Makefile

@@ -8,7 +8,11 @@ bdist:
 	python setup.py bdist --formats=egg
 
 install:
-	python setup.py install
+	@which pip > /dev/null
+	@pip freeze|grep 'pbcore=='>/dev/null \
+      && pip uninstall -y pbcore \
+      || echo -n ''
+	@pip install ./
 
 pylint:
 	pylint --errors-only pbcore/
@@ -59,3 +63,8 @@ pip-install:
 publish-to-pypi:
 	@echo "I'm not going to do this for you, but you can do it by:"
 	@echo "    % python setup.py sdist upload -r pypi"
+
+
+xsd-codegen:
+	rm -f pbcore/io/dataset/pyxb/DataSetXsd.py
+	./bin/updateXSDs.py ../xsd-datamodels/PacBioDatasets.xsd pbcore/io/dataset/pyxb/

bamboo_build.sh

@@ -2,17 +2,17 @@
 type module >& /dev/null || . /mnt/software/Modules/current/init/bash
 set -ex
 
-NX3PBASEURL=http://nexus/repository/unsupported/pitchfork/gcc-4.9.2
+NX3PBASEURL=http://nexus/repository/unsupported/pitchfork/gcc-6.4.0
 export PATH=$PWD/build/bin:/mnt/software/a/anaconda2/4.2.0/bin:$PATH
 export PYTHONUSERBASE=$PWD/build
 export CFLAGS="-I/mnt/software/a/anaconda2/4.2.0/include"
 PIP="pip --cache-dir=$bamboo_build_working_directory/.pip"
-module load gcc/4.9.2
+module load gcc
 
 rm -rf   build
 mkdir -p build/bin build/lib build/include build/share
 $PIP install --user \
-  $NX3PBASEURL/pythonpkgs/pysam-0.9.1.4-cp27-cp27mu-linux_x86_64.whl
+  $NX3PBASEURL/pythonpkgs/pysam-0.13-cp27-cp27mu-linux_x86_64.whl
 $PIP install --user -r requirements.txt
 $PIP install --user -r requirements-dev.txt
 $PIP install --user -e ./    

bin/updateXSDs.py

 #!/usr/bin/env python
 
+from __future__ import print_function
 import argparse
 import tempfile
 import shutil
@@ -10,7 +11,7 @@ import shlex
 
 
 def get_files(xsd_dir):
-    print "Searching ", xsd_dir
+    print("Searching ", xsd_dir)
     files = []
     for path, subdirs, fns in os.walk(xsd_dir):
         for fn in fns:
@@ -22,16 +23,16 @@ def copy_xsds(xsd, dest):
     """Go ahead and copy all xsds, there will likely be many dependencies. If
     not, xsds are small"""
     files = get_files(os.path.dirname(xsd))
-    print "Copying:"
+    print("Copying:")
     for f in files:
-        print f
+        print(f)
     for fn in files:
         shutil.copy(fn, dest)
 
 def generate_pyxb(xsd, outdir, modname):
     cmd = "pyxbgen -u {x} -m {m} --binding-root {p}".format(x=xsd, m=modname,
                                                             p=outdir)
-    print cmd
+    print(cmd)
     subprocess.call(shlex.split(cmd))
 
 if __name__ == "__main__":
@@ -47,4 +48,4 @@ if __name__ == "__main__":
     xsd_name = os.path.basename(args.xsd)
     generate_pyxb(os.path.join(tempd, xsd_name), args.outdir, args.mod_name)
     shutil.rmtree(tempd)
-
+    print("please view commit b7ef4238b63 for additional diffs required for python3 support")

debian/changelog

-python-pbcore (1.4.2+dfsg-1) UNRELEASED; urgency=medium
+python-pbcore (1.5.0+git20180606.43fcd9d+dfsg-1) UNRELEASED; urgency=medium
 
   [ Afif Elghraoui ]
   * New upstream version (git f3bcf3a)
@@ -7,10 +7,10 @@ python-pbcore (1.4.2+dfsg-1) UNRELEASED; urgency=medium
   * d/control: use build profile declarations
  
