Refactored the makefile build system

.gitignore

@@ -7,5 +7,14 @@
 # ignore .x files
 *.x
 
+# ignore .so files
+*.so
+
+# ignore .dat files in root directory
+/*.dat
+
 # ignore any VScode settings
 .vscode/*
+
+# ignore any macOS folder settings
+.DS_store

README.md

@@ -5,8 +5,29 @@ Capt'n General: $q^{2n}$ and $v^{2m}$ dependent solar dark matter capture and en
 
 Capt'n Oper: Solar capture using the NREO formalism as adapted from [https://arxiv.org/abs/1501.03729]().
 
-Can be built using `make` as a library by default (or by explicitly calling `make gencaplib.so`), or can be built as a standalone executable using `make gentest.x`.
+## Installation
+
+Run the `install.sh` script to install the `gencap` library and an optional testing executable.
+Use `install.sh -h` to learn more.
+Run the `cleanup.sh` script to clear all installed files and temporary `.dat` files produced by the testing executable.
+
+## Development
+
+Can be built using `make` as a library by default (or by explicitly calling `make libgencap.so`), or can be built as a standalone executable using `make gentest.x`.
+To enable (or disable) debugging, set (or unset) the shell variable `debug` to any non-empty value:
+
+```shell
+export debug=foo
+unset debug
+```
+
+This can be done for a single `make` call by adding the assignment after the make target(s): `make bar debug=foo`.
+The debug compiled objects, modules, library, and executable can be found in directories appended with **-debug**.
+This keeps the debug build files seperate from the regular build files.
+The debug files can be cleaned by passing the same `debug` variable to either of the `clean` or `nuke` make targets.
 
 See `main.f90` for examples of how to call the executable, `gentest.x`.
 
+## Citing Captn General
+
 If you use this code, you can cite [https://arxiv.org/abs/2105.06810]() and/or [https://arxiv.org/abs/1808.10465]() where it was first deployed.

cleanup.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+# Move into script's directory
+cd "$(realpath "$(dirname -- "${BASH_SOURCE[0]}")")"
+
+# Nuke all built objects, modules, libraries, and executables
+echo "Nuking built files..."
+make nuke
+echo
+
+# Remove the empty build directories
+echo "Removing build directories from $(pwd)..."
+if [[ -d obj ]]; then rmdir obj/* && rmdir obj; fi
+if [[ -d lib ]]; then rmdir lib; fi
+if [[ -d bin ]]; then rmdir bin; fi
+echo
+
+# Nuke all built debug objects, modules, libraries, and executables
+echo "Nuking built debug files..."
+make nuke debug=true
+echo
+
+# Remove the empty debug build directories
+echo "Removing build directories from $(pwd)..."
+if [[ -d obj-debug ]]; then rmdir obj-debug/* && rmdir obj-debug; fi
+if [[ -d lib-debug ]]; then rmdir lib-debug; fi
+if [[ -d bin-debug ]]; then rmdir bin-debug; fi
+echo
+
+# Removing data files created by the test executable
+echo "Deleting temporary *.dat files from $(pwd)..."
+rm -f *.dat

install.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+# Move into script's directory
+cd "$(realpath "$(dirname -- "${BASH_SOURCE[0]}")")"
+
+HELPMSG="Usage: $(basename "$0") [-h] [-x] [-g]
+Builds the gencap library in the ./lib/ directory. Optionally toggle building
+of the testing executable in the ./bin/ directory, and building in debug mode
+for development.
+
+Launch Options:
+HELP:
+  -h  shows this help text
+
+TEST EXECUTABLE:
+  -x  the script will also install the test executable that demonstrates the
+      library's capabilities
+
+DEBUGGING MODE:
+  -g  enables the debugging flags 'g', 'Og', 'Wall', and other helpful flags
+      for gfortran"
+
+unset do_exe
+while getopts hxg FLAG; do
+    case "${FLAG}" in
+        h)
+            echo "$HELPMSG"
+            exit 0
+            ;;
+        x) do_exe=true;;
+        g) export debug=true;;
+    esac
+done
+
+# Making library
+echo "Making the library..."
+if make; then
+    echo "Completed library!"
+else
+    echo "Failed to make the library."
+    exit 2
+fi
+echo
+
+if [[ "${do_exe}" == true ]]; then
+	# Making test executable
+	echo "Making the test executable..."
+	if make gentest.x; then
+        echo "Completed executable!"
+    else
+        echo "Failed to make the executable."
+        exit 3
+    fi
+fi

