New test suite is working and takes account of round-off problems.

Closes genetics-statistics#247
Closes genetics-statistics#242

Makefile

@@ -237,16 +237,19 @@ fast-check: all unittests
 	rm -vf output/*
 	ruby -Eutf-8 -Itest ./test/dev_tests.rb | tee ./dev_test.log
 
+# Note the following tests are not robust for different architectures
 old-check: all unittests
 	rm -vf test/output/*
 	cd test && ./dev_test_suite.sh | tee ../test.log
 	grep -q 'success rate: 100%' test.log
 
+# Note the following tests are not robust for different architectures
 slow-check: all
 	rm -vf test/output/*
 	cd test && ./test_suite.sh | tee ../test.log
 	grep -q 'success rate: 100%' test.log
 
+# Note the following tests are not robust for different architectures
 lengthy-check: all
 	rm -vf test/output/*
 	cd test && ./lengthy_test_suite.sh | tee ../lengthy_test.log

RELEASE-NOTES.md

@@ -11,6 +11,7 @@ and
 * Documented `-lmm 9` which adds additive effect to `-lmm 2`
 * Fix of GSL ERROR: function value is not finite in brent.c at line 202 errno 9, see #210
 * Added profiler support in Guix profile and make file. Profiling issue #243
+* Added new test suite to replace shunit2 scripts - should make it more robust for different architectures, see github issues #242 and #247.
 
 ## ChangeLog v0.98.4 (2021/01/29)
 

test/dev_test_suite.sh

@@ -1,5 +1,7 @@
 #!/bin/sh
 
+echo "WARNING: THIS TEST SUITE IS NO LONGER USED"
+
 gemma=../bin/gemma
 # gemmaopts="-debug -strict"
 gemmaopts="-debug -check"

test/dev_tests.rb

@@ -10,7 +10,7 @@ def setup
   end
 
   def test_linear_model
-    assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \
+    gemma("-g ./example/mouse_hs1940.geno.txt.gz \
            -p ./example/mouse_hs1940.pheno.txt \
            -n 1 \
            -a ./example/mouse_hs1940.anno.txt \
@@ -23,14 +23,14 @@ def test_linear_model
   end
 
   def test_BXD
-    assert gemma("-g ./example/BXD_geno.txt.gz \
+    gemma("-g ./example/BXD_geno.txt.gz \
            -p ./example/BXD_pheno.txt \
            -c ./example/BXD_covariates2.txt \
            -a ./example/BXD_snps.txt \
            -gk \
            -o BXD")
 
-    assert gemma("-g ./example/BXD_geno.txt.gz \
+    gemma("-g ./example/BXD_geno.txt.gz \
            -p ./example/BXD_pheno.txt \
            -c ./example/BXD_covariates2.txt \
            -a ./example/BXD_snps.txt \
@@ -39,18 +39,18 @@ def test_BXD
            -o BXDLMM")
 
     expect("output/BXDLMM.assoc.txt",[[2,9,"1.234747e-01"],
-                                      [:max,9,"9.997119e-01"]])
+                                      [:max,"p_lrt","9.997119e-01"]])
   end
 
   def test_mouse_hs1940_loco
-    assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \
+    gemma("-g ./example/mouse_hs1940.geno.txt.gz \
            -p ./example/mouse_hs1940.pheno.txt \
            -a ./example/mouse_hs1940.anno.txt \
            -snps ./example/mouse_hs1940_snps.txt \
            -nind 400 -loco 1 -gk \
            -o mouse_hs1940_loco")
 
-    assert gemma("-g ./example/mouse_hs1940.geno.txt.gz \
+    gemma("-g ./example/mouse_hs1940.geno.txt.gz \
            -p ./example/mouse_hs1940.pheno.txt \
 	   -n 1 \
 	   -loco 1 \
@@ -61,6 +61,26 @@ def test_mouse_hs1940_loco
 	   -nind 400 -no-check \
            -o mouse_hs1940_loco")
     expect("output/mouse_hs1940_loco.assoc.txt",[[2,9,"-3.073643e+02"],
-                                                 [:max,11,"9.716047e-01"]])
+                                                 [:max,"p_wald","9.716047e-01"]])
   end
+
+  # Test for https://github.com/genetics-statistics/GEMMA/issues/58
+  # fixed GSLv2 NaN's that appeared with covariates.
+  def test_plink_covariates_lmm
+    gemma("-bfile example/HLC -gk 2 -o testPlinkStandardRelatednessMatrixK")
+
+    gemma("-bfile example/HLC \
+           -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
+           -lmm 1 \
+           -maf 0.1 \
+           -c example/HLC_covariates.txt \
+           -no-check \
+           -o plink_lmm1_cov")
+    expect("output/plink_lmm1_cov.assoc.txt",[[100,"p_wald","5.189953e-01"],
+                                              [:max,"logl_H1","279.2689"],
+                                              [:max,"l_remle","1.686062"],
+                                              [:max,"p_wald","0.9999996"]])
+  end
+
+
 end

test/lengthy_test_suite.sh

@@ -2,6 +2,8 @@
 #
 # Long running tests go here
 
+echo "WARNING: THIS TEST SUITE IS NO LONGER USED"
+
 gemma=../bin/gemma
 export GSL_RNG_SEED=100
 

test/lib/test-helpers.rb

@@ -2,7 +2,7 @@ module TestHelpers
 
   # Runs gemma and returns true if successful
   def gemma(opts)
-    system("./bin/gemma #{opts}")
+    assert system("./bin/gemma #{opts}")
   end
 
   def read(fn, line=0)
@@ -18,11 +18,15 @@ def expect(fn, list)
     lines = lines.map { |l| l.split("\t") } # avoid this for large files
     list.each do | l |
       line,colnum,value = l
-      if line == :max
-        cols = lines.max_by {|a| a[colnum].to_f}
-      else
-        cols = lines[line]
+      if colnum.is_a? String
+        colnum = lines[0].index(colnum)
       end
+      cols =
+        if line == :max
+          lines.max_by {|a| a[colnum].to_f}
+        else
+          lines[line]
+        end
       # assert_equal value,cols[colnum]
       assert_in_delta value.to_f,cols[colnum].to_f, 0.001
     end

test/test_suite.sh

@@ -1,5 +1,7 @@
 #!/bin/sh
 
+echo "WARNING: THIS TEST SUITE IS NO LONGER USED"
+
 gemma=../bin/gemma
 gemmaopts="-debug"
 export GSL_RNG_SEED=10