   [ Andreas Tille ]
-  * Adapt to numpy 1.14 (thanks to Graham Inggs for cherry-picking from
-    upstream)
+  * New upstream version
     Closes: #900485
   * Relax test constraint which is rather a rounding issue
+  * d/watch: mode=git
 
  -- Afif Elghraoui <afif@debian.org>  Sun, 07 Jan 2018 02:03:14 -0500
 

debian/patches/enable-build-time-testing.patch

@@ -5,17 +5,17 @@ Description: Modify setuptools configuration to use nosetests
 Author: Afif Elghraoui <afif@ghraoui.name>
 Forwarded: not-needed
 Last-Update: 2015-08-06
---- python-pbcore.orig/setup.cfg
-+++ python-pbcore/setup.cfg
+--- a/setup.cfg
++++ b/setup.cfg
 @@ -1,2 +1,5 @@
  [metadata]
  description-file = README.md
 +[nosetests]
 +verbosity=2
 +where=tests
---- python-pbcore.orig/setup.py
-+++ python-pbcore/setup.py
-@@ -50,6 +50,7 @@
+--- a/setup.py
++++ b/setup.py
+@@ -48,6 +48,7 @@ setup(
                                 'data/datasets/yieldtest/*.*']
                                 },
      zip_safe = False,

debian/patches/ignore-pyxb.patch

@@ -6,10 +6,10 @@ Description: Ignore hard-coded pyxb version check
 Author: Afif Elghraoui <afif@debian.org>
 Forwarded: not-needed
 Last-Update: 2016-10-09
---- python-pbcore.orig/pbcore/io/dataset/pyxb/DataSetXsd.py
-+++ python-pbcore/pbcore/io/dataset/pyxb/DataSetXsd.py
-@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
+--- a/pbcore/io/dataset/pyxb/DataSetXsd.py
++++ b/pbcore/io/dataset/pyxb/DataSetXsd.py
+@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:4c2de410-68d0-11e8-b8c4-1803730e031b')
  
  # Version of PyXB used to generate the bindings
 -_PyXBVersion = '1.2.4'
@@ -22,10 +22,10 @@ Last-Update: 2016-10-09
  
  # Import bindings for namespaces imported into schema
  import _pbbase as _ImportedBinding__pbbase
---- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbbase.py
-+++ python-pbcore/pbcore/io/dataset/pyxb/_pbbase.py
-@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
+--- a/pbcore/io/dataset/pyxb/_pbbase.py
++++ b/pbcore/io/dataset/pyxb/_pbbase.py
+@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:4c2de410-68d0-11e8-b8c4-1803730e031b')
  
  # Version of PyXB used to generate the bindings
 -_PyXBVersion = '1.2.4'
@@ -38,10 +38,10 @@ Last-Update: 2016-10-09
  
  # Import bindings for namespaces imported into schema
  import pyxb.binding.datatypes
---- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbmeta.py
-+++ python-pbcore/pbcore/io/dataset/pyxb/_pbmeta.py
-@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
+--- a/pbcore/io/dataset/pyxb/_pbmeta.py
++++ b/pbcore/io/dataset/pyxb/_pbmeta.py
+@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:4c2de410-68d0-11e8-b8c4-1803730e031b')
  
  # Version of PyXB used to generate the bindings
 -_PyXBVersion = '1.2.4'
@@ -53,11 +53,11 @@ Last-Update: 2016-10-09
 +#    raise pyxb.PyXBVersionError(_PyXBVersion)
  
  # Import bindings for namespaces imported into schema
- import _pbrk as _ImportedBinding__pbrk
---- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbrk.py
-+++ python-pbcore/pbcore/io/dataset/pyxb/_pbrk.py
-@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
+ import _pbbase as _ImportedBinding__pbbase
+--- a/pbcore/io/dataset/pyxb/_pbrk.py
++++ b/pbcore/io/dataset/pyxb/_pbrk.py
+@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:4c2de410-68d0-11e8-b8c4-1803730e031b')
  
