Use non-recursive make, as far as possible

.gitignore

@@ -20,4 +20,5 @@ src/cubeit
 src/reintegrate
 src/estimate_background
 src/check_hkl
+src/.dirstamp
 *~

Makefile.am

 EXTRA_DIST = configure m4/gnulib-cache.m4
-SUBDIRS = lib src data doc doc/examples scripts
+SUBDIRS = lib
 ACLOCAL_AMFLAGS = -I m4
+
+bin_PROGRAMS = src/pattern_sim src/process_hkl src/get_hkl src/indexamajig \
+               src/compare_hkl src/powder_plot src/render_hkl \
+               src/calibrate_detector src/facetron src/reintegrate \
+               src/estimate_background src/check_hkl
+
+if HAVE_GTK
+bin_PROGRAMS += src/hdfsee
+endif
+
+if HAVE_CAIRO
+bin_PROGRAMS += src/cubeit
+endif
+
+AM_CFLAGS = -Wall
+AM_CPPFLAGS = -DDATADIR=\""$(datadir)"\" -I$(top_builddir)/lib -I$(top_srcdir)/lib
+LDADD = $(top_builddir)/lib/libgnu.a
+
+src_pattern_sim_SOURCES = src/pattern_sim.c src/diffraction.c src/utils.c \
+                      src/image.c src/cell.c src/hdf5-file.c src/detector.c \
+                      src/sfac.c src/peaks.c src/reflections.c \
+                      src/beam-parameters.c src/symmetry.c
+if HAVE_OPENCL
+src_pattern_sim_SOURCES += src/diffraction-gpu.c src/cl-utils.c
+endif
+
+src_process_hkl_SOURCES = src/process_hkl.c src/sfac.c src/statistics.c src/cell.c \
+                      src/utils.c src/reflections.c src/symmetry.c \
+                      src/stream.c src/beam-parameters.c
+
+src_indexamajig_SOURCES = src/indexamajig.c src/hdf5-file.c src/utils.c src/cell.c \
+                      src/image.c src/peaks.c src/index.c src/filters.c \
+                      src/diffraction.c src/detector.c src/sfac.c src/dirax.c \
+                      src/mosflm.c src/reflections.c src/templates.c \
+                      src/symmetry.c src/geometry.c src/thread-pool.c \
+                      src/beam-parameters.c
+if HAVE_OPENCL
+src_indexamajig_SOURCES += src/diffraction-gpu.c src/cl-utils.c
+endif
+
+
+if HAVE_GTK
+src_hdfsee_SOURCES = src/hdfsee.c src/displaywindow.c src/render.c src/hdf5-file.c \
+                 src/utils.c src/image.c src/filters.c
+endif
+
+src_get_hkl_SOURCES = src/get_hkl.c src/sfac.c src/cell.c src/utils.c \
+                  src/reflections.c src/symmetry.c src/beam-parameters.c
+
+src_compare_hkl_SOURCES = src/compare_hkl.c src/sfac.c src/cell.c src/utils.c \
+                      src/reflections.c src/statistics.c src/symmetry.c
+
+src_check_hkl_SOURCES = src/check_hkl.c src/sfac.c src/cell.c src/utils.c \
+                    src/reflections.c src/statistics.c src/symmetry.c
+
+src_powder_plot_SOURCES = src/powder_plot.c src/cell.c src/utils.c src/image.c \
+                      src/hdf5-file.c src/detector.c
+
+src_render_hkl_SOURCES = src/render_hkl.c src/cell.c src/reflections.c src/utils.c \
+                     src/povray.c src/symmetry.c src/render.c src/hdf5-file.c \
+                     src/image.c src/filters.c
+
+src_calibrate_detector_SOURCES = src/calibrate_detector.c src/utils.c \
+                             src/hdf5-file.c src/image.c src/filters.c \
+                             src/peaks.c src/detector.c src/cell.c \
+                             src/thread-pool.c
+
+src_facetron_SOURCES = src/facetron.c src/cell.c src/hdf5-file.c src/utils.c \
+                   src/detector.c src/peaks.c src/image.c src/geometry.c \
+                   src/reflections.c src/stream.c src/thread-pool.c \
+                   src/beam-parameters.c src/symmetry.c src/post-refinement.c \
+                   src/hrs-scaling.c
+
+if HAVE_CAIRO
+src_cubeit_SOURCES = src/cubeit.c src/cell.c src/hdf5-file.c src/utils.c \
+                 src/detector.c src/render.c src/filters.c src/image.c \
+                 src/symmetry.c src/stream.c src/thread-pool.c
+endif
+
+src_reintegrate_SOURCES = src/reintegrate.c src/cell.c src/hdf5-file.c src/utils.c \
