Adds "makedep" script to replace mkmf

`mkmf` is an external dependency that that uses a multi-stage
approach to building a Makefile with dependencies but fails to yield
an optimal link stage (it links everything, including unused modules).

`makedep` is a bash script that constructs the link stage for as many
programs as found, links only the necessary object files*, and is coded
solely in bash thus removing an external dependency. The addition of this
script is the bulk of this commit.

Code changes:
- when more than one program is encountered the executable is given
  the name following "program". Since all the programs were named
  "MOM_main" I have had to change them to provide unique names:
  - MOM_sum_driver.F90, "program MOM_main" has been changed to
    "MOM_sum_driver"
  - solo_driver/MOM_driver.F90, "program MOM_main" has been
    changed to "MOM6"

Script changes:
- Makefile.in now has a target "depend" to generate dependencies
  using makedep
- configure.ac no longer checks for list_paths and mkmf
- configure.ac now invokes "make depend" in place of mkmf
- Added target "unit" to .testing/Makefile to build all programs
  in config_src/drivers/unit_drivers

Ugliness:
- I had to add a -f option to makedep to handle FMS non-standard macros
  - To compile FMS, the dependencies Makefile is passed CPPDEFS in addition
    to CPPFLAGS.
  - The first version of makedep was consistent with the standard gmake
    rules which were sufficient to build MOM6. Adding -f "rule command"
    allows FMS to be built:
      makemake -f '$(FC) $(FFLAGS) $(CPPFLAGS) $(CPPDEFS) -c $<' -x libFMS.a ../src
- .inc suffix is included when searching for include directories
  - FMS has includes of .inc files which modify the search path passed
    to /lib/cpp .
- Handling of badly formatted comments when searching for modules
  - FMS fm_util.F90, that generates fm_util_mod.mod, has some odd strings
    in a comment on the module declaration line. This was causing wierdness
    in the script.
- Not just Fortran dependencies
  - makedep needs to also generate rules for C files in order to
    build FMS

Todo:
[ ] *A work around is used for TEOS10 (gsw_*) functions that are in separate
    object files even though accessed via a module (WTFortran!!!)

.testing/Makefile

@@ -119,10 +119,6 @@ DIMS ?= t l h z q r
 # Dependencies
 DEPS = deps
 
-# mkmf, list_paths (GFDL build toolchain)
-LIST_PATHS := $(DEPS)/bin/list_paths
-MKMF := $(DEPS)/bin/mkmf
-
 
 #---
 # Test configuration
@@ -295,7 +291,7 @@ build/%/MOM6: build/%/Makefile
 
 # Use autoconf to construct the Makefile for each target
 .PRECIOUS: $(foreach b,$(BUILDS),build/$(b)/Makefile)
-build/%/Makefile: ../ac/configure ../ac/Makefile.in $(DEPS)/lib/libFMS.a $(MKMF) $(LIST_PATHS)
+build/%/Makefile: ../ac/configure ../ac/Makefile.in $(DEPS)/lib/libFMS.a
 	mkdir -p $(@D)
 	cd $(@D) \
 	  && $(MOM_ENV) ../../../ac/configure $(MOM_ACFLAGS) --with-framework=$(FRAMEWORK) \
@@ -308,7 +304,7 @@ build/%/Makefile: ../ac/configure ../ac/Makefile.in $(DEPS)/lib/libFMS.a $(MKMF)
 
 # Fetch the regression target codebase
 build/target/Makefile build/opt_target/Makefile: \
-  $(TARGET_CODEBASE)/ac/configure $(DEPS)/lib/libFMS.a $(MKMF) $(LIST_PATHS)
+  $(TARGET_CODEBASE)/ac/configure $(DEPS)/lib/libFMS.a
 	mkdir -p $(@D)
 	cd $(@D) \
 	  && $(MOM_ENV) ../../$(TARGET_CODEBASE)/ac/configure $(MOM_ACFLAGS) \
@@ -337,7 +333,7 @@ $(DEPS)/lib/libFMS.a: $(DEPS)/fms/build/libFMS.a
 $(DEPS)/fms/build/libFMS.a: $(DEPS)/fms/build/Makefile
 	$(MAKE) -C $(DEPS) fms/build/libFMS.a
 
-$(DEPS)/fms/build/Makefile: $(DEPS)/fms/src/configure $(DEPS)/Makefile.fms.in $(MKMF) $(LIST_PATHS)
+$(DEPS)/fms/build/Makefile: $(DEPS)/fms/src/configure $(DEPS)/Makefile.fms.in
 	$(FMS_ENV) $(MAKE) -C $(DEPS) fms/build/Makefile
 	$(MAKE) -C $(DEPS) fms/build/Makefile
 
