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 <[email protected]> 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 <[email protected]> Uploaders: Charles Plessy <[email protected]>, Andreas Tille <[email protected]>, - Etienne Mollier <[email protected]> + Étienne Mollier <[email protected]> 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 <[email protected]> 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 <[email protected]> -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 You're receiving this email because of your account on salsa.debian.org.
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