Adjust header files to compile with submodules.

scripts/version_update.pl

@@ -0,0 +1,218 @@
+#!/usr/bin/env perl
+
+###############################################################################
+ #
+ #  This file is part of canu, a software program that assembles whole-genome
+ #  sequencing reads into contigs.
+ #
+ #  This software is based on:
+ #    'Canu' v2.0              (https://github.com/marbl/canu)
+ #  which is based on:
+ #    'Celera Assembler' r4587 (http://wgs-assembler.sourceforge.net)
+ #    the 'kmer package' r1994 (http://kmer.sourceforge.net)
+ #
+ #  Except as indicated otherwise, this is a 'United States Government Work',
+ #  and is released in the public domain.
+ #
+ #  File 'README.licenses' in the root directory of this distribution
+ #  contains full conditions and disclaimers.
+ ##
+
+use strict;
+use File::Compare;
+use Cwd qw(getcwd);
+
+my $cwd = getcwd();
+
+#  This script expects a module name on the command line, e.g.,
+#  'version-update.pl canu'.  This name is used is the non-git based version
+#  string.
+#
+#  On release change $label to 'release', update $major and $minor.  Make the
+#  release, then change label back to 'snapshot'.  This will result in the
+#  released code having a version string of "$modName 1.9".
+
+my $modName  = shift @ARGV;
+my $MODNAME  = $modName;       $MODNAME =~ tr/a-z-/A-Z_/;
+
+my $verFile  = shift @ARGV;
+
+my $label    = "snapshot";      #  If not 'release' print this in the version output.
+my $major    = "2";             #  Bump before release.
+my $minor    = "0";             #  Bump before release.
+
+my $branch   = "master";
+my $version  = "v$major.$minor";
+
+my @submodules;
+
+my $commits  = undef;
+my $hash1    = undef;          #  This from 'git describe'
+my $hash2    = undef;          #  This from 'git rev-list'
+my $revCount = 0;
+my $dirty    = undef;
+my $dirtya   = undef;
+my $dirtyc   = undef;
+
+#  Required module name on the command line.
+
+if (($modName eq "") || ($modName eq undef) || ($verFile eq undef)) {
+    die "usage: $0 module-name version-file.H\n";
+}
+
+#  If in a git repo, we can get the actual values.
+
+if (-d "../.git") {
+    $label = "snapshot";
+
+    #  Count the number of changes since the last release.
+    open(F, "git rev-list HEAD |") or die "Failed to run 'git rev-list'.\n";
+    while (<F>) {
+        chomp;
+
+        $hash2 = $_  if (!defined($hash2));
+        $revCount++;
+    }
+    close(F);
+
+    #  Find the commit and version we're at.
+    open(F, "git describe --tags --long --always --abbrev=40 |") or die "Failed to run 'git describe'.\n";
+    while (<F>) {
+        chomp;
+        if (m/^v(\d+)\.(.+)-(\d+)-g(.{40})$/) {
+            $major   = $1;
+            $minor   = $2;
+            $commits = $3;
+            $hash1   = $4;
+
+            $version = "v$major.$minor";
+        } else {
+            die "Failed to parse describe string '$_'.\n";
+        }
+    }
+    close(F);
+
+    #  Decide if we've got locally committed changes.
+    open(F, "git status |");
+    while (<F>) {
+        if (m/is\s+ahead\s/) {
+            $dirtya = "ahead of github";
+        }
+        if (m/not\s+staged\s+for\s+commit/) {
+            $dirtyc = "uncommitted changes";
+        }
+    }
+    close(F);
+
+    if    (defined($dirtya) && defined($dirtyc)) {
+        $dirty = "ahead of github w/changes";
+    }
+    elsif (defined($dirtya)) {
+        $dirty = "ahead of github";
+    }
+    elsif (defined($dirtyc)) {
+        $dirty = "w/changes";
+    }
+    else {
+        $dirty = "sync'd with github";
+    }
+
+
+    #  But if we're on a branch, replace the version with the name of the branch.
+    open(F, "git rev-parse --abbrev-ref HEAD |");
+    while (<F>) {
+        chomp;
+        $branch  = $_;
+    }
+
+    if ($branch ne "master") {
+        if ($branch =~ m/v(\d+)\.(\d+)/) {
+            $major = $1;
+            $minor = $2;
+        }
+
+        $label   = "branch";
+        $version = $branch;
+    }
+
+
+    #  Get information on any submodules here.
+    open(F, "git submodule status |");
+    while (<F>) {
+        if (m/^(.*)\s+(.*)\s+\((.*)\)$/) {
+            push @submodules, "$2 $3 $1";
+        }
+    }
+    close(F);
+}
+
+
+#  If not in a git repo, we might be able to figure things out based on the directory name.
+
+elsif ($cwd =~ m/$modName-(.{40})\/src/) {
+    $label   = "snapshot";
+    $hash1   = $1;
+    $hash2   = $1;
+}
+
+elsif ($cwd =~ m/$modName-master\/src/) {
+    $label   = "master-snapshot";
+}
+
+
+#  Report what we found.  This is really for the gmake output.
+
+if (defined($commits)) {
+    print STDERR "Building $label $version +$commits changes (r$revCount $hash1) ($dirty)\n";
+    foreach my $s (@submodules) {
+        print STDERR "         $s\n";
+    }
+    print STDERR "\n";
+} else {
+    print STDERR "Building $label $version\n";
+    print STDERR "\n";
+}
+
+#  Dump a new file, but don't overwrite the original.
+
+open(F, "> ${verFile}.new") or die "Failed to open '${verFile}.new' for writing: $!\n";
+print F "//  Automagically generated by version_update.pl!  Do not commit!\n";
+print F "#define ${MODNAME}_VERSION_LABEL     \"$label\"\n";
+print F "#define ${MODNAME}_VERSION_MAJOR     \"$major\"\n";
+print F "#define ${MODNAME}_VERSION_MINOR     \"$minor\"\n";
+print F "#define ${MODNAME}_VERSION_COMMITS   \"$commits\"\n";
+print F "#define ${MODNAME}_VERSION_REVISION  \"$revCount\"\n";
+print F "#define ${MODNAME}_VERSION_HASH      \"$hash1\"\n";
+print F "\n";
+
+if      (defined($commits)) {
+    print F "#define ${MODNAME}_VERSION           \"$modName $label $version +$commits changes (r$revCount $hash1)\\n\"\n";
+} elsif (defined($hash1)) {
+    print F "#define ${MODNAME}_VERSION           \"$modName snapshot ($hash1)\\n\"\n";
+} elsif ($label  =~ m/release/) {
+    print F "#define ${MODNAME}_VERSION           \"$modName $major.$minor\\n\"\n";
+} else {
+    print F "#define ${MODNAME}_VERSION           \"$modName $label ($version)\\n\"\n";
+}
+
+if ($MODNAME ne "MERYL_UTILITY") {
+    print F "\n";
+    print F "#undef  MERYL_UTILITY_VERSION\n";
+    print F "#define MERYL_UTILITY_VERSION ${MODNAME}_VERSION\n";
+}
+
+close(F);
+
+#  If they're the same, don't replace the original.
+
+if (compare("${verFile}", "${verFile}.new") == 0) {
+    unlink "${verFile}.new";
+} else {
+    unlink "${verFile}";
+    rename "${verFile}.new", "${verFile}";
+}
+
+#  That's all, folks!
+
+exit(0);
+

