[med-svn] [python-pbcore] 01/11: Drop non-functional python3 package
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Aug 11 07:48:18 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbcore.
commit dafea9c3a095d483965d16cef85465861fefb3c4
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Mon Aug 10 21:50:39 2015 -0700
Drop non-functional python3 package
It needed quite a bit of work and is not supported upstream at
the moment [1]. This also removes the need to split the data
package, so that has been dropped as well.
1. https://github.com/PacificBiosciences/pbcore/issues/18
---
debian/control | 46 +++-----------------------
debian/patches/enable-build-time-testing.patch | 6 ++--
debian/patches/remove-convenience-script.patch | 4 +--
debian/patches/series | 1 -
debian/patches/support-python3.patch | 38 ---------------------
debian/python-pbcore-data.install | 1 -
debian/python-pbcore.links | 1 -
debian/python-pbcore.pyremove | 1 -
debian/python3-pbcore.links | 1 -
debian/python3-pbcore.pyremove | 1 -
debian/rules | 5 +--
debian/tests/control | 8 ++---
12 files changed, 12 insertions(+), 101 deletions(-)
diff --git a/debian/control b/debian/control
index e15cd42..1b18d06 100644
--- a/debian/control
+++ b/debian/control
@@ -11,16 +11,9 @@ Build-Depends: debhelper (>= 9),
python-h5py (>= 2.0.1),
python-numpy (>= 1.7.1),
python-pysam (>= 0.8.1),
- python3-all,
- python3-setuptools,
- python3-nose,
- python3-h5py (>= 2.0.1),
- python3-numpy (>= 1.7.1),
- python3-pysam (>= 0.8.1),
python-sphinx
Standards-Version: 3.9.6
X-Python-Version: >= 2.7
-X-Python3-Version: >= 3.2
Homepage: https://github.com/PacificBiosciences/pbcore
Vcs-Git: git://anonscm.debian.org/debian-med/python-pbcore.git
Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbcore.git
@@ -28,47 +21,16 @@ Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbcore.git
Package: python-pbcore
Architecture: all
Depends: ${misc:Depends},
- ${python:Depends},
- python-six
-Suggests: python-pbcore-doc
-Description: Python library for processing PacBio data files (Python 2)
+ ${python:Depends}
+Suggests: python-pbcore-doc (= ${source:Version})
+Description: Python library for processing PacBio data files
The pbcore package provides Python modules for processing Pacific Biosciences
data files and building PacBio bioinformatics applications. These modules
include tools to read/write PacBio data formats, sample data files for
testing and debugging, base classes, and utilities for building bioinformatics
applications.
.
- This package is part of the SMRTAnalysis suite. It provides the Python2
- module
-
-Package: python3-pbcore
-Architecture: all
-Depends: ${misc:Depends},
- ${python3:Depends},
- python3-six
-Suggests: python-pbcore-doc
-Description: Python library for processing PacBio data files (Python 3)
- The pbcore package provides Python modules for processing Pacific Biosciences
- data files and building PacBio bioinformatics applications. These modules
- include tools to read/write PacBio data formats, sample data files for
- testing and debugging, base classes, and utilities for building bioinformatics
- applications.
- .
- This package is part of the SMRTAnalysis suite. It provides the Python3
- module.
-
-Package: python-pbcore-data
-Architecture: all
-Depends: ${misc:Depends}
-Description: Python library for processing PacBio data files (data)
- The pbcore package provides Python modules for processing Pacific Biosciences
- data files and building PacBio bioinformatics applications. These modules
- include tools to read/write PacBio data formats, sample data files for
- testing and debugging, base classes, and utilities for building bioinformatics
- applications.
- .
- pbcore is part of the SMRTAnalysis suite. This package provides sample
- data files.
+ This package is part of the SMRTAnalysis suite.
Package: python-pbcore-doc
Architecture: all
diff --git a/debian/patches/enable-build-time-testing.patch b/debian/patches/enable-build-time-testing.patch
index 88c722b..9cdbd64 100644
--- a/debian/patches/enable-build-time-testing.patch
+++ b/debian/patches/enable-build-time-testing.patch
@@ -12,12 +12,12 @@ Last-Update: 2015-08-06
description-file = README.md
+[nosetests]
+verbosity=2
-+where=temptests
++where=tests
--- python-pbcore.orig/setup.py
+++ python-pbcore/setup.py
-@@ -29,6 +29,7 @@
+@@ -30,6 +30,7 @@
+ 'data/datasets/yieldtest/*.*']
},
- use_2to3 = True,
zip_safe = False,
+ test_suite = 'nose.collector',
install_requires=[
diff --git a/debian/patches/remove-convenience-script.patch b/debian/patches/remove-convenience-script.patch
index d32a7c8..6282ad9 100644
--- a/debian/patches/remove-convenience-script.patch
+++ b/debian/patches/remove-convenience-script.patch
@@ -10,9 +10,9 @@ Last-Update: 2015-08-05
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-pbcore.orig/setup.py
+++ python-pbcore/setup.py
-@@ -29,8 +29,6 @@
+@@ -30,8 +30,6 @@
+ 'data/datasets/yieldtest/*.*']
},
- use_2to3 = True,
zip_safe = False,
- entry_points = { "console_scripts" : [ ".open = pbcore.io.opener:entryPoint" ] },
- scripts=['bin/dataset.py'],
diff --git a/debian/patches/series b/debian/patches/series
index c6733f2..8f4e122 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-support-python3.patch
remove-convenience-script.patch
doc-theme.patch
enable-build-time-testing.patch
diff --git a/debian/patches/support-python3.patch b/debian/patches/support-python3.patch
deleted file mode 100644
index 32fdc85..0000000
--- a/debian/patches/support-python3.patch
+++ /dev/null
@@ -1,38 +0,0 @@
-Description: Run 2to3 at build time to allow making a Python 3 package
- Following directions at <https://pythonhosted.org/setuptools/python3.html>
- we run 2to3 at build time to more easily support both Python 2 and Python 3.
