adding build versions and consistent version function across modules

dentearl · Sep 6, 2012 · 79cb943 · 79cb943
1 parent 1d76f6e
commit 79cb943
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Showing 22 changed files with 203 additions and 87 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,4 @@ bin
 *.o
 *.pyc
 *.a
+buildVersion*
diff --git a/mafComparator/src/createVersionSources.py → include/createVersionSources.py b/mafComparator/src/createVersionSources.py → include/createVersionSources.py
@@ -34,7 +34,6 @@
  */
 '''
 g_git = mtt.which('git')
-
 def runCommand(cmd):
     p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
     pout, perr = p.communicate()
@@ -47,7 +46,6 @@ def getBranch():
             return b[2:]
 def getSha():
     return runCommand([g_git, 'rev-parse', 'HEAD']).strip()
-
 def writeHeader(location):
     f = open(os.path.join(location, 'buildVersion.h'), 'w')
     f.write(g_BoilerPlate)
@@ -58,7 +56,6 @@ def writeHeader(location):
     f.write('extern const char g_build_git_sha[];\n')
     f.write('#endif // _BUILD_VERSION_H_\n')
     f.close()
-
 def writeSource(location, buildDate, buildBranch, buildSha):
     f = open(os.path.join(location, 'buildVersion.c'), 'w')
     f.write(g_BoilerPlate)
@@ -67,7 +64,6 @@ def writeSource(location, buildDate, buildBranch, buildSha):
     f.write('const char g_build_git_branch[] = "%s";\n' % buildBranch)
     f.write('const char g_build_git_sha[] = "%s";\n' % buildSha)
     f.close()
-
 def main():
     location = os.path.join(os.curdir, 'src')
     buildDate = time.strftime('%Y-%m-%dT%H:%M%Z', time.localtime()) # gmtime()

diff --git a/mafBlockDuplicateFilter/Makefile b/mafBlockDuplicateFilter/Makefile
@@ -4,12 +4,14 @@ args = -Wall -Wextra -Werror -std=c99 -pedantic -I ../external -I ../include
 bin = ../bin
 PROGS = mafBlockDuplicateFilter
 dependencies = $(wildcard ../include/common.*) $(wildcard ../include/sharedMaf.*)
-objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a
-testObjects := test/sharedMaf.o test/common.o ../external/CuTest.a 
+objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a src/buildVersion.o
+testObjects := test/sharedMaf.o test/common.o ../external/CuTest.a  test/buildVersion.o
 
-.PHONY: all clean test
+.PHONY: all clean test buildVersion
 
-all: $(foreach f,${PROGS}, ${bin}/$f)
+all: buildVersion $(foreach f,${PROGS}, ${bin}/$f)
+buildVersion:
+	@python ../include/createVersionSources.py
 
 ${bin}/mafBlockDuplicateFilter: src/mafBlockDuplicateFilter.c ${dependencies} ${objects}
 	mkdir -p $(dir $@)

diff --git a/mafBlockDuplicateFilter/src/mafBlockDuplicateFilter.c b/mafBlockDuplicateFilter/src/mafBlockDuplicateFilter.c
@@ -31,6 +31,9 @@
 #include <string.h>
 #include "common.h"
 #include "sharedMaf.h"
+#include "buildVersion.h"
+
+const char *g_version = "version 0.1 September 2012";
 
 typedef struct scoredMafLine {
     // augmented data structure
@@ -47,6 +50,7 @@ typedef struct duplicate {
 } duplicate_t;
 
 void usage(void);
+void version(void);
 void processBody(mafFileApi_t *mfa);
 void checkBlock(mafBlock_t *block);
 // void destroyBlock(mafLine_t *m);
@@ -63,20 +67,25 @@ void parseOptions(int argc, char **argv, char *filename) {
     int c;
     int setMName = 0;
     while (1) {
-        static struct option long_options[] = {
+        static struct option longOptions[] = {
             {"debug", no_argument, 0, 'd'},
             {"verbose", no_argument, 0, 'v'},
             {"help", no_argument, 0, 'h'},
+            {"version", no_argument, 0, 0},
             {"maf",  required_argument, 0, 'm'},            
             {0, 0, 0, 0}
         };
-        int option_index = 0;
+        int longIndex = 0;
         c = getopt_long(argc, argv, "d:m:h:v",
-                        long_options, &option_index);
+                        longOptions, &longIndex);
         if (c == -1)
             break;
         switch (c) {
         case 0:
+            if (strcmp("version", longOptions[longIndex].name) == 0) {
+                version();
+                exit(EXIT_SUCCESS);
+            }
             break;
         case 'm':
             setMName = 1;
@@ -113,7 +122,12 @@ void parseOptions(int argc, char **argv, char *filename) {
         usage();
     }
 }
+void version(void) {
+    fprintf(stderr, "mafBlockDuplicateFilter, %s\nbuild: %s, %s, %s\n\n", g_version, g_build_date, 
+            g_build_git_branch, g_build_git_sha);
+}
 void usage(void) {
+    version();
     fprintf(stderr, "Usage: mafBlockDuplicateFilter --maf mafWithDuplicates.maf > pruned.maf \n\n"
             "mafBlockDuplicateFilter is a program to filter out duplications from a Multiple \n"
             "Alignment Format (maf) file. This program assumes the sequence name field is \n"

