Added reporting of version number to all program and stream file

18 files changed, 175 insertions, 8 deletions

diff --git a/.gitignore b/.gitignore
index 5091a898..6fd9164e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -51,3 +51,4 @@ lib/.libs/
 lib/dummy.lo
 lib/libgnu.la
 libcrystfel/crystfel.pc
+version.h
diff --git a/Makefile.am b/Makefile.am
index a4efba1c..e9f427c7 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,5 +1,5 @@
 docdir = ${datadir}/doc/${PACKAGE}
-EXTRA_DIST = configure m4/gnulib-cache.m4
+EXTRA_DIST = configure m4/gnulib-cache.m4 version.sh version.h.in
 SUBDIRS = lib doc/reference/libcrystfel libcrystfel
 ACLOCAL_AMFLAGS = -I m4
 
@@ -184,3 +184,13 @@ EXTRA_DIST += $(script_DATA)
 
 
 DISTCHECK_CONFIGURE_FLAGS=--enable-gtk-doc
+
+mostlyclean-local: mostlyclean-version
+.PHONY: mostlyclean-version
+mostlyclean-version:
+	rm -f $(top_builddir)/version.h
+
+all: update_version_header
+.PHONY: version_header
+update_version_header:
+	$(top_srcdir)/version.sh $(top_srcdir)
diff --git a/libcrystfel/Makefile.am b/libcrystfel/Makefile.am
index 7d028b20..318dcd24 100644
--- a/libcrystfel/Makefile.am
+++ b/libcrystfel/Makefile.am
@@ -18,10 +18,11 @@ endif
 
 libcrystfel_la_includedir=$(includedir)/crystfel/
 
-libcrystfel_la_include_HEADERS = src/beam-parameters.h src/hdf5-file.h \
-                                 src/reflist.h src/symmetry.h src/cell.h \
-                                 src/reflist-utils.h src/thread-pool.h \
-                                 src/statistics.h src/utils.h src/detector.h \
+libcrystfel_la_include_HEADERS = ${top_srcdir}/version.h src/beam-parameters.h \
+                                 src/hdf5-file.h src/reflist.h src/symmetry.h \
+                                 src/cell.h src/reflist-utils.h \
+                                 src/thread-pool.h  src/statistics.h \
+                                 src/utils.h src/detector.h \
                                  src/geometry.h src/peaks.h src/stream.h \
                                  src/render.h src/index.h src/image.h \
                                  src/filters.h src/dirax.h src/mosflm.h \
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 4470d098..34c14573 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -42,6 +42,7 @@
 #include <sys/stat.h>
 #include <fcntl.h>
 
+#include "version.h"
 #include "cell.h"
 #include "cell-utils.h"
 #include "utils.h"
@@ -821,7 +822,7 @@ Stream *open_stream_fd_for_write(int fd)
 
 	fprintf(st->fh, "CrystFEL stream format %i.%i\n",
 	        st->major_version, st->minor_version);
-
+	fprintf(st->fh, "Generated by CrystFEL "CRYSTFEL_VERSIONSTRING"\n");
 	return st;
 }
 
diff --git a/src/ambigator.c b/src/ambigator.c
index bbc89c32..1c11578d 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -44,6 +44,7 @@
 #include <gsl/gsl_permutation.h>
 #include <gsl/gsl_randist.h>
 
+#include "version.h"
 #include <image.h>
 #include <utils.h>
 #include <symmetry.h>
@@ -63,6 +64,7 @@ static void show_help(const char *s)
 "\n"
 "  -h, --help                  Display this help message.\n"
 "\n"
+"      --version               Print CrystFEL version number and exit.\n"
 "  -o, --output=<filename>     Output stream.\n"
 "  -y, --symmetry=<sym>        Actual (\"target\") symmetry.\n"
 "  -w <sym>                    Apparent (\"source\" or \"twinned\") symmetry.\n"
@@ -824,6 +826,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,               10 },
 		{"output",             1, NULL,               'o'},
 		{"symmetry",           1, NULL,               'y'},
 		{"iterations",         1, NULL,               'n'},
@@ -852,6 +855,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 10 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'o' :
 			outfile = strdup(optarg);
 			break;
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index 1087ce54..0df5032c 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -40,6 +40,7 @@
 #include <gdk/gdkkeysyms.h>
 #include <gsl/gsl_multifit_nlin.h>
 
+#include "version.h"
 #include "stream.h"
 #include "image.h"
 #include "utils.h"
@@ -55,6 +56,8 @@ static void show_help(const char *s)
 "Examine cell parameter histograms.\n"
 "\n"
 " -h, --help              Display this help message.\n"
+"     --version           Print CrystFEL version number and exit.\n"
+
 );
 }
 
