debian/changelog

-python-pbcore (1.6.5+dfsg-1) UNRELEASED; urgency=medium
+python-pbcore (1.6.5+dfsg-1) unstable; urgency=medium
 
   * Team upload.
   * Upstream is now tagging releases - adjust watch file
@@ -8,7 +8,7 @@ python-pbcore (1.6.5+dfsg-1) UNRELEASED; urgency=medium
   * Remove trailing whitespace in debian/changelog
   * Build-Depends: s/python-sphinx/python3-sphinx/
 
- -- Andreas Tille <tille@debian.org>  Wed, 31 Oct 2018 15:30:29 +0100
+ -- Andreas Tille <tille@debian.org>  Wed, 31 Oct 2018 18:45:13 +0100
 
 python-pbcore (1.5.0+git20180606.43fcd9d+dfsg-3) UNRELEASED; urgency=medium
 

debian/control

@@ -7,13 +7,26 @@ Build-Depends: debhelper (>= 11~),
                dh-python,
                python-all,
                python-setuptools,
-               python-h5py,
-               python-numpy,
-               python-pysam (>= 0.9.0),
+               python-h5py (>= 2.0.1),
+               python-numpy (>= 1.7.1),
+               python-pysam (>= 0.13),
                python3-sphinx <!nodoc>,
-               python-nose <!nocheck>,
-               python-pyxb <!nocheck>,
-               python-coverage
+               python-nose (>= 1.3.4) <!nocheck>,
+               python-pyxb (>= 1.2.4) <!nocheck>,
+               python-uritools <!nocheck>,
+#               python-parse,
+               pylint,
+               python-coverage,
+#               python3-all,
+#               python3-setuptools,
+#               python3-h5py (>= 2.0.1),
+#               python3-numpy (>= 1.7.1),
+#               python3-pysam (>= 0.13),
+#               python3-nose (>= 1.3.4) <!nocheck>,
+#               python3-pyxb (>= 1.2.4) <!nocheck>,
+#               python3-uritools <!nocheck>,
+#               pylint3,
+#               python3-coverage
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-pbcore
 Vcs-Git: https://salsa.debian.org/med-team/python-pbcore.git
@@ -26,7 +39,7 @@ Depends: ${misc:Depends},
          python-pkg-resources
 Recommends: python-h5py
 Suggests: python-pbcore-doc (= ${source:Version})
-Description: Python library for processing PacBio data files
+Description: Python 2 library for processing PacBio data files
  The pbcore package provides Python modules for processing Pacific Biosciences
  data files and building PacBio bioinformatics applications. These modules
  include tools to read/write PacBio data formats, sample data files for
@@ -34,6 +47,26 @@ Description: Python library for processing PacBio data files
  applications.
  .
  This package is part of the SMRTAnalysis suite.
+ .
+ This is the Python 2 module.
+
+#Package: python3-pbcore
+#Architecture: all
+#Depends: ${misc:Depends},
+#         ${python3:Depends},
+#         python3-pkg-resources
+#Recommends: python3-h5py
+#Suggests: python-pbcore-doc (= ${source:Version})
+#Description: Python 3 library for processing PacBio data files
+# The pbcore package provides Python modules for processing Pacific Biosciences
+# data files and building PacBio bioinformatics applications. These modules
+# include tools to read/write PacBio data formats, sample data files for
+# testing and debugging, base classes, and utilities for building bioinformatics
+# applications.
+# .
+# This package is part of the SMRTAnalysis suite.
+# .
+# This is the Python 3 module.
 
 Package: python-pbcore-doc
 Architecture: all

debian/patches/accept_debian_packaged_pylint.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 31 Oct 2018 15:36:38 +0100
+Description: Relax version condition and accept Debian packaged pylint
+
+--- a/requirements-dev.txt
++++ b/requirements-dev.txt
+@@ -3,4 +3,4 @@ nose==1.3.4
+ pyxb >= 1.2.4
+ h5py >= 2.0.1
+ pysam >= 0.13
+-pylint==1.6.4
++pylint >= 1.6.4

debian/patches/exclude_test_missing_data.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 31 Oct 2018 15:36:38 +0100
+Description: Missing data for this test
+
+--- a/tests/test_pbdataset_metadata.py
++++ b/tests/test_pbdataset_metadata.py
+@@ -165,15 +165,3 @@ class TestDataSet(unittest.TestCase):
+         aln = AlignmentSet(outXml)
+         self.assertEqual(aln.uuid, oldUuid)
+ 
+-    def test_merge(self):
+-        sset_fn = ('/pbi/dept/secondary/siv/testdata/'
+-                'SA3-Sequel/lambda/roche_SAT/'
+-                'm54013_151205_032353.subreadset.xml')
+-        sset = SubreadSet(sset_fn)
+-        orig_metadata = copy.deepcopy(sset.metadata)
+-        self.assertEqual(len(sset.metadata.collections), 1)
+-        sset.metadata.collections.merge(orig_metadata.collections)
+-        self.assertEqual(len(sset.metadata.collections), 2)
+-        sset = SubreadSet(sset_fn)
+-        sset.metadata.collections.merge(orig_metadata.collections, forceUnique=True)
+-        self.assertEqual(len(sset.metadata.collections), 1)

debian/patches/ignore-pyxb.patch

@@ -86,3 +86,13 @@ Last-Update: 2016-10-09
  
  # Import bindings for namespaces imported into schema
  import pyxb.binding.datatypes
+--- a/requirements-dev.txt
++++ b/requirements-dev.txt
+@@ -1,6 +1,6 @@
+ coverage
+ nose==1.3.4
+-pyxb==1.2.4
++pyxb >= 1.2.4
+ sphinx
+ h5py >= 2.0.1
+ pysam >= 0.13

debian/patches/relax_test_constraint.patch

@@ -17,3 +17,14 @@ Description: Relax test constraint which is rather a rounding issue
                           2322.16060475)
          # uses the bins, not the previous values for mean, std, etc.:
          self.assertEqual(ds3.metadata.summaryStats.readLenDist.sampleMed, 45)
+--- a/requirements-dev.txt
++++ b/requirements-dev.txt
+@@ -1,7 +1,6 @@
+ coverage
+-nose==1.3.4
++nose >= 1.3.4
+ pyxb >= 1.2.4
+-sphinx
+ h5py >= 2.0.1
+ pysam >= 0.13
+ pylint==1.6.4

debian/patches/series

@@ -2,3 +2,6 @@ doc-theme.patch
 enable-build-time-testing.patch
 ignore-pyxb.patch
 relax_test_constraint.patch
+accept_debian_packaged_pylint.patch
+exclude_test_missing_data.patch
+# python3_support.patch