  # Version of PyXB used to generate the bindings
 -_PyXBVersion = '1.2.4'
@@ -69,11 +69,11 @@ Last-Update: 2016-10-09
 +#    raise pyxb.PyXBVersionError(_PyXBVersion)
  
  # Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- python-pbcore.orig/pbcore/io/dataset/pyxb/_pbsample.py
-+++ python-pbcore/pbcore/io/dataset/pyxb/_pbsample.py
-@@ -18,10 +18,10 @@
- _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:7fa6c9c0-a3d6-11e7-96cb-0026b9fe0a90')
+ import _pbbase as _ImportedBinding__pbbase
+--- a/pbcore/io/dataset/pyxb/_pbsample.py
++++ b/pbcore/io/dataset/pyxb/_pbsample.py
+@@ -18,10 +18,10 @@ import pyxb.utils.six as _six
+ _GenerationUID = pyxb.utils.utility.UniqueIdentifier('urn:uuid:4c2de410-68d0-11e8-b8c4-1803730e031b')
  
  # Version of PyXB used to generate the bindings
 -_PyXBVersion = '1.2.4'
@@ -85,13 +85,14 @@ Last-Update: 2016-10-09
 +#    raise pyxb.PyXBVersionError(_PyXBVersion)
  
  # Import bindings for namespaces imported into schema
- import pyxb.binding.datatypes
---- python-pbcore.orig/requirements-dev.txt
-+++ python-pbcore/requirements-dev.txt
-@@ -1,5 +1,5 @@
+ import _pbbase as _ImportedBinding__pbbase
+--- a/requirements-dev.txt
++++ b/requirements-dev.txt
+@@ -1,6 +1,6 @@
  coverage
  nose
 -pyxb==1.2.4
 +pyxb
  sphinx
  h5py >= 2.0.1
+ pysam >= 0.13

