[med-svn] [Git][med-team/python-bx][master] 2 commits: d/control: now run the autopkgtesting using pybuild-autopkgtest.
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Tue Feb 27 18:34:24 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / python-bx
Commits:
4438273f by Michael R. Crusoe at 2024-02-27T18:57:39+01:00
d/control: now run the autopkgtesting using pybuild-autopkgtest.
- - - - -
5e79d014 by Michael R. Crusoe at 2024-02-27T18:57:39+01:00
routine-update: Ready to upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- + debian/patches/post-install-testing
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,13 @@
-python-bx (0.11.0-2) UNRELEASED; urgency=medium
+python-bx (0.11.0-2) unstable; urgency=medium
* d/rules: use dh_numpy3 to inject a dependency on the appropriate
numpy ABI.
* mark the fix_BIN_OFFSETS_MAX patch as being forwarded upstream.
* d/control: switch to pyproject based building.
* d/patches/pytest8: add pytest 8.x compatability.
+ * d/control: use pybuild-autopkgtest to provide non-superficial autopkgtests
- -- Michael R. Crusoe <crusoe at debian.org> Tue, 27 Feb 2024 16:05:18 +0100
+ -- Michael R. Crusoe <crusoe at debian.org> Tue, 27 Feb 2024 18:54:18 +0100
python-bx (0.11.0-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Steffen Moeller <moeller at debian.org>,
Michael R. Crusoe <crusoe at debian.org>
Section: python
-Testsuite: autopkgtest-pkg-python
+Testsuite: autopkgtest-pkg-pybuild
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
=====================================
debian/patches/post-install-testing
=====================================
@@ -0,0 +1,132 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: enable post-installation testing
+Forwarded: https://github.com/bxlab/bx-python/pull/93
+--- python-bx.orig/lib/bx/align/sitemask/sitemask_tests.py
++++ python-bx/lib/bx/align/sitemask/sitemask_tests.py
+@@ -6,7 +6,7 @@
+ from io import StringIO
+
+ import bx.align.maf
+-from . import cpg
++from bx.align.sitemask import cpg
+
+ test_maf_cpg = """##maf version=1 scoring=none
+ a score=0
+--- python-bx.orig/lib/bx/binned_array_tests.py
++++ python-bx/lib/bx/binned_array_tests.py
+@@ -10,7 +10,7 @@
+ )
+ from numpy.random import random_sample as random
+
+-from .binned_array import (
++from bx.binned_array import (
+ BinnedArray,
+ BinnedArrayWriter,
+ FileBinnedArray,
+--- python-bx.orig/lib/bx/interval_index_file_tests.py
++++ python-bx/lib/bx/interval_index_file_tests.py
+@@ -1,8 +1,8 @@
+ import random
+ from tempfile import mktemp
+
+-from . import interval_index_file
+-from .interval_index_file import Indexes
++from bx import interval_index_file
++from bx.interval_index_file import Indexes
+
+
+ def test_offsets():
+--- python-bx.orig/lib/bx/intervals/cluster_tests.py
++++ python-bx/lib/bx/intervals/cluster_tests.py
+@@ -2,13 +2,7 @@
+ import sys
+ import unittest
+
+-try:
+- sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
+-except Exception:
+- sys.path.insert(0, os.path.dirname(os.path.abspath(".")))
+-
+-# from bx.intervals.cluster import ClusterTree
+-from .cluster import ClusterTree
++from bx.intervals.cluster import ClusterTree
+
+
+ class TestCluster(unittest.TestCase):
+--- python-bx.orig/lib/bx/misc/seekbzip2_tests.py
++++ python-bx/lib/bx/misc/seekbzip2_tests.py
+@@ -7,7 +7,7 @@
+ import random
+ from codecs import encode
+
+-from . import seekbzip2
++from bx.misc import seekbzip2
+
+ F = None
+ T = None
+--- python-bx.orig/lib/bx/motif/io/transfac_tests.py
++++ python-bx/lib/bx/motif/io/transfac_tests.py
+@@ -2,7 +2,7 @@
+
+ from numpy import allclose
+
+-from . import transfac
++from bx.motif.io import transfac
+
+ sample = """
+ VV TRANSFAC MATRIX TABLE, Rel.3.2 26-06-1997
+--- python-bx.orig/lib/bx/motif/pwm_tests.py
++++ python-bx/lib/bx/motif/pwm_tests.py
+@@ -3,7 +3,7 @@
+ isnan,
+ )
+
+-from . import pwm
++from bx.motif import pwm
+
+
+ def test_create():
+--- python-bx.orig/lib/bx/seq/fasta_tests.py
++++ python-bx/lib/bx/seq/fasta_tests.py
+@@ -4,7 +4,7 @@
+
+ import unittest
+
+-from . import fasta
++from bx.seq import fasta
+
+ test_fa = "test_data/seq_tests/test.fa"
+
+--- python-bx.orig/lib/bx/seq/nib_tests.py
++++ python-bx/lib/bx/seq/nib_tests.py
+@@ -4,7 +4,7 @@
+
+ import unittest
+
+-from . import nib
++from bx.seq import nib
+
+ test_nib = "test_data/seq_tests/test.nib"
+
+--- python-bx.orig/lib/bx/seq/qdna_tests.py
++++ python-bx/lib/bx/seq/qdna_tests.py
+@@ -4,7 +4,7 @@
+
+ import unittest
+
+-from . import qdna
++from bx.seq import qdna
+
+ test_qdna = "test_data/seq_tests/test.qdna"
+
+--- python-bx.orig/lib/bx/seq/twobit_tests.py
++++ python-bx/lib/bx/seq/twobit_tests.py
+@@ -2,7 +2,7 @@
+
+ import pytest
+
+-from . import twobit
++from bx.seq import twobit
+
+
+ def quick_fasta_iter(f):
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+post-install-testing
pytest8
shebang.patch
fix_BIN_OFFSETS_MAX
=====================================
debian/rules
=====================================
@@ -7,8 +7,8 @@ export LC_ALL=C.UTF-8
export NOSE_VERBOSE=2
export PYBUILD_NAME=bx-python
-export PYBUILD_BEFORE_TEST=cp -r {dir}/test_data {build_dir}/
-
+export PYBUILD_BEFORE_TEST=export PYTHONPATH={install_dir} ; cp -r {dir}/test_data {build_dir}/
+export PYBUILD_AFTER_TEST=rm -Rf {build_dir}/test_data
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
%:
@@ -22,6 +22,13 @@ override_dh_auto_clean:
# Changes perpetually redone
rm -rf lib/bx_python.egg-info
+before-pybuild-autopkgtest:
+ find lib -name "*_tests.py" > debian/pybuild.testfiles
+ echo pytest.ini >> debian/pybuild.testfiles
+
+after-pybuild-autopkgtest:
+ rm debian/pybuild.testfiles
+
override_dh_python3:
dh_python3 --shebang=/usr/bin/python3
dh_numpy3
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/ad9cf2d25fc899d03f67a3690b52042fa9d7a8ac...5e79d01420f3f46edc7677e968f15d3e2c23750f
--
View it on GitLab: https://salsa.debian.org/med-team/python-bx/-/compare/ad9cf2d25fc899d03f67a3690b52042fa9d7a8ac...5e79d01420f3f46edc7677e968f15d3e2c23750f
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