+                      src/detector.c src/peaks.c src/image.c src/stream.c \
+                      src/index.c src/dirax.c src/mosflm.c src/templates.c \
+                      src/geometry.c src/symmetry.c src/thread-pool.c
+
+src_estimate_background_SOURCES = src/estimate_background.c src/stream.c \
+                              src/utils.c src/cell.c
+
+INCLUDES = "-I$(top_srcdir)/data"
+
+EXTRA_DIST += src/cell.h src/hdf5-file.h src/image.h src/utils.h \
+              src/diffraction.h src/detector.h src/sfac.h src/reflections.h \
+              src/list_tmp.h src/statistics.h src/displaywindow.h \
+              src/render.h src/hdfsee.h src/dirax.h src/mosflm.h src/peaks.h \
+              src/index.h src/filters.h src/diffraction-gpu.h src/cl-utils.h \
+              src/symmetry.h src/povray.h src/index-priv.h src/geometry.h \
+              src/templates.h src/render_hkl.h src/stream.h src/thread-pool.h \
+              src/beam-parameters.h src/post-refinement.h src/hrs-scaling.h
+
+hdfseedir = $(datadir)/hdfsee
+hdfsee_DATA = data/displaywindow.ui
+
+crystfeldir = $(datadir)/crystfel
+crystfel_DATA = data/diffraction.cl data/defs.h data/sfac/Ca.nff \
+                data/sfac/C.nff data/sfac/Fe.nff data/sfac/H.nff \
+                data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
+                data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat
+
+EXTRA_DIST += data/sfac/Ca.nff data/sfac/C.nff data/sfac/Fe.nff \
+              data/sfac/H.nff data/sfac/Mg.nff data/sfac/N.nff data/sfac/O.nff \
+              data/sfac/P.nff data/sfac/S.nff data/sfac/f0_WaasKirf.dat \
+              data/defs.h data/diffraction.cl data/displaywindow.ui
+
+crystfeldocdir = $(docdir)
+crystfeldoc_DATA = doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
+                   doc/process_hkl.txt doc/symmetry.txt \
+                   doc/twin-calculator.pdf \
+                   doc/0-INDEX doc/examples/lcls-dec.geom \
+                   doc/examples/lcls-dec.beam \
+                   doc/examples/lcls-june-r0013-r0128.geom \
+                   doc/examples/lcls-june.beam \
+                   doc/examples/lcls-xpp-estimate.geom \
+                   doc/examples/lcls-xpp-estimate.beam \
+                   doc/examples/simple.geom
+
+EXTRA_DIST += doc/geometry.txt doc/indexamajig.txt doc/pattern_sim.txt \
+              doc/process_hkl.txt doc/symmetry.txt doc/twin-calculator.pdf \
+              doc/0-INDEX doc/examples/lcls-dec.geom \
+              doc/examples/lcls-june-r0013-r0128.geom \
+              doc/examples/lcls-xpp-estimate.geom doc/examples/simple.geom
+
+scriptdir = $(docdir)/scripts
+script_DATA = scripts/check-near-bragg scripts/double-hit \
+              scripts/random-image scripts/stream-split scripts/wibbletron \
+              scripts/zone-axis scripts/create-mtz scripts/frequency \
+              scripts/i0-analysis scripts/mtz2hkl scripts/sequence-image \
+              scripts/test-facetron scripts/zone-axes \
+              scripts/alternate-stream scripts/README scripts/indexing-rate \
+              scripts/observed-peak-rate scripts/cell-please \
+              scripts/check-hkl-completeness.gp scripts/check-hkl-quality.gp \
+              scripts/compare-hkl.gp
+
+EXTRA_DIST += scripts/check-near-bragg scripts/double-hit scripts/random-image \
+              scripts/stream-split scripts/wibbletron scripts/zone-axis \
+              scripts/create-mtz scripts/frequency scripts/i0-analysis \
+              scripts/mtz2hkl scripts/sequence-image scripts/test-facetron \
+              scripts/zone-axes scripts/alternate-stream scripts/README \
+              scripts/indexing-rate scripts/observed-peak-rate \
+              scripts/cell-please scripts/check-hkl-completeness.gp \
+              scripts/check-hkl-quality.gp scripts/compare-hkl.gp

