1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
#!/usr/bin/make -f
# Uncomment this to turn on verbose mode.
export DH_VERBOSE=1
#export PYBUILD_NAME=biopython
#export PYBUILD_DESTDIR_python2=debian/python-biopython/
#export PYBUILD_DESTDIR_python3=debian/python3-biopython/
# export DEB_BUILD_MAINT_OPTIONS = hardening=+all ... does not build
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
# Fails to build with this option switched on
# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
BUILDARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH)
# If `$(CURDIR)/setup.py test` would be called these tests need to be excluded since they require to be online
#EXCLUDEONLINE=Entrez_online HotRand NCBI_qblast SCOP_online SeqIO_online TogoWS
# Since `run_texts.py --online` is used the test requiring online connections are excluded by the test suite
EXCLUDEONLINE=
# 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# avoid testing tools that are not packaged for Debian yet (or will never be packaged since they might be outdated)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 NACCESS_tool PopGen_DFDist PopGen_FDist PopGen_GenePop PopGen_GenePop_EasyController PopGen_SimCoal XXmotif_tool
# avoid amd64 only tools on other architectures
ifeq ($(BUILDARCH),amd64)
EXCLUDEARCHamd64=
else
EXCLUDEARCHamd64=BWA_tool raxml_tool
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
# With recent phyml we get:
# ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa', message 'beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware'
# See https://bugs.debian.org/813262
EXCLUDEFAILINGTESTS=phyml_tool
# FIXME: Currently it is not sure for what architecture samtools will be available
# to anable a smooth migration to testing the build-dependency will be dropped
# for the moment
# .
# The samtools test also fails on amd64. This is reported upstream
# see https://github.com/biopython/biopython/issues/625
EXCLUDEPACKAGEINFLUX=samtools_tool
%:
dh $@ --with python2,python3 --buildsystem=pybuild
override_dh_auto_clean:
dh_auto_clean
cd Doc && make distclean
override_dh_auto_build:
dh_auto_build
cd Doc && make
override_dh_auto_install:
dh_auto_install
dh_numpy -ppython-biopython
dh_numpy3 -ppython3-biopython
override_dh_auto_test:
ifeq ($(BUILDARCH),mips)
echo "***************************************************************************"
echo "* Attention: Build time tests for mips architecture are skipped. *"
echo "* The reason is that the tests are known to fail for Python3 and the *"
echo "* effort to simply run only for Python 2.7 seems to be error prone. *"
echo "* Upstream is working on a solution so this should be dropped for *"
echo "* next upstream version. See: *"
echo "* http://mailman.open-bio.org/pipermail/biopython/2014-August/015383.html *"
echo "***************************************************************************"
else
mkdir -p Tests_avoid
for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \
; do \
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
# We also keep the tests we need to avoid for later inspection
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.tex {build_dir}/Doc; \
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'
mv Tests_avoid/* Tests
rmdir Tests_avoid
endif
override_dh_installdocs-indep:
dh_installdocs
find debian -name __pycache__ -type d | xargs rm -rf
find debian -name example.fastq.gz
# 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
cp -a debian/tmp_tests/* $(CURDIR)/debian/python-biopython-doc/usr/share/doc/python-biopython-doc/
find debian -name .cvsignore -delete
cd debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc && make clean
find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name Makefile -delete
find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name "*.aux" -delete
find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -name "*.lyx" -delete
find debian/python-biopython-doc/usr/share/doc/python-biopython-doc/Doc -type d -empty -delete
override_dh_auto_clean:
dh_auto_clean
if [ -d Tests_avoid ] ; then \
mv Tests_avoid/* Tests ; \
rmdir Tests_avoid ; \
fi
rm -rf debian/tmp_tests
|
