Updating the tests to remove only one that is really redundant and not needed while also commenting to explain the workaround, which should be included in the github workflows

Author: andrewdavidsmith

Makefile.am

@@ -67,7 +67,6 @@ EXTRA_DIST = \
              data/two_epialleles.states \
              data/araTha1_simulated.counts.gz \
              test_scripts/test_abismalidx.test \
-             test_scripts/test_simreads.test \
              test_scripts/test_abismal.test \
              test_scripts/test_format.test \
              test_scripts/test_uniq.test \
@@ -96,8 +95,15 @@ AM_CPPFLAGS = -I $(top_srcdir)/src/common -I $(top_srcdir)/src/smithlab_cpp -I $
 
 CXXFLAGS = -Wall -O3 $(OPENMP_CXXFLAGS) # default has optimization on
 
-TESTS = test_scripts/test_simreads.test \
-        test_scripts/test_abismalidx.test \
+### 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
+### warnings, probably for good reason. Defining a check-local only
+### adds to functionality and does not remove the dependency that
+### causes the recursion. The preferred alternative is to do `make`
+### first and then `make check-TESTS` after. This will not do tests
+### recursively.
+TESTS = test_scripts/test_abismalidx.test \
         test_scripts/test_abismal.test \
         test_scripts/test_format.test \
         test_scripts/test_uniq.test \
@@ -230,8 +236,6 @@ CLEANFILES = \
     tests/reads.mstats \
     tests/reads.sam \
     tests/reads.ustats \
-    tests/simreads_1.fq \
-    tests/simreads_2.fq \
     tests/tRex1.idx \
     tests/tRex1_promoters.roi.bed \
     tests/reads.counts.select \

data/md5sum.txt

@@ -14,8 +14,6 @@ af8b97ef25af8a16ced1537ca4a74d07  tests/reads.hmr
 916fe07a1d03449b65dfc1458d7c1c40  tests/reads.mstats
 65816bee34b977adf1dd798fbf85d758  tests/reads.sam
 1aecbb2b12bd867405118eae42de6743  tests/reads.ustats
-ae8e662c3ab23ba742a45a9784390e63  tests/simreads_1.fq
-d2723d2e99d2a3492af508633d61b30a  tests/simreads_2.fq
 bcbf01be810cbf4051292813eb6b9225  tests/tRex1.idx
 7c84dafb85252a04a45704da71eba7c4  tests/tRex1_promoters.roi.bed
 e7e9590475a7f9b1ae41701d81892e57  tests/two_epialleles.amr