diff --git a/mafBlockExtractor/Makefile b/mafBlockExtractor/Makefile
@@ -4,13 +4,15 @@ args = -Wall -Wextra -std=c99 -pedantic -I ../external -I ../include
 bin = ../bin
 PROGS = mafBlockExtractor
 dependencies = $(wildcard ../include/common.*) $(wildcard ../include/sharedMaf.*) src/mafBlockExtractor.h
-API = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a src/mafBlockExtractorAPI.o
-testAPI = test/sharedMaf.o ../external/CuTest.a test/common.o test/mafBlockExtractorAPI.o
+API = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a src/mafBlockExtractorAPI.o src/buildVersion.o
+testAPI = test/sharedMaf.o ../external/CuTest.a test/common.o test/mafBlockExtractorAPI.o test/buildVersion.o
 testObjects := test/test.mafBlockExtractor.o
 
-.PHONY: all clean test
+.PHONY: all clean test buildVersion
 
-all: $(foreach f,${PROGS}, ${bin}/$f)
+all: buildVersion $(foreach f,${PROGS}, ${bin}/$f)
+buildVersion:
+	@python ../include/createVersionSources.py
 
 ${bin}/mafBlockExtractor: src/mafBlockExtractor.c ${dependencies} ${API}
 	mkdir -p $(dir $@)

diff --git a/mafBlockExtractor/src/mafBlockExtractor.c b/mafBlockExtractor/src/mafBlockExtractor.c
@@ -32,8 +32,16 @@
 #include "sharedMaf.h"
 #include "mafBlockExtractor.h"
 #include "mafBlockExtractorAPI.h"
+#include "buildVersion.h"
 
+const char *g_version = "version 0.2 September 2012";
+
+void version(void) {
+    fprintf(stderr, "mafBlockExtractor, %s\nbuild: %s, %s, %s\n\n", g_version, g_build_date, 
+            g_build_git_branch, g_build_git_sha);
+}
 void usage(void) {
+    version();
     fprintf(stderr, "Usage: mafBlockExtractor --maf [maf file] --seq [sequence name (and possibly chr)] "
             "--start [start of region, inclusive, 0 based] --stop [end of region, inclusive] "
             "[options]\n\n"
@@ -58,42 +66,46 @@ void parseOptions(int argc, char **argv, char *filename, char *seqName, uint32_t
     bool setSName = false, setStart = false, setStop = false, setMName = false;
     int32_t value = 0;
     while (1) {
-        static struct option long_options[] = {
+        static struct option longOptions[] = {
             {"debug", no_argument, 0, 'd'},
             {"verbose", no_argument, 0, 'v'},
             {"help", no_argument, 0, 'h'},
+            {"version", no_argument, 0, 0},
             {"maf", required_argument, 0, 'm'},
             {"seq", required_argument, 0, 's'},
             {"start", required_argument, 0, 0},
             {"stop", required_argument, 0, 0},
             {"soft", no_argument, 0, 0},
             {0, 0, 0, 0}
         };
-        int option_index = 0;
+        int longIndex = 0;
         c = getopt_long(argc, argv, "m:s:h:v:d",
-                        long_options, &option_index);
+                        longOptions, &longIndex);
         if (c == -1)
             break;
         switch (c) {
         case 0:
-            if (strcmp("start", long_options[option_index].name) == 0) {
+            if (strcmp("start", longOptions[longIndex].name) == 0) {
                 value = strtoll(optarg, NULL, 10);
                 if (value < 0) {
                     fprintf(stderr, "Error, --start %d must be nonnegative.\n", value);
                     usage();
                 }
                 *start = value;
                 setStart = true;
-            } else if (strcmp("stop", long_options[option_index].name) == 0) {
+            } else if (strcmp("stop", longOptions[longIndex].name) == 0) {
                 value = strtoll(optarg, NULL, 10);
                 if (value < 0) {
                     fprintf(stderr, "Error, --stop %d must be nonnegative.\n", value);
                     usage();
                 }
                 *stop = value;
                 setStop = true;
-            } else if (strcmp("soft", long_options[option_index].name) == 0) {
+            } else if (strcmp("soft", longOptions[longIndex].name) == 0) {
                 *isSoft = true;
+            } else if (strcmp("version", longOptions[longIndex].name) == 0) {
+                version();
+                exit(EXIT_SUCCESS);
             }
             break;
         case 'm':

