[med-svn] [Git][med-team/python-biopython][master] 3 commits: remove unused patches
Michael R. Crusoe
gitlab at salsa.debian.org
Mon Dec 16 09:00:19 GMT 2019
Michael R. Crusoe pushed to branch master at Debian Med / python-biopython
Commits:
fbd4aa44 by Michael R. Crusoe at 2019-12-16T08:26:26Z
remove unused patches
- - - - -
9d0a7bf4 by Michael R. Crusoe at 2019-12-16T08:27:58Z
bwa is now arch: any, phyml no longer has bug
- - - - -
bb5b2863 by Michael R. Crusoe at 2019-12-16T09:00:00Z
mips port is no more
- - - - -
6 changed files:
- debian/README.source
- debian/control
- − debian/patches/5af680b5043c9f160a19e4bb0deab0ccc271280d.patch
- − debian/patches/reportlab3.5.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/README.source
=====================================
@@ -63,17 +63,4 @@ The tools which are not packaged yet (item 4.) are:
But it does not need to be explicitly excluded since the
test suite itself checks the existence
-There is a package only available on amd64 architectures:
-
- bwa: The package is limited to amd64 only.
-
-So the Build-Depends from bwa is only on these architectures and the
-test is consequently only run there.
-
-As described in Bug https://bugs.debian.org/813262 there is a problem
-with phyml when using recent libhmsbeagle and the test is running in a
-chroot that has no proper GPU (emulator). So for the moment we also
-need to exclude phyml from testing.
-
-
-- Andreas Tille <tille at debian.org> Tue, 04 Mar 2014 11:16:02 +0100
=====================================
debian/control
=====================================
@@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 12),
texlive-latex-base,
texlive-latex-extra,
texlive-fonts-recommended,
- bwa [any-amd64],
+ bwa,
clustalo,
clustalw,
dialign,
@@ -25,7 +25,7 @@ Build-Depends: debhelper-compat (= 12),
muscle,
ncbi-blast+,
phylip,
- phyml [any-amd64 any-i386 arm64 armhf sparc64],
+ phyml,
prank,
probcons,
python3-networkx,
@@ -57,7 +57,7 @@ Depends: ${python3:Depends},
Recommends: python-biopython-doc (= ${source:Version}),
ncbi-blast+
Suggests: python3-tk,
- bwa [any-amd64],
+ bwa,
clustalo,
clustalw,
dialign,
@@ -67,7 +67,7 @@ Suggests: python3-tk,
mafft,
muscle,
phylip,
- phyml [any-amd64 any-i386 arm64 armhf sparc64],
+ phyml,
prank,
probcons,
python3-mysqldb,
=====================================
debian/patches/5af680b5043c9f160a19e4bb0deab0ccc271280d.patch deleted
=====================================
@@ -1,30 +0,0 @@
-From 5af680b5043c9f160a19e4bb0deab0ccc271280d Mon Sep 17 00:00:00 2001
-From: Peter Cock <p.j.a.cock at googlemail.com>
-Date: Tue, 19 Nov 2019 09:59:16 +0000
-Subject: [PATCH] Ignore C modules with no docstrings
- Does not work as expected
-
----
- Tests/run_tests.py | 9 +++++++++
- 1 file changed, 9 insertions(+)
-
-diff --git a/Tests/run_tests.py b/Tests/run_tests.py
-index 15503f65d5..084df08afc 100644
---- a/Tests/run_tests.py
-+++ b/Tests/run_tests.py
-@@ -358,6 +358,15 @@ def runTest(self, name):
- except MissingPythonDependencyError:
- sys.stderr.write("skipped, missing Python dependency\n")
- return True
-+ except ValueError as e:
-+ if str(e).startswith("module ") and str(e).endswith("has no docstrings"):
-+ # Seen with some C modules via Debian build testing
-+ sys.stderr.write("skipped, has no docstrings\n")
-+ return True
-+ sys.stderr.write("FAIL, ValueError\n")
-+ result.stream.write("ERROR while importing %s: %s\n" % (name, e))
-+ result.printErrors()
-+ return False
- except ImportError as e:
- sys.stderr.write("FAIL, ImportError\n")