makefile

@@ -1,74 +1,154 @@
+# Default target is the library
+CAPTNGEN_LIBNAME = gencap
+lib$(CAPTNGEN_LIBNAME).so:
+# -------------------------------- Directories ---------------------------------
+SRCDIR = src
+NUMDIR = numerical
+QAGDIR = dqag
+WDIR = Wfunctions
+RDIR = Rfunctions
+OBJDIR_name = obj
+BINDIR_name = bin
+LIBDIR_name = lib
+DEBUG_name = debug
+
+# Put debug-compiled files in a seperate directory
+ifneq ($(strip $(debug)),)
+	OBJDIR = $(OBJDIR_name)-$(DEBUG_name)
+	BINDIR = $(BINDIR_name)-$(DEBUG_name)
+	LIBDIR = $(LIBDIR_name)-$(DEBUG_name)
+else
+	OBJDIR = $(OBJDIR_name)
+	BINDIR = $(BINDIR_name)
+	LIBDIR = $(LIBDIR_name)
+endif
+
+
+# ----------------------- Source Files and their Targets -----------------------
+# The file module call dependencies are defined here:
+# gencap.f90 and opercap.f90 use sharedcap.f90
+$(addprefix $(OBJDIR)/, \
+	gencap.o \
+	opercap.o \
+): $(addprefix $(OBJDIR)/, \
+	sharedcap.o \
+)
+
+# spergelpressmod.f90 and fastevap.f90 use gencap.f90
+$(addprefix $(OBJDIR)/, \
+	spergelpressmod.o \
+	fastevap.o \
+): $(addprefix $(OBJDIR)/, \
+	gencap.o \
+)
+
+# transgen.f90 uses gencap.f90, spergelpressmod.f90, and alphakappamod.f90
+$(addprefix $(OBJDIR)/, \
+	transgen.o \
+): $(addprefix $(OBJDIR)/, \
+	gencap.o \
+	spergelpressmod.o \
+	alphakappamod.o \
+)
+
+# Grab the f and f90 source files via wildcards
+CAPTNSRCS = $(wildcard $(SRCDIR)/*.f90)
+MAINSRC = $(SRCDIR)/main.f90
+WRSRCS = $(wildcard $(SRCDIR)/$(WDIR)/*.f $(SRCDIR)/$(RDIR)/*.f)
+NUMSRCS = $(wildcard $(SRCDIR)/$(NUMDIR)/*.f*)
+QAGSRCS = $(wildcard $(SRCDIR)/$(QAGDIR)/*.f)
+
+# Use a string replace to get target directory/filename.o for each source file
+CAPTNOBJS = $(CAPTNSRCS:$(SRCDIR)/%.f90=$(OBJDIR)/%.o)
+MAINOBJ = $(MAINSRC:$(SRCDIR)/%.f90=$(OBJDIR)/%.o)
+WROBJS = $(WRSRCS:$(SRCDIR)/%.f=$(OBJDIR)/%.o)
+temp = $(NUMSRCS:$(SRCDIR)/%.f90=$(OBJDIR)/%.o)
+NUMOBJS = $(temp:$(SRCDIR)/%.f=$(OBJDIR)/%.o)
+QAGOBJS = $(QAGSRCS:$(SRCDIR)/%.f=$(OBJDIR)/%.o)
+
+# Name of the testing executable
+TESTING_EXE = gentest.x
+
+
+# ----------------------------- Compiler and Flags -----------------------------
 FC=gfortran
-FOPT= -O3 -fPIC -std=legacy -fopenmp# -Wall -fbounds-check -g  #legacy is required if you are running gcc 10 or later 
-NUMDIR = ./numerical
-QAGDIR = ./numerical/dqag
-# TSDIR = ./numerical/TSPACK
-WDIR = ./Wfunctions
-RDIR = ./Rfunctions
+#legacy is required if you are running gcc 10 or later due to the arguement-mismatch warning being promoted to error
+FFLAGS=-fopenmp -fPIC -std=legacy -J $(OBJDIR)
+ifneq ($(strip $(debug)),)
+	FFLAGS+= -g -O0 -Wall -Wextra -Wconversion
+	FFLAGS+= -fbacktrace -fcheck=all -ffpe-trap=invalid,zero,overflow
+	FFLAGS+= -fdebug-aux-vars# -fimplicit-none --- numerical/dgamic.f misbehaves with the implicit-none restriction!
+else
+	FFLAGS+= -O3
+endif
 
