Merge pull request #218 from smithlabcode/makefile-am-updates

makefile am updates

Makefile.am

@@ -14,6 +14,20 @@
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 # General Public License for more details.
 
+### ADS: the file md5sum.txt can be regenerated by running the tests
+### with "make check" and then doing `md5sum tests/* > md5sum.txt`
+### from the build directory.
+
+ACLOCAL_AMFLAGS = -I m4
+
+SUBDIRS := src/smithlab_cpp src/abismal
+install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp src/abismal, $(SUBDIRS))
+AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
+
+AM_CXXFLAGS = $(OPENMP_CXXFLAGS)
+CXXFLAGS = -Wall -Wextra -Wpedantic -Wno-unknown-attributes
+CXXFLAGS += -O3 -DNDEBUG # default has optimization on
+
 EXTRA_DIST = \
              README.md \
              code_of_conduct.md \
@@ -87,19 +101,6 @@ EXTRA_DIST = \
              test_scripts/test_diff.test \
              test_scripts/test_mlml.test
 
-### ADS: the file md5sum.txt can be regenerated by running the tests
-### with "make check" and then doing `md5sum tests/* > md5sum.txt`
-### from the build directory.
-
-ACLOCAL_AMFLAGS = -I m4
-
-SUBDIRS := src/smithlab_cpp src/abismal
-install installdirs: SUBDIRS := $(filter-out src/smithlab_cpp src/abismal, $(SUBDIRS))
-AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $(top_srcdir)/src/bamxx
-
-AM_CXXFLAGS = $(OPENMP_CXXFLAGS)
-CXXFLAGS = -Wall -O3 # default has optimization on
-
 ### ADS: Testing with `make check` can be a long process. Testing with
 ### `make check` is designed to work recursively. Modifying this
 ### behavior requires overriding build-in rules which generates