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
130
131
132
133
134
135
136
137
138
139
140
141
|
#!/usr/bin/make -f
# See debhelper(7) (uncomment to enable)
# output every command that modifies files on the build system.
#export DH_VERBOSE = 1
export PYBUILD_NAME=mdanalysis
export PYBUILD_DIR=package
# skip tests on these arches
ARCH_NO_TEST_LIST = hurd-i386
empty :=
space := $(empty)$(empty)
# run tests, or not
#RUNTEST=yes
# always skip all tests for now, see Bug#1108309
RUNTEST=no
ifneq (,$(findstring $(space)$(DEB_HOST_ARCH)$(space), $(space)$(ARCH_NO_TEST_LIST)$(space)))
RUNTEST=no
endif
ifeq (nocheck,$(findstring nocheck,$(DEB_BUILD_OPTIONS)))
RUNTEST=no
endif
# parallel and openmp tests are unstable, often timing out
SKIP_TEST_LIST += parallel multiprocess openmp
# gsd tends to induce test time-outs, https://github.com/MDAnalysis/mdanalysis/issues/4209
SKIP_TEST_LIST += gsd GSD
# NSGrid is flaky and causes distance tests to often (randomly) fail
# https://github.com/MDAnalysis/mdanalysis/issues/4906
SKIP_TEST_LIST += test_distances
# mdahole2, pathsimanalysis are not yet packaged for debian
# (duecredit test journal.pcbi.1004568 accesses pathsimanalysis)
SKIP_TEST_LIST += test_all_import[.analysis.hole2] journal.pcbi.1004568
ifneq (,$(findstring $(DEB_HOST_ARCH), i386))
export DEB_CFLAGS_MAINT_APPEND += -ffloat-store -fexcess-precision=fast
SKIP_TEST_LIST += test_multiprocess_COG[u4] test_ramachandran
SKIP_TEST_LIST += test_clustering_three_ensembles_two_identical test_hbond_analysis
endif
ifneq (,$(findstring $(DEB_HOST_ARCH), s390x))
SKIP_TEST_LIST += test_start_stop_step test_count_by_time \
test_rmsd test_mass_weighted test_custom_weighted test_ref_mobile_mass_mismapped \
test_time test_dt test_total_time test_iter test_last_frame test_frame_jump \
test_next_gives_second_frame test_set_time test_write_istart \
test_write_trajectory_atomgroup test_write_trajectory_universe test_Timestep_time \
test_rename_aux test_namdbin ref_reader25 ref_reader_extra_args25
endif
ifneq (,$(findstring $(DEB_HOST_ARCH), hppa))
SKIP_TEST_LIST += Parallel parallel Serial \
test_frame_bool_fail FrameAnalysis test_start_stop_step test_AnalysisFromFunction_args_content \
test_bat_multifragments_atomgroup test_distance_box test_n_initial_contacts \
test_density_analysis_conversion_default_unit \
test_trajectory[client_DSSP test_atomgroup[client_DSSP test_trajectory_with_hydrogens[client_DSSP \
test_get_distance_matrix TestHydrogenBondAnalysisTIP3P \
test_cosine_content TestRMSD \
"(TestChainReader and test_time)" TestChainReaderFormats TestChainReaderContinuous test_issue_4008 \
TestDCDReader test_write_istart TestDCDWriter test_writer_dt test_other_writer \
test_writer_no_h5py TestLAMMPSDCDReader TestMemoryReader TestNAMDBINReader TestNCDFWriter \
test_xdr test_write_frame_none test_tpr_fragments test_reader_wo_timeseries test_libmdaxdr \
test_universe_creation_from_coordinates test_universe_unpickle_in_new_process test_creating_multiple_universe_without_offset \
test_universe_with_minimal test_streamplot test_frame_slice[run_kwargs TestDensityAnalysis \
