From: Steffen Moeller <moeller@debian.org>
Date: Fri, 14 Sep 2018 10:13:43 +0000 (+0200)
Subject: Adjustments
X-Git-Tag: archive/raspbian/0.22.0+ds-1+rpi1~1^2^2~106
X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=ccef4ca24c6f77a419a473ea44a9a5d074d4efe8;p=python-pysam.git

Adjustments
---

diff --git a/debian/patches/series b/debian/patches/series
index c6285a7..a5807b9 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-skip_test_needing_missing_data.patch
 skip_test_remote.patch
+#skip_test_needing_missing_data.patch
diff --git a/debian/patches/skip_test_remote.patch b/debian/patches/skip_test_remote.patch
index e088109..4065c70 100644
--- a/debian/patches/skip_test_remote.patch
+++ b/debian/patches/skip_test_remote.patch
@@ -2,9 +2,11 @@ Author: Andreas Tille <tille@debian.org>
 Last-Update: Tue, 11 Sep 2018 14:12:55 +0200
 Description: Skip tests trying to access remote site
 
---- a/tests/AlignmentFile_test.py
-+++ b/tests/AlignmentFile_test.py
-@@ -1596,6 +1596,7 @@ class TestDoubleFetchCRAMWithReference(T
+Index: python-pysam/tests/AlignmentFile_test.py
+===================================================================
+--- python-pysam.orig/tests/AlignmentFile_test.py
++++ python-pysam/tests/AlignmentFile_test.py
+@@ -1623,6 +1623,7 @@ class TestDoubleFetchCRAMWithReference(T
      reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
  
  
@@ -12,8 +14,10 @@ Description: Skip tests trying to access remote site
  class TestRemoteFileFTP(unittest.TestCase):
  
      '''test remote access.
---- a/tests/tabix_test.py
-+++ b/tests/tabix_test.py
+Index: python-pysam/tests/tabix_test.py
+===================================================================
+--- python-pysam.orig/tests/tabix_test.py
++++ python-pysam/tests/tabix_test.py
 @@ -1039,6 +1039,7 @@ for vcf_file in vcf_files:
      globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
  
diff --git a/debian/rules b/debian/rules
index f47200a..e03ce13 100755
--- a/debian/rules
+++ b/debian/rules
@@ -52,7 +52,7 @@ clean-tests: pysam_data.clean cbcf_data.clean
 	#find . -name "tmp_*" -delete # This deletes samtools/tmp_file.* which is needed to build successfully
 	find . -name "*.bai*" -delete
 	find . -name "*.cram*" -delete
-	find . -name "*.bam" -delete
+	#find . -name "*.bam" -delete # which deletes files tested
 	rm -rf	tests/pysam_test_work \
 		tests/example_htslib.gtf.gz.tbi \
 		tests/log.txt \
@@ -66,4 +66,5 @@ clean-tests: pysam_data.clean cbcf_data.clean
 		tests/pysam_data/ex1.fa.gz \
 		tests/pysam_data/ex1.fa.gz.gzi \
 		tests/pysam_data/ex1_csi.bam.csi
+	rm -rf .pytest_cache/