debian/patches/numpy1.14.patch

-Description: Fix FTBFS with NumPy 1.14
-Bug-Debian: https://bugs.debian.org/900485
-Origin: upstream, https://github.com/PacificBiosciences/pbcore/commit/b7ef4238b6388f984a264b8a912450b652177dbf
-Author: David Seifert <dseifert@pacificbiosciences.com>
-Last-Update: 2018-01-10
-
---- a/tests/test_pbdataset.py
-+++ b/tests/test_pbdataset.py
-@@ -1693,7 +1693,7 @@ class TestDataSet(unittest.TestCase):
-         self.assertEqual(len(readers[0].referenceInfoTable), 59)
-         obstbl = [readers[0].referenceInfo('E.faecalis.1')]
-         exptbl = [(27, 27, 'E.faecalis.1', 'E.faecalis.1', 1482,
--                   'a1a59c267ac1341e5a12bce7a7d37bcb', 0L, 0L)]
-+                   'a1a59c267ac1341e5a12bce7a7d37bcb', 0, 0)]
-         self.assertListOfTuplesEqual(obstbl, exptbl)
-         # TODO: add a bam with a different referenceInfoTable to check merging
-         # and id remapping:
-@@ -2220,7 +2220,7 @@ class TestDataSet(unittest.TestCase):
-         self.assertEqual(len3, 338114)
-         obstbl = aln.referenceInfoTable
-         exptbl = [(1, 1, 'lambda_NEB3011', 'lambda_NEB3011',
--                   48502, 'a1319ff90e994c8190a4fe6569d0822a', 0L, 338113L)]
-+                   48502, 'a1319ff90e994c8190a4fe6569d0822a', 0, 338113)]
-         self.assertListOfTuplesEqual(obstbl, exptbl)
-         self.assertEqual(set(aln.tId), {1})
-         # + 1, because bounds are inclusive, rather than exclusive
-@@ -2247,9 +2247,9 @@ class TestDataSet(unittest.TestCase):
-         self.assertEqual(len3, 57147)
-         obstbl = aln.referenceInfoTable
-         exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
--                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 57034L),
-+                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 57034),
-                   (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,
--                   'a1319ff90e994c8190a4fe6569d0822a', 57035L, 57146L)]
-+                   'a1319ff90e994c8190a4fe6569d0822a', 57035, 57146)]
-         self.assertListOfTuplesEqual(obstbl, exptbl)
-         self.assertEqual(set(aln.tId), {0, 1})
-         # + 1, because bounds are inclusive, rather than exclusive
-@@ -2282,7 +2282,7 @@ class TestDataSet(unittest.TestCase):
-         self.assertEqual(len3, 65346)
-         obstbl = aln.referenceInfoTable
-         exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
--                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]
-+                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]
-         self.assertListOfTuplesEqual(obstbl, exptbl)
-         self.assertEqual(set(aln.tId), {0})
-         self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
-@@ -2306,7 +2306,7 @@ class TestDataSet(unittest.TestCase):
-         self.assertEqual(len1 + len2, len3)
-         self.assertEqual(len3, 160264)
-         exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
--                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L)]
-+                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0)]
-         obstbl = aln.referenceInfoTable
-         self.assertListOfTuplesEqual(obstbl, exptbl)
-         self.assertEqual(set(aln.tId), {0})
-@@ -2338,9 +2338,9 @@ class TestDataSet(unittest.TestCase):
-         # and endrow fields for bams someday...
-         obstbl = aln.referenceInfoTable
-         exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
--                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L),
-+                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0),
-                   (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,
--                   'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]
-+                   'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]
-         self.assertListOfTuplesEqual(obstbl, exptbl)
-         self.assertEqual(set(aln.tId), {0, 1})
-         self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),
-@@ -2372,9 +2372,9 @@ class TestDataSet(unittest.TestCase):
-         self.assertEqual(len4, 160376)
-         obstbl = aln.referenceInfoTable
-         exptbl = [(0, 0, 'ecoliK12_pbi_March2013', 'ecoliK12_pbi_March2013',
--                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0L, 0L),
-+                   4642522, '52cd7c5fa92877152fa487906ae484c5', 0, 0),
-                   (1, 1, 'lambda_NEB3011', 'lambda_NEB3011', 48502,
--                   'a1319ff90e994c8190a4fe6569d0822a', 0L, 0L)]
-+                   'a1319ff90e994c8190a4fe6569d0822a', 0, 0)]
-         self.assertListOfTuplesEqual(obstbl, exptbl)
-         self.assertEqual(set(aln.tId), {0, 1})
-         self.assertEqual(aln.referenceInfo('ecoliK12_pbi_March2013'),

debian/patches/relax_test_constraint.patch

@@ -8,7 +8,7 @@ Description: Relax test constraint which is rather a rounding issue
 
 --- a/tests/test_pbdataset.py
 +++ b/tests/test_pbdataset.py
-@@ -2121,7 +2121,7 @@ class TestDataSet(unittest.TestCase):
+@@ -2122,7 +2122,7 @@ class TestDataSet(unittest.TestCase):
                           2322.805559802698)
          self.assertEqual(ds2.metadata.summaryStats.readLenDist.sampleStd,
                           2322.805559802698)

debian/patches/remove-unnecessary-cython-dep.patch

@@ -5,9 +5,9 @@ Description: Remove cython from requirements.txt
 Author: Afif Elghraoui <afif@ghraoui.name
 Forwarded: no
 Last-Update: 2015-12-13
---- python-pbcore.orig/requirements.txt
-+++ python-pbcore/requirements.txt
+--- a/requirements.txt
++++ b/requirements.txt
 @@ -1,3 +1,2 @@
 -cython
  numpy >= 1.7.1
- pysam >= 0.9.0
+ pysam >= 0.13

debian/patches/series

@@ -2,5 +2,4 @@ doc-theme.patch
 enable-build-time-testing.patch
 remove-unnecessary-cython-dep.patch
 ignore-pyxb.patch
-numpy1.14.patch
 relax_test_constraint.patch