aclocal.m4

@@ -1004,6 +1004,41 @@ AC_MSG_RESULT([$_am_result])
 rm -f confinc confmf
 ])
 
+# Copyright (C) 1999, 2000, 2001, 2003, 2004, 2005, 2008
+# Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# serial 6
+
+# AM_PROG_CC_C_O
+# --------------
+# Like AC_PROG_CC_C_O, but changed for automake.
+AC_DEFUN([AM_PROG_CC_C_O],
+[AC_REQUIRE([AC_PROG_CC_C_O])dnl
+AC_REQUIRE([AM_AUX_DIR_EXPAND])dnl
+AC_REQUIRE_AUX_FILE([compile])dnl
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $[2] | sed ['s/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/']`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+   # Losing compiler, so override with the script.
+   # FIXME: It is wrong to rewrite CC.
+   # But if we don't then we get into trouble of one sort or another.
+   # A longer-term fix would be to have automake use am__CC in this case,
+   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+   CC="$am_aux_dir/compile $CC"
+fi
+dnl Make sure AC_PROG_CC is never called again, or it will override our
+dnl setting of CC.
+m4_define([AC_PROG_CC],
+          [m4_fatal([AC_PROG_CC cannot be called after AM_PROG_CC_C_O])])
+])
+
 # Fake the existence of programs that GNU maintainers use.  -*- Autoconf -*-
 