diff --git a/mafBlockExtractor/src/mafBlockExtractor.h b/mafBlockExtractor/src/mafBlockExtractor.h
@@ -30,6 +30,7 @@
 #include "common.h"
 #include "sharedMaf.h"
 
+void version(void);
 void usage(void);
 void parseOptions(int argc, char **argv, char *filename, char *seqName, uint32_t *start, 
                   uint32_t *stop, bool *isSoft);

diff --git a/mafBlockFilter/Makefile b/mafBlockFilter/Makefile
@@ -4,12 +4,14 @@ args = -Wall -Wextra -Werror -std=c99 -pedantic -I ../external -I ../include
 bin = ../bin
 PROGS = mafBlockFilter
 dependencies = $(wildcard ../include/common.*) $(wildcard ../include/sharedMaf.*)
-objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a
-testObjects = ./test/common.o ./test/sharedMaf.o ../external/CuTest.a
+objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a src/buildVersion.o
+testObjects = test/common.o test/sharedMaf.o ../external/CuTest.a test/buildVersion.o
 
-.PHONY: all clean test
+.PHONY: all clean test buildVersion
 
-all: $(foreach f,${PROGS}, ${bin}/$f)
+all: buildVersion $(foreach f,${PROGS}, ${bin}/$f)
+buildVersion:
+	@python ../include/createVersionSources.py
 
 ${bin}/mafBlockFilter: src/mafBlockFilter.c ${dependencies} ${objects}
 	mkdir -p $(dir $@)

diff --git a/mafBlockFilter/src/mafBlockFilter.c b/mafBlockFilter/src/mafBlockFilter.c
@@ -36,13 +36,22 @@
 #include <unistd.h>
 #include "common.h"
 #include "sharedMaf.h"
+#include "buildVersion.h"
 
+const char *g_version = "version 0.1 September 2012";
+
+void version(void);
 void usage(void);
 void parseOptions(int argc, char **argv, char *filename, char *nameList, bool *isInclude, int64_t *blockDegLT, int64_t *blockDegGT);
 void checkRegion(unsigned lineno, char *fullname, uint32_t pos, uint32_t start, 
                  uint32_t length, uint32_t sourceLength, char strand);
 
+void version(void) {
+    fprintf(stderr, "mafBlockFilter, %s\nbuild: %s, %s, %s\n\n", g_version, g_build_date, 
+            g_build_git_branch, g_build_git_sha);
+}
 void usage(void) {
+    version();
     fprintf(stderr, "Usage: mafBlockFilter --maf [path to maf] "
             "[options]\n\n"
             "mafBlockFilter is a program that will look through a\n"
@@ -68,25 +77,30 @@ void parseOptions(int argc, char **argv, char *filename, char *nameList, bool *i
     int c;
     bool setMafName = false, setNames = false, setBlockLimits = false;
     while (1) {
-        static struct option long_options[] = {
+        static struct option longOptions[] = {
             {"debug", no_argument, &g_debug_flag, 1},
             {"verbose", no_argument, 0, 'v'},
             {"help", no_argument, 0, 'h'},
+            {"version", no_argument, 0, 0},
             {"maf",  required_argument, 0, 'm'},
             {"includeSeq",  required_argument, 0, 'i'},
             {"excludeSeq",  required_argument, 0, 'e'},
             {"noDegreeGT", required_argument, 0, 'g'},
             {"noDegreeLT", required_argument, 0, 'l'},
             {0, 0, 0, 0}
         };
-        int option_index = 0;
+        int longIndex = 0;
         c = getopt_long(argc, argv, "m:i:e:g:l:v:h",
-                        long_options, &option_index);
+                        longOptions, &longIndex);
         if (c == -1) {
             break;
         }
         switch (c) {
         case 0:
+            if (strcmp("version", longOptions[longIndex].name) == 0) {
+                version();
+                exit(EXIT_SUCCESS);
+            }
             break;
         case 'm':
             setMafName = true;

