[med-svn] [python-pbcore] 03/06: Update patches
Afif Elghraoui
afif at moszumanska.debian.org
Sun Jan 7 07:06:17 UTC 2018
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository python-pbcore.
commit 6d80e0f6a6f4f9fbe8f99cff67af01c528ea84f7
Author: Afif Elghraoui <afif at debian.org>
Date: Sun Jan 7 01:21:57 2018 -0500
Update patches
---
debian/patches/deprecate-dataset.patch | 14 --------
debian/patches/enable-build-time-testing.patch | 4 +--
debian/patches/ignore-pyxb.patch | 40 ++++++++++++----------
debian/patches/remove-unnecessary-cython-dep.patch | 3 +-
debian/patches/series | 1 -
5 files changed, 24 insertions(+), 38 deletions(-)
diff --git a/debian/patches/deprecate-dataset.patch b/debian/patches/deprecate-dataset.patch
deleted file mode 100644
index 450fd2c..0000000
--- a/debian/patches/deprecate-dataset.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Description: pbdataset was moved to another package
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
-Last-Update: 2016-04-11
---- python-pbcore.orig/setup.py
-+++ python-pbcore/setup.py
-@@ -51,7 +51,6 @@
- zip_safe = False,
- test_suite = 'nose.collector',
- entry_points = { "console_scripts" : [ ".open = pbcore.io.opener:entryPoint" ] },
-- scripts=['bin/dataset.py'],
- install_requires=_get_local_requirements(_REQUIREMENTS_FILE),
- tests_require=_get_local_requirements(_REQUIREMENTS_TEST_FILE)
- )
diff --git a/debian/patches/enable-build-time-testing.patch b/debian/patches/enable-build-time-testing.patch
index 61b3f48..74e8823 100644
--- a/debian/patches/enable-build-time-testing.patch
+++ b/debian/patches/enable-build-time-testing.patch
@@ -15,11 +15,11 @@ Last-Update: 2015-08-06
+where=tests
--- python-pbcore.orig/setup.py
+++ python-pbcore/setup.py
-@@ -49,6 +49,7 @@
+@@ -50,6 +50,7 @@
'data/datasets/yieldtest/*.*']
},
zip_safe = False,
+ test_suite = 'nose.collector',
entry_points = { "console_scripts" : [ ".open = pbcore.io.opener:entryPoint" ] },
- scripts=['bin/dataset.py'],
install_requires=_get_local_requirements(_REQUIREMENTS_FILE),
+ tests_require=_get_local_requirements(_REQUIREMENTS_TEST_FILE)
diff --git a/debian/patches/ignore-pyxb.patch b/debian/patches/ignore-pyxb.patch
index 015b60b..d8421ff 100644
--- a/debian/patches/ignore-pyxb.patch
+++ b/debian/patches/ignore-pyxb.patch
@@ -6,10 +6,10 @@ Description: Ignore hard-coded pyxb version check
Author: Afif Elghraoui <afif at debian.org>
Forwarded: not-needed
Last-Update: 2016-10-09
---- python-pbcore.orig/pbcore/io/dataset/DataSetXsd.py
-+++ python-pbcore/pbcore/io/dataset/DataSetXsd.py
+--- python-pbcore.orig/pbcore/io/dataset/pyxb/DataSetXsd.py
++++ python-pbcore/pbcore/io/dataset/pyxb/DataSetXsd.py
@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:8749368c-9df1-11e5-86b0-001a4acb6b14')
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
# Version of PyXB used to generate the bindings
-_PyXBVersion = '1.2.4'
@@ -21,11 +21,11 @@ Last-Update: 2016-10-09
+# raise pyxb.PyXBVersionError(_PyXBVersion)
# Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- python-pbcore.orig/pbcore/io/dataset/_pbbase.py
-+++ python-pbcore/pbcore/io/dataset/_pbbase.py
+ import _pbbase as _ImportedBinding__pbbase
+--- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbbase.py
++++ python-pbcore/pbcore/io/dataset/pyxb/_pbbase.py
@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:8749368c-9df1-11e5-86b0-001a4acb6b14')
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
# Version of PyXB used to generate the bindings
-_PyXBVersion = '1.2.4'
@@ -38,10 +38,10 @@ Last-Update: 2016-10-09
# Import bindings for namespaces imported into schema
import pyxb.binding.datatypes
---- python-pbcore.orig/pbcore/io/dataset/_pbmeta.py
-+++ python-pbcore/pbcore/io/dataset/_pbmeta.py
+--- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbmeta.py
++++ python-pbcore/pbcore/io/dataset/pyxb/_pbmeta.py
@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:8749368c-9df1-11e5-86b0-001a4acb6b14')
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
# Version of PyXB used to generate the bindings
-_PyXBVersion = '1.2.4'
@@ -53,11 +53,11 @@ Last-Update: 2016-10-09
+# raise pyxb.PyXBVersionError(_PyXBVersion)
# Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- python-pbcore.orig/pbcore/io/dataset/_pbrk.py
-+++ python-pbcore/pbcore/io/dataset/_pbrk.py
+ import _pbrk as _ImportedBinding__pbrk
+--- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbrk.py
++++ python-pbcore/pbcore/io/dataset/pyxb/_pbrk.py
@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:8749368c-9df1-11e5-86b0-001a4acb6b14')
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
# Version of PyXB used to generate the bindings
-_PyXBVersion = '1.2.4'
@@ -70,10 +70,10 @@ Last-Update: 2016-10-09
# Import bindings for namespaces imported into schema
import pyxb.binding.datatypes
---- python-pbcore.orig/pbcore/io/dataset/_pbsample.py
-+++ python-pbcore/pbcore/io/dataset/_pbsample.py
+--- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbsample.py
++++ python-pbcore/pbcore/io/dataset/pyxb/_pbsample.py
@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:8749368c-9df1-11e5-86b0-001a4acb6b14')
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
# Version of PyXB used to generate the bindings
-_PyXBVersion = '1.2.4'
@@ -88,8 +88,10 @@ Last-Update: 2016-10-09
import pyxb.binding.datatypes
--- python-pbcore.orig/requirements-dev.txt
+++ python-pbcore/requirements-dev.txt
-@@ -1,3 +1,3 @@
- sphinx
+@@ -1,5 +1,5 @@
+ coverage
nose
-pyxb==1.2.4
+pyxb
+ sphinx
+ h5py >= 2.0.1
diff --git a/debian/patches/remove-unnecessary-cython-dep.patch b/debian/patches/remove-unnecessary-cython-dep.patch
index 79a01c3..26c3053 100644
--- a/debian/patches/remove-unnecessary-cython-dep.patch
+++ b/debian/patches/remove-unnecessary-cython-dep.patch
@@ -7,8 +7,7 @@ Forwarded: no
Last-Update: 2015-12-13
--- python-pbcore.orig/requirements.txt
+++ python-pbcore/requirements.txt
-@@ -1,4 +1,3 @@
+@@ -1,3 +1,2 @@
-cython
numpy >= 1.7.1
- h5py >= 2.0.1
pysam >= 0.9.0
diff --git a/debian/patches/series b/debian/patches/series
index 00dca95..def20f1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,4 @@
doc-theme.patch
enable-build-time-testing.patch
remove-unnecessary-cython-dep.patch
-deprecate-dataset.patch
ignore-pyxb.patch
--
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