[med-svn] [Git][med-team/aevol][master] Adapt autopkgtest to new upstream version Closes: #1131937

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / aevol


Commits:
fd72f5b7 by Andreas Tille at 2026-05-24T22:20:28+02:00
Adapt autopkgtest to new upstream version Closes: #1131937

- - - - -


2 changed files:

- debian/changelog
- debian/tests/run-unit-tests


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+aevol (9.3.0-2) UNRELEASED; urgency=medium
+
+  * Adapt autopkgtest to new upstream version
+    Closes: #1131937
+
+ -- Andreas Tille <tille at debian.org>  Sun, 24 May 2026 22:18:24 +0200
+
 aevol (9.3.0-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/tests/run-unit-tests
=====================================
@@ -16,118 +16,17 @@ cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
 cd "${AUTOPKGTEST_TMP}"
 gunzip -r *
 
-# Run simulation
-cd workflow/wild_type
-aevol_create
-xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_run -n 100 -p -1
-
-# Test setup
-outdirsA="line01 line02 line03 line04 line05"
-outdirsB="line06 line07 line08 line09 line10"
-outdirsC="line11 line12 line13 line14 line15"
-for mydir in $outdirsA $outdirsB $outdirsC
-do
-  xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_propagate -o ../$mydir
-done
-
-cd ..
-
-# For each experiment, create a file with the parameters to change
-echo "# New environment
-ENV_GAUSSIAN  0.5   0.2   0.05
-ENV_GAUSSIAN  0.5   0.4   0.05
-ENV_GAUSSIAN  0.5   0.8   0.05
-ENV_VARIATION none
-# New rearrangement rates
-DUPLICATION_RATE    1e-4
-DELETION_RATE       1e-4
-TRANSLOCATION_RATE  1e-4
-INVERSION_RATE      1e-4" > newparam-groupA.in
-
-echo "# New environment
-ENV_GAUSSIAN  0.5   0.2   0.05
-ENV_GAUSSIAN  0.5   0.4   0.05
-ENV_GAUSSIAN  0.5   0.8   0.05
-ENV_VARIATION none
-# New rearrangement rates
-DUPLICATION_RATE    1e-6
-DELETION_RATE       1e-6
-TRANSLOCATION_RATE  1e-6
-INVERSION_RATE      1e-6" > newparam-groupB.in
-
-echo "# New environment
-ENV_GAUSSIAN  0.5   0.2   0.05
-ENV_GAUSSIAN  0.5   0.4   0.05
-ENV_GAUSSIAN  0.5   0.8   0.05
-ENV_VARIATION none" > newparam-groupC.in
-
-
-# Apply these modifications
-#
-for mydir in $outdirsA
-do
-   cd $mydir
-   xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_modify -f ../newparam-groupA.in
-   cd ..
-done
-
-for mydir in $outdirsB
-do
-  cd $mydir
-  xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_modify -f ../newparam-groupB.in
+for exampledir in $(find . -maxdepth 1 -mindepth 1 -type d) ; do
+  cd $exampledir
+  if [ $(basename $exampledir) = "eukaryote" ] ; then
+    echo "Advise in README.md fails with:"
+    echo "  ERROR in param file "param.in" on line 14: selfing is only valid in the eukaryote setting."
+    echo "aevol_create_2b param.in --fasta WT0.fa"
+    echo "aevol_eukaryote_2b_run --begin 0 --end 1000 --parallel -1"
+  else
+    aevol_create_2b param.in
+    aevol_run_2b
+  fi
   cd ..
 done
 
-for mydir in $outdirsC
-do
-  cd $mydir
-  xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_modify -f ../newparam-groupC.in
-  cd ..
-done
-
-# Run the simulations
-#
-for mydir in $outdirsA $outdirsB $outdirsC
-do
-  cd $mydir
-  xvfb-run --auto-servernum --server-args="-screen 0 1024x768x24" aevol_run -e 200 -p -1
-  cd ..
-done
-
-# aevol_misc_create_eps 
-for mydir in $outdirsA $outdirsB $outdirsC
-do
-  cd $mydir
-  aevol_misc_create_eps &
-  cd ..
-done
-
-
-# aevol_misc_robustness 
-for mydir in $outdirsA $outdirsB $outdirsC
-do
-   cd $mydir
-   aevol_misc_robustness &
-   cd ..
-done
-
-
-# aevol_misc_lineage 
-for mydir in $outdirsA $outdirsB $outdirsC
-do
-   cd $mydir
-   # FIXME: Added '|| true' since this test contains errors
-   #        We want to see those errors in the test logs but
-   #        it should not make the whole test fail
-   aevol_misc_lineage || true
-   cd ..
-done
-
-
-# aevol_misc_ancstats 
-for mydir in $outdirsA $outdirsB $outdirsC
-do
-   cd $mydir
-   aevol_misc_ancestor_stats lineage-*.ae -M &
-   cd ..
-done



View it on GitLab: https://salsa.debian.org/med-team/aevol/-/commit/fd72f5b7a305a5f844128c6f97e492876848ad94

-- 
View it on GitLab: https://salsa.debian.org/med-team/aevol/-/commit/fd72f5b7a305a5f844128c6f97e492876848ad94
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