@@ -1214,6 +1217,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                1 },
 		{0, 0, NULL, 0}
 	};
 
@@ -1227,6 +1231,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 1 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			default :
 			return 1;
 
diff --git a/src/check_hkl.c b/src/check_hkl.c
index 1ba55313..dc376779 100644
--- a/src/check_hkl.c
+++ b/src/check_hkl.c
@@ -39,6 +39,7 @@
 #include <getopt.h>
 #include <gsl/gsl_fit.h>
 
+#include "version.h"
 #include "utils.h"
 #include "statistics.h"
 #include "symmetry.h"
@@ -54,6 +55,7 @@ static void show_help(const char *s)
 "Characterise an intensity list.\n"
 "\n"
 "  -h, --help                 Display this help message.\n"
+"      --version              Print CrystFEL version number and exit.\n"
 "  -y, --symmetry=<sym>       The symmetry of the input file.\n"
 "  -p, --pdb=<filename>       PDB file to use.\n"
 "      --rmin=<res>           Low resolution cutoff (1/d in m^-1).\n"
@@ -710,6 +712,7 @@ int main(int argc, char *argv[])
 	const struct option longopts[] = {
 
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                9 },
 		{"symmetry",           1, NULL,               'y'},
 		{"pdb",                1, NULL,               'p'},
 
@@ -738,6 +741,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 9 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'y' :
 			sym_str = strdup(optarg);
 			break;
diff --git a/src/compare_hkl.c b/src/compare_hkl.c
index d2173aff..e10b93aa 100644
--- a/src/compare_hkl.c
+++ b/src/compare_hkl.c
@@ -42,13 +42,13 @@
 #include <gsl/gsl_errno.h>
 #include <gsl/gsl_statistics.h>
 
+#include "version.h"
 #include "utils.h"
 #include "statistics.h"
 #include "symmetry.h"
 #include "reflist-utils.h"
 #include "cell-utils.h"
 
-
 enum fom
 {
 	FOM_R1I,
@@ -109,6 +109,7 @@ static void show_help(const char *s)
 "      --intensity-shells     Use shells of intensity instead of resolution.\n"
 "\n"
 "  -h, --help                 Display this help message.\n"
+"      --version              Print CrystFEL version number and exit.\n"
 );
 }
 
@@ -935,6 +936,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,               10 },
 		{"symmetry",           1, NULL,               'y'},
 		{"pdb",                1, NULL,               'p'},
 		{"rmin",               1, NULL,                2},
@@ -962,6 +964,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 10 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'y' :
 			sym_str = strdup(optarg);
 			break;
diff --git a/src/get_hkl.c b/src/get_hkl.c
index ae82858c..caeccd60 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -38,6 +38,7 @@
 #include <unistd.h>
 #include <getopt.h>
 
+#include "version.h"
 #include "utils.h"
 #include "reflist-utils.h"
 #include "symmetry.h"
@@ -53,6 +54,7 @@ static void show_help(const char *s)
 "Manipulate reflection lists.\n"
 "\n"
 "  -h, --help                 Display this help message.\n"
+"      --version              Print CrystFEL version number and exit.\n"
 "\n"
 "  -i, --input=<file>         Read reflections from <file>.\n"
 "  -y, --symmetry=<sym>       The symmetry of the input reflection list.\n"
@@ -418,6 +420,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                5 },
 		{"template",           1, NULL,               't'},
 		{"poisson",            0, &config_poisson,     1},
 		{"noise",              0, &config_noise,       1},
@@ -446,6 +449,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 5 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 't' :
 			template = strdup(optarg);
 			break;
diff --git a/src/hdfsee.c b/src/hdfsee.c
index ea6de2b2..fa10cfa6 100644
--- a/src/hdfsee.c
+++ b/src/hdfsee.c
@@ -37,6 +37,7 @@
 #include <gtk/gtk.h>
 #include <getopt.h>
 
+#include "version.h"
 #include "dw-hdfsee.h"
 #include "utils.h"
 #include "render.h"
@@ -54,6 +55,7 @@ static void show_help(const char *s)
 "Quick HDF5 image viewer.\n"
 "\n"
 "  -h, --help                       Display this help message.\n"
+"      --version                    Print CrystFEL version number and exit.\n"
 "\n"
 "  -p, --peak-overlay=<filename>    Draw circles in positions listed in file.\n"
 "      --ring-size=<n>              Set the size for those circles.\n"
@@ -131,6 +133,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                4 },
 		{"peak-overlay",       1, NULL,               'p'},
 		{"int-boost",          1, NULL,               'i'},
 		{"binning",            1, NULL,               'b'},
@@ -168,6 +171,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 4 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'p' :
 			peaks = strdup(optarg);
 			break;
diff --git a/src/indexamajig.c b/src/indexamajig.c
index c41b1487..143a0d82 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -54,6 +54,7 @@
 #include <sys/time.h>
 #endif
 