- Doing this, there was an issue with converting the doctests similar to what is
- described at <http://bugs.python.org/issue12611>. To get around this,
- we disable converting doctests as described in the first link above.
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: no
-Last-Update: 2015-08-04
---- python-pbcore.orig/setup.py
-+++ python-pbcore/setup.py
-@@ -1,15 +1,13 @@
- #!/usr/bin/env python
- # -*- coding: utf-8 -*-
-
--from setuptools import setup, Extension, find_packages
-+from setuptools import setup, Extension, find_packages, setuptools
- import sys
-
--if ("install" in sys.argv) and sys.version_info < (2, 7, 0):
-- print "pbcore requires Python 2.7"
-- sys.exit(-1)
-+setuptools.run_2to3_on_doctests = False
-
- globals = {}
--execfile("pbcore/__init__.py", globals)
-+exec(open("pbcore/__init__.py").read(), globals)
- __VERSION__ = globals["__VERSION__"]
-
- setup(
-@@ -29,6 +27,7 @@
- 'data/datasets/*.*',
- 'data/datasets/yieldtest/*.*']
- },
-+ use_2to3 = True,
- zip_safe = False,
- entry_points = { "console_scripts" : [ ".open = pbcore.io.opener:entryPoint" ] },
- scripts=['bin/dataset.py'],
diff --git a/debian/python-pbcore-data.install b/debian/python-pbcore-data.install
deleted file mode 100644
index 62d1de1..0000000
--- a/debian/python-pbcore-data.install
+++ /dev/null
@@ -1 +0,0 @@
-pbcore/data usr/share/doc/python-pbcore
diff --git a/debian/python-pbcore.links b/debian/python-pbcore.links
deleted file mode 100644
index fb69ca0..0000000
--- a/debian/python-pbcore.links
+++ /dev/null
@@ -1 +0,0 @@
-/usr/share/doc/python-pbcore/data /usr/lib/python2.7/dist-packages/pbcore/data
diff --git a/debian/python-pbcore.pyremove b/debian/python-pbcore.pyremove
deleted file mode 100644
index f9d2565..0000000
--- a/debian/python-pbcore.pyremove
+++ /dev/null
@@ -1 +0,0 @@
-pbcore/data
diff --git a/debian/python3-pbcore.links b/debian/python3-pbcore.links
deleted file mode 100644
index f355287..0000000
--- a/debian/python3-pbcore.links
+++ /dev/null
@@ -1 +0,0 @@
-/usr/share/doc/python-pbcore/data /usr/lib/python3/dist-packages/pbcore/data
diff --git a/debian/python3-pbcore.pyremove b/debian/python3-pbcore.pyremove
deleted file mode 100644
index f9d2565..0000000
--- a/debian/python3-pbcore.pyremove
+++ /dev/null
@@ -1 +0,0 @@
-pbcore/data
diff --git a/debian/rules b/debian/rules
index 52a551c..ad7edae 100755
--- a/debian/rules
+++ b/debian/rules
@@ -6,7 +6,7 @@ include /usr/share/dpkg/default.mk
export PYBUILD_NAME = pbcore
%:
- LC_ALL=C.UTF-8 dh $@ --with python2,python3 --buildsystem=pybuild
+ LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
override_dh_auto_build:
dh_auto_build
@@ -21,9 +21,6 @@ override_dh_auto_clean:
override_dh_auto_test:
PYBUILD_SYSTEM=custom \
- PYBUILD_BEFORE_TEST="cp -rv {dir}/tests {dir}/temptests" \
- PYBUILD_BEFORE_TEST_python3="cp -rv {dir}/tests {dir}/temptests; 2to3 -w --no-diffs {dir}/temptests" \
- PYBUILD_AFTER_TEST="rm -rfv {dir}/temptests" \
PYBUILD_TEST_ARGS="{interpreter} setup.py test" \
dh_auto_test
diff --git a/debian/tests/control b/debian/tests/control
index 3402daf..5ef6767 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1,7 +1,3 @@
-Test-Command: make test
-Depends: @, python-sphinx, python-nose
-Restrictions: allow-stderr
-
-Test-Command: nosetests3 --with-xunit tests -v
-Depends: @, python3-nose
+Test-Command: nosetests -v tests
+Depends: python-pbcore-data, python-nose
Restrictions: allow-stderr
--
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