Merge pull request #15 from sfiligoi/igor_static_hfd5

Fix static hdf5 linking

.github/workflows/main.yml

@@ -88,6 +88,13 @@ jobs:
         popd
         pushd test
         ./capi_test 1
+        # explicitly check that we do not have hdf5 dependencies
+        if [[ "$(uname -s)" == "Linux" ]];
+        then
+          ldd ./capi_test |awk 'BEGIN{a=0}/hdf/{a=a+1;print $0}END{if (a==0) {print "No dynamic hdf5 found"} else {exit 2}}'
+        else
+          otool -L ./capi_test|awk 'BEGIN{a=0}/hdf/{a=a+1;print $0}END{if (a==0) {print "No dynamic hdf5 found"} else {exit 2}}'
+        fi
         popd
         pushd src/testdata
         conda install --yes -c conda-forge h5py

src/Makefile

@@ -110,7 +110,7 @@ faithpd: faithpd.cpp tree.o biom.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_F
 	$(CXX) $(CPPFLAGS) $(EXEFLAGS) faithpd.cpp -o faithpd tree.o biom.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lhdf5_cpp -llz4 $(BLASLIB) -lpthread
 
 libssu.so: tree.o biom.o unifrac.o cmd.o skbio_alt.o api.o $(UNIFRAC_FILES)
-	$(CXX) $(LDDFLAGS) -o libssu.so tree.o biom.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -lhdf5_cpp -llz4 $(BLASLIB) -L$(PREFIX)/lib
+	$(CXX) $(LDDFLAGS) -o libssu.so tree.o biom.o $(UNIFRAC_FILES) unifrac.o cmd.o skbio_alt.o api.o -lc -llz4 $(BLASLIB) -L$(PREFIX)/lib -noshlib -lhdf5_cpp -lhdf5_hl_cpp -lhdf5_hl -lhdf5
 
 api.o: api.cpp api.hpp unifrac.hpp skbio_alt.hpp biom.hpp tree.hpp
 	$(CXX) $(CPPFLAGS) api.cpp -c -o api.o -fPIC