Makedep (#1)

* Autoconf: Fix makedep path

The current path of makedep in the autoconf build assumes a directory tree as in .testing.  This patch uses the 
generalized @SrcDir@ to support more general autoconf builds.

Other minor changes:
* The `depend` rule was split into an explicit Makefile.dep rule and a phony rule to support `make depend`

* SRC_DIRS shell assignment is replaced with an Autoconf macro.

* A "self-generate" rule was added to `Makefile.in`, so that changes to `Makefile.in` do not trigger a full `./configure` run and regeneration of `.config.status`.

  This could possibly be extended to support `make depend` but let's first see how this one goes.

* Autoconf: makedep uses autoconf var conventions

This patch changes the makedep script to use autoconf environment variable conventions rather than mkmf ones:

* FCFLAGS in place of FFLAGS

* DEFS in place of CPPDEFS

* LDFLAGS and LIBS rather than just LDFLAGS
  (NOTE: This differs from Makefile's LDLFLAGS/LDLIBS)

This also allowed us to remove the custom build rule in the FMS build. Note that we now use an autoconf-friendly rule, rather than the default Makefile rule (which was arguably for fixed-format Fortran anyway).

The description of autoconf->mkmf translation from the Makefile templates has also been removed, since they're no longer relevant.

Some other minor changes in this build:

* The `make depend` rule was added to the FMS Makefile template.

* @SrcDir@ is directly passed to FMS makedep, rather than identically re-defining it in a variable.

* Testing: Resolve makedep paths

This patch resolves some issues relating to finding the path to makedep in both .testing and more generalized autoconf builds.

An explicit autoconf test for makedep has been added, with a default path which includes the `ac` directory relative to `deps`.

The .testing directory, which does not lie within `ac`, instead modifies the PATH to allow autoconf to find makedep.

The absolute path is determined and substituted into the appropriate Makefile.in template.

Some redundant operations in .testing/Makefile have been removed, but I suspect there are even more.  Much of the structure required to support mkmf and list_paths is probably no longer needed.

.testing/Makefile

@@ -324,7 +324,7 @@ $(TARGET_CODEBASE):
 # FMS
 
 # Set up the FMS build environment variables
-FMS_ENV = PATH="${PATH}:../../bin" FCFLAGS="$(FCFLAGS_DEBUG)"
+FMS_ENV = PATH="${PATH}:$(realpath ../ac)" FCFLAGS="$(FCFLAGS_DEBUG)"
 
 # TODO: *.mod dependencies?
 $(DEPS)/lib/libFMS.a: $(DEPS)/fms/build/libFMS.a
@@ -335,7 +335,6 @@ $(DEPS)/fms/build/libFMS.a: $(DEPS)/fms/build/Makefile
 
 $(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
 
 $(DEPS)/Makefile.fms.in: ../ac/deps/Makefile.fms.in $(DEPS)/Makefile
 	cp $< $(DEPS)

ac/Makefile.in

@@ -2,65 +2,34 @@
 #
 # Compiler flags are configured by autoconf's configure script.
 #
-# Source code dependencies are configured by mkmf and list_paths, specified in
-# the `Makefile.mkmf` file.
-#
-# mkmf conventions are close, but not identical, to autoconf.  We attempt to
-# map the autoconf variables to the mkmf variables.
-#
-# The following variables are used by Makefiles generated by mkmf.
-#
-#   CC      C compiler
-#   CXX     C++ compiler
-#   FC      Fortran compiler (f77 and f90)
-#   LD      Linker
-#   AR      Archiver
-#
-#   CPPDEFS     Preprocessor macros
-#   CPPFLAGS    C preprocessing flags
-#   CXXFLAGS    C++ preprocessing flags
-#   FPPFLAGS    Fortran preprocessing flags
-#
-#   CFLAGS      C compiler flags
-#   FFLAGS      Fortran compiler flags
-#   LDFLAGS     Linker flags + libraries
-#   ARFLAGS     Archiver flags
-#
-#   OTHERFLAGS      Additional flags for all languages (C, C++, Fortran)
-#   OTHER_CFLAGS    Optional C flags
-#   OTHER_CXXFLAGS  Optional C++ flags
-#   OTHER_FFLAGS    Optional Fortran flags
-#   TMPFILES        Placeholder for `make clean` deletion (as `make neat`).
-#
-#
-#   NOTES:
-#    - FPPFLAGS and FFLAGS always appear as a pair, and autoconf does not use
-#      FPPFLAGS, so FPPFLAGS does not serve much purpose.
-#
-#    - mkmf's FFLAGS does not distinguish between autoconf's fixed-format
-#      FFLAGS and free-format FCFLAGS.
-#
-#    - LDFLAGS does not distinguish between autoconf's LDFLAGS and LIBS.
-#      It also places both after the executable rather than just LIBS.
+# Source code dependencies are configured by makedep and saved to Makefile.dep.
 
