From e0671a336595deddaa287a1f1f4f718897d01b90 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 9 Jul 2017 07:38:29 +0000
Subject: Add test framework based on shunit2

---
 test/test_suite.sh | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)
 create mode 100755 test/test_suite.sh

(limited to 'test')

diff --git a/test/test_suite.sh b/test/test_suite.sh
new file mode 100755
index 0000000..c6aa38e
--- /dev/null
+++ b/test/test_suite.sh
@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+
+gemma=../bin/gemma
+
+testCenteredRelatednessMatrix() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+                 -a ../example/mouse_hs1940.anno.txt -gk -o mouse_hs1940
+    assertEquals "3763600" `wc -w < output/mouse_hs1940.cXX.txt`
+}
+
+shunit2=`which shunit2`
+if [ -x "$shunit2" ]; then
+    . $shunit2
+else
+    # try to run the locally installed shunit2
+    . ../shunit2-2.0.3/src/shell/shunit2
+fi
-- 
cgit v1.2.3


From 35405450385ded8797a9a6388e6e2801381f2894 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 9 Jul 2017 08:07:46 +0000
Subject: Test: check result

---
 test/test_suite.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'test')

diff --git a/test/test_suite.sh b/test/test_suite.sh
index c6aa38e..effc056 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -2,10 +2,13 @@
 
 gemma=../bin/gemma
 
-testCenteredRelatednessMatrix() {
+testCenteredRelatednessMatrixK() {
     $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
-                 -a ../example/mouse_hs1940.anno.txt -gk -o mouse_hs1940
+           -a ../example/mouse_hs1940.anno.txt -gk -o mouse_hs1940
     assertEquals "3763600" `wc -w < output/mouse_hs1940.cXX.txt`
+    # assertEquals "15f680c" `md5sum < output/mouse_hs1940.cXX.txt | head -c 7`
+    assertEquals "0.335" `head -c 5 output/mouse_hs1940.cXX.txt`
+    assertEquals "29.691" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt`
 }
 
 shunit2=`which shunit2`
-- 
cgit v1.2.3


From 0792aee7269e4bf1c2903267e17a12dfebd14884 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 9 Jul 2017 08:33:41 +0000
Subject: Tests: added test for univariate and multivariate LMM

Also added 'make check' command in Makefile and documented in INSTALL.md
---
 .gitignore         |  4 +++-
 INSTALL.md         |  4 ++++
 Makefile           |  2 ++
 test/test_suite.sh | 17 +++++++++++++++++
 4 files changed, 26 insertions(+), 1 deletion(-)

(limited to 'test')

diff --git a/.gitignore b/.gitignore
index 108e607..d6c227e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,9 +2,11 @@
 *.tar.gz
 src/Eigen
 example/output
+test/output
+./output
 doc/manual.aux
 doc/manual.bbl
 doc/manual.blg
 doc/manual.log
 doc/manual.out
-doc/manual.toc
\ No newline at end of file
+doc/manual.toc
diff --git a/INSTALL.md b/INSTALL.md
index f6eb0c0..32d37f3 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -48,3 +48,7 @@ if you get an Eigen error you may need to override the include
 path. E.g. on GNU Guix with shared libs this may work
 
     make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1
+
+to run GEMMA tests
+
+    make check
diff --git a/Makefile b/Makefile
index 0f25d88..a15c043 100644
--- a/Makefile
+++ b/Makefile
@@ -95,6 +95,8 @@ $(OBJS) : $(HDR)
 	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
 .SUFFIXES : .cpp .c .o $(SUFFIXES)
 
+check:
+	./run_tests.sh
 
 clean:
 	rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT)
diff --git a/test/test_suite.sh b/test/test_suite.sh
index effc056..8adc5c9 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -11,6 +11,23 @@ testCenteredRelatednessMatrixK() {
     assertEquals "29.691" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt`
 }
 
+testUnivariateLinearMixedModel() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt -n 1 \
+           -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm \
+           -o mouse_hs1940_CD8_lmm
+    assertEquals "118459" `wc -w < output/mouse_hs1940_CD8_lmm.assoc.txt`
+    assertEquals "92047" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940_CD8_lmm.assoc.txt`
+}
+
+testMultivariateLinearMixedModel() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+           -n 1 6 -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt \
+           -lmm -o mouse_hs1940_CD8MCH_lmm
+    outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
+    assertEquals "139867" `wc -w < $outfn`
+    assertEquals "92079" `awk '{s+=substr($1,0,6)}END{print s}' $outfn`
+}
+
 shunit2=`which shunit2`
 if [ -x "$shunit2" ]; then
     . $shunit2
-- 
cgit v1.2.3


From d2ea25218f28c01afcb2480960fdf090318a864b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 9 Jul 2017 08:42:07 +0000
Subject: Tests: more tests

---
 test/test_suite.sh | 10 ++++++++++
 1 file changed, 10 insertions(+)