-MAIN = main.o
-MFSHR = sharedcap.o
-MFOBJ = gencap.o
-MFCAP = opercap.o
-TRGOBJ = alphakappamod.o spergelpressmod.o transgen.o fastevap.o
-NUMFOBJ =  dgamic.o d1mach.o
-NUMF90OBJ = sgolay.o spline.o pchip.o fftpack5.o
-QAG=  dsntdqagse.o dqelg.o dqk21.o dqpsrt.o dsntdqk21.o
-WFUNC = WM.o WS2.o WS1.o WP2.o WMP2.o WP1.o WD.o WS1D.o
-RFUNC = RM.o RS2.o RS1.o RP2.o RMP2.o RP1.o RD.o RS1D.o
+# -L tells where the linker to look at compile time
+# -Wl sends a comma separated list of arguments to the linker
+# -rpath tells the exe where to look at runtime (hence the use of the full path)
+LDFLAGS=-L $(LIBDIR) -Wl,-rpath,"$(realpath $(LIBDIR))"
+LDLIBS=-l $(CAPTNGEN_LIBNAME)
 
 
-# TSOBJ = ENDSLP.o SIGS.o SNHCSH.o STORE.o YPCOEF.o YPC1.o YPC1P.o YPC2.o YPC2P.o TSPSI.o \
- INTRVL.o HVAL.o HPVAL.o
+# ------------------------------- Phony Targets --------------------------------
+# debug=true isn't an actual target, but PHONY makes it appear in tab completion
+.PHONY: lib$(CAPTNGEN_LIBNAME).so $(TESTING_EXE) clean nuke debug=true
 
+lib$(CAPTNGEN_LIBNAME).so: $(LIBDIR)/lib$(CAPTNGEN_LIBNAME).so
+$(TESTING_EXE): $(BINDIR)/$(TESTING_EXE)
+clean: # clears all objects and modules
+	rm -f $(SRCDIR)/*.mod $(OBJDIR)/*.mod $(OBJDIR)/*/*.mod
+	rm -f $(OBJDIR)/*.o $(OBJDIR)/*/*.o
+nuke: clean # and also clears the testing executable and library
+	rm -f $(LIBDIR)/lib$(CAPTNGEN_LIBNAME).so
+	rm -f $(BINDIR)/$(TESTING_EXE)
 
-gencaplib.so: $(MFSHR) $(MFOBJ) $(MFCAP) $(TRGOBJ) $(NUMFOBJ) $(NUMF90OBJ) $(QAG) $(WFUNC) $(RFUNC)
-	$(FC) $(FOPT) -shared -o $@ $(MFSHR) $(MFOBJ) $(MFCAP) $(TRGOBJ) $(NUMFOBJ) $(NUMF90OBJ) $(QAG) $(WFUNC) $(RFUNC)
 
