	vlc output.mp4
+
+# upgrade rules 
+
+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.$$(grep . VER.txt).zip > DL_FILE.txt 
+	rm -f VER.txt
+	$$(curl -L $$(grep . DL_FILE.txt) --output PhysiCell_upgrade.zip)
+	rm -f DL_FILE.txt 
+
+PhysiCell_upgrade.zip: 
+	make get-upgrade 
+
+upgrade: $(SOURCE)
+	unzip $(SOURCE) PhysiCell/VERSION.txt
+	mv -f PhysiCell/VERSION.txt . 
+	unzip $(SOURCE) PhysiCell/core/* 
+	cp -r PhysiCell/core/* core 
+	unzip $(SOURCE) PhysiCell/modules/* 
+	cp -r PhysiCell/modules/* modules 
+	unzip $(SOURCE) PhysiCell/sample_projects/* 
+	cp -r PhysiCell/sample_projects/* sample_projects 
+	unzip $(SOURCE) PhysiCell/BioFVM/* 
+	cp -r PhysiCell/BioFVM/* BioFVM
+	unzip $(SOURCE) PhysiCell/documentation/User_Guide.pdf
+	mv -f PhysiCell/documentation/User_Guide.pdf documentation
+	rm -f -r PhysiCell
+	rm -f $(SOURCE) 
+
+# use: make save PROJ=your_project_name
+PROJ := my_project
+
+save: 
+	echo "Saving project as $(PROJ) ... "
+	mkdir -p ./user_projects
+	mkdir -p ./user_projects/$(PROJ)
+	mkdir -p ./user_projects/$(PROJ)/custom_modules
+	mkdir -p ./user_projects/$(PROJ)/config 
+	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
+
+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/ 
+
+pack:
+	@echo " "
+	@echo "Preparing project $(PROJ) for sharing ... "
+	@echo " " 
+	cd ./user_projects && zip -r $(PROJ).zip $(PROJ)
+	@echo " "
+	@echo "Share ./user_projects/$(PROJ).zip ... "
+	@echo "Other users can unzip $(PROJ).zip in their ./user_projects, compile, and run."
+	@echo " " 
+
+unpack:
+	@echo " "
+	@echo "Preparing shared project $(PROJ).zip for use ... "
+	@echo " " 
+	cd ./user_projects && unzip $(PROJ).zip 
+	@echo " "
+	@echo "Load this project via make load PROJ=$(PROJ) ... "
+	@echo " " 	
+
+list-user-projects:
+	@echo "user projects::"
+	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'