 FC = @FC@
 LD = @FC@
+MAKEDEP = @MAKEDEP@
 
-CPPDEFS = @DEFS@
+DEFS = @DEFS@
 CPPFLAGS = @CPPFLAGS@
-FFLAGS = @FCFLAGS@
-LDFLAGS = @LDFLAGS@ @LIBS@
-
+FCFLAGS = @FCFLAGS@
+LDFLAGS = @LDFLAGS@
+LIBS = @LIBS@
 SRC_DIRS = @SRC_DIRS@
 
-# Gather modulefiles
-TMPFILES = $(wildcard *.mod)
 
 -include Makefile.dep
 
+
+# Generate Makefile from template
+Makefile: @srcdir@/ac/Makefile.in config.status
+	./config.status
+
+
+# Generate dependencies
 .PHONY: depend
-depend:
-	../../../ac/makedep -o Makefile.dep $(SRC_DIRS)
+depend: Makefile.dep
+Makefile.dep:
+	$(MAKEDEP) -o Makefile.dep $(SRC_DIRS)
+
 
 # Delete any files associated with configuration (including the Makefile).
 .PHONY: distclean

ac/configure.ac

@@ -223,13 +223,20 @@ AC_COMPILE_IFELSE(
   ]
 )
 
-SRC_DIRS="${srcdir}/src ${MODEL_FRAMEWORK} ${srcdir}/config_src/external ${DRIVER_DIR} ${MEM_LAYOUT}"
-AC_CONFIG_COMMANDS([Makefile.dep],
-  [make depend])
+
+# Verify that makedep is available
+AC_PATH_PROG([MAKEDEP], [makedep], [${srcdir}/ac/makedep])
+AC_SUBST([MAKEDEP])
+
+
+# Generate source list and configure dependency command
+AC_SUBST([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_SUBST([CPPFLAGS])
 AC_CONFIG_FILES([Makefile:${srcdir}/ac/Makefile.in])
 AC_OUTPUT
 

ac/deps/Makefile

@@ -6,7 +6,6 @@ SHELL = bash
 # Disable implicit variables
 MAKEFLAGS += -R
 
-
 # FMS framework
 FMS_URL ?= https://github.com/NOAA-GFDL/FMS.git
 FMS_COMMIT ?= 2019.01.03
@@ -26,14 +25,8 @@ FMS_SOURCE = $(call SOURCE,fms/src)
 # Rules
 
 .PHONY: all
-all: bin/makedep lib/libFMS.a
-
-#---
-# makedep script
+all: lib/libFMS.a
 
-bin/makedep: ../../ac/makedep
-	mkdir -p $(@D)
-	cp $^ $@
 
 #---
 # FMS build
@@ -45,7 +38,7 @@ bin/makedep: ../../ac/makedep
 
 
 # TODO: track *.mod copy?
-lib/libFMS.a: fms/build/libFMS.a fms/build/Makefile
+lib/libFMS.a: fms/build/libFMS.a
 	mkdir -p {lib,include}
 	cp fms/build/libFMS.a lib/libFMS.a
 	cp fms/build/*.mod include
@@ -55,7 +48,7 @@ fms/build/libFMS.a: fms/build/Makefile
 	make -C fms/build libFMS.a
 