 # Copyright (C) 1997, 1999, 2000, 2001, 2003, 2004, 2005, 2008

build-aux/compile

+#! /bin/sh
+# Wrapper for compilers which do not understand `-c -o'.
+
+scriptversion=2009-10-06.20; # UTC
+
+# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2009  Free Software
+# Foundation, Inc.
+# Written by Tom Tromey <tromey@cygnus.com>.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# As a special exception to the GNU General Public License, if you
+# distribute this file as part of a program that contains a
+# configuration script generated by Autoconf, you may include it under
+# the same distribution terms that you use for the rest of that program.
+
+# This file is maintained in Automake, please report
+# bugs to <bug-automake@gnu.org> or send patches to
+# <automake-patches@gnu.org>.
+
+case $1 in
+  '')
+     echo "$0: No command.  Try \`$0 --help' for more information." 1>&2
+     exit 1;
+     ;;
+  -h | --h*)
+    cat <<\EOF
+Usage: compile [--help] [--version] PROGRAM [ARGS]
+
+Wrapper for compilers which do not understand `-c -o'.
+Remove `-o dest.o' from ARGS, run PROGRAM with the remaining
+arguments, and rename the output as expected.
+
+If you are trying to build a whole package this is not the
+right script to run: please start by reading the file `INSTALL'.
+
+Report bugs to <bug-automake@gnu.org>.
+EOF
+    exit $?
+    ;;
+  -v | --v*)
+    echo "compile $scriptversion"
+    exit $?
+    ;;
+esac
+
+ofile=
+cfile=
+eat=
+
+for arg
+do
+  if test -n "$eat"; then
+    eat=
+  else
+    case $1 in
+      -o)
+	# configure might choose to run compile as `compile cc -o foo foo.c'.
+	# So we strip `-o arg' only if arg is an object.
+	eat=1
+	case $2 in
+	  *.o | *.obj)
+	    ofile=$2
+	    ;;
+	  *)
+	    set x "$@" -o "$2"
+	    shift
+	    ;;
+	esac
+	;;
+      *.c)
+	cfile=$1
+	set x "$@" "$1"
+	shift
+	;;
+      *)
+	set x "$@" "$1"
+	shift
+	;;
+    esac
+  fi
+  shift
+done
+
+if test -z "$ofile" || test -z "$cfile"; then
+  # If no `-o' option was seen then we might have been invoked from a
+  # pattern rule where we don't need one.  That is ok -- this is a
+  # normal compilation that the losing compiler can handle.  If no
+  # `.c' file was seen then we are probably linking.  That is also
+  # ok.
+  exec "$@"
+fi
+
+# Name of file we expect compiler to create.
+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
+
+# Create the lock directory.
+# Note: use `[/\\:.-]' here to ensure that we don't use the same name
+# that we are using for the .o file.  Also, base the name on the expected
+# object file name, since that is what matters with a parallel build.
+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
+while true; do
+  if mkdir "$lockdir" >/dev/null 2>&1; then
+    break
+  fi
+  sleep 1
+done
+# FIXME: race condition here if user kills between mkdir and trap.
+trap "rmdir '$lockdir'; exit 1" 1 2 15
+
+# Run the compile.
+"$@"
+ret=$?
+
+if test -f "$cofile"; then
+  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
+elif test -f "${cofile}bj"; then
+  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
+fi
+
+rmdir "$lockdir"
+exit $ret
+
+# Local Variables:
+# mode: shell-script
+# sh-indentation: 2
+# eval: (add-hook 'write-file-hooks 'time-stamp)
+# time-stamp-start: "scriptversion="
+# time-stamp-format: "%:y-%02m-%02d.%02H"
+# time-stamp-time-zone: "UTC"
+# time-stamp-end: "; # UTC"
+# End:

config.h.in

@@ -161,6 +161,9 @@
 /* Define to a substitute value for mmap()'s MAP_ANONYMOUS flag. */
 #undef MAP_ANONYMOUS
 
+/* Define to 1 if your C compiler doesn't accept -c and -o together. */
+#undef NO_MINUS_C_MINUS_O
+
 /* Name of package */
 #undef PACKAGE
 

configure

@@ -700,6 +700,8 @@ GNULIB_MEMCHR
 GL_COND_LIBTOOL_FALSE
 GL_COND_LIBTOOL_TRUE
 LIBOBJS
+AM_BACKSLASH
+AM_DEFAULT_VERBOSITY
 LN_S
 EGREP
 GREP
@@ -752,8 +754,6 @@ am__isrc
 INSTALL_DATA
 INSTALL_SCRIPT
 INSTALL_PROGRAM
-AM_BACKSLASH
-AM_DEFAULT_VERBOSITY
 target_alias
 host_alias
 build_alias
@@ -795,8 +795,8 @@ SHELL'
 ac_subst_files=''
 ac_user_opts='
 enable_option_checking
-enable_silent_rules
 enable_dependency_tracking
+enable_silent_rules
 with_hdf5
 with_gsl
 enable_opencl
@@ -1440,10 +1440,10 @@ Optional Features:
   --disable-option-checking  ignore unrecognized --enable/--with options
   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-  --enable-silent-rules          less verbose build output (undo: `make V=1')
-  --disable-silent-rules         verbose build output (undo: `make V=0')
   --disable-dependency-tracking  speeds up one-time build
   --enable-dependency-tracking   do not reject slow dependency extractors
+  --enable-silent-rules          less verbose build output (undo: `make V=1')
+  --disable-silent-rules         verbose build output (undo: `make V=0')
   --enable-opencl         Enable the use of OpenCL
   --disable-gtk           Disable GTK+/GLib
   --disable-gtktest       do not try to compile and run a test GTK+ program
@@ -2304,19 +2304,6 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $
 ac_compiler_gnu=$ac_cv_c_compiler_gnu
 
