New upstream version 1.6.5+dfsg

xsd-codegen:

	rm -f pbcore/io/dataset/pyxb/DataSetXsd.py

	./bin/updateXSDs.py ../xsd-datamodels/PacBioDatasets.xsd pbcore/io/dataset/pyxb/

validate-metadata:

	xmllint --schema ../xsd-datamodels/PacBioCollectionMetadata.xsd pbcore/data/datasets/CollectionMetadata.xml

The `pbcore` package provides Python APIs for interacting with PacBio

data files and writing bioinformatics applications.

## Installation:

## Availability

Latest version can be installed via bioconda package `pbcore`.

    % pip install -r requirements.txt

    % python setup.py install

Note that h5py is now considered an "optional" dependency, since the old

RSII sequencing files are no longer generated by current systems and

software.  The underlying functionality has been left in place for backwards

compatibility with existing code, but you will need to install h5py manually

to use these parts of the API:

    % pip install h5py

Please refer to our [official pbbioconda page](https://github.com/PacificBiosciences/pbbioconda)

for information on Installation, Support, License, Copyright, and Disclaimer.

## Documentation:

#!/bin/bash

type module >& /dev/null || . /mnt/software/Modules/current/init/bash

module load python/2.7.9-mobs-pbcore

set -ex

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 PATH=$PWD/build/bin:$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

PIP="pip --cache-dir=${bamboo_build_working_directory:-$PWD}/.pip"

if [[ -z ${bamboo_repository_branch_name+x} ]]; then

  WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop

elif [[ ${bamboo_repository_branch_name} == develop ]]; then

  WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop

elif [[ ${bamboo_repository_branch_name} == master ]]; then

  WHEELHOUSE=/mnt/software/p/python/wheelhouse/master

else

  WHEELHOUSE=/mnt/software/p/python/wheelhouse/develop

fi

rm -rf   build

mkdir -p build/bin build/lib build/include build/share

$PIP install --user \

  $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 ./    

$PIP install --no-compile --find-link $WHEELHOUSE --user -r requirements.txt

$PIP install --no-compile --find-link $WHEELHOUSE --user -r requirements-dev.txt

$PIP install --no-compile --find-link $WHEELHOUSE --user -e ./

set +e

make pylint # way too many errors right now

import sys, os

# don't forget to update setup.py and pbcore/__init__.py too

__VERSION__ = '1.5.0'

__VERSION__ = '1.6.5'

# If extensions (or modules to document with autodoc) are in another directory,

from __future__ import absolute_import

# don't forget to update setup.py and doc/conf.py too

__VERSION__ = "1.5.0"

__VERSION__ = "1.6.5"