New upstream version 0.8.0

*.bak

cythonize.dat

docs/source/autodocs/*.rst

MANIFEST

# os:

#   - linux

#   - osx

# make edits to this line to trigger a new travis build.

# (sometimes it errors out trying to download from PyPI)

language: python

python:

    - "2.7"

    #- "3.3"

    - "3.4"

    - "3.5"

    - "3.6"

# see https://github.com/travis-ci/travis-ci/issues/9815 for py3.7 support

matrix:

  include:

    - python: 3.7

      dist: xenial

      sudo: true

notifications:

    email:

    - conda update -q conda

    - conda info -a

    # Base env only needs to cythonize sources; test script takes care of

    # everything else.

    - conda install cython

script:

    - ./condatest.sh "$TRAVIS_PYTHON_VERSION"

include src/*

recursive-include pybedtools/include/ *

include README.rst

include LICENSE.txt

include ez_setup.py

recursive-include docs/source *.rst

recursive-include docs/source *.py

recursive-include docs/source/images *

recursive-include docs/source/_templates *

recursive-include pybedtools/test/data *

recursive-include pybedtools/test *

include docs/Makefile

include docs/make.bat

recursive-include pybedtools *.cxx

recursive-include pybedtools *.cpp

recursive-include pybedtools *.c

recursive-exclude * __pycache__

recursive-exclude * *.py[co]

#!/bin/bash

# Installs pybedtools and requirements into a fresh Python 2 or 3 environment

# and runs tests.

#

# Note that this script needs to be called from an environment with Cython

# since this does a clean/sdist operation which will Cythonize the source

set -e

PY_VERSION=$1

usage="Usage: $0 py_version[2|3]"

: ${PY_VERSION:?$usage}

log () {

    echo

    echo "[`date`] TEST HARNESS: $1"

    echo

}

log "removing existing env pbtpy${PY_VERSION}"

name=pbtpy${PY_VERSION}

conda env list | grep -q $name && conda env remove -y -n $name

log "starting with basic environment"

conda create -y -n $name --channel bioconda python=${PY_VERSION} \

    bedtools \

    "htslib<1.4" \

    ucsc-bedgraphtobigwig \

    ucsc-bigwigtobedgraph

source activate $name

log "temporarily install cython"

conda install cython

log "force re-cythonizing"

rm -rf dist build

python setup.py clean

python setup.py build

python setup.py sdist

log "uninstall cython"

conda remove cython

log "test installation of sdist"

set -x

(cd dist && pip install pybedtools-*.tar.gz && python -c 'import pybedtools')

set +x

python setup.py clean

log "install test requirements"

# ----------------------------------------------------------------------------

# sdist and pip install tests

# ----------------------------------------------------------------------------

# Build an environment with just Python and Cython. We do this fresh each time.

log "building fresh environment with just python and cython"

with_cy="pbtpy${PY_VERSION}_sdist_cython"

if conda env list | grep -q $with_cy; then

    conda env remove -y -n $with_cy

fi

conda create -n $with_cy -y --channel conda-forge --channel bioconda python=${PY_VERSION} cython

source activate $with_cy

# Clone the repo -- so we're only catching things committed to git -- into

# a temp dir

log "cloning into temp dir"

HERE="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

TMP=/tmp/pybedtools-deploy

rm -rf $TMP

git clone $HERE $TMP

cd $TMP

log "cythonizing source files and building source package"

# Cythonize the .pyx filex to .cpp, and build a source package

python setup.py clean cythonize sdist

log "installing source package with pip"

# Install into the environment to verify that everything works (just an import

# test)

(cd dist && pip install pybedtools-*.tar.gz && python -c 'import pybedtools; print(pybedtools.__file__)')

# ----------------------------------------------------------------------------

# Unit tests

# ----------------------------------------------------------------------------

# Deactivate that env, and build another one with all requirements that we'll

# use for unit tests.

source deactivate

conda env list | grep -q $name && conda env remove -y -n $name

conda create -y -n $name --channel bioconda python=${PY_VERSION} \

    --file "requirements.txt" \

    --file "test-requirements.txt" \

    --file "optional-requirements.txt"

source activate $name

log "install pybedtools from setup.py in develop mode to trigger re-cythonizing"

python setup.py develop

log "run tests"

nosetests

(cd docs && make clean && make doctest)

no_cy="pbtpy${PY_VERSION}_conda_no_cython"

if ! conda env list | grep -q $no_cy; then

    log "creating environment"

    # pysam not available from bioconda for py37 so remove it from

    # requirements.

    TMPREQS=$(tempfile)

    grep -v pysam requirements.txt > $TMPREQS

    if [[ "$PY_VERSION" == "3.7" ]]; then

        REQS=$TMPREQS

    else

        REQS=requirements.txt

    fi

    conda create -n $no_cy -y \

        --channel conda-forge \

        --channel bioconda \

        python=${PY_VERSION} \

        --file $REQS \

        --file test-requirements.txt \

        --file optional-requirements.txt

else

    echo "Using existing environment '${no_cy}'"

fi

source activate $no_cy

log "unpacking source package and install with pip install -e into $no_cy env"

mkdir -p /tmp/pybedtools-uncompressed

cd /tmp/pybedtools-uncompressed

tar -xf $TMP/dist/pybedtools-*.tar.gz

cd pybedtools-*

pip install -e .

log "Unit tests"

pytest -v --doctest-modules

# ----------------------------------------------------------------------------

# sphinx doctests

# ----------------------------------------------------------------------------

# Since the docs aren't included in the MANIFEST and therefore aren't included

# in the source distribution, we copy them over from the repo we checked out.

log "copying over docs directory from repo"

cp -r $TMP/docs .

log "sphinx doctests"

(cd docs && make clean doctest)

cython

matplotlib

nose

numpydoc

pandas

pyyaml