New upstream version 1.1.1

	find . -name "*.err" | xargs rm -f;\

	find . -name "*.log" | xargs rm -f;\

	rm -rf dist;\

	rm -rf docs/_build

	rm -rf docs/build

	rm -f FileTypes.h

test:

test-nose:

	nosetests -s --verbose --with-xunit --logging-config log_nose.cfg tests/test_*.py

test: test-nose run-pylint run-pep8

doc:

	cd docs && make html

	python -m pbcommand.cli.examples.dev_scatter_fasta_app --emit-tool-contract > ./tests/data/tool-contracts/dev_scatter_fasta_app_tool_contract.json

	python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contracts -o ./tests/data/tool-contracts

run-pylint:

	pylint --errors-only pbcommand

run-pep8:

	find pbcommand -name "*.py" -exec pep8 --ignore=E501,E265,E731,E402,W292 {} \;

	# use xargs to propagate exit code

	find pbcommand -name "*.py" | xargs pep8 --ignore=E501,E265,E731,E402,W292

run-auto-pep8:

	find pbcommand -name "*.py" -exec autopep8 -i --ignore=E501,E265,E731,E402,W292 {} \;

build-avro-schema-docs:

	# this requires nodejs + https://github.com/ept/avrodoc

	avrodoc pbcommand/schemas/*.avsc > index.html

cpp-header:

	python extras/make_cpp_file_types_header.py FileTypes.h

                        Min Sequence Length filter (default: 25)

```

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----------

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avro

requests

iso8601

pytz

nose

coverage

tox

autopep8

pylint

# Putting these here for RTD

sphinx-argparse

sphinx-bootstrap-theme

# I think this is a bug in jupyter client

# for some reason jupyter_client.manager is called

# which generates an ImportError

# maybe related https://github.com/jupyter/nbconvert/issues/495

jupyter_client

# for ipython notebooks in sphinx docs

nbsphinx

avro

requests

iso8601

#!/bin/bash -ex

NX3PBASEURL=http://nexus/repository/unsupported/pitchfork/gcc-4.9.2

export PATH=$PWD/bin:/mnt/software/a/anaconda2/4.2.0/bin:$PATH

export PYTHONUSERBASE=$PWD

export CFLAGS="-I/mnt/software/a/anaconda2/4.2.0/include"

PIP="pip --cache-dir=$bamboo_build_working_directory/.pip"

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

module load gcc/4.9.2

rm -rf bin lib include share

mkdir  bin lib include share

$PIP install --user \

  iso8601

$PIP install --user \

  $NX3PBASEURL/pythonpkgs/xmlbuilder-1.0-cp27-none-any.whl \

  $NX3PBASEURL/pythonpkgs/tabulate-0.7.5-cp27-none-any.whl \

  $NX3PBASEURL/pythonpkgs/pysam-0.9.1.4-cp27-cp27mu-linux_x86_64.whl \

  $NX3PBASEURL/pythonpkgs/avro-1.7.7-cp27-none-any.whl

$PIP install --user --upgrade pylint

$PIP install --user -r  REQUIREMENTS.txt

$PIP install --user -r  REQUIREMENTS_TEST.txt

$PIP install --user -e ./

nosetests -s --verbose --with-xunit --xunit-file=nosetests.xml --with-coverage --cover-xml --cover-xml-file=coverage.xml --logging-config \

    log_nose.cfg tests/test_*.py

sed -i -e 's@filename="@filename="./@g' coverage.xml

make run-pylint run-pep8