[med-svn] [Git][med-team/python-cobra][master] 2 commits: Drop Python 2 package since it has no reverse dependencies
Andreas Tille
gitlab at salsa.debian.org
Tue Sep 4 20:16:10 BST 2018
Andreas Tille pushed to branch master at Debian Med / python-cobra
Commits:
ec8cae51 by Andreas Tille at 2018-09-04T18:43:25Z
Drop Python 2 package since it has no reverse dependencies
- - - - -
10917aa9 by Andreas Tille at 2018-09-04T19:05:11Z
Drop failing test (needs further investigation)
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/drop_failing_test2.patch
- debian/patches/series
- − debian/python-cobra.links
- − debian/python-cobra.pyremove
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -9,15 +9,17 @@ python-cobra (0.13.3-1) UNRELEASED; urgency=medium
* Drop obsolete patch
[ Andreas Tille ]
- * Standards-Version: 4.2.0
+ * Standards-Version: 4.2.1
* Point Vcs-fields to Salsa
* debhelper 11
* Build-Depends: python*-requests, python*-pip
* Drop failing test TestCobraFluxSampling.test_fixed_seed
* Rename debian/tests/control to control.autodep8
* Testsuite: autopkgtest-pkg-python
- * Build-Depends: python-depinfo, python-pipdeptree
- TODO: packaging python-depinfo, python-pipdeptree
+ * Drop Python2 package since it has no reverse dependencies
+ * Build-Depends: python3-depinfo, python3-pipdeptree
+ * Drop failing test: test_show_versions
+ ---> needs further investigation
-- Andreas Tille <tille at debian.org> Sat, 28 Apr 2018 22:36:04 +0200
=====================================
debian/control
=====================================
@@ -8,23 +8,6 @@ Build-Depends:
debhelper (>= 11~),
dh-python,
libglpk-dev,
-# Python2
- python-all,
- python-all-dev,
- python-setuptools,
- python-depinfo,
- python-future,
- python-numpy (>= 1.6),
- python-optlang,,
- python-pandas (>= 0.17.0),
- python-pip,
- python-pipdeptree,
- python-requests,
- python-ruamel.yaml,
- python-swiglpk,
- python-tabulate,
- cython,
-# Python3
python3-all,
python3-all-dev,
python3-setuptools,
@@ -41,40 +24,14 @@ Build-Depends:
python3-tabulate,
cython3,
# Test-Depends:
- python-pytest,
- python-pytest-benchmark,
python3-pytest,
python3-pytest-benchmark,
- python-jsonschema (>> 2.5.0),
python3-jsonschema (>> 2.5.0)
-Standards-Version: 4.2.0
+Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/python-cobra
Vcs-Git: https://salsa.debian.org/med-team/python-cobra.git
Homepage: http://opencobra.github.io/cobrapy/
-Package: python-cobra
-Architecture: any
-Depends:
- ${shlibs:Depends},
- ${misc:Depends},
- ${python:Depends},
- python-cobra-data (= ${source:Version}),
-Recommends:
- libsbml5-python,
-Suggests:
- python-matplotlib,
- qsopt-ex,
-Description: constraint-based modeling of biological networks (Python 2)
- COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely
- used for genome-scale modeling of metabolic networks in both prokaryotes
- and eukaryotes. COBRApy is a constraint-based modeling package that is
- designed to accommodate the biological complexity of the next generation
- of COBRA models and provides access to commonly used COBRA methods, such
- as flux balance analysis, flux variability analysis, and gene deletion
- analyses.
- .
- This package provides the Python 2 module.
-
Package: python3-cobra
Architecture: any
Depends:
@@ -85,7 +42,7 @@ Depends:
Suggests:
python3-matplotlib,
qsopt-ex,
-Description: constraint-based modeling of biological networks (Python 3)
+Description: constraint-based modeling of biological networks with Python 3
COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely
used for genome-scale modeling of metabolic networks in both prokaryotes
and eukaryotes. COBRApy is a constraint-based modeling package that is
@@ -93,8 +50,6 @@ Description: constraint-based modeling of biological networks (Python 3)
of COBRA models and provides access to commonly used COBRA methods, such
as flux balance analysis, flux variability analysis, and gene deletion
analyses.
- .
- This package provides the Python 3 module.
Package: python-cobra-data
Architecture: all
=====================================
debian/patches/drop_failing_test2.patch
=====================================
@@ -0,0 +1,24 @@
+Description: Drop another failing test leaving investigation for later point in time
+ FIXME
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 04 Sep 2018 21:03:58 +0200
+
+--- a/cobra/test/test_util.py
++++ b/cobra/test/test_util.py
+@@ -294,16 +294,3 @@ class TestDictList:
+ assert len(test_list) == 2
+ assert test_list.index("test2") == 1
+
+-
+-def test_show_versions(capsys):
+- show_versions()
+- captured = capsys.readouterr()
+- lines = captured.out.split("\n")
+- assert lines[1].startswith("System Information")
+- assert lines[2].startswith("==================")
+- assert lines[3].startswith("OS")
+- assert lines[4].startswith("OS-release")
+- assert lines[5].startswith("Python")
+-
+- assert lines[7].startswith("Package Versions")
+- assert lines[8].startswith("================")
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
mathjax.patch
drop_failing_test.patch
+drop_failing_test2.patch
=====================================
debian/python-cobra.links deleted
=====================================
@@ -1 +0,0 @@
-/usr/share/python-cobra/data /usr/lib/python2.7/dist-packages/cobra/test/data
=====================================
debian/python-cobra.pyremove deleted
=====================================
@@ -1 +0,0 @@
-cobra/test/data
=====================================
debian/rules
=====================================
@@ -7,7 +7,7 @@ export PYBUILD_NAME=cobra
%:
- dh $@ --with python2,python3 --buildsystem=pybuild
+ dh $@ --with python3 --buildsystem=pybuild
# Disable building of documentation (see README.source)
#override_dh_auto_build:
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/compare/28d2177f3e206bf8ec4053300db58540cbb9dc12...10917aa9c5c04206ead2d366bd6ee6d246531984
--
View it on GitLab: https://salsa.debian.org/med-team/python-cobra/compare/28d2177f3e206bf8ec4053300db58540cbb9dc12...10917aa9c5c04206ead2d366bd6ee6d246531984
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