Merge pull request #40 from sfiligoi/multi_230328

Fix Makefile and GitHub CI script
biocore · Apr 28, 2023 · 5213eb1 · 5213eb1
2 parents badf2e1 + d02dd66
commit 5213eb1
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Showing 3 changed files with 12 additions and 6 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -14,10 +14,10 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, linux-gpu-cuda]
-        fullopt: [True, False]
+        fullopt: ["True", "False"]
         exclude:
         - os: linux-gpu-cuda
-          fullopt: False
+          fullopt: "False"
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v3
@@ -201,7 +201,7 @@ jobs:
         ./compare_unifrac_pcoa.py test500.unweighted_fp32.f.h5 t1.h5 3 0.3
         rm -f t1.h5
         time ssu -m unweighted -i test500.biom  -t test500.tre --pcoa 4  -r hdf5_nodist --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 -o t1.h5
-        python compare_unifrac_stats.py t1.h5 5 99 1.001112 0.456  0.05 0.5
+        python compare_unifrac_stats.py t1.h5 5 99 1.001112 0.456  0.05 0.6
         ls -l t1.h5
         rm -f t1.h5
         # multi
@@ -211,7 +211,7 @@ jobs:
         ls -l t1.h5
         rm -f t1.h5
         time ssu -m unweighted -i test500.biom  -t test500.tre --pcoa 4  --mode multi --n-subsamples 10 --permanova 99 -g test500.tsv -c empo_2 --subsample-depth 100 -o t1.h5
-        python compare_unifrac_stats_multi.py t1.h5 10 5 99 1.001112 0.456  0.08 0.5
+        python compare_unifrac_stats_multi.py t1.h5 10 5 99 1.001112 0.456  0.08 0.6
         ls -l t1.h5
         rm -f t1.h5
         popd

diff --git a/src/Makefile b/src/Makefile
@@ -28,12 +28,15 @@ ifeq ($(PREFIX),)
 	PREFIX := $(CONDA_PREFIX)
 endif
 
+BLASLIB=-llapacke -lcblas
+
 ifeq ($(PLATFORM),Darwin)
 	AVX2 := $(shell sysctl -a | grep -c AVX2)
 	LDDFLAGS = -dynamiclib -install_name @rpath/libssu.so
 else
 	AVX2 := $(shell grep "^flags" /proc/cpuinfo | head -n 1 | grep -c avx2)
 	LDDFLAGS = -shared
+	BLASLIB += -lgfortran -lquadmath
 endif
 
 EXEFLAGS =
@@ -99,8 +102,6 @@ ifeq (,$(findstring pgi,$(COMPILER)))
     endif
 endif
 
-BLASLIB=-llapacke -lcblas
-
 
 CPPFLAGS += -Wall  -std=c++14 -pedantic -I. $(OPT) -fPIC -L$(PREFIX)/lib
 

diff --git a/test/Makefile b/test/Makefile
@@ -7,6 +7,11 @@ ifeq ($(PREFIX),)
 	PREFIX := $(CONDA_PREFIX)
 endif
 
+ifneq ($(PLATFORM),Darwin)
+	CC := gcc
+	LD := ld
+endif
+
 test: capi_test
 	./capi_test 1