[med-svn] [Git][med-team/python-pbcore][master] pbtestdata is not yet packaged
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Dec 23 11:50:52 GMT 2021
Andreas Tille pushed to branch master at Debian Med / python-pbcore
Commits:
9fd62d52 by Andreas Tille at 2021-12-23T12:50:20+01:00
pbtestdata is not yet packaged
- - - - -
6 changed files:
- debian/control
- debian/patches/b24746790c7105212e45dc2f40115d231bd8baae.patch
- − debian/patches/do_not_call_pip_to_fetch_wheel.patch
- debian/patches/exclude_test_missing_data.patch
- − debian/patches/ignore-pyxb.patch
- debian/patches/series
Changes:
=====================================
debian/control
=====================================
@@ -18,7 +18,7 @@ Build-Depends: debhelper-compat (= 12),
python3-pytest-xdist <!nocheck>,
python3-pytest-cov <!nocheck>,
python3-biopython (>= 1.74) <!nocheck>,
- python3-wheel <!nocheck>,
+ python3-xmlschema <!nocheck>,
pylint,
python3-coverage
Standards-Version: 4.5.0
=====================================
debian/patches/b24746790c7105212e45dc2f40115d231bd8baae.patch
=====================================
@@ -15353,7 +15353,7 @@ Fixes #122
-
--- a/setup.py
+++ b/setup.py
-@@ -10,13 +10,13 @@ test_deps = [
+@@ -9,13 +9,13 @@ test_deps = [
'pytest',
'pytest-cov',
'pytest-xdist',
=====================================
debian/patches/do_not_call_pip_to_fetch_wheel.patch deleted
=====================================
@@ -1,11 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -73,6 +73,6 @@ validate-metadata:
- xmllint --schema ../xsd-datamodels/PacBioCollectionMetadata.xsd pbcore/data/datasets/CollectionMetadata.xml
-
- wheel:
-- which pip
-- pip wheel --wheel-dir=${WHEELHOUSE} --no-deps .
-+ # which pip
-+ echo "Do not call 'pip wheel --wheel-dir=${WHEELHOUSE} --no-deps .'"
- ls -larth ${WHEELHOUSE}
=====================================
debian/patches/exclude_test_missing_data.patch
=====================================
@@ -4,23 +4,30 @@ Description: Missing data for this test
--- a/tests/test_pbdataset_metadata.py
+++ b/tests/test_pbdataset_metadata.py
-@@ -153,19 +153,6 @@ class TestDataSet(unittest.TestCase):
+@@ -134,6 +134,7 @@ class TestDataSet:
aln = AlignmentSet(outXml)
- self.assertEqual(aln.uuid, oldUuid)
+ assert aln.uuid == oldUuid
-- def test_merge(self):
-- sset_fn = ('/pbi/dept/secondary/siv/testdata/'
-- 'SA3-Sequel/lambda/roche_SAT/'
-- 'm54013_151205_032353.subreadset.xml')
-- sset = SubreadSet(sset_fn)
-- orig_metadata = copy.deepcopy(sset.metadata)
-- self.assertEqual(len(sset.metadata.collections), 1)
-- sset.metadata.collections.merge(orig_metadata.collections)
-- self.assertEqual(len(sset.metadata.collections), 2)
-- sset = SubreadSet(sset_fn)
-- sset.metadata.collections.merge(orig_metadata.collections, forceUnique=True)
-- self.assertEqual(len(sset.metadata.collections), 1)
--
- @skip_if_no_pbtestdata
- def test_merge_biosamples(self):
- import pbtestdata
++ @pytest.mark.skip(reason="pbtestdata is not packaged yet")
+ @pytest.mark.internal_data
+ def test_merge(self):
+ sset_fn = ('/pbi/dept/secondary/siv/testdata/'
+--- a/pytest.ini
++++ b/pytest.ini
+@@ -1,6 +1,5 @@
+ [pytest]
+ markers =
+- pbtestdata: requires the 'PacBioTestData' package to be installed
+ internal_data: requires access to internal data on '/pbi/dept/secondary/siv/testdata'
+ constools: requires 'pbindex', 'samtools' and 'pbmerge' in PATH
+
+--- a/setup.py
++++ b/setup.py
+@@ -5,7 +5,6 @@ from setuptools import setup, find_packa
+
+ test_deps = [
+ 'coverage',
+- 'pbtestdata',
+ 'pylint',
+ 'pytest',
+ 'pytest-cov',
=====================================
debian/patches/ignore-pyxb.patch deleted
=====================================
@@ -1,90 +0,0 @@
-Description: Ignore hard-coded pyxb version check
- Upstream does not really care to keep up with pyxb versions
- (see https://github.com/PacificBiosciences/pbcore/pull/105/commits/2b2782e68a0117e0844279a001a010376e18b644)
- Dataset is not an interesting part of pbcore either. Disabling the hardcoded
- version check, the test suite still passes.