- result.stream.write("ERROR while importing %s: %s\n" % (name, e))
=====================================
debian/patches/reportlab3.5.patch deleted
=====================================
@@ -1,19 +0,0 @@
-Description: Fix compatibility with ReportLab 3.5
-Bug: https://github.com/biopython/biopython/issues/1737
-Bug-Debian: https://bugs.debian.org/913064
-Origin: upstream, https://github.com/biopython/biopython/commit/c7b909e842139f82d87639f3080bc45ff9613cca
-Origin: upstream, https://github.com/biopython/biopython/commit/a5fe524925f42370349ceb50aa57aa1129d384d8
-Author: Peter Cock <p.j.a.cock at googlemail.com>
-Last-Update: 2018-08-13
-
---- a/Tests/test_GenomeDiagram.py
-+++ b/Tests/test_GenomeDiagram.py
-@@ -49,6 +49,8 @@ from Bio.Graphics.GenomeDiagram._Colors
- from reportlab import rl_config
- rl_config.invariant = True
-
-+from reportlab import rl_config
-+rl_config.invariant = True
-
- def fill_and_border(base_color, alpha=0.5):
- """Return fill and border colors given a base color."""
=====================================
debian/patches/series
=====================================
@@ -1,8 +1,6 @@
remove_mathml-qname.patch
privacy_breach.patch
-reportlab3.5.patch
python_3.8_iteration_fix.patch
-# 5af680b5043c9f160a19e4bb0deab0ccc271280d.patch
exclude_docstring_tests.patch
arm.patch
fix_doctests
=====================================
debian/rules
=====================================
@@ -31,18 +31,13 @@ EXCLUDENOTPACKAGED=MSAProbs_tool NACCESS_tool PopGen_GenePop PopGen_GenePop_Easy
ifeq ($(BUILDARCH),amd64)
EXCLUDEARCHamd64=
else
- EXCLUDEARCHamd64=BWA_tool raxml_tool
+ EXCLUDEARCHamd64=raxml_tool
endif
# avoid tests requiring data base connections if no server is running while we are doing the build
# This would not trigger a failure but bloats the build log with irrelevant noise
EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
-# With recent phyml we get:
-# ApplicationError: Non-zero return code 255 from 'phyml -i Phylip/interlaced2.phy -d aa', message 'beignet-opencl-icd: no supported GPU found, this is probably the wrong opencl-icd package for this hardware'
-# See https://bugs.debian.org/813262
-EXCLUDEFAILINGTESTS=phyml_tool
-
%:
dh $@ --with python3 --buildsystem=pybuild
@@ -74,16 +69,6 @@ override_dh_auto_install:
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-ifeq ($(BUILDARCH),mips)
- # FIXME: Do the tests *really* fail any more?
- echo "***************************************************************************"
- echo "* Attention: Build time tests for mips architecture are skipped. *"
- echo "* The reason is that the tests are known to fail for Python3 *"
- echo "* Upstream is working on a solution so this should be dropped for *"
- echo "* next upstream version. See: *"
- echo "* http://mailman.open-bio.org/pipermail/biopython/2014-August/015383.html *"
- echo "***************************************************************************"
-else
mkdir -p Tests_avoid
for avoid in $(EXCLUDEONLINE) $(EXCLUDENONFREE) $(EXCLUDENOTPACKAGED) $(EXCLUDEARCHamd64) $(EXCLUDEDATABASE) $(EXCLUDEFAILINGTESTS) $(EXCLUDEPACKAGEINFLUX) \
; do \
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/compare/ec554598c0fab2487133de8937c463e56d1ca2f6...bb5b286367fa9033b18c4ab79d13a802956b18eb
--
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/compare/ec554598c0fab2487133de8937c463e56d1ca2f6...bb5b286367fa9033b18c4ab79d13a802956b18eb
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20191216/57cd255d/attachment-0001.html>
More information about the debian-med-commit
mailing list