[med-svn] [Git][med-team/hhsuite][master] make sure tests do not overwrite example files

[Sascha Steinbiss (@satta)]

Sascha Steinbiss pushed to branch master at Debian Med / hhsuite


Commits:
4596d8d1 by Sascha Steinbiss at 2021-11-20T13:16:20+01:00
make sure tests do not overwrite example files

- - - - -


2 changed files:

- debian/changelog
- debian/patches/test_without_mpi


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+hhsuite (3.3.0+ds-6) UNRELEASED; urgency=medium
+
+  * Adjust patch to not overwrite example files in tests.
+    This caused a modified file to be packaged containing the build time,
+    leaving the package unreproducible (and is likely not intended here?)
+
+ -- Sascha Steinbiss <satta at debian.org>  Sat, 20 Nov 2021 13:14:10 +0100
+
 hhsuite (3.3.0+ds-5) unstable; urgency=medium
 
   * Fix watchfile to detect new versions on github


=====================================
debian/patches/test_without_mpi
=====================================
@@ -3,17 +3,18 @@ Date: Tue, 1 Sep 2020 22:23:03 +0200
 Subject: Make test script work without MPI
 Origin: upstream, https://github.com/soedinglab/hh-suite/commit/c296b369410900b193a6b74f0554ac90ccfd7d08
 Forwarded: not-needed
---- hhsuite.orig/data/test.sh
-+++ hhsuite/data/test.sh
-@@ -2,36 +2,49 @@
+--- a/data/test.sh
++++ b/data/test.sh
+@@ -2,36 +2,51 @@
  
  rm -f single* search_* blits_*
  
+-hhalign -i query.a3m -t query.a3m
 +if $(command -v "ffindex_apply_mpi" >/dev/null 2>&1); then
 +    MPI=1
 +fi
 +
- hhalign -i query.a3m -t query.a3m
++hhalign -i query.a3m -o result.hhr -t query.a3m
  
  ffindex_build -s single.ffdata single.ffindex query.a3m
  
@@ -44,7 +45,8 @@ Forwarded: not-needed
 +    cstranslate -i single -o single_cs219 -b -x 0.3 -c 4 -I a3m -f
 +fi
  
- hhblits -i query.a3m -d single -blasttab blits_app_res -n 1
+-hhblits -i query.a3m -d single -blasttab blits_app_res -n 1
++hhblits -i query.a3m -o result.hhr -d single -blasttab blits_app_res -n 1
  hhblits_omp -i single -d single -blasttab blits_omp_res -n 1
 -mpirun -np 2 hhblits_mpi -i single -d single -blasttab blits_mpi_res -n 1
 -
@@ -55,7 +57,8 @@ Forwarded: not-needed
 +    diff <(tr -d '\000' < blits_mpi_res.ffdata) blits_app_res
 +fi
  
- hhsearch -i query.a3m -d single -blasttab search_app_res
+-hhsearch -i query.a3m -d single -blasttab search_app_res
++hhsearch -i query.a3m -o result.hhr -d single -blasttab search_app_res
  hhsearch_omp -i single -d single -blasttab search_omp_res
 -mpirun -np 2 hhsearch_mpi -i single -d single -blasttab search_mpi_res
 -
@@ -68,3 +71,5 @@ Forwarded: not-needed
 +fi
  
  diff <(cut -f 1-10,12 blits_app_res) <(cut -f 1-10,12 search_app_res)
++
++rm -f result.hhr



View it on GitLab: https://salsa.debian.org/med-team/hhsuite/-/commit/4596d8d1546690a8f9c00294e73e8cac3f56ee72

-- 
View it on GitLab: https://salsa.debian.org/med-team/hhsuite/-/commit/4596d8d1546690a8f9c00294e73e8cac3f56ee72
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