 
-# Check whether --enable-silent-rules was given.
-if test "${enable_silent_rules+set}" = set; then :
-  enableval=$enable_silent_rules;
-fi
-
-case $enable_silent_rules in
-yes) AM_DEFAULT_VERBOSITY=0;;
-no)  AM_DEFAULT_VERBOSITY=1;;
-*)   AM_DEFAULT_VERBOSITY=0;;
-esac
-AM_BACKSLASH='\'
-
-VERSION=0.2.0
 ac_aux_dir=
 for ac_dir in build-aux "$srcdir"/build-aux; do
   for ac_t in install-sh install.sh shtool; do
@@ -2340,7 +2327,6 @@ ac_config_sub="$SHELL $ac_aux_dir/config.sub"  # Please don't use this var.
 ac_configure="$SHELL $ac_aux_dir/configure"  # Please don't use this var.
 
 
-
 ac_config_headers="$ac_config_headers config.h"
 
 am__api_version='1.11'
@@ -2781,8 +2767,8 @@ fi
 
 
 # Define the identity of the package.
- PACKAGE=crystfel
- VERSION="$VERSION"
+ PACKAGE='crystfel'
+ VERSION='0.2.0'
 
 
 cat >>confdefs.h <<_ACEOF
@@ -4456,6 +4442,132 @@ $as_echo "$ac_cv_safe_to_define___extensions__" >&6; }
   # Code from module strnlen:
   # Code from module warn-on-use:
 
+if test "x$CC" != xcc; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC and cc understand -c and -o together" >&5
+$as_echo_n "checking whether $CC and cc understand -c and -o together... " >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether cc understands -c and -o together" >&5
+$as_echo_n "checking whether cc understands -c and -o together... " >&6; }
+fi
+set dummy $CC; ac_cc=`$as_echo "$2" |
+		      sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+if { as_var=ac_cv_prog_cc_${ac_cc}_c_o; eval "test \"\${$as_var+set}\" = set"; }; then :
+  $as_echo_n "(cached) " >&6
+else
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+int
+main ()
+{
+
+  ;
+  return 0;
+}
+_ACEOF
+# Make sure it works both with $CC and with simple cc.
+# We do the test twice because some compilers refuse to overwrite an
+# existing .o file with -o, though they will create one.
+ac_try='$CC -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+rm -f conftest2.*
+if { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } &&
+   test -f conftest2.$ac_objext && { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; };
+then
+  eval ac_cv_prog_cc_${ac_cc}_c_o=yes
+  if test "x$CC" != xcc; then
+    # Test first that cc exists at all.
+    if { ac_try='cc -c conftest.$ac_ext >&5'
+  { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; }; }; then
+      ac_try='cc -c conftest.$ac_ext -o conftest2.$ac_objext >&5'
+      rm -f conftest2.*
+      if { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; } &&
+	 test -f conftest2.$ac_objext && { { case "(($ac_try" in
+  *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;;
+  *) ac_try_echo=$ac_try;;
+esac
+eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\""
+$as_echo "$ac_try_echo"; } >&5
+  (eval "$ac_try") 2>&5
+  ac_status=$?
+  $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
+  test $ac_status = 0; };
+      then
+	# cc works too.
+	:
+      else
+	# cc exists but doesn't like -o.
+	eval ac_cv_prog_cc_${ac_cc}_c_o=no
+      fi
+    fi
+  fi
+else
+  eval ac_cv_prog_cc_${ac_cc}_c_o=no
+fi
+rm -f core conftest*
+
+fi
+if eval test \$ac_cv_prog_cc_${ac_cc}_c_o = yes; then
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+else
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+
+$as_echo "#define NO_MINUS_C_MINUS_O 1" >>confdefs.h
+
+fi
+
+# FIXME: we rely on the cache variable name because
+# there is no other way.
+set dummy $CC
+am_cc=`echo $2 | sed 's/[^a-zA-Z0-9_]/_/g;s/^[0-9]/_/'`
+eval am_t=\$ac_cv_prog_cc_${am_cc}_c_o
+if test "$am_t" != yes; then
+   # Losing compiler, so override with the script.
+   # FIXME: It is wrong to rewrite CC.
+   # But if we don't then we get into trouble of one sort or another.
+   # A longer-term fix would be to have automake use am__CC in this case,
+   # and then we could set am__CC="\$(top_srcdir)/compile \$(CC)"
+   CC="$am_aux_dir/compile $CC"
+fi
+
+
 for ac_prog in gawk mawk nawk awk
 do
   # Extract the first word of "$ac_prog", so it can be a program name with args.
@@ -4602,6 +4714,17 @@ else
   RANLIB="$ac_cv_prog_RANLIB"
 fi
 
