[med-svn] [Git][med-team/prottest][master] 2 commits: Unfortunately we can only do a superficial for the moment

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / prottest


Commits:
fbbbfaa8 by Andreas Tille at 2021-02-21T15:52:35+01:00
Unfortunately we can only do a superficial for the moment

- - - - -
4fb1f613 by Andreas Tille at 2021-02-21T15:58:15+01:00
Upload to unstable

- - - - -


3 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-prottest (3.4.2+dfsg-5) UNRELEASED; urgency=medium
+prottest (3.4.2+dfsg-5) unstable; urgency=medium
 
   * Team upload
 
@@ -8,6 +8,9 @@ prottest (3.4.2+dfsg-5) UNRELEASED; urgency=medium
 
   [ Tassia Camoes Araujo ]
   * Add functional test
+    Unfortunately we can only do a superficial for the moment until there
+    will be a way to run with phyml provided in Debian (see
+      https://github.com/ddarriba/prottest3/issues/12 )
 
   [ Pierre Gruet ]
   * Adding libbetter-appframework-java in runtime dependencies and its


=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
 Tests: run-unit-test
 Depends: @
-Restrictions: allow-stderr
+Restrictions: allow-stderr, superficial


=====================================
debian/tests/run-unit-test
=====================================
@@ -21,7 +21,22 @@ cd $AUTOPKGTEST_TMP
 cp -a /usr/share/doc/${pkg}/examples/* .
 
 # Run simulations with demo models
-prottest -i COX2_PF0016/alignment -t COX2_PF0016/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5
-prottest -i Ribosomal_L5_PF00673/alignment -t Ribosomal_L5_PF00673/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5
+# Unfortunately there are issues with the Debian packaged phyml as described here
+#   https://github.com/ddarriba/prottest3/issues/12
+#
+# Model optimization exception: there was an error while executing there was an error parsing PhyML stats file: Stats file does not exist. Please check if PhyML is working.
+# Model................................ : FLU+I+G+F
+#   Number of parameters............... : 74 (21 + 53 branch length estimates)
+# 
+# ************************************************************
+# Date   :  Sun Feb 21 14:44:46 UTC 2021
+# Runtime:  0h:02:29
+# 
+# 
+# Lk not initialized
+
+# For the moment we'll leave the trivial test
+#prottest -i COX2_PF0016/alignment -t COX2_PF0016/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5
+#prottest -i Ribosomal_L5_PF00673/alignment -t Ribosomal_L5_PF00673/tree -S 0 -all-distributions -F -AIC -BIC -tc 0.5
 
 echo "PASS"



View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/006ef64028fe70f877338d448b31d83bd46581ed...4fb1f6138726ee947b043fac7f156cd005d5f582

-- 
View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/006ef64028fe70f877338d448b31d83bd46581ed...4fb1f6138726ee947b043fac7f156cd005d5f582
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