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#!/usr/bin/make -f
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
# Fails to build with hardening=+all switched on
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
# Fix partially build reproducibility issues. Also, refrain from
# meddling with build user's home directory.
export HOME = /nonexistent
# Directory mainly holding chemical components data for dssp.
export LIBCIFPP_DATA_DIR = $(CURDIR)/libcifpp-data
BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
# avoid PAML_tools and EmbossPhylipNew since paml resp. embassy-phylip
# are non-free This would not trigger a failure but bloats the build log
# with irrelevant noise
EXCLUDENONFREE=PAML_tools EmbossPhylipNew
# avoid testing tools that are not packaged for Debian yet (or will
# never be packaged since they might be outdated). This would not
# trigger a failure but bloats the build log with irrelevant noise
EXCLUDENOTPACKAGED=\
MSAProbs_tool \
PopGen_GenePop \
PopGen_GenePop_EasyController \
XXmotif_tool \
PDB_ResidueDepth \
mmtf \
mmtf_online \
GraphicsBitmaps
# avoid amd64 only tools on other architectures
ifneq ($(BUILDARCH),amd64)
EXCLUDEARCH=raxml_tool
endif
ifeq ($(BUILDARCH),riscv64)
# FIXME: the below test is affected by #1080479, and can be
# restored once it is resolved.
EXCLUDEARCH+=NCBI_BLAST_tools
endif
ifeq ($(BUILDARCH),mips64el)
# FIXME: bwa on mips64el is affected by the following issue, so
# skipping for now:
#
# Bio.Application.ApplicationError: Non-zero return code 138 from
# 'bwa mem BWA/human_g1k_v37_truncated.fasta
# BWA/HNSCC1_1_truncated.fastq BWA/HNSCC1_2_truncated.fastq',
# message '[M::bwa_idx_load_from_disk] read 0 ALT contigs'
EXCLUDEARCH+=BWA_tool
endif
ifeq ($(BUILDARCH),s390x)
# PDB binary cif parsing is non-working on big endian platforms.
# The parsing is fed to C code which would need potientially
# heavier-than-first-thought rewrite to get the issue sorted.
EXCLUDEARCH+=PDB_binary_cif
EXCLUDEARCH+=Tutorial
endif
# avoid tests requiring data base connections if no server is running
# while we are doing the build This would not trigger a failure but
# bloats the build log with irrelevant noise
EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
%:
dh $@ --with python3 --buildsystem=pybuild
override_dh_auto_clean:
dh_auto_clean
cd Doc && make clean
rm -f Doc/install/Installation.pdf
rm -f Doc/install/Installation.txt
rm -f Doc/install/Installation.html
rm -f Doc/Tutorial.pdf Doc/biopdb_faq.pdf
rm -f Doc/Tutorial/*.aux
find Doc -name "*.pygtex" -o -name "*.pygstyle" -delete
rm -rf biopython.egg-info
rm -rf .pybuild
if [ -d Tests_avoid ] ; then \
mv Tests_avoid/* Tests ; \
rmdir Tests_avoid ; \
fi
rm -rf debian/tmp_tests
override_dh_auto_build:
dh_auto_build
ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS)))
PYTHONPATH=$(CURDIR)/.pybuild/cpython3_$(shell py3versions -dv)/build \
$(MAKE) -C Doc html
endif
override_dh_auto_install:
dh_auto_install
dh_numpy3 -ppython3-biopython
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
set -e \
; for avoid in \
$(EXCLUDENONFREE) \
$(EXCLUDENOTPACKAGED) \
$(EXCLUDEARCH) \
$(EXCLUDEDATABASE) \
; do mkdir -p Tests_avoid \
; mv Tests/test_$${avoid}.py Tests_avoid \
; done
# For the doc package we need a clean testsuite without all the
# remaining files. So keep a clean copy here
mkdir -p debian/tmp_tests
cp -a Tests debian/tmp_tests
# remove duplicated file
rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz
# Prepare resources necessary to dssp.
mkdir -pv $(LIBCIFPP_DATA_DIR)
cp -v /usr/share/libcifpp/mmcif_pdbx.dic $(LIBCIFPP_DATA_DIR)
cp -v /usr/share/libcifpp/mmcif_ma.dic $(LIBCIFPP_DATA_DIR)
cp -v debian/tests/mini-ccd.cif $(LIBCIFPP_DATA_DIR)/components.cif
# We also keep the tests we need to avoid for later inspection
test ! -d Tests_avoid || cp -a Tests_avoid debian/tmp_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
LC_ALL=C.UTF-8 \
dh_auto_test -- \
--test \
--system=custom \
--test-args=' \
set -e; \
mkdir -p {build_dir}/home; \
mkdir -p {build_dir}/Doc/examples; \
cp -a Doc/Tutorial {build_dir}/Doc; \
cp -a Doc/examples {build_dir}/Doc; \
cp -a Tests {build_dir}; \
cd {build_dir}/Tests; \
env DIALIGN2_DIR=/usr/share/dialign \
EMBOSS_ROOT=/usr/lib/emboss \
HOME={build_dir}/home \
{interpreter} run_tests.py --offline'
# Cleanup steps after tests.
set -e \
; if [ -d Tests_avoid ] \
; then mv Tests_avoid/* Tests \
; rmdir Tests_avoid \
; fi
rm -r $(LIBCIFPP_DATA_DIR)
endif
DOCPKG = python-biopython-doc
DOCDIR = $(CURDIR)/debian/$(DOCPKG)/usr/share/doc/$(DOCPKG)
override_dh_installdocs-indep:
ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS)))
dh_installdocs -i
find debian -name __pycache__ -type d | xargs rm -rf
# dh_installdocs seems to refuse copying zero length files (for
# instance Tests/Blast/tab_2226_tblastn_002.txt) but these are
# needed for the tests as well
# The following line breaks the build with nocheck, but
# we can't remove it yet because doing so seems to break autopkgtests
cp -a debian/tmp_tests/* $(DOCDIR)
# Tackle privacy breaches caused by MathML.
sed -i 's@https://cdn.jsdelivr.net/npm/mathjax\@3/es5/tex-mml-chtml.js@file:///usr/share/nodejs/mathjax-full/es5/tex-mml-chtml.js@' \
$(DOCDIR)/html/Tutorial/*.html \
$(DOCDIR)/html/index.html
# Clean fonts that made their way to the documentation package.
rm -rvf $(DOCDIR)/html/_static/fonts/
# Use Debian provided Javascript files.
rm -v $(DOCDIR)/html/_static/jquery.js
ln -sv /usr/share/javascript/jquery/jquery.js \
$(DOCDIR)/html/_static/jquery.js
rm -v $(DOCDIR)/html/_static/doctools.js
ln -sv /usr/share/javascript/sphinxdoc/1.0/doctools.js \
$(DOCDIR)/html/_static/doctools.js
rm -v $(DOCDIR)/html/_static/language_data.js
ln -sv /usr/share/javascript/sphinxdoc/1.0/language_data.js \
$(DOCDIR)/html/_static/language_data.js
rm -v $(DOCDIR)/html/_static/searchtools.js
ln -sv /usr/share/javascript/sphinxdoc/1.0/searchtools.js \
$(DOCDIR)/html/_static/searchtools.js
endif
override_dh_fixperms:
dh_fixperms
find debian -name "*.dtd" -exec chmod -x \{\} \;
|