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
-Last-Update: 2016-10-09
-Bug-Debian: https://bugs.debian.org/950336
-
---- a/pbcore/io/dataset/pyxb/DataSetXsd.py
-+++ b/pbcore/io/dataset/pyxb/DataSetXsd.py
-@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:a9ab3db6-517a-11e9-bbae-005056872f45')
-
- # Version of PyXB used to generate the bindings
--_PyXBVersion = '1.2.4'
-+#_PyXBVersion = '1.2.4'
- # Generated bindings are not compatible across PyXB versions
--if pyxb.__version__ != _PyXBVersion:
-- raise pyxb.PyXBVersionError(_PyXBVersion)
-+#if pyxb.__version__ != _PyXBVersion:
-+# raise pyxb.PyXBVersionError(_PyXBVersion)
-
- # Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- a/pbcore/io/dataset/pyxb/_pbbase.py
-+++ b/pbcore/io/dataset/pyxb/_pbbase.py
-@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:a9ab3db6-517a-11e9-bbae-005056872f45')
-
- # Version of PyXB used to generate the bindings
--_PyXBVersion = '1.2.4'
-+#_PyXBVersion = '1.2.4'
- # Generated bindings are not compatible across PyXB versions
--if pyxb.__version__ != _PyXBVersion:
-- raise pyxb.PyXBVersionError(_PyXBVersion)
-+#if pyxb.__version__ != _PyXBVersion:
-+# raise pyxb.PyXBVersionError(_PyXBVersion)
-
- # Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- a/pbcore/io/dataset/pyxb/_pbmeta.py
-+++ b/pbcore/io/dataset/pyxb/_pbmeta.py
-@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:a9ab3db6-517a-11e9-bbae-005056872f45')
-
- # Version of PyXB used to generate the bindings
--_PyXBVersion = '1.2.4'
-+#_PyXBVersion = '1.2.4'
- # Generated bindings are not compatible across PyXB versions
--if pyxb.__version__ != _PyXBVersion:
-- raise pyxb.PyXBVersionError(_PyXBVersion)
-+#if pyxb.__version__ != _PyXBVersion:
-+# raise pyxb.PyXBVersionError(_PyXBVersion)
-
- # Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- a/pbcore/io/dataset/pyxb/_pbrk.py
-+++ b/pbcore/io/dataset/pyxb/_pbrk.py
-@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:a9ab3db6-517a-11e9-bbae-005056872f45')
-
- # Version of PyXB used to generate the bindings
--_PyXBVersion = '1.2.4'
-+#_PyXBVersion = '1.2.4'
- # Generated bindings are not compatible across PyXB versions
--if pyxb.__version__ != _PyXBVersion:
-- raise pyxb.PyXBVersionError(_PyXBVersion)
-+#if pyxb.__version__ != _PyXBVersion:
-+# raise pyxb.PyXBVersionError(_PyXBVersion)
-
- # Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- a/pbcore/io/dataset/pyxb/_pbsample.py
-+++ b/pbcore/io/dataset/pyxb/_pbsample.py
-@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:a9ab3db6-517a-11e9-bbae-005056872f45')
-
- # Version of PyXB used to generate the bindings
--_PyXBVersion = '1.2.4'
-+#_PyXBVersion = '1.2.4'
- # Generated bindings are not compatible across PyXB versions
--if pyxb.__version__ != _PyXBVersion:
-- raise pyxb.PyXBVersionError(_PyXBVersion)
-+#if pyxb.__version__ != _PyXBVersion:
-+# raise pyxb.PyXBVersionError(_PyXBVersion)
-
- # Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,4 @@
doc-theme.patch
enable-build-time-testing.patch
-# ignore-pyxb.patch
-# exclude_test_missing_data.patch
+exclude_test_missing_data.patch
b24746790c7105212e45dc2f40115d231bd8baae.patch
-do_not_call_pip_to_fetch_wheel.patch
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/commit/9fd62d52e99a3b7467f9f7a262dcddc15ffa1a96
--
View it on GitLab: https://salsa.debian.org/med-team/python-pbcore/-/commit/9fd62d52e99a3b7467f9f7a262dcddc15ffa1a96
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