 
-fms/build/Makefile: Makefile.fms.in fms/src/configure bin/makedep
+fms/build/Makefile: Makefile.fms.in fms/src/configure
 	mkdir -p fms/build
 	cp Makefile.fms.in fms/src/Makefile.in
 	cd $(@D) && ../src/configure --srcdir=../src
@@ -67,14 +60,15 @@ fms/src/configure: configure.fms.ac $(FMS_SOURCE) | fms/src
 	cp -r m4 $(@D)
 	cd $(@D) && autoreconf -i
 
+
 fms/src:
 	git clone $(FMS_URL) $@
 	git -C $@ checkout $(FMS_COMMIT)
 
 
 .PHONY: clean
 clean:
-	rm -rf fms/build lib include bin
+	rm -rf fms/build lib include
 
 .PHONY: distclean
 distclean: clean

ac/deps/Makefile.fms.in

@@ -1,66 +1,25 @@
-# Makefile template for autoconf builds using mkmf
+# Makefile template for FMS
 #
 # Compiler flags are configured by autoconf's configure script.
 #
-# Source code dependencies are configured by mkmf and list_paths, specified in
-# the `Makefile.mkmf` file.
-#
-# mkmf conventions are close, but not identical, to autoconf.  We attempt to
-# map the autoconf variables to the mkmf variables.
-#
-# The following variables are used by Makefiles generated by mkmf.
-#
-#   CC      C compiler
-#   CXX     C++ compiler
-#   FC      Fortran compiler (f77 and f90)
-#   LD      Linker
-#   AR      Archiver
-#
-#   CPPDEFS     Preprocessor macros
-#   CPPFLAGS    C preprocessing flags
-#   CXXFLAGS    C++ preprocessing flags
-#   FPPFLAGS    Fortran preprocessing flags
-#
-#   CFLAGS      C compiler flags
-#   FFLAGS      Fortran compiler flags
-#   LDFLAGS     Linker flags + libraries
-#   ARFLAGS     Archiver flags
-#
-#   OTHERFLAGS      Additional flags for all languages (C, C++, Fortran)
-#   OTHER_CFLAGS    Optional C flags
-#   OTHER_CXXFLAGS  Optional C++ flags
-#   OTHER_FFLAGS    Optional Fortran flags
-#   TMPFILES        Placeholder for `make clean` deletion (as `make neat`).
-#
-#
-#   NOTES:
-#    - FPPFLAGS and FFLAGS always appear as a pair, and autoconf does not use
-#      FPPFLAGS, so FPPFLAGS does not serve much purpose.
-#
-#    - mkmf's FFLAGS does not distinguish between autoconf's fixed-format
-#      FFLAGS and free-format FCFLAGS.
-#
-#    - LDFLAGS does not distinguish between autoconf's LDFLAGS and LIBS.
-#      It also places both after the executable rather than just LIBS.
+# Source code dependencies are configured by makedep and saved to Makefile.dep.
 
 CC = @CC@
 FC = @FC@
 LD = @FC@
 AR = @AR@
+MAKEDEP = @MAKEDEP@
 
-CPPDEFS = @DEFS@
+DEFS = @DEFS@
 CPPFLAGS = @CPPFLAGS@
-FFLAGS = @FCFLAGS@
+FCFLAGS = @FCFLAGS@
 LDFLAGS = @LDFLAGS@
+LIBS = @LIBS@
 ARFLAGS = @ARFLAGS@
 
-SRC_DIRS = @SRC_DIRS@
-
-# Gather modulefiles
-TMPFILES = $(wildcard *.mod)
-
 -include Makefile.dep
 
 .PHONY: depend
-depend:
-	../../bin/makedep -o Makefile.dep -f '$$(FC) $$(CPPFLAGS) $$(CPPDEFS) $$(FFLAGS) -c $$<' -x libFMS.a -d $(SRC_DIRS)
+depend: Makefile.dep
+Makefile.dep:
+	$(MAKEDEP) -o Makefile.dep -x libFMS.a @srcdir@

ac/deps/configure.fms.ac

@@ -158,20 +158,26 @@ AX_FC_ALLOW_ARG_MISMATCH
 FCFLAGS="$FCFLAGS $ALLOW_ARG_MISMATCH_FCFLAGS"
 
