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#!/bin/bash
set -e
pkg=bppsuite
ARCH=$(dpkg --print-architecture)
export LC_ALL=C.UTF-8
if [ "${AUTOPKGTEST_TMP}" = "" ]; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
# Double quote below to expand the temporary directory variable now versus
# later is on purpose.
# shellcheck disable=SC2064
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
gunzip -r *
run_test() {
# $1: test number
# $2: command
# $3: path to file
# $4: filename
# $5: outfile
# $6: reference
echo -e "\e[93m\e[1mTest $1\e[0m"
cd $3
$2 param=$4
if [ "$?" -ne "0" ]; then
echo -e "\e[31m\e[1mTest $1 could not be run.\e[0m"
exit 1
fi
# discard digits after the fourth decimal place
# in outfile and refence both
sed -e "s/\([0-9]\.[0-9]\{4\}\)[0-9]\+/\1/g" < $5 > $5.approx
sed -e "s/\([0-9]\.[0-9]\{4\}\)[0-9]\+/\1/g" < $6 > $6.approx
if [ $1 -eq 5 -a "$ARCH" = "arm64" ] ; then
echo "Test $1 is known to diverge on $ARCH which is accepted here"
else
diff $5.approx $6.approx --suppress-common-lines
if [ "$?" -ne "0" ]; then
echo -e "\e[31m\e[1mOutput did not match the reference.\e[0m"
exit 1
fi
echo -e "\e[92m\e[1mPassed\e[0m"
fi
}
run_test 1 bppml MaximumLikelihood/Codons/BranchModel ML.bpp lysozymeLarge.ML.dnd ../../../ref/branch-lysozymeLarge.ML.dnd
run_test 2 bppml ../CladeModel ML.bpp lysozymeLarge.ML.dnd ../../../ref/clade-lysozymeLarge.ML.dnd
run_test 3 bppml ../M0 ML.bpp lysozymeLarge.ML.dnd ../../../ref/m0-lysozymeLarge.ML.dnd
run_test 4 bppml ../../Nucleotides/Homogeneous ML.bpp LSU.ML.dnd ../../../ref/LSU.ML.dnd
run_test 5 bppml ../../Proteins/Homogeneous ML.bpp Myo.ML.dnd ../../../ref/Myo.ML.dnd
run_test 6 bppseqgen ../../../SequenceSimulation/Homogeneous "SeqGen.bpp --seed=5" LSUSim.fasta ../../ref/Homogeneous-LSUSim.fasta
run_test 7 bppseqgen ../HomogeneousCovarion "SeqGen.bpp --seed=5" LSUSim.fasta ../../ref/HomogeneousCovarion-LSUSim.fasta
run_test 8 bppseqgen ../NonHomogeneous "SeqGen.bpp --seed=5" LSUSim.fasta ../../ref/NonHomogeneous-LSUSim.fasta
run_test 9 bppseqgen ../WithSiteSpecificSettings "SeqGen.bpp --seed=5" LSUSim.fasta ../../ref/WithSiteSpecificSettings-LSUSim.fasta
run_test 10 bppdist ../../Distance Dist.bpp LSU.mat ../ref/dist-LSU.mat
run_test 11 bpppars ../Parsimony Pars.bpp Pars.bpp Pars.bpp
# No comparison since output appears to be different everytime
# and no seed parameter can be provided
# comparing imput file against itself to obey function rules
run_test 12 bppreroot ../ReRooting ReRoot.bpp treeList2_rooted.dnd ../ref/treeList2_rooted.dnd
run_test 13 bppseqman ../SequenceManipulation SeqMan.bpp LSU.fas ../ref/seqman-LSU.fas
run_test 14 bppalnscore ../AlignmentScoring AlnScores.bpp HIV1_REF_2010_gag.scores.txt ../ref/HIV1_REF_2010_gag.scores.txt
run_test 15 bpppopstats ../PopStats PopStatsCodonSites.bpp alignment.codons.csv ../ref/popstats-alignment.codons.csv
run_test 16 bpptreedraw ../Drawing TreeDraw.bpp LSU.svg ../ref/treedraw-LSU.svg
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