Merge pull request #788 from kdmurray91/libmakefile

./lib Makefile rewrite, create libkhmer.{a,so} and install target

ChangeLog

@@ -1,3 +1,17 @@
+2015-03-27  Michael R. Crusoe  <mcrusoe@msu.edu>
+
+   * lib/read_parsers.{cc,hh}: Obfuscate SeqAn SequenceStream objects with a
+   wrapper struct, to avoid #include-ing the SeqAn headers.
+   * lib/Makefile: Don't install the SeqAn headers.
+
+2015-03-27  Kevin Murray  <spam@kdmurray.id.au>
+
+   * lib/Makefile: Add libkhmer targets, clean up
+   * lib/get_version.py: Rewrite to use versioneer.py
+   * lib/.gitignore,third-party/.gitignore: Add more compiled outputs
+   * lib/.check_openmp.cc: add source that checks compiler for openmp support.
+   * lib/khmer.pc.in: add pkg-config file for khmer
+
 2015-03-23  Kevin Murray  <spam@kdmurray.id.au>
 
    * lib/counting.hh: Add CountingHash::n_tables() accessor

Makefile

@@ -184,6 +184,24 @@ lib:
 	cd lib && \
 	$(MAKE)
 
+# Runs a test of ./lib
+libtest: FORCE
+	rm -rf install_target
+	mkdir -p install_target
+	cd lib && \
+	 $(MAKE) clean && \
+	 $(MAKE) all && \
+	 $(MAKE) install PREFIX=../install_target
+	test -d install_target/include
+	test -f install_target/include/khmer.hh
+	test -d install_target/lib
+	test -f install_target/lib/libkhmer.a
+	$(CXX) -o install_target/test-prog-static -I install_target/include \
+		lib/test-compile.cc install_target/lib/libkhmer.a
+	$(CXX) -o install_target/test-prog-dynamic -I install_target/include \
+		-L install_target/lib lib/test-compile.cc -lkhmer
+	rm -rf install_target
+
 ## test        : run the khmer test suite
 test: FORCE
 	./setup.py develop

jenkins-build.sh

@@ -68,4 +68,6 @@ fi
 
 # takes too long to run on every build
 #bash -ex -c 'cd examples/stamps/; ./do.sh' || { echo examples/stamps/do.sh no longer runs; /bin/false; }
-
+
+make lib
+make libtest

lib/.check_openmp.cc

@@ -0,0 +1,17 @@
+//
+// This file is part of khmer, http://github.com/ged-lab/khmer/, and is
+// Copyright (C) Michigan State University, 2015. It is licensed under
+// the three-clause BSD license; see doc/LICENSE.txt.
+// Contact: khmer-project@idyll.org
+//
+
+// File to be used to check for openmp
+#include <omp.h>
+#include <stdio.h>
+
+int main()
+{
+	#pragma omp parallel
+	printf("Hello from thread %d, nthreads %d\n",
+	       omp_get_thread_num(), omp_get_num_threads());
+}

lib/.gitignore

@@ -1,9 +1,10 @@
-test-StreamReader
-test-CacheManager
 test-Parser
 test-HashTables
-smpFiltering
-bittest
-ktable_test
+test-read-aligner
 ht-diff
+chkomp
+*.pc
 *.swp
+*.so
+*.so.*
+*.a