@@ -353,13 +349,6 @@ $(DEPS)/fms/src/configure: ../ac/deps/configure.fms.ac $(DEPS)/Makefile $(FMS_SO
 $(DEPS)/fms/src: $(DEPS)/Makefile
 	make -C $(DEPS) fms/src
 
-# mkmf
-$(MKMF) $(LIST_PATHS): $(DEPS)/mkmf
-	$(MAKE) -C $(DEPS) bin/$(@F)
-
-$(DEPS)/mkmf: $(DEPS)/Makefile
-	$(MAKE) -C $(DEPS) mkmf
-
 # Dependency init
 $(DEPS)/Makefile: ../ac/deps/Makefile
 	mkdir -p $(@D)
@@ -693,7 +682,7 @@ test.summary:
 .PHONY: unit.cov
 unit.cov: build/unit/MOM_new_unit_tests.gcov
 
-work/unit/std.out: build/unit/MOM6
+work/unit/std.out: build/unit/MOM_unit_tests
 	if [ $(REPORT_COVERAGE) ]; then \
 	  find build/unit -name *.gcda -exec rm -f '{}' \; ; \
 	fi

ac/Makefile.in

@@ -51,11 +51,16 @@ CPPFLAGS = @CPPFLAGS@
 FFLAGS = @FCFLAGS@
 LDFLAGS = @LDFLAGS@ @LIBS@
 
+SRC_DIRS = @SRC_DIRS@
+
 # Gather modulefiles
 TMPFILES = $(wildcard *.mod)
 
-include Makefile.mkmf
+-include Makefile.dep
 
+.PHONY: depend
+depend:
+	../../../ac/makedep -o Makefile.dep $(SRC_DIRS)
 
 # Delete any files associated with configuration (including the Makefile).
 .PHONY: distclean
@@ -64,9 +69,8 @@ distclean: clean
 	rm -f config.log
 	rm -f config.status
 	rm -f Makefile
-	# mkmf output
 	rm -f path_names
-	rm -f Makefile.mkmf
+	rm -f Makefile.dep
 
 
 # This deletes all files generated by autoconf, including configure.

ac/configure.ac

@@ -223,46 +223,13 @@ AC_COMPILE_IFELSE(
   ]
 )
 
-
-# Search for mkmf build tools
-AC_PATH_PROG([LIST_PATHS], [list_paths])
-AS_IF([test -z "$LIST_PATHS"], [
-  AC_PATH_PROG([LIST_PATHS], [list_paths], [], ["$PATH:${srcdir}/ac/deps/bin"])
-  AS_IF([test -z "$LIST_PATHS"],
-    [AC_MSG_ERROR([Could not find list_paths.])],
-    [AC_SUBST(PATH, ["$PATH:${srcdir}/ac/deps/bin"])])
-  ]
-)
-
-AC_PATH_PROG([MKMF], [mkmf])
-AS_IF([test -z "$MKMF"], [
-  AC_PATH_PROG([MKMF], [mkmf], [], ["$PATH:${srcdir}/ac/deps/bin"])
-  AS_IF([test -z "$MKMF"],
-    [AC_MSG_ERROR([Could not find mkmf.])],
-    [AC_SUBST(PATH, ["$PATH:${srcdir}/ac/deps/bin"])])
-  ]
-)
-
-
-# NOTE: MEM_LAYOUT unneeded if we shift to MOM_memory.h.in template
-AC_CONFIG_COMMANDS([path_names],
-  [list_paths -l \
-    ${srcdir}/src \
-    ${MODEL_FRAMEWORK} \
-    ${srcdir}/config_src/ext* \
-    ${DRIVER_DIR} \
-    ${MEM_LAYOUT}],
-  [MODEL_FRAMEWORK=$MODEL_FRAMEWORK
-    MEM_LAYOUT=$MEM_LAYOUT
-    DRIVER_DIR=$DRIVER_DIR]
-)
-
-
-AC_CONFIG_COMMANDS([Makefile.mkmf],
-  [mkmf -p MOM6 -m Makefile.mkmf path_names])
-
+SRC_DIRS="${srcdir}/src ${MODEL_FRAMEWORK} ${srcdir}/config_src/external ${DRIVER_DIR} ${MEM_LAYOUT}"
+AC_CONFIG_COMMANDS([Makefile.dep],
+  [make depend])
 
