Allow for parallelisation of unit tests.

andi (0.12-3) UNRELEASED; urgency=medium

  * Allow for parallelisation of unit tests. Really fixes build failures.

 -- Fabian Klötzl <kloetzl@evolbio.mpg.de>  Wed, 07 Mar 2018 12:12:24 +0100

andi (0.12-2) unstable; urgency=medium

  [ Fabian Klötzl ]

From: =?utf-8?q?Fabian_Kl=C3=B6tzl?= <fabian@kloetzl.info>

Date: Wed, 7 Mar 2018 11:26:26 +0100

Subject: prefix files in unit tests

Applied-Upstream: https://github.com/EvolBioInf/andi/commit/e35d1a51f71541f246919a277386817f69c94a3e

Unit tests can be run in parallel (see debian builds). Thus they should

work on different files, otherwise bad and confusing things happen.

---

 test/low_homo.sh  | 16 ++++++++--------

 test/nan.sh       | 10 +++++-----

 test/test_join.sh | 48 ++++++++++++++++++++++++------------------------

 3 files changed, 37 insertions(+), 37 deletions(-)

diff --git a/test/low_homo.sh b/test/low_homo.sh

index 11e889e..1f16a79 100755

--- a/test/low_homo.sh

+++ b/test/low_homo.sh

@@ -9,21 +9,21 @@ if test $SEED -ne 0; then

 	SEED3=$((SEED + 3))

 fi

-./test/test_fasta -s $SEED -l 100000 > a.fa

-./test/test_fasta -s $SEED2 -l 100000 > b.fa

-./test/test_fasta -s $SEED3 -l 100 > both.fa

+./test/test_fasta -s $SEED -l 100000 > a_low.fa

+./test/test_fasta -s $SEED2 -l 100000 > b_low.fa

+./test/test_fasta -s $SEED3 -l 100 > both_low.fa

-cat both.fa a.fa | awk -vRS='>' '{if($1 == "S0")print ">"$0 > "S0.fa"}'

-cat both.fa b.fa | awk -vRS='>' '{if($1 == "S1")print ">"$0 > "S1.fa"}'

+cat both_low.fa a_low.fa | awk -vRS='>' '{if($1 == "S0")print ">"$0 > "S0_low.fa"}'

+cat both_low.fa b_low.fa | awk -vRS='>' '{if($1 == "S1")print ">"$0 > "S1_low.fa"}'

 # this is expected to trigger the low homology warning

-./src/andi -j S0.fa S1.fa 2>&1 | grep 'homology'

+./src/andi -j S0_low.fa S1_low.fa 2>&1 | grep 'homology'

 EXIT_VAL=$?

 if [[ EXIT_VAL -ge 1 ]]; then

 	echo "Triggering low homology failed" >&2

-	grep '^>' a.fa b.fa both.fa

+	grep '^>' a_low.fa b_low.fa both_low.fa

 fi

-rm -f a.fa b.fa both.fa S0.fa S1.fa

+rm -f a_low.fa b_low.fa both_low.fa S0_low.fa S1_low.fa

 exit $EXIT_VAL

diff --git a/test/nan.sh b/test/nan.sh

index 60db0e2..97fa167 100755

--- a/test/nan.sh

+++ b/test/nan.sh

@@ -8,18 +8,18 @@ if test $SEED -ne 0; then

 fi

-./test/test_fasta -s $SEED -l 10000 > a.fa

-./test/test_fasta -s $SEED2 -l 10000 > b.fa

+./test/test_fasta -s $SEED -l 10000 > a_nan.fa

+./test/test_fasta -s $SEED2 -l 10000 > b_nan.fa

 # this is expected to trigger the nan warning

-./src/andi -j a.fa b.fa 2>&1 | grep 'nan'

+./src/andi -j a_nan.fa b_nan.fa 2>&1 | grep 'nan'

 EXIT_VAL=$?

 if [[ EXIT_VAL -ge 1 ]]; then

 	echo "Triggering nan failed" >&2

-	grep '^>' a.fa b.fa both.fa

+	grep '^>' a_nan.fa b_nan.fa

 fi

-rm -f a.fa b.fa

+rm -f a_nan.fa b_nan.fa

 exit $EXIT_VAL

diff --git a/test/test_join.sh b/test/test_join.sh

index 33cc2c6..a0616bf 100755

--- a/test/test_join.sh

+++ b/test/test_join.sh

@@ -12,17 +12,17 @@ if test $SEED -ne 0; then

 fi

 # Simple join test

-./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta

-./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta

-./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta

+./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta

+./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta

+./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta

-head -qn 2 p1.fasta p2.fasta p3.fasta > S0.fasta

-tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta

+head -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S0_join.fasta

+tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta

-rm p1.fasta p2.fasta p3.fasta;

