debian/changelog

+pbh5tools (0.8.0+git20181212.9fa8fc4+dfsg-2) UNRELEASED; urgency=medium
+
+  * Afif Elghraoui removed himself from Uploaders
+  * Add myself to Uploaders
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.1
+  * Secure URI in copyright format
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Build-Depends: s/python-sphinx/python3-sphinx/
+  * Remove patches enable-nosetests that are missing from
+    debian/patches/series.
+  * Use 2to3 to convert from Python2 to Python3
+    Closes: #937256
+
+ -- Andreas Tille <tille@debian.org>  Sat, 07 Dec 2019 09:23:30 +0100
+
 pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) unstable; urgency=medium
 
   * Team upload.

debian/compat

-11

debian/control

 Source: pbh5tools
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python,
-               python-setuptools,
-               python-pbcore,
-               python-sphinx,
-               python-nose,
-               python-h5py,
-               python-cram
-Standards-Version: 4.1.5
+               python3,
+               python3-setuptools,
+               python3-pbcore,
+               python3-sphinx,
+               python3-nose <!nocheck>,
+               python3-h5py <!nocheck>,
+               python3-cram <!nocheck>
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/pbh5tools
 Vcs-Git: https://salsa.debian.org/med-team/pbh5tools.git
 Homepage: https://github.com/PacificBiosciences/pbh5tools
@@ -19,9 +20,9 @@ Homepage: https://github.com/PacificBiosciences/pbh5tools
 Package: pbh5tools
 Architecture: all
 Depends: ${misc:Depends},
-         ${python:Depends},
-         python-pbh5tools (>= ${binary:Version}),
-         python-pkg-resources
+         ${python3:Depends},
+         python3-pbh5tools (>= ${binary:Version}),
+         python3-pkg-resources
 Description: tools for manipulating Pacific Biosciences HDF5 files
  This package provides functionality for manipulating and extracting data
  from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.
@@ -30,20 +31,20 @@ Description: tools for manipulating Pacific Biosciences HDF5 files
  .
  This package is part of the SMRTAnalysis suite.
 
-Package: python-pbh5tools
+Package: python3-pbh5tools
 Architecture: any
 Section: python
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${python:Depends}
-Description: tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library
+         ${python3:Depends}
+Description: tools for manipulating Pacific Biosciences HDF5 files -- Python 3 library
  This package provides functionality for manipulating and extracting data
  from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.
  cmp.h5 files contain alignment information while bas.h5 files contain
  base-call information.
  .
  pbh5tools is part of the SMRTAnalysis suite. This package provides the
- Python 2 backend library
+ Python 3 backend library
 
 Package: python-pbh5tools-doc
 Architecture: all

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: pbh5tools
 Source: https://github.com/PacificBiosciences/pbh5tools
 Files-Excluded: doc/pacbio-theme/*

debian/patches/enable-nosetests

-Description: Configure nosetests to run with setup.py test
-Author: Afif Elghraoui <afif@ghraoui.name>
-Forwarded: not-needed
-Last-Update: 2015-08-12
---- python-pbh5tools.orig/setup.py
-+++ python-pbh5tools/setup.py
-@@ -26,6 +26,7 @@
-                'bin/cmph5tools.py'],
-     packages = find_packages("."),
-     package_dir = {'':'.'},
-+    test_suite = 'nose.collector',
-     ext_modules=[Extension('pbh5tools/ci', ['pbh5tools/ci.c'],
-                            extra_compile_args=["-O3","-shared"])],
-     zip_safe = False,
---- /dev/null
-+++ python-pbh5tools/setup.cfg
-@@ -0,0 +1,3 @@
-+[nosetests]
-+verbosity=2
-+where=tests

debian/patches/multiarch-module-path.patch

@@ -2,9 +2,9 @@ Author: Afif Elghraoui
 Last-Update: 2016-03-20 00:45:22 -0700
 Description: Enable multiarch modules
 
---- python-pbh5tools.orig/pbh5tools/Indexer.py
-+++ python-pbh5tools/pbh5tools/Indexer.py
-@@ -32,10 +32,11 @@
+--- a/pbh5tools/Indexer.py
++++ b/pbh5tools/Indexer.py
+@@ -32,10 +32,11 @@ import ctypes
  import os
  import numpy
  import pkg_resources

debian/patches/series

@@ -6,3 +6,4 @@ ignore-cram-results.patch
 fix-type-in-test.patch
 multiarch-module-path.patch
 # enable-nosetests
+2to3.patch

debian/rules

@@ -8,7 +8,7 @@ BINDIR=$(CURDIR)/debian/pbh5tools/usr/bin
 export PYBUILD_NAME = pbh5tools
 
 %:
-	LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
+	LC_ALL=C.UTF-8 dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_auto_build:
 	dh_auto_build
@@ -19,13 +19,15 @@ override_dh_install:
 	# We do this here rather than in .install files so that debhelper
 	# takes care of the #!/usr/bin/env lines for us
 	mkdir -p $(BINDIR)
-	mv debian/python-pbh5tools/usr/bin/bash5tools.py $(BINDIR)/bash5tools
-	mv debian/python-pbh5tools/usr/bin/cmph5tools.py $(BINDIR)/cmph5tools
+	mv debian/python3-pbh5tools/usr/bin/bash5tools.py $(BINDIR)/bash5tools
+	mv debian/python3-pbh5tools/usr/bin/cmph5tools.py $(BINDIR)/cmph5tools
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	PYBUILD_SYSTEM=custom \
 	PYBUILD_TEST_ARGS="PATH=$(CURDIR)/build/scripts-2.7:$$PATH $(MAKE) test" \
 	  dh_auto_test
+endif
 
 override_dh_auto_clean:
 	dh_auto_clean

doc/index.rst

@@ -28,6 +28,14 @@ To install ``pbh5tools``, run the following command from the ``pbh5tools`` root
 
    python setup.py install
 
+If you do not have `root` or `sudo` permissions, you can install locally by:  
+
+1. Installing pysam, numpy, Cython, and h5py to your home directory.  
+              pip install --user --upgrade numpy h5py pysam cython
+2. Running 
+              python setup.py install --user
+
+
 ####################
 Tool: bash5tools.py
 ####################
@@ -80,10 +88,10 @@ Usage
 Examples
 --------
 
-Extracting all Raw reads from ``input.bas.h5`` without any filtering
-and exporting to FASTA (``myreads.fasta``): ::
+Extracting all subreads reads from ``input.bas.h5`` without any filtering
+and exporting to a FASTA file named ``myreads.fasta``: ::
 
-    python bash5tools.py input.bas.h5 --outFilePrefix myreads --outType fasta --readType Raw
+    python bash5tools.py --outFilePrefix myreads --outType fasta --readType subreads input.bas.h5
 
 Extracting all CCS reads from ``input.bas.h5`` that have read lengths
 larger than 100 and exporting to FASTQ (``myreads.fastq``): ::