debian/watch

-version=3
+version=4
 
-# For GitHub projects you can use the tags or releases page.  Since the archive
-# URLs use only the version as the name, it is recommended to use a
-# filenamemangle to adjust the name of the downloaded file:
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/pbcore-$1.tar.gz/" \
-  https://github.com/PacificBiosciences/pbcore/tags (?:.*/)?v?(\d[\d\.]*)\.tar\.gz
+# Upstream is not tagging releases regularly - thus we use mode=git
+opts="mode=git,pretty=1.5.0+git%cd.%h,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+  https://github.com/PacificBiosciences/pbcore.git HEAD

doc/conf.py

@@ -12,9 +12,9 @@
 # serve to show the default.
 
 import sys, os
-globals = {}
-execfile("../pbcore/__init__.py", globals)
-__VERSION__ = globals["__VERSION__"]
+
+# don't forget to update setup.py and pbcore/__init__.py too
+__VERSION__ = '1.5.0'
 
 
 # If extensions (or modules to document with autodoc) are in another directory,

pbcore/__init__.py

-#################################################################################
-# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
-#
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of Pacific Biosciences nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-#
-# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
-# THIS LICENSE.  THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
-# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
-# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
-# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#################################################################################
+from __future__ import absolute_import
 
-__VERSION__ = "1.4.2"
+# don't forget to update setup.py and doc/conf.py too
+__VERSION__ = "1.5.0"

pbcore/chemistry/__init__.py

-#################################################################################
-# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
-#
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of Pacific Biosciences nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-#
-# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
-# THIS LICENSE.  THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
-# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
-# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
-# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#################################################################################
+from __future__ import absolute_import
 
 from .chemistry import *

pbcore/chemistry/chemistry.py

-#################################################################################
-# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
-#
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of Pacific Biosciences nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-#
-# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
-# THIS LICENSE.  THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
-# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
-# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
-# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#################################################################################
-
+from __future__ import absolute_import
 
 __all__ = ["tripleFromMetadataXML",
            "decodeTriple",
@@ -54,7 +25,7 @@ def _loadBarcodeMappingsFromFile(mapFile):
             mappings[(bindingKit, sequencingKit, softwareVersion)] = sequencingChemistry
         return mappings
     except:
-        raise ChemistryLookupError, "Error loading chemistry mapping xml"
+        raise ChemistryLookupError("Error loading chemistry mapping xml")
 
 def _loadBarcodeMappings():
     mappingFname = resource_filename(Requirement.parse('pbcore'),'pbcore/chemistry/resources/mapping.xml')
@@ -87,8 +58,7 @@ def tripleFromMetadataXML(metadataXmlPath):
         instrumentControlVersion = ".".join(verComponents)
         return (bindingKit, sequencingKit, instrumentControlVersion)
     except Exception as e:
-        raise ChemistryLookupError, \
-            ("Could not find, or extract chemistry information from, %s" % (metadataXmlPath,))
+        raise ChemistryLookupError("Could not find, or extract chemistry information from, %s" % (metadataXmlPath,))
 
 def decodeTriple(bindingKit, sequencingKit, softwareVersion):
     """