src/Makefile

@@ -730,9 +730,7 @@ $(foreach TGT,${ALL_TGTS},\
 #  A fake target, to regenerate the canu_version.H file on every build.
 .PHONY: UPDATE_VERSION
 UPDATE_VERSION:
-	@./canu_version_update.pl
-
-AS_global.C: UPDATE_VERSION
+	@../scripts/version_update.pl canu utility/src/utility/version.H
 
 #  A fake target, to make the directory for the canu perl modules.
 .PHONY: MAKE_DIRS

src/bogart/AS_BAT_AssemblyGraph.H

@@ -26,7 +26,7 @@
 #ifndef INCLUDE_AS_BAT_ASSEMBLYGRAPH
 #define INCLUDE_AS_BAT_ASSEMBLYGRAPH
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "AS_BAT_OverlapCache.H"
 #include "AS_BAT_BestOverlapGraph.H"  //  For ReadEnd
 #include "AS_BAT_Unitig.H"            //  For SeqInterval

src/bogart/AS_BAT_BestOverlapGraph.H

@@ -42,7 +42,7 @@
 #ifndef INCLUDE_AS_BAT_BESTOVERLAPGRAPH
 #define INCLUDE_AS_BAT_BESTOVERLAPGRAPH
 
-#include "AS_global.H"
+#include "runtime.H"
 
 #include "AS_BAT_ReadInfo.H"
 #include "AS_BAT_OverlapCache.H"

src/bogart/AS_BAT_ChunkGraph.H

@@ -38,7 +38,7 @@
 #ifndef INCLUDE_AS_BAT_CHUNKGRAPH
 #define INCLUDE_AS_BAT_CHUNKGRAPH
 
-#include "AS_global.H"
+#include "runtime.H"
 
 //  Returns a list of read IDs sorted by the number of reads in a BOG path
 //  seeded by that read.