 # Prepare output
 AC_SUBST(CPPFLAGS)
+AC_SUBST(SRC_DIRS)
 AC_CONFIG_FILES([Makefile:${srcdir}/ac/Makefile.in])
 AC_OUTPUT
+

ac/deps/Makefile

@@ -7,10 +7,6 @@ SHELL = bash
 MAKEFLAGS += -R
 
 
-# mkmf, list_paths (GFDL build toolchain)
-MKMF_URL ?= https://github.com/NOAA-GFDL/mkmf.git
-MKMF_COMMIT ?= master
-
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
 FMS_COMMIT ?= 2019.01.03
@@ -30,19 +26,14 @@ FMS_SOURCE = $(call SOURCE,fms/src)
 # Rules
 
 .PHONY: all
-all: bin/mkmf bin/list_paths lib/libFMS.a
+all: bin/makedep lib/libFMS.a
 
 #---
-# mkmf checkout
+# makedep script
 
-bin/mkmf bin/list_paths: mkmf
+bin/makedep: ../../ac/makedep
 	mkdir -p $(@D)
-	cp $^/$@ $@
-
-mkmf:
-	git clone $(MKMF_URL) $@
-	git -C $@ checkout $(MKMF_COMMIT)
-
+	cp $^ $@
 
 #---
 # FMS build
@@ -64,7 +55,7 @@ fms/build/libFMS.a: fms/build/Makefile
 	make -C fms/build libFMS.a
 
 
-fms/build/Makefile: Makefile.fms.in fms/src/configure bin/mkmf bin/list_paths
+fms/build/Makefile: Makefile.fms.in fms/src/configure bin/makedep
 	mkdir -p fms/build
 	cp Makefile.fms.in fms/src/Makefile.in
 	cd $(@D) && ../src/configure --srcdir=../src
@@ -87,4 +78,4 @@ clean:
 
 .PHONY: distclean
 distclean: clean
-	rm -rf fms mkmf
+	rm -rf fms

ac/deps/Makefile.fms.in

@@ -54,7 +54,13 @@ FFLAGS = @FCFLAGS@
 LDFLAGS = @LDFLAGS@
 ARFLAGS = @ARFLAGS@
 
+SRC_DIRS = @SRC_DIRS@
+
 # Gather modulefiles
 TMPFILES = $(wildcard *.mod)
 
-include Makefile.mkmf
+-include Makefile.dep
+
+.PHONY: depend
+depend:
+	../../bin/makedep -o Makefile.dep -f '$$(FC) $$(CPPFLAGS) $$(CPPDEFS) $$(FFLAGS) -c $$<' -x libFMS.a -d $(SRC_DIRS)

ac/deps/configure.fms.ac

@@ -158,38 +158,6 @@ AX_FC_ALLOW_ARG_MISMATCH
 FCFLAGS="$FCFLAGS $ALLOW_ARG_MISMATCH_FCFLAGS"
 
 
-# Search for mkmf build tools
-AC_PATH_PROG([LIST_PATHS], [list_paths])
-AS_IF([test -z "$LIST_PATHS"], [
-  AC_PATH_PROG([LIST_PATHS], [list_paths], [], ["$PATH:${srcdir}/../../bin"])
-  AS_IF([test -z "$LIST_PATHS"],
-    [AC_MSG_ERROR([Could not find list_paths.])],
-    [AC_SUBST(PATH, ["$PATH:${srcdir}/../../bin"])])
-  ]
-)
-
-AC_PATH_PROG([MKMF], [mkmf])
-AS_IF([test -z "$MKMF"], [
-  AC_PATH_PROG([MKMF], [mkmf], [], ["$PATH:${srcdir}/../../bin"])
-  AS_IF([test -z "$MKMF"],
-    [AC_MSG_ERROR([Could not find mkmf.])],
-    [AC_SUBST(PATH, ["$PATH:${srcdir}/../../bin"])])
-  ]
-)
-
-
-# MKMF commands
-AC_CONFIG_COMMANDS([path_names],
-  [${LIST_PATHS} -l ${srcdir}],
-  [LIST_PATHS=${LIST_PATHS}]
-)
-
-
-AC_CONFIG_COMMANDS([mkmf],
-  [${MKMF} -p libFMS.a -m Makefile.mkmf path_names],
-  [MKMF=${MKMF}]
-)
-
 
 # Autoconf does not configure the archiver (ar), as it is handled by Automake.
 # TODO: Properly configure this tool.  For now, we hard-set this to `ar`.
@@ -198,8 +166,12 @@ ARFLAGS=rv
 AC_SUBST(AR)
 AC_SUBST(ARFLAGS)
 
+SRC_DIRS="../src"
+AC_CONFIG_COMMANDS([Makefile.dep],
+  [make depend])
 
 # Prepare output
 AC_SUBST(CPPFLAGS)
+AC_SUBST(SRC_DIRS)
 AC_CONFIG_FILES(Makefile)
 AC_OUTPUT