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debian/README.source
View file @ bb5b2863
......@@ -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@debian.org> Tue, 04 Mar 2014 11:16:02 +0100
debian/control
View file @ bb5b2863
......@@ -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 100644 → 0
View file @ ec554598
From 5af680b5043c9f160a19e4bb0deab0ccc271280d Mon Sep 17 00:00:00 2001
From: Peter Cock <p.j.a.cock@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 100644 → 0
View file @ ec554598
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@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
View file @ bb5b2863
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
View file @ bb5b2863
......@@ -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 \
......