src/bogart/AS_BAT_Logging.H

@@ -38,7 +38,7 @@
 #ifndef INCLUDE_AS_BAT_LOGGING
 #define INCLUDE_AS_BAT_LOGGING
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "files.H"
 
 void    setLogFile(char const *prefix, char const *name);

src/bogart/AS_BAT_MergeOrphans.H

@@ -30,7 +30,7 @@
 #ifndef INCLUDE_AS_BAT_MERGEORPHANS
 #define INCLUDE_AS_BAT_MERGEORPHANS
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "AS_BAT_BestOverlapGraph.H"
 #include "AS_BAT_Unitig.H"
 

src/bogart/AS_BAT_OptimizePositions.C

@@ -40,7 +40,7 @@
  *  full conditions and disclaimers for each license.
  */
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "AS_BAT_Unitig.H"
 #include "AS_BAT_ReadInfo.H"
 #include "AS_BAT_BestOverlapGraph.H"

src/bogart/AS_BAT_OverlapCache.H

@@ -42,7 +42,7 @@
 #ifndef INCLUDE_AS_BAT_OVERLAPCACHE
 #define INCLUDE_AS_BAT_OVERLAPCACHE
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "ovStore.H"
 #include "sqStore.H"
 

src/bogart/AS_BAT_ReadInfo.H

@@ -26,7 +26,7 @@
 #ifndef INCLUDE_AS_BAT_READ_INFO
 #define INCLUDE_AS_BAT_READ_INFO
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "ovStore.H"
 #include "sqStore.H"
 

src/bogart/AS_BAT_TigGraph.H

@@ -26,7 +26,7 @@
 #ifndef INCLUDE_AS_BAT_TIGGRAPH
 #define INCLUDE_AS_BAT_TIGGRAPH
 
-#include "AS_global.H"
+#include "runtime.H"
 
 #include "AS_BAT_Unitig.H"
 #include "AS_BAT_TigVector.H"

src/bogart/AS_BAT_TigVector.H

@@ -26,7 +26,7 @@
 #ifndef INCLUDE_AS_BAT_TIGVECTOR
 #define INCLUDE_AS_BAT_TIGVECTOR
 
-#include "AS_global.H"
+#include "runtime.H"
 
 class Unitig;
 

src/bogart/AS_BAT_Unitig.C

@@ -35,7 +35,7 @@
  *  full conditions and disclaimers for each license.
  */
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "AS_BAT_Unitig.H"
 #include "AS_BAT_ReadInfo.H"
 #include "AS_BAT_BestOverlapGraph.H"

src/bogart/AS_BAT_Unitig.H

@@ -42,7 +42,7 @@
 #ifndef INCLUDE_AS_BAT_UNITIG
 #define INCLUDE_AS_BAT_UNITIG
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "AS_BAT_TigVector.H"
 #include "AS_BAT_OverlapCache.H"
 

src/bogart/analyzeBest.C

@@ -35,7 +35,7 @@
  *  full conditions and disclaimers for each license.
  */
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "AS_PER_seqStore.H"
 #include "strings.H"
 

src/bogart/bogart.mk

@@ -35,7 +35,7 @@ SOURCES  := bogart.C \
             AS_BAT_Unitig_AddRead.C \
             AS_BAT_Unitig_PlaceReadUsingEdges.C
 
-SRC_INCDIRS  := .. ../utility ../stores
+SRC_INCDIRS  := .. ../utility/src/utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

src/bogus/bogus.mk

@@ -11,7 +11,7 @@ TARGET   := bogus
 SOURCES  := bogus.C \
             bogusUtil.C
 
-SRC_INCDIRS  := .. ../utility ../stores
+SRC_INCDIRS  := .. ../utility/src/utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

src/bogus/bogusUtil.H

@@ -39,7 +39,7 @@
 #ifndef INCLUDE_BOGUSUTIL
 #define INCLUDE_BOGUSUTIL
 
-#include "AS_global.H"
+#include "runtime.H"
 
 #include "files.H"
 

src/bogus/bogusness.mk

@@ -10,7 +10,7 @@ endif
 TARGET   := bogusness
 SOURCES  := bogusness.C
 
-SRC_INCDIRS  := .. ../utility ../stores
+SRC_INCDIRS  := .. ../utility/src/utility ../stores
 
 TGT_LDFLAGS := -L${TARGET_DIR}/lib
 TGT_LDLIBS  := -lcanu

src/correction/computeGlobalScore.H

@@ -38,7 +38,7 @@
 #ifndef COMPUTEGLOBALSCORES_H
 #define COMPUTEGLOBALSCORES_H
 
-#include "AS_global.H"
+#include "runtime.H"
 #include "ovStore.H"
 
 class globalScoreStats {