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commit 6d80e0f6a6f4f9fbe8f99cff67af01c528ea84f7 Author: Afif Elghraoui <[email protected]> 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 <[email protected]> -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 <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pbcore.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
