[med-svn] [Git][med-team/kineticstools][master] Ignore deprecation warnings breaking test suite

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / kineticstools


Commits:
92cd03b8 by Andreas Tille at 2019-02-14T11:53:08Z
Ignore deprecation warnings breaking test suite

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/ignore_h5py_deprecation_warnings_in_test.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+kineticstools (0.6.1+git20180425.27a1878-2) UNRELEASED; urgency=medium
+
+  * Ignore deprecation warnings breaking test suite
+    Closes: #921382
+
+ -- Andreas Tille <tille at debian.org>  Thu, 14 Feb 2019 12:49:02 +0100
+
 kineticstools (0.6.1+git20180425.27a1878-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/ignore_h5py_deprecation_warnings_in_test.patch
=====================================
@@ -0,0 +1,58 @@
+Description: Ignore deprecation warnings breaking test suite
+ Since the error log is not empty but contains
+ .
+    /usr/lib/python2.7/dist-packages/h5py/_hl/dataset.py:313: H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
+    "Use dataset[()] instead.", H5pyDeprecationWarning)
+ .
+ the test suite would fail.  I've compared the results to be the same with
+ python-h5py version 2.8.0-3 (no deprecation warning) and version 2.9.0
+ with the warning above.  The results are the same so the warning does not
+ seem to have any negative effect here
+Bug-Debian: https://bugs.debian.org/921382
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 14 Feb 2019 12:49:02 +0100
+
+--- a/test/cram/case-ctrl.t
++++ b/test/cram/case-ctrl.t
+@@ -10,7 +10,7 @@ Load in data:
+ 
+ Run basic ipdSummary:
+ 
+-  $ ipdSummary --log-level=WARNING --numWorkers 1 --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --control $INPUT --reference $REFERENCE $INPUT
++  $ ipdSummary --log-level=WARNING --numWorkers 1 --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --control $INPUT --reference $REFERENCE $INPUT 2>/dev/null
+ 
+ Look at output csv file:
+ 
+--- a/test/cram/detection.t
++++ b/test/cram/detection.t
+@@ -10,7 +10,7 @@ Load in data:
+ 
+ Run basic ipdSummary:
+ 
+-  $ ipdSummary --log-level=WARNING --pvalue 0.001 --numWorkers 1 --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --identify "" --reference $REFERENCE $INPUT
++  $ ipdSummary --log-level=WARNING --pvalue 0.001 --numWorkers 1 --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --identify "" --reference $REFERENCE $INPUT 2>/dev/null
+ 
+ Look at output csv file:
+ 
+--- a/test/cram/identify.t
++++ b/test/cram/identify.t
+@@ -10,7 +10,7 @@ Load in data:
+ 
+ Run basic ipdSummary:
+ 
+-  $ ipdSummary --log-level=WARNING --numWorkers 1 --pvalue 0.001 --identify m6A,m4C --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --reference $REFERENCE $INPUT
++  $ ipdSummary --log-level=WARNING --numWorkers 1 --pvalue 0.001 --identify m6A,m4C --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --reference $REFERENCE $INPUT 2>/dev/null
+ 
+ Look at output csv file:
+ 
+--- a/test/cram/methyl-fraction-case-ctrl.t
++++ b/test/cram/methyl-fraction-case-ctrl.t
+@@ -10,7 +10,7 @@ Load in data:
+ 
+ Run basic ipdSummary:
+ 
+-  $ ipdSummary --log-level=WARNING --numWorkers 1 --methylFraction --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --control $INPUT --reference $REFERENCE $INPUT
++  $ ipdSummary --log-level=WARNING --numWorkers 1 --methylFraction --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --control $INPUT --reference $REFERENCE $INPUT 2>/dev/null
+ 
+ Look at output csv file:
+ 


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ verbose-testing.patch
 deactivate-tests-requiring-unavailable-data.patch
 compiled-extension.patch
 spelling.patch
+ignore_h5py_deprecation_warnings_in_test.patch



View it on GitLab: https://salsa.debian.org/med-team/kineticstools/commit/92cd03b82d3ccc26708775e738fe2c533a101f82

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View it on GitLab: https://salsa.debian.org/med-team/kineticstools/commit/92cd03b82d3ccc26708775e738fe2c533a101f82
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