[med-svn] [Git][med-team/python-biopython][master] 5 commits: Revert "routine-update: Ready to upload to unstable"

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / python-biopython


Commits:
5eb9ae49 by Étienne Mollier at 2020-10-05T18:35:35+02:00
Revert "routine-update: Ready to upload to unstable"

This reverts commit 632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc.

- - - - -
78a0389a by Étienne Mollier at 2020-10-05T18:43:47+02:00
d/rules: erased makeblastdb override

should be properly handled by all architectures now.

- - - - -
b1bfd6c8 by Étienne Mollier at 2020-10-05T18:44:48+02:00
d/tests/run-unit-tests: removed makeblastdb override

this should be properly handled on all architectures, including
mipsel, since ncbi-blast+ 2.10.1-3.  Also, the override that was still
present in that file could have been a source of autopkgtest failures.

- - - - -
4046757b by Étienne Mollier at 2020-10-05T18:49:17+02:00
d/control: bump requirement to ncbi-blast+ 2.10.1-3

- - - - -
2b9339e1 by Étienne Mollier at 2020-10-05T19:26:14+02:00
updated d/changelog to reflect changes appropriately

- - - - -


4 changed files:

- debian/changelog
- debian/control
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,10 +1,9 @@
-python-biopython (1.78+dfsg-3) unstable; urgency=medium
+python-biopython (1.78+dfsg-3) UNRELEASED; urgency=medium
 
-  * mpisel build still failing on buildd (host arch mips64el, schroot mipsel)
-      - overred makeblastdb memory allocation for that arch on build and test;
-      - updated run-unit-test to reflect that change.
+  * Bumped ncbi-blast+ version requirement to 2.10.1-3
+  * Made sure run-unit-test did not attempt memory allocation override
 
- -- Étienne Mollier <etienne.mollier at mailoo.org>  Sun, 04 Oct 2020 22:18:45 +0200
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Sat, 03 Oct 2020 10:34:12 +0200
 
 python-biopython (1.78+dfsg-2) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13),
                fasttree <!nocheck>,
                mafft <!nocheck>,
                muscle <!nocheck>,
-               ncbi-blast+ (>= 2.10.1-2) <!nocheck>,
+               ncbi-blast+ (>= 2.10.1-3) <!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+ (>= 2.10.0-3)
+            ncbi-blast+ (>= 2.10.1-3)
 Suggests: python3-tk,
           bwa,
           clustalo,


=====================================
debian/rules
=====================================
@@ -34,14 +34,6 @@ else
     EXCLUDEARCHamd64=raxml_tool
 endif
 
-# virtualized environment, esp. with schroot, may be too constrained for the
-# memory allocation required by the test_NCBI_BLAST_tools.  See #969608 for
-# more details:
-#     https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40
-ifeq ($(BUILD_ARCH),mipsel)
-    export BLASTDB_LMDB_MAP_SIZE = 3000000000
-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


=====================================
debian/tests/run-unit-test
=====================================
@@ -27,15 +27,6 @@ if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" != "amd64" ]; then
     rm -f test_BWA_tool.py
 fi
 
-# virtualized environment, esp. with schroot, may be too constrained for the
-# memory allocation required by the test_NCBI_BLAST_tools.  See #969608 for
-# more details:
-#     https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=969608#40
-if [ "$(dpkg-architecture -qDEB_BUILD_ARCH)" = "mipsel" ]; then
-    BLASTDB_LMDB_MAP_SIZE=3000000000
-    export BLASTDB_LMDB_MAP_SIZE
-fi
-
 # execute tests
 ################################################################################
 # in the Debian package dialign it is not needed to set DIALIGN2_DIR but the



View it on GitLab: https://salsa.debian.org/med-team/python-biopython/-/compare/632894cbc01ded9ad6a97f57fc1f3fb6ee64c9dc...2b9339e183b1d4999bbeaddab1b5d92184594c98

-- 
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