 
+# Verify makedep
+AC_PATH_PROGS([MAKEDEP], [makedep], [], ["${PATH}:${srcdir}/../../.."])
+AS_IF([test -n "${MAKEDEP}"], [
+  AC_SUBST([MAKEDEP])
+], [
+  AC_MSG_ERROR(["Could not find makedep."])
+])
+
 
 # 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`.
 AR=ar
 ARFLAGS=rv
-AC_SUBST(AR)
-AC_SUBST(ARFLAGS)
+AC_SUBST([AR])
+AC_SUBST([ARFLAGS])
+
+AC_CONFIG_COMMANDS([Makefile.dep], [make depend])
 
-SRC_DIRS="../src"
-AC_CONFIG_COMMANDS([Makefile.dep],
-  [make depend])
+AC_SUBST([CPPFLAGS])
 
 # Prepare output
-AC_SUBST(CPPFLAGS)
-AC_SUBST(SRC_DIRS)
-AC_CONFIG_FILES(Makefile)
+AC_CONFIG_FILES([Makefile])
 AC_OUTPUT

ac/makedep

@@ -16,15 +16,15 @@ usage() {
     echo "  -x EXEC  Name of executable to build. Fails if more than one"
     echo "           is found. If EXEC ends in .a then a library is built."
     echo "  -f CMD   String to use in compile rule. Default is:"
-    echo "             '$(FC) $(FFLAGS) $(CPPFLAGS) -c $<'"
+    echo "             '$(FC) $(DEFS) $(FCFLAGS) $(CPPFLAGS) -c $<'"
 }
 
 # Defaults
 makefile=Makefile.dep
 debug=0
 executable=""
 librarymode=0
-compile_line='$(FC) $(FFLAGS) $(CPPFLAGS) -c $<'
+compile_line='$(FC) $(DEFS) $(FCFLAGS) $(CPPFLAGS) -c $<'
 
 while getopts dho:x:f: option
 do
@@ -61,7 +61,7 @@ for F in ${A}; do # F is the relative path to source file
         u=`echo $u | sed s:$m::g`
     fi
     if [ ${#u} -ne 0 ]; then o2use["$o"]=$u; fi
-    H=$(/lib/cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
+    H=$(cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
     o2H["$o"]=$H
     h=`echo ${H} | cut -d\  -f3- ` # header files
     if [ ${#h} -ne 0 ]; then o2head["$o"]=$h; fi
@@ -91,7 +91,7 @@ for F in ${A}; do # F is the relative path to source file
     f=`basename $F` # file name stripped of path
     o=${f/.c/}.o # object file name
     o2c["$o"]=$F
-    H=$(/lib/cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
+    H=$(cpp -E -MM $I $F | tr -d '\n' | sed 's:\\::g') # line of form a.o: a.F b.h c.h ...
     o2H["$o"]=$H
     h=`echo ${H} | cut -d\  -f3- ` # header files
     if [ ${#h} -ne 0 ]; then o2head["$o"]=$h; fi
@@ -189,7 +189,7 @@ for o in ${OC[@]}; do
         echo "#   incpath:" $i >> ${makefile}
     fi
     echo $H ${U[@]} >> ${makefile} # a.mod a.o: a.F b.mod
-    echo -e '\t$(CC) $(CPPDEFS) $(CPPFLAGS) $(CFLAGS) -c $<' ${i} >> ${makefile} # compile rule
+    echo -e '\t$(CC) $(DEFS) $(CPPFLAGS) $(CFLAGS) -c $<' ${i} >> ${makefile} # compile rule
 done
 
 if [ ${#lib} -ne 0 ]; then # rule to build library
@@ -207,7 +207,7 @@ if [ ${#p2o[@]} -ne 0 ]; then # write rules for linking executables
         o=${p2o[$p]}
         l=$(make -f ${makefile} -B -n -t $o | egrep "\.o$" | sed 's:touch ::' | sort)
         echo $p: $l ${externals[@]} >> ${makefile}
-        echo -e '\t$(LD) -o $@ $^ $(LDFLAGS)' >> ${makefile} # link rule
+        echo -e '\t$(LD) $(LDFLAGS) -o $@ $^ $(LIBS)' >> ${makefile} # link rule
     done
 elif [ -z "$lib" ]; then
     echo "Warning: no library target specified (with -x) and no programs found!"