(limited to 'test')

diff --git a/test/test_suite.sh b/test/test_suite.sh
index 8adc5c9..763c981 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -5,6 +5,9 @@ gemma=../bin/gemma
 testCenteredRelatednessMatrixK() {
     $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
            -a ../example/mouse_hs1940.anno.txt -gk -o mouse_hs1940
+    assertEquals 0 $?
+    grep "total computation time" < output/mouse_hs1940.log.txt
+    assertEquals 0 $?
     assertEquals "3763600" `wc -w < output/mouse_hs1940.cXX.txt`
     # assertEquals "15f680c" `md5sum < output/mouse_hs1940.cXX.txt | head -c 7`
     assertEquals "0.335" `head -c 5 output/mouse_hs1940.cXX.txt`
@@ -15,6 +18,9 @@ testUnivariateLinearMixedModel() {
     $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt -n 1 \
            -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm \
            -o mouse_hs1940_CD8_lmm
+    assertEquals 0 $?
+    grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt
+    assertEquals 0 $?
     assertEquals "118459" `wc -w < output/mouse_hs1940_CD8_lmm.assoc.txt`
     assertEquals "92047" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940_CD8_lmm.assoc.txt`
 }
@@ -23,6 +29,10 @@ testMultivariateLinearMixedModel() {
     $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
            -n 1 6 -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt \
            -lmm -o mouse_hs1940_CD8MCH_lmm
+    assertEquals 0 $?
+    grep "total computation time" < output/mouse_hs1940_CD8MCH_lmm.log.txt
+    assertEquals 0 $?
+
     outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
     assertEquals "139867" `wc -w < $outfn`
     assertEquals "92079" `awk '{s+=substr($1,0,6)}END{print s}' $outfn`
-- 
cgit v1.2.3


From d92fc5359540d7c860140f74f9f905d83b24f82d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 9 Jul 2017 12:25:44 +0000
Subject: Makefile: force unit tests to throw a make error on less than 100%
 success

---
 Makefile           | 3 +--
 test/test_suite.sh | 1 +
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'test')

diff --git a/Makefile b/Makefile
index 8b5b113..748c4f2 100644
--- a/Makefile
+++ b/Makefile
@@ -102,8 +102,7 @@ $(OBJS) : $(HDR)
 .SUFFIXES : .cpp .c .o $(SUFFIXES)
 
 check: all
-	cd test && ./test_suite.sh
-
+	cd test && ./test_suite.sh | grep -q 'success rate: 100%'
 clean:
 	rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT)
 
diff --git a/test/test_suite.sh b/test/test_suite.sh
index 763c981..d65bf40 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -11,6 +11,7 @@ testCenteredRelatednessMatrixK() {
     assertEquals "3763600" `wc -w < output/mouse_hs1940.cXX.txt`
     # assertEquals "15f680c" `md5sum < output/mouse_hs1940.cXX.txt | head -c 7`
     assertEquals "0.335" `head -c 5 output/mouse_hs1940.cXX.txt`
+    # FIXME: The following test fails in the Guix build system (https://github.com/xiangzhou/GEMMA/issues/55)
     assertEquals "29.691" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt`
 }
 
-- 
cgit v1.2.3


From d6098a5f318543b525878c6cf45ddfe8ec923d9d Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 16 Jul 2017 11:05:39 +0000
Subject: sunit2: added instructions

---
 .gitignore         |  1 +
 INSTALL.md         | 17 +++++++++++++++++
 run_tests.sh       |  3 +--
 test/test_suite.sh | 12 +++++++++---
 4 files changed, 28 insertions(+), 5 deletions(-)

(limited to 'test')

diff --git a/.gitignore b/.gitignore
index d6c227e..5088ec4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@ doc/manual.blg
 doc/manual.log
 doc/manual.out
 doc/manual.toc
+contrib/
diff --git a/INSTALL.md b/INSTALL.md
index de6558b..e4da6ff 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -52,3 +52,20 @@ path. E.g. on GNU Guix with shared libs this may work
 to run GEMMA tests
 
     make check
+
+## Run tests
+
+GEMMA uses the shunit2 test framework (version 2.0) and can be found
+[here](https://github.com/genenetwork/shunit2)
+
+In the source tree:
+
+    git clone https://github.com/genenetwork/shunit2 contrib/shunit2
+
+and run
+
+    make check
+
+or
+
+    ./run_tests.sh
diff --git a/run_tests.sh b/run_tests.sh
index e8b7d49..181f687 100755
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -1,7 +1,6 @@
 #!/usr/bin/env bash
 
-# download shunit2 in order to run tests:
-# curl -L "https://dl.dropboxusercontent.com/u/7916095/shunit2-2.0.3.tgz" | tar zx --overwrite
+# download shunit2 in order to run tests (see INSTALL.md)
 
 cd test
 ./test_suite.sh | tee /dev/stderr | grep -q 'success rate: 100%'
diff --git a/test/test_suite.sh b/test/test_suite.sh
index d65bf40..f1a1c6f 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -40,9 +40,15 @@ testMultivariateLinearMixedModel() {
 }
 
 shunit2=`which shunit2`
-if [ -x "$shunit2" ]; then
+if [ -e "../contrib/shunit2/source/2.0/src/shell/shunit2" ]; then
+    echo try to run the locally installed shunit2
+    . ../contrib/shunit2/source/2.0/src/shell/shunit2
+elif [ -e "../shunit2-2.0.3/src/shell/shunit2" ]; then
+    echo try to run the older locally installed shunit2
+    . ../shunit2-2.0.3/src/shell/shunit2
+elif [ -x "$shunit2" ]; then
+    echo run system shunit2
     . $shunit2
 else
-    # try to run the locally installed shunit2
-    . ../shunit2-2.0.3/src/shell/shunit2
+    echo "Can not find shunit2 - see INSTALL.md"
 fi
-- 
cgit v1.2.3