Adjustments

diff --git a/debian/patches/series b/debian/patches/series
index c6285a7b0dc7ed7873d60ec4cbc26b6b64a69f34..a5807b9fc35f52473584da255af73b5836237b14 100644 (file)
--- 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 e088109d83db2d5ba5ac5c093d4dd31a2d33dc0d..4065c70dac5618f7761f9f82643dc9a02311eb1f 100644 (file)
--- 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 f47200a2b0c1e430f6f451e522ea248390d5d1fc..e03ce13d181d810ce98d5a516d7d83d41085ae78 100755 (executable)
--- 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/