diff --git a/mafBlockFinder/Makefile b/mafBlockFinder/Makefile
@@ -4,12 +4,14 @@ args = -Wall -Wextra -std=c99 -pedantic -I ../external -I ../include
 bin = ../bin
 PROGS = mafBlockFinder
 dependencies = $(wildcard ../include/common.*) $(wildcard ../include/sharedMaf.*)
-objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a
-testObjects = test/common.o test/sharedMaf.o ../external/CuTest.a
+objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a src/buildVersion.o
+testObjects = test/common.o test/sharedMaf.o ../external/CuTest.a test/buildVersion.o
 
-.PHONY: all clean test
+.PHONY: all clean test buildVersion
 
-all: $(foreach f,${PROGS}, ${bin}/$f)
+all: buildVersion $(foreach f,${PROGS}, ${bin}/$f)
+buildVersion:
+	@python ../include/createVersionSources.py
 
 ${bin}/mafBlockFinder: src/mafBlockFinder.c ${dependencies} ${objects}
 	mkdir -p $(dir $@)

diff --git a/mafBlockFinder/src/mafBlockFinder.c b/mafBlockFinder/src/mafBlockFinder.c
@@ -37,14 +37,23 @@
 #include <unistd.h>
 #include "common.h"
 #include "sharedMaf.h"
+#include "buildVersion.h"
 
+const char *g_version = "version 0.1 September 2012";
+
+void version(void);
 void usage(void);
 void parseOptions(int argc, char **argv, char *filename, char *seqName, uint32_t *position);
 void checkRegion(unsigned lineno, char *fullname, uint32_t pos, uint32_t start, 
                  uint32_t length, uint32_t sourceLength, char strand);
 void searchInput(mafFileApi_t *mfa, char *fullname, unsigned long pos);
 
+void version(void) {
+    fprintf(stderr, "mafBlockDuplicateFilter, %s\nbuild: %s, %s, %s\n\n", g_version, g_build_date, 
+            g_build_git_branch, g_build_git_sha);
+}
 void usage(void) {
+    version();
     fprintf(stderr, "Usage: mafBlockFinder --maf [path to maf] "
             "--seq [sequence name (and possibly chr)] "
             "--pos [position to search for, zero based coords] [options]\n\n"
@@ -72,6 +81,7 @@ void parseOptions(int argc, char **argv, char *filename, char *seqName, uint32_t
             {"debug", no_argument, &g_debug_flag, 1},
             {"verbose", no_argument, 0, 'v'},
             {"help", no_argument, 0, 'h'},
+            {"version", no_argument, 0, 0},
             {"maf",  required_argument, 0, 'm'},
             {"seq",  required_argument, 0, 's'},
             {"sequence",  required_argument, 0, 's'},
@@ -87,6 +97,10 @@ void parseOptions(int argc, char **argv, char *filename, char *seqName, uint32_t
         }
         switch (c) {
         case 0:
+            if (strcmp("version", long_options[option_index].name) == 0) {
+                version();
+                exit(EXIT_SUCCESS);
+            }
             break;
         case 'm':
             setMName = 1;

diff --git a/mafBlockSorter/Makefile b/mafBlockSorter/Makefile
@@ -4,12 +4,14 @@ args = -Wall -Wextra -Werror -std=c99 -pedantic -I ../external -I ../include
 bin = ../bin
 PROGS = mafBlockSorter
 dependencies = $(wildcard ../include/common.*) $(wildcard ../include/sharedMaf.*)
-objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a
-testObjects = ./test/common.o ./test/sharedMaf.o ../external/CuTest.a
+objects = ../include/common.o ../include/sharedMaf.o ../external/CuTest.a src/buildVersion.o
+testObjects = ./test/common.o ./test/sharedMaf.o ../external/CuTest.a test/buildVersion.o
 
-.PHONY: all clean test
+.PHONY: all clean test buildVersion
 
-all: $(foreach f,${PROGS}, ${bin}/$f)
+all: buildVersion $(foreach f,${PROGS}, ${bin}/$f)
+buildVersion:
+	@python ../include/createVersionSources.py
 
 ${bin}/mafBlockSorter: src/mafBlockSorter.c ${dependencies} ${objects}
 	mkdir -p $(dir $@)
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,3 +2,4 @@ bin @@
     *.o
     *.pyc
     *.a
+    buildVersion*