test_diffusionmap test_dihedrals test_gnm test_random_walk_u_simple test_rdf_s TestRMSF \
TestXVGReader TestXVGFileReader "(test_copying and test_reader_)" test_timestep_copied test_positions_share_memory \
NAMDBINWriter test_NullWriter TestBaseTimestepInterface test_center_compounds_ TestSelectionsTPR \
test_group_traj_access TestAllCoordinatesKwarg TestUpdatingSelection \
test_multiprocess_COG[u1 test_readers_pickle[ref_reader17] test_readers_pickle[ref_reader20] test_readers_pickle[ref_reader30] \
test_nojump_iterate_twice test_posavging_
endif
ifneq (,$(findstring $(DEB_HOST_ARCH), ppc64))
SKIP_TEST_LIST += test_start_stop_step TestHydrogenBondAnalysisTIP3P \
TestRMSD "(TestChainReader and test_time)" TestDCDReader TestDCDWriter \
test_write_istart TestLAMMPSDCDReader "(TestMemoryReader and (test_rename_aux or test_iter_as_aux))" \
TestNAMDBINReader NAMDBINWriter "(test_copying and test_reader)" \
test_timestep_copied[ref_reader25] test_positions_share_memory[ref_reader25]
endif
SKIP_TESTS=$(shell skip_tests=""; list_initialised=0; \
for t in $(SKIP_TEST_LIST); do \
if [ $${list_initialised} = 0 ]; then \
skip_tests=$$t; \
list_initialised=1; \
else \
skip_tests="$${skip_tests} or $$t"; \
fi; \
done; \
if [ "x$${skip_tests}" != "x" ]; then \
echo "not ( $${skip_tests} )"; \
fi )
%:
dh $@ --with sphinxdoc --buildsystem=pybuild
execute_after_dh_auto_clean:
rm -f .duecredit.p
rm -f package/MDAnalysis/authors.py
rm -f package/MDAnalysis/analysis/encore/clustering/affinityprop.c \
package/MDAnalysis/analysis/encore/cutils.c \
package/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c \
package/MDAnalysis/coordinates/timestep.cpp \
package/MDAnalysis/lib/_augment.cpp \
package/MDAnalysis/lib/_cutil.cpp \
package/MDAnalysis/lib/c_distances.c \
package/MDAnalysis/lib/c_distances_openmp.c \
package/MDAnalysis/lib/formats/cython_util.c \
package/MDAnalysis/lib/formats/libdcd.c \
package/MDAnalysis/lib/formats/libmdaxdr.c \
package/MDAnalysis/lib/nsgrid.cpp \
package/MDAnalysis/lib/qcprot.c
rm -rf package/MDAnalysis.egg-info
rm -f testsuite/MDAnalysisTests/data/.*_offsets.npz testsuite/MDAnalysisTests/data/*/.*_offsets.npz
rm -rf testsuite/.pytest_cache
override_dh_auto_test:
ifeq (yes,$(findstring yes,$(RUNTEST)))
set -e; \
for py in $(shell py3versions -rv); do \
echo "=== testing with python$$py ==="; \
pydir=`pybuild -p $$py --system=distutils --print {build_dir}`; \
MPLBACKEND=agg PYTHONPATH=$$pydir python$$py -mpytest -v -k "$(SKIP_TESTS)" --disable-pytest-warnings testsuite; \
rm -rf $$pydir/MDAnalysis/.hypothesis; \
rm -rf $$pydir/MDAnalysis/.duecredit.p; \
done
endif
execute_after_dh_python3:
dh_numpy3
rm -rf debian/python3-mdanalysis/usr/lib/python3.*
execute_after_dh_auto_build-indep: export http_proxy=127.0.0.1:9
execute_after_dh_auto_build-indep: export https_proxy=127.0.0.1:9
execute_after_dh_auto_build-indep:
PYTHONPATH=$(shell pybuild --pyver `py3versions --default -v` --print {build_dir}) make html -C package/doc/sphinx/ BUILDDIR=$(CURDIR)/.pybuild # HTML generator
|
