[med-svn] [Git][med-team/python-biopython][master] 5 commits: d/control: register with uppercase 'e' acute
Étienne Mollier
gitlab at salsa.debian.org
Tue Sep 8 21:57:37 BST 2020
Étienne Mollier pushed to branch master at Debian Med / python-biopython
Commits:
c64dced5 by Etienne Mollier at 2020-09-07T21:08:19+02:00
d/control: register with uppercase 'e' acute
- - - - -
39affaf3 by Etienne Mollier at 2020-09-07T21:09:43+02:00
d/control: bump deps to ncbi-blast+ >= 2.10.0-2
- - - - -
abc06652 by Etienne Mollier at 2020-09-08T21:15:43+02:00
bump build-dep on ncbi-blast+ 2.10.0-3
2.10.0-2 had a bug on amd64 architecture
- - - - -
414e0f60 by Etienne Mollier at 2020-09-08T21:17:53+02:00
removed blastdbv4-test.patch
- - - - -
9c4c52a4 by Etienne Mollier at 2020-09-08T22:55:43+02:00
blastdbv4-impl.patch applied-upstream
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/blastdbv4-impl.patch
- − debian/patches/blastdbv4-test.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+python-biopython (1.77+dfsg-4) UNRELEASED; urgency=medium
+
+ * Bumped build requirement on ncbi-blast+ 2.10.0-3 and greater,
+ * Removed patch against tests to work makeblastdb bug around on 32 bit archs.
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org> Mon, 07 Sep 2020 20:37:27 +0200
+
python-biopython (1.77+dfsg-3) unstable; urgency=medium
[ Etienne Mollier ]
=====================================
debian/control
=====================================
@@ -2,7 +2,7 @@ Source: python-biopython
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>,
- Etienne Mollier <etienne.mollier at mailoo.org>
+ Étienne Mollier <etienne.mollier at mailoo.org>
Section: python
Priority: optional
Build-Depends: debhelper-compat (= 12),
@@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 12),
fasttree <!nocheck>,
mafft <!nocheck>,
muscle <!nocheck>,
- ncbi-blast+ <!nocheck>,
+ ncbi-blast+ (>= 2.10.0-3) <!nocheck>,
phylip <!nocheck>,
phyml [any-amd64 any-i386] <!nocheck>,
prank <!nocheck>,
@@ -58,7 +58,7 @@ Depends: ${python3:Depends},
${misc:Depends},
python3-reportlab
Recommends: python-biopython-doc (= ${source:Version}),
- ncbi-blast+
+ ncbi-blast+ (>= 2.10.0-3)
Suggests: python3-tk,
bwa,
clustalo,
=====================================
debian/patches/blastdbv4-impl.patch
=====================================
@@ -5,7 +5,8 @@ Description: Implement BLAST database version 4 switch
as well, hence a separation of the implementation and test.
Author: Étienne Mollier <etienne.mollier at mailoo.org>
Forwarded: https://github.com/biopython/biopython/pull/2987
-Last-Update: 2020-06-10
+Applied-Upstream: 1.79
+Last-Update: 2020-09-08
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- python-biopython.orig/Bio/Blast/Applications.py
=====================================
debian/patches/blastdbv4-test.patch deleted
=====================================
@@ -1,51 +0,0 @@
-Description: adapt makeblastdb wrapper test for 32 bits architecture
- This patch works around issues with testing the wrapper to makeblastdb, which
- fails to execute on 32 bit CPU architectures due to starvation of the virtual
- memory address space. This issue is apparently specific to the construction
- of BLAST databases in version 5 format, and does not occur when falling back
- to version 4. This requires the wrapper to know about falling back to version
- 4, which is addressed by another patch.
-Author: Étienne Mollier <etienne.mollier at mailoo.org>
-Bug-Debian: https://bugs.debian.org/960756
-Forwarded: not-needed
-Last-Update: 2020-06-10
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- python-biopython.orig/Tests/test_NCBI_BLAST_tools.py
-+++ python-biopython/Tests/test_NCBI_BLAST_tools.py
-@@ -217,6 +217,7 @@
- global exe_names
- cline = Applications.NcbimakeblastdbCommandline(
- exe_names["makeblastdb"],
-+ blastdb_version=4,
- input_file="GenBank/NC_005816.faa",
- dbtype="prot",
- hash_index=True,
-@@ -228,7 +229,8 @@
- self.assertEqual(
- str(cline),
- _escape_filename(exe_names["makeblastdb"])
-- + " -dbtype prot -in GenBank/NC_005816.faa"
-+ + " -blastdb_version 4"
-+ " -dbtype prot -in GenBank/NC_005816.faa"
- " -parse_seqids -hash_index -max_file_sz 20MB"
- " -taxid 10",
- )
-@@ -263,6 +265,7 @@
- global exe_names
- cline = Applications.NcbimakeblastdbCommandline(
- exe_names["makeblastdb"],
-+ blastdb_version=4,
- input_file="GenBank/NC_005816.fna",
- dbtype="nucl",
- hash_index=True,
-@@ -274,7 +277,8 @@
- self.assertEqual(
- str(cline),
- _escape_filename(exe_names["makeblastdb"])
-- + " -dbtype nucl -in GenBank/NC_005816.fna"
-+ + " -blastdb_version 4"
-+ " -dbtype nucl -in GenBank/NC_005816.fna"
- " -parse_seqids -hash_index -max_file_sz 20MB"
- " -taxid 10",
- )
=====================================
debian/patches/series
=====================================
@@ -1,6 +1,5 @@
remove_mathml-qname.patch
privacy_breach.patch
blastdbv4-impl.patch
-blastdbv4-test.patch
71d9f4e2398d542d04001eabb1b467a6f3fdeecf.patch
1c3504736d41e6f6d0931e6f2685f95e486b27c8.patch
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/ee2dda9191503b47799c5e56af43ded65e942020...9c4c52a4df0dd86c77057eeea5f9b50414552f68
--
View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/ee2dda9191503b47799c5e56af43ded65e942020...9c4c52a4df0dd86c77057eeea5f9b50414552f68
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