+# Check whether --enable-silent-rules was given.
+if test "${enable_silent_rules+set}" = set; then :
+  enableval=$enable_silent_rules;
+fi
+
+case $enable_silent_rules in
+yes) AM_DEFAULT_VERBOSITY=0;;
+no)  AM_DEFAULT_VERBOSITY=1;;
+*)   AM_DEFAULT_VERBOSITY=0;;
+esac
+AM_BACKSLASH='\'
 
 
 { $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
@@ -6797,9 +6920,7 @@ CFLAGS="$CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE $libPNG_CFLAGS $Cairo_CFLAGS"
 LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
 LIBS="$LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS"
 
-ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile doc/Makefile"
-
-ac_config_files="$ac_config_files scripts/Makefile doc/examples/Makefile lib/Makefile"
+ac_config_files="$ac_config_files Makefile lib/Makefile"
 
 cat >confcache <<\_ACEOF
 # This file is a shell script that caches the results of configure
@@ -7562,11 +7683,6 @@ do
     "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;;
     "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;;
     "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-    "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;;
-    "data/Makefile") CONFIG_FILES="$CONFIG_FILES data/Makefile" ;;
-    "doc/Makefile") CONFIG_FILES="$CONFIG_FILES doc/Makefile" ;;
-    "scripts/Makefile") CONFIG_FILES="$CONFIG_FILES scripts/Makefile" ;;
-    "doc/examples/Makefile") CONFIG_FILES="$CONFIG_FILES doc/examples/Makefile" ;;
     "lib/Makefile") CONFIG_FILES="$CONFIG_FILES lib/Makefile" ;;
 
   *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;;

configure.ac

 dnl Process this file with autoconf to produce a configure script.
 
 AC_INIT(crystfel, 0.2.0, taw@physics.org)
-AM_SILENT_RULES([yes])
-VERSION=AC_PACKAGE_VERSION
 AC_CONFIG_AUX_DIR([build-aux])
-
 AM_CONFIG_HEADER(config.h)
-AM_INIT_AUTOMAKE(crystfel, "$VERSION")
+AM_INIT_AUTOMAKE([subdir-objects])
 
 AC_PROG_CC
 gl_EARLY
+AM_PROG_CC_C_O
 AC_PROG_AWK
 AC_PROG_INSTALL
 AC_PROG_LN_S
 AC_PROG_RANLIB
-
+AM_SILENT_RULES([yes])
 
 AC_HEADER_STDC
 AC_CHECK_HEADERS([fcntl.h stdlib.h unistd.h])
@@ -151,6 +149,5 @@ CFLAGS="$CFLAGS $LIBTIFF_CFLAGS -D_GNU_SOURCE $libPNG_CFLAGS $Cairo_CFLAGS"
 LIBS="$LIBS $HDF5_LIBS -lm -lz $GSL_LIBS $GTK_LIBS $OPENCL_LIBS -pthread"
 LIBS="$LIBS $LIBTIFF_LIBS $libPNG_LIBS $Cairo_LIBS"
 
-AC_CONFIG_FILES(Makefile src/Makefile data/Makefile doc/Makefile)
-AC_CONFIG_FILES(scripts/Makefile doc/examples/Makefile lib/Makefile)
+AC_CONFIG_FILES(Makefile lib/Makefile)
 AC_OUTPUT