[med-svn] [Git][med-team/prottest][master] 3 commits: Add patch to fix autopkgtests (Closes: #997886)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / prottest


Commits:
fa47ffe0 by Nilesh Patra at 2021-10-29T18:05:12+05:30
Add patch to fix autopkgtests (Closes: #997886)

- - - - -
7c4fb987 by Nilesh Patra at 2021-10-29T18:06:59+05:30
d/t/run-unit-tests: Remove un-necessary template

- - - - -
37b0d72e by Nilesh Patra at 2021-10-29T18:06:59+05:30
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/read-stats-file.patch
- debian/patches/series
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+prottest (3.4.2+dfsg-7) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix autopkgtests (Closes: #997886)
+
+ -- Nilesh Patra <nilesh at debian.org>  Fri, 29 Oct 2021 18:05:16 +0530
+
 prottest (3.4.2+dfsg-6) unstable; urgency=medium
 
   * Re-activate real test suggested by Tassia


=====================================
debian/patches/read-stats-file.patch
=====================================
@@ -0,0 +1,24 @@
+Description: properly resolve stats and tree files, add missing dot
+Author: Nilesh Patra <nilesh at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=997886
+Last-Update: 2021-10-29
+--- a/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
++++ b/src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java
+@@ -378,7 +378,7 @@
+         if (!(statsFile.exists() && statsFile.canRead()))
+         {
+         	/* try with txt suffix */
+-        	statsFile = new File(workAlignment + STATS_FILE_SUFFIX + "txt");
++        	statsFile = new File(workAlignment + STATS_FILE_SUFFIX + ".txt");
+         	if (!(statsFile.exists() && statsFile.canRead()))
+         		throw new StatsFileFormatException("PhyML", 
+         				"Stats file does not exist. Please check if PhyML is working.");
+@@ -389,7 +389,7 @@
+         if (!(treeFile.exists() && treeFile.canRead()))
+         {
+         	/* try with txt suffix */
+-        	treeFile = new File(workAlignment + TREE_FILE_SUFFIX + "txt");
++        	treeFile = new File(workAlignment + TREE_FILE_SUFFIX + ".txt");
+         	if (!(treeFile.exists() && treeFile.canRead()))
+         		throw new TreeFormatException(
+         				"Tree file does not exist. Please check if PhyML is working correctly.");


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 use_debian_packaged_phyml.patch
 build.patch
 alter-import.patch
+read-stats-file.patch


=====================================
debian/tests/run-unit-test
=====================================
@@ -20,21 +20,6 @@ cd $AUTOPKGTEST_TMP
 
 cp -a /usr/share/doc/${pkg}/examples/* .
 
-# Run simulations with demo models
-# 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
-
 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
 



View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3

-- 
View it on GitLab: https://salsa.debian.org/med-team/prottest/-/compare/0078b6b6f9c161ca9fe2089b128794001ca1cc6b...37b0d72eff823911de381fc822af716e07dd9ad3
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