+#include "version.h"
 #include "utils.h"
 #include "hdf5-file.h"
 #include "index.h"
@@ -78,6 +79,7 @@ static void show_help(const char *s)
 "Process and index FEL diffraction images.\n"
 "\n"
 " -h, --help               Display this help message.\n"
+"     --version            Print CrystFEL version number and exit.\n"
 "\n"
 " -i, --input=<filename>   Specify file containing list of images to process.\n"
 "                           '-' means stdin, which is the default.\n"
@@ -247,6 +249,7 @@ int main(int argc, char *argv[])
 		{"image",              1, NULL,               'e'},
 
 		/* Long-only options with no arguments */
+		{"version",            0, NULL,                     20},
 		{"filter-noise",       0, &iargs.noisefilter,        1},
 		{"no-check-prefix",    0, &config_checkprefix,       0},
 		{"basename",           0, &config_basename,          1},
@@ -296,6 +299,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 20 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'i' :
 			filename = strdup(optarg);
 			break;
diff --git a/src/partial_sim.c b/src/partial_sim.c
index e1e0a4b4..17603d70 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -41,6 +41,7 @@
 #include <pthread.h>
 #include <gsl/gsl_rng.h>
 
+#include "version.h"
 #include "image.h"
 #include "utils.h"
 #include "reflist-utils.h"
@@ -214,7 +215,8 @@ static void show_help(const char *s)
 	printf(
 "Generate a stream containing partials from a reflection list.\n"
 "\n"
-" -h, --help              Display this help message.\n"
+" -h, --help               Display this help message.\n"
+"     --version            Print CrystFEL version number and exit.\n"
 "\n"
 "You need to provide the following basic options:\n"
 " -i, --input=<file>       Read reflections from <file>.\n"
@@ -440,6 +442,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                8 },
 		{"output",             1, NULL,               'o'},
 		{"input",              1, NULL,               'i'},
 		{"beam",               1, NULL,               'b'},
@@ -471,6 +474,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 8 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'i' :
 			input_file = strdup(optarg);
 			break;
diff --git a/src/partialator.c b/src/partialator.c
index c1dedad8..e6069057 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -51,6 +51,7 @@
 #include <reflist.h>
 #include <reflist-utils.h>
 
+#include "version.h"
 #include "post-refinement.h"
 #include "hrs-scaling.h"
 #include "scaling-report.h"
@@ -63,6 +64,7 @@ static void show_help(const char *s)
 "Scaling and post refinement for coherent nanocrystallography.\n"
 "\n"
 "  -h, --help                 Display this help message.\n"
+"      --version              Print CrystFEL version number and exit.\n"
 "\n"
 "  -i, --input=<filename>     Specify the name of the input 'stream'.\n"
 "  -o, --output=<filename>    Output filename.  Default: partialator.hkl.\n"
@@ -353,6 +355,7 @@ int main(int argc, char *argv[])
 	const struct option longopts[] = {
 
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                3 },
 		{"input",              1, NULL,               'i'},
 		{"output",             1, NULL,               'o'},
 		{"symmetry",           1, NULL,               'y'},
@@ -388,6 +391,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 3 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'i' :
 			infile = strdup(optarg);
 			break;
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index b8cc1c68..fca12bab 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -40,6 +40,7 @@
 #include <unistd.h>
 #include <getopt.h>
 
+#include "version.h"
 #include "image.h"
 #include "diffraction.h"
 #include "diffraction-gpu.h"
@@ -65,6 +66,7 @@ static void show_help(const char *s)
 "pulses of X-rays from a free electron laser.\n"
 "\n"
 " -h, --help                Display this help message.\n"
+"     --version             Print CrystFEL version number and exit.\n"
 "\n"
 " -p, --pdb=<file>          PDB file from which to get the unit cell.\n"
 "                            (The actual Bragg intensities come from the\n"
@@ -261,6 +263,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                7 },
 		{"gpu",                0, &config_gpu,         1},
 		{"random-orientation", 0, NULL,               'r'},
 		{"number",             1, NULL,               'n'},
@@ -297,6 +300,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 7 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'r' :
 			config_randomquat = 1;
 			break;
diff --git a/src/process_hkl.c b/src/process_hkl.c
index d5fba397..1916a1ae 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -41,6 +41,7 @@
 #include <unistd.h>
 #include <getopt.h>
 
