Generate header dependencies so header edits trigger a rebuild

.gitignore

@@ -30,6 +30,9 @@ Studio.zip
 /worm
 /*.exe
 
+# generated header-dependency files (-MMD)
+*.d
+
 # boolean intracellular project executables
 /invasion_model
 /PhysiBoSS_Cell_Lines

Makefile

@@ -35,7 +35,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -435,6 +440,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -560,3 +566,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/Makefile-default

@@ -35,7 +35,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -435,6 +440,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -560,3 +566,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/asymmetric_division/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -187,6 +192,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/biorobots/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -187,6 +192,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/cancer_biorobots/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -187,6 +192,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/cancer_immune/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -183,6 +188,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -313,3 +319,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/celltypes3/Makefile

@@ -41,7 +41,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -184,6 +189,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/custom_division/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -187,6 +192,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/episode/Makefile

@@ -51,7 +51,12 @@ else
 endif
 
 CFLAGS_LINK := $(shell echo $(CFLAGS) | sed -e "s/-fopenmp//g")
-COMPILE_COMMAND := $(CC) $(CFLAGS)  $(EXTRA_FLAGS)
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS)  $(EXTRA_FLAGS) $(DEPFLAGS)
 LINK_COMMAND := $(CC) $(CFLAGS_LINK) $(EXTRA_FLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
@@ -198,6 +203,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -323,3 +329,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/heterogeneity/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -187,6 +192,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/immune_function/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -187,6 +192,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/interactions/Makefile

@@ -49,7 +49,12 @@ else
 endif
 
 CFLAGS_LINK := $(shell echo $(CFLAGS) | sed -e "s/-fopenmp//g")
-COMPILE_COMMAND := $(CC) $(CFLAGS)  $(EXTRA_FLAGS)
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS)  $(EXTRA_FLAGS) $(DEPFLAGS)
 LINK_COMMAND := $(CC) $(CFLAGS_LINK) $(EXTRA_FLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
@@ -196,6 +201,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -321,3 +327,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)

sample_projects/mechano/Makefile

@@ -44,7 +44,12 @@ else
 	endif
 endif
 
-COMPILE_COMMAND := $(CC) $(CFLAGS) 
+# -MMD emits a .d file beside each .o listing the headers it included; -MP adds
+# a dummy target for each so that deleting or renaming a header does not break
+# the build. The .d files are read back in at the bottom of this file.
+DEPFLAGS := -MMD -MP
+
+COMPILE_COMMAND := $(CC) $(CFLAGS) $(DEPFLAGS)
 
 BioFVM_OBJECTS := BioFVM_vector.o BioFVM_mesh.o BioFVM_microenvironment.o BioFVM_solvers.o BioFVM_matlab.o \
 BioFVM_utilities.o BioFVM_basic_agent.o BioFVM_MultiCellDS.o BioFVM_agent_container.o 
@@ -187,6 +192,7 @@ reset:
 
 clean:
 	rm -f *.o
+	rm -f *.d
 	rm -f $(PROGRAM_NAME)*
 
 data-cleanup:
@@ -312,3 +318,7 @@ unpack:
 list-user-projects:
 	@echo "user projects::"
 	@cd ./user_projects && ls -dt1 * | grep . | sed 's!empty.txt!!'
+
+# Keep this at the end of the file: each .d declares rules for its own .o, so
+# including them any earlier would replace `all` as the default goal.
+-include $(ALL_OBJECTS:.o=.d)