pbcore/chemistry/resources/mapping.xml

@@ -329,71 +329,68 @@
     <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
-  <!--=====================================-->
-  <!-- Updating PA version from 5.0 -> 5.1 -->
-  <!--=====================================-->
-
-  <!-- PA5.1 backward compatibility with iguana chemistry -->
+  <!-- 2.1 binding kit with 2.0 sequencing plate -->
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>100-862-200</BindingKit>
+    <BindingKit>101-365-900</BindingKit>
     <SequencingKit>100-861-800</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>100-862-200</BindingKit>
+    <BindingKit>101-365-900</BindingKit>
     <SequencingKit>101-093-700</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
-  <!-- Sequel® Sequencing Plate Silwet -->
+  <!-- 2.1 binding kit with 2.1 sequencing plate (silwet) -->
+  <!-- SG1/16509P Chemistry update (binding kit only) with 5.0 basecaller (no new training) -->
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>100-862-200</BindingKit>
+    <BindingKit>101-365-900</BindingKit>
     <SequencingKit>101-309-500</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
-  <!-- Sequel® Sequencing Plate Silwet (4 rxn) -->
+  <!-- SG1/16509P Chemistry update (binding kit only) with 5.0 basecaller (no new training) -->
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>100-862-200</BindingKit>
+    <BindingKit>101-365-900</BindingKit>
     <SequencingKit>101-309-400</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
-  <!-- 2.1 binding kit with 2.0 sequencing plate -->
+  <!-- SG1/16509P Chemistry update (binding kit only) with 5.0 basecaller (no new training, prototype parts) -->
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>101-365-900</BindingKit>
-    <SequencingKit>100-861-800</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <BindingKit>101-490-800</BindingKit>
+    <SequencingKit>101-490-900</SequencingKit>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
+  <!-- SG1/16509P Chemistry update (binding kit only) with 5.0 basecaller (no new training, prototype parts) -->
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>101-365-900</BindingKit>
-    <SequencingKit>101-093-700</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <BindingKit>101-490-800</BindingKit>
+    <SequencingKit>101-491-000</SequencingKit>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
-  <!-- 2.1 binding kit with 2.1 sequencing plate (silwet) -->
-  <!-- SG1/16509P Chemistry update (binding kit only) with 5.1 primary (no new training) -->
+  <!-- SG1/16509P Chemistry update (binding kit only) with 5.0 basecaller (no new training, prototype parts) -->
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>101-365-900</BindingKit>
-    <SequencingKit>101-309-500</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <BindingKit>101-500-400</BindingKit>
+    <SequencingKit>101-490-900</SequencingKit>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
-  <!-- SG1/16509P Chemistry update (binding kit only) with 5.1 primary (no new training) -->
+  <!-- SG1/16509P Chemistry update (binding kit only) with 5.0 basecaller (no new training, prototype parts) -->
   <Mapping>
     <SequencingChemistry>S/P2-C2/5.0</SequencingChemistry>
-    <BindingKit>101-365-900</BindingKit>
-    <SequencingKit>101-309-400</SequencingKit>
-    <SoftwareVersion>5.1</SoftwareVersion>
+    <BindingKit>101-500-400</BindingKit>
+    <SequencingKit>101-491-000</SequencingKit>
+    <SoftwareVersion>5.0</SoftwareVersion>
   </Mapping>
 
 </MappingTable>

pbcore/data/__init__.py

-#################################################################################
-# Copyright (c) 2011-2015, Pacific Biosciences of California, Inc.
-#
-# All rights reserved.
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions are met:
-# * Redistributions of source code must retain the above copyright
-#   notice, this list of conditions and the following disclaimer.
-# * Redistributions in binary form must reproduce the above copyright
-#   notice, this list of conditions and the following disclaimer in the
-#   documentation and/or other materials provided with the distribution.
-# * Neither the name of Pacific Biosciences nor the names of its
-#   contributors may be used to endorse or promote products derived from
-#   this software without specific prior written permission.
-#
-# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY
-# THIS LICENSE.  THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS
-# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
-# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR
-# ITS CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
-# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
-# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-# IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-# POSSIBILITY OF SUCH DAMAGE.
-#################################################################################
+from __future__ import absolute_import
 
 from pkg_resources import Requirement, resource_filename
 
@@ -177,3 +149,6 @@ def getEmptyAlignedBam():
 
 def getMappingXml():
     return _getAbsPath("chemistry.xml")
+
+def getWeird():
+    return _getAbsPath("weird.fa")

pbcore/data/datasets/__init__.py

 """Doctest resources"""
+from __future__ import absolute_import
 
 import os
 from pkg_resources import Requirement, resource_filename

pbcore/data/weird.fa

+>chr1
+acgtacgtacgtact
\ No newline at end of file

pbcore/data/weird.fa.fai

+chr1	15	7	15	15