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#!/bin/sh -e
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/python-biopython-test.XXXXXX`
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
# Preconfigure CCD data bank for test_PDB* and dssp.
LIBCIFPP_DATA_DIR="$AUTOPKGTEST_TMP/libcifpp-data"
export LIBCIFPP_DATA_DIR
mkdir -p "$LIBCIFPP_DATA_DIR"
cp /usr/share/libcifpp/mmcif_pdbx.dic "$LIBCIFPP_DATA_DIR"
cp /usr/share/libcifpp/mmcif_ma.dic "$LIBCIFPP_DATA_DIR"
# Note that as mini-ccd.cif is shipped by python-biopython source
# package, this makes self testing python3-biopython impossible using
# only binary packages as a regular en user.
cp debian/tests/mini-ccd.cif "$LIBCIFPP_DATA_DIR/components.cif"
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/python-biopython-doc/Tests $AUTOPKGTEST_TMP
mkdir -p Doc/
unset GZIP
find . -name "*.gz" -exec gunzip \{\} \;
SUBSMAT_DIR="Bio/Align/substitution_matrices/data"
mkdir -pv "$SUBSMAT_DIR/"
cp -av "/usr/lib/python3/dist-packages/$SUBSMAT_DIR"/* "$SUBSMAT_DIR/"
cd Tests
# we really need this gzipped duplicate of the example.fastq and E3MFGYR02_random_10_reads.sff files to pass the BGZF compression test
gzip --keep Quality/example.fastq
gzip --keep Roche/E3MFGYR02_random_10_reads.sff
gzip --keep Fasta/flowers.pro
gzip --keep PDB/1gbt.bcif
gzip --keep PDB/3jqh.bcif
gzip --keep PDB/6wg6.bcif
# bwa is only available on amd64
BUILDARCH=
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "amd64" ]; then
rm -f test_BWA_tool.py
fi
# FIXME: PDB bcif is currently broken on s390x
if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "s390x" ]; then
rm -f test_PDB_binary_cif.py
find . -name test_Tutorial.py -delete
fi
# execute tests
################################################################################
# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the
# test is verifying this dir to run the EMBOSS test
# test_Emboss also requires to have the environment variable EMBOSS_ROOT set
for pi in $(py3versions -s); do
LC_ALL=C.UTF-8 DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss HOME=$AUTOPKGTEST_TMP ${pi} run_tests.py --offline
done
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