+#include "version.h"
 #include "utils.h"
 #include "statistics.h"
 #include "reflist-utils.h"
@@ -61,6 +62,7 @@ static void show_help(const char *s)
 "Assemble and process FEL Bragg intensities.\n"
 "\n"
 "  -h, --help                Display this help message.\n"
+"      --version             Print CrystFEL version number and exit.\n"
 "  -i, --input=<filename>    Specify input filename (\"-\" for stdin).\n"
 "  -o, --output=<filename>   Specify output filename for merged intensities\n"
 "                             Default: processed.hkl).\n"
@@ -452,6 +454,7 @@ int main(int argc, char *argv[])
 		{"min-res",            1, NULL,                5},
 		{"push-res",           1, NULL,                6},
 		{"res-push",           1, NULL,                6}, /* compat */
+		{"version",            0, NULL,                7},
 		{0, 0, NULL, 0}
 	};
 
@@ -554,6 +557,11 @@ int main(int argc, char *argv[])
 			push_res = push_res*1e9;
 			break;
 
+			case 7 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case '?' :
 			break;
 
diff --git a/src/render_hkl.c b/src/render_hkl.c
index 2eb9ef9a..bdf1bbe6 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -45,6 +45,7 @@
 #include <gsl/gsl_linalg.h>
 #include <gsl/gsl_blas.h>
 
+#include "version.h"
 #include "utils.h"
 #include "symmetry.h"
 #include "render.h"
@@ -96,6 +97,7 @@ static void show_help(const char *s)
 "                           current directory.\n"
 "\n"
 "  -h, --help              Display this help message.\n"
+"      --version           Print CrystFEL version and exit.\n"
 );
 }
 
@@ -764,6 +766,7 @@ int main(int argc, char *argv[])
 	/* Long options */
 	const struct option longopts[] = {
 		{"help",               0, NULL,               'h'},
+		{"version",            0, NULL,                5 },
 		{"zone-axis",          0, &config_zawhinge,    1},
 		{"output",             1, NULL,               'o'},
 		{"pdb",                1, NULL,               'p'},
@@ -791,6 +794,11 @@ int main(int argc, char *argv[])
 			show_help(argv[0]);
 			return 0;
 
+			case 5 :
+			printf("CrystFEL: " CRYSTFEL_VERSIONSTRING "\n");
+			printf(CRYSTFEL_BOILERPLATE"\n");
+			return 0;
+
 			case 'p' :
 			pdb = strdup(optarg);
 			break;
diff --git a/version.h.in b/version.h.in
new file mode 100644
index 00000000..6451a0d9
--- /dev/null
+++ b/version.h.in
@@ -0,0 +1,33 @@
+/*
+ * CrystFEL version header
+ *
+ * Copyright © 2014 Deutsches Elektronen-Synchrotron DESY,
+ *                  a research centre of the Helmholtz Association.
+ *
+ * Author:
+ *   2014 Valerio Mariani <valerio.mariani@desy.de>
+ *
+ * This file is part of CrystFEL.
+ *
+ * CrystFEL 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 3 of the License, or
+ * (at your option) any later version.
+ *
+ * CrystFEL 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 CrystFEL.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#define CRYSTFEL_VERSIONSTRING "$u$$e$"
+#define CRYSTFEL_BOILERPLATE \
+"License GPLv3+: GNU GPL version 3 or later"\
+" <http://gnu.org/licenses/gpl.html>.\n"\
+"This is free software: you are free to change and redistribute it.\n"\
+"There is NO WARRANTY, to the extent permitted by law.\n\n"\
+"Written by Thomas White and others."
diff --git a/version.sh b/version.sh
new file mode 100755
index 00000000..1be14f69
--- /dev/null
+++ b/version.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+
+top_srcdir=$1
+
+CRYSTFEL_BASE_VERSION=$( cf=( `grep PACKAGE_VERSION config.h` ); echo ${cf[2]} | sed -n 's/"//gp' )
+sed 's/\$u\$/'${CRYSTFEL_BASE_VERSION}'/g' $top_srcdir/version.h.in > version1.tmp
+command -v git > /dev/null 2>&1
+if [ $? -eq 0 ]; then
+  if [ -d ".git" ]; then
+    git log -1 --pretty=%B | grep 'This is CrystFEL' > /dev/null
+    if [ $? -eq 0 ]; then
+      CRYSTFEL_GIT_COMMIT=""
+    else
+      CRYSTFEL_GIT_COMMIT="+"`git rev-parse HEAD`
+    fi
+  fi
+fi
+sed 's/\$e\$/'${CRYSTFEL_GIT_COMMIT}'/g' version1.tmp > version2.tmp
+diff version.h version2.tmp > /dev/null
+if [ $? -ne 0 ]; then
+  mv version2.tmp version.h
+  rm version1.tmp
+else
+  rm version1.tmp version2.tmp
+fi