-# -L tells the linker where to look for shared libraries
-# -rpath puts the location of the libraries in the executable so the load can find them at runtime
-# -Wl lets us send options to the linker (which are comma seperated)
-gentest.x: $(MAIN) gencaplib.so
-	${FC} $(FOPT) -L. -Wl,-rpath,. -o gentest.x $(MAIN) gencaplib.so
-#	rm $(MFOBJ) $(NUMFOBJ) $(QAG)
+# -------------------------------- Main Targets --------------------------------
+# Targets with recipes to put the library and executable in the correct folders
+$(LIBDIR)/lib$(CAPTNGEN_LIBNAME).so: $(NUMOBJS) $(QAGOBJS) $(CAPTNOBJS) $(WROBJS) | $(LIBDIR)
+	$(FC) $(FFLAGS) -shared $^ -o $@
 
+$(BINDIR)/$(TESTING_EXE): $(MAINOBJ) $(LIBDIR)/lib$(CAPTNGEN_LIBNAME).so | $(BINDIR)
+	$(FC) $(FFLAGS) $(LDFLAGS) $< $(LDLIBS) -o $@
 
-$(NUMFOBJ): %.o : $(NUMDIR)/%.f
-	$(FC) $(FOPT) -c  $<
 
-$(NUMF90OBJ): %.o : $(NUMDIR)/%.f90
-	$(FC) $(FOPT) -Wno-argument-mismatch -c  $<
+# ------------------------------- Object Targets -------------------------------
+# Targets with recipes for each object file in directory structure
+$(OBJDIR)/%.o: $(SRCDIR)/%.f90 | $(OBJDIR)
+	$(FC) $(FFLAGS) -c $< -o $@
 
-$(TSOBJ): %.o : $(TSDIR)/%.f
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(WDIR)/%.o: $(SRCDIR)/$(WDIR)/%.f | $(OBJDIR)/$(WDIR)
+	$(FC) $(FFLAGS) -c $< -o $@
 
-$(MFSHR): %.o: %.f90
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(RDIR)/%.o: $(SRCDIR)/$(RDIR)/%.f | $(OBJDIR)/$(RDIR)
+	$(FC) $(FFLAGS) -c $< -o $@
 
-$(MFOBJ): %.o: %.f90
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(NUMDIR)/%.o: $(SRCDIR)/$(NUMDIR)/%.f* | $(OBJDIR)/$(NUMDIR)
+	$(FC) $(FFLAGS) -c $< -o $@
 
-$(MFCAP): %.o: %.f90
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(QAGDIR)/%.o: $(SRCDIR)/$(QAGDIR)/%.f | $(OBJDIR)/$(QAGDIR)
+	$(FC) $(FFLAGS) -c $< -o $@
 
-$(TRGOBJ): %.o: %.f90
-	$(FC) $(FOPT) -c $<
 
-$(MAIN): %.o: %.f90
-	$(FC) $(FOPT) -c  $<
+# ----------------------------- Directory Targets ------------------------------
+# Targets with recipes to create the output directories if they don't exist yet
+$(OBJDIR):
+	mkdir -p $(OBJDIR)
 
-$(NUMOBJ): %.o: $(NUMDIR)/%.f
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(WDIR):
+	mkdir -p $(OBJDIR)/$(WDIR)
 
-$(QAG): %.o: $(QAGDIR)/%.f
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(RDIR):
+	mkdir -p $(OBJDIR)/$(RDIR)
 
-$(WFUNC): %.o: $(WDIR)/%.f
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(NUMDIR):
+	mkdir -p $(OBJDIR)/$(NUMDIR)
 
-$(RFUNC): %.o: $(RDIR)/%.f
-	$(FC) $(FOPT) -c  $<
+$(OBJDIR)/$(QAGDIR):
+	mkdir -p $(OBJDIR)/$(QAGDIR)
 
+$(BINDIR):
+	mkdir -p $(BINDIR)
 
-clean:
-	rm -f *.o *.mod *.so gentest.x
+$(LIBDIR):
+	mkdir -p $(LIBDIR)

mkmesalib.sh

@@ -1,3 +1,3 @@
-make gencaplib.so
+make
 cp -r ak_files $DARKMESADIR
-cp gencaplib.so $DARKMESADIR
+cp lib/libgencap.so $DARKMESADIR