+rm p1_join.fasta p2_join.fasta p3_join.fasta;

-RES=$(./src/andi -m RAW -t 1 -j S0.fasta S1.fasta |

+RES=$(./src/andi -m RAW -t 1 -j S0_join.fasta S1_join.fasta |

 	tail -n 1 |

 	awk '{print ($2 - 0.1)}' |

 	awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'

@@ -30,7 +30,7 @@ RES=$(./src/andi -m RAW -t 1 -j S0.fasta S1.fasta |

 if test $RES -ne 1; then

 	echo "The last test computed a distance deviating more than three percent from its intended value."

-	echo "See S0.fasta and S1.fasta for the used sequences."

+	echo "See S0_join.fasta and S1_join.fasta for the used sequences."

 	exit 1;

 fi

@@ -42,16 +42,16 @@ if test $SEED -ne 0; then

 fi

 #unbalanced number of contigs

-./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2.fasta

-./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3.fasta

+./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p2_join.fasta

+./test/test_fasta -s $SEED2 -l 10000 -L 10000 -d 0.1 > p3_join.fasta

-head -qn 2 p3.fasta > S0.fasta

-tail -qn 2 p2.fasta p3.fasta > S1.fasta

+head -qn 2 p3_join.fasta > S0_join.fasta

+tail -qn 2 p2_join.fasta p3_join.fasta > S1_join.fasta

-rm p2.fasta p3.fasta;

+rm p2_join.fasta p3_join.fasta;

-RES=$(./src/andi -m RAW -t1 -j S0.fasta S1.fasta |

+RES=$(./src/andi -m RAW -t1 -j S0_join.fasta S1_join.fasta |

         tail -n 1 |

         awk '{print ($2 - 0.1)}' |

         awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'

@@ -59,7 +59,7 @@ RES=$(./src/andi -m RAW -t1 -j S0.fasta S1.fasta |

 if test $RES -ne 1; then

         echo "The last test computed a distance deviating more than three percent from its intended value."

-        echo "See S0.fasta and S1.fasta for the used sequences."

+        echo "See S0_join.fasta and S1_join.fasta for the used sequences."

         exit 1;

 fi

@@ -73,17 +73,17 @@ if test $SEED -ne 0; then

 fi

 #unbalanced number of contigs 2

-./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1.fasta

-./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2.fasta

-./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3.fasta

+./test/test_fasta -s $SEED -l 1000 -L 1000 -d 0.1 > p1_join.fasta

+./test/test_fasta -s $SEED2 -l 1000 -L 1000 -d 0.1 > p2_join.fasta

+./test/test_fasta -s $SEED3 -l 10000 -L 10000 -d 0.1 > p3_join.fasta

-head -qn 2 p1.fasta p3.fasta > S0.fasta

-tail -qn 2 p1.fasta p2.fasta p3.fasta > S1.fasta

+head -qn 2 p1_join.fasta p3_join.fasta > S0_join.fasta

+tail -qn 2 p1_join.fasta p2_join.fasta p3_join.fasta > S1_join.fasta

-rm p1.fasta p2.fasta p3.fasta;

+rm p1_join.fasta p2_join.fasta p3_join.fasta;

-RES=$(./src/andi -mRAW -t 1 -j S0.fasta S1.fasta |

+RES=$(./src/andi -mRAW -t 1 -j S0_join.fasta S1_join.fasta |

         tail -n 1 |

         awk '{print ($2 - 0.1)}' |

         awk 'function abs(x){return ((x < 0.0) ? -x : x)} {print abs($1-$2) < 0.03}'

@@ -91,9 +91,9 @@ RES=$(./src/andi -mRAW -t 1 -j S0.fasta S1.fasta |

 if test $RES -ne 1; then

         echo "The last test computed a distance deviating more than three percent from its intended value."

-        echo "See S0.fasta and S1.fasta for the used sequences."

+        echo "See S0_join.fasta and S1_join.fasta for the used sequences."

         exit 1;

 fi

-rm S0.fasta S1.fasta

+rm S0_join.fasta S1_join.fasta

0001-Make-unit-tests-reproducible.patch

0002-prefix-files-in-unit-tests.patch