Initial commit

.github/workflows/pythonpackage.yml

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+name: Python package
+
+on: [push]
+env:
+  POETRY_VERSION: 1.1
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        PYTHON_VERSION: ["3.6", "3.7"]
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{matrix.PYTHON_VERSION}}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{matrix.PYTHON_VERSION}}
+
+    - name: Get full Python version
+      id: full-python-version
+      shell: bash
+      run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+
+    - name: Install poetry
+      shell: bash
+      run: |
+        python -m pip install --upgrade pip
+        pip install poetry==${{env.POETRY_VERSION}}
+
+    - name: Configure poetry
+      shell: bash
+      run: poetry config virtualenvs.in-project true
+
+    - name: Set up cache
+      uses: actions/cache@v2
+      id: cache
+      with:
+        path: .venv
+        key: venv-${{ runner.os }}-${{ steps.full-python-version.outputs.version }}-${{ hashFiles('**/poetry.lock') }}
+
+    - name: Ensure cache is healthy
+      if: steps.cache.outputs.cache-hit == 'true'
+      shell: bash
+      run: poetry run pip --version >/dev/null 2>&1 || rm -rf .venv
+
+    - name: Install deps
+      shell: bash
+      run: |
+        poetry install --extras docs
+
+    - name: Run pytest
+      shell: bash
+      run: |
+        poetry run python -m pytest --cov=pybedlite --cov-report=xml --cov-branch 
+
+    - name: Style checking
+      shell: bash
+      run: |
+        poetry run black --line-length 99 --check pybedlite
+
+    - name: Run lint
+      shell: bash
+      run: |
+        poetry run flake8 --config=ci/flake8.cfg pybedlite
+
+    - name: Run mypy
+      shell: bash
+      run: |
+        poetry run mypy -p pybedlite --config=ci/mypy.ini
+
+    - name: Run docs
+      shell: bash
+      run: |
+        set -euo pipefail
+        pushd docs
+        poetry run make html
+        popd
+
+    - name: Upload code coverage
+      uses: codecov/[email protected]

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# VSCode configurations
+.vscode/

.readthedocs.yml

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+build:
+    image: latest
+version: 2
+sphinx:
+  configuration: docs/conf.py
+python:
+    version: 3.6
+    install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

LICENSE

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+The MIT License
+
+Copyright (c) 2021 Fulcrum Genomics LLC, with the exception of 
+  - pybedlite/overlap_detector.py
+  - pybedlite/tests/test_overlap_detector.py
+ which are Copyright 2020 Myriad Genetics Inc. and are copied from https://github.com/myriad-opensource/samwell under MIT license.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

README.md

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+
+[![Language][language-badge]][language-link]
+[![Code Style][code-style-badge]][code-style-link]
+[![Type Checked][type-checking-badge]][type-checking-link]
+[![PEP8][pep-8-badge]][pep-8-link]
+[![Code Coverage][code-coverage-badge]][code-coverage-link]
+[![License][license-badge]][license-link]
+
+---
+
+[![Python package][python-package-badge]][python-package-link]
+[![PyPI version][pypi-badge]][pypi-link]
+[![PyPI download total][pypi-downloads-badge]][pypi-downloads-link]
+
+---
+
+[language-badge]:       http://img.shields.io/badge/language-python-brightgreen.svg
+[language-link]:        http://www.python.org/
+[code-style-badge]:     https://img.shields.io/badge/code%20style-black-000000.svg
+[code-style-link]:      https://black.readthedocs.io/en/stable/ 
+[type-checking-badge]:  http://www.mypy-lang.org/static/mypy_badge.svg
+[type-checking-link]:   http://mypy-lang.org/
+[pep-8-badge]:          https://img.shields.io/badge/code%20style-pep8-brightgreen.svg
+[pep-8-link]:           https://www.python.org/dev/peps/pep-0008/
+[code-coverage-badge]:  https://codecov.io/gh/fulcrumgenomics/pybedlite/branch/master/graph/badge.svg
+[code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/pybedlite
+[license-badge]:        http://img.shields.io/badge/license-MIT-blue.svg
+[license-link]:         https://github.com/fulcrumgenomics/pybedlite/blob/master/LICENSE
+[python-package-badge]: https://github.com/fulcrumgenomics/pybedlite/workflows/Python%20package/badge.svg
+[python-package-link]:  https://github.com/fulcrumgenomics/pybedlite/actions?query=workflow%3A%22Python+package%22
+[pypi-badge]:           https://badge.fury.io/py/pybedlite.svg
+[pypi-link]:            https://pypi.python.org/pypi/pybedlite
+[pypi-downloads-badge]: https://img.shields.io/pypi/dm/pybedlite
+[pypi-downloads-link]:  https://pypi.python.org/pypi/pybedlite
+
+# pybedlite
+
+`pip install pybedlite`
+
+**Requires python 3.6+**
+
+# Getting Setup
+
+[Poetry][poetry-link] is used to manage the python development environment. 
+
+A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link].  E.g.:
+
+```bash
+conda create -n pybedlite python=3.6 poetry
+conda activate pybedlite
+poetry install
+```
+
+If, during `poetry install` on Mac OS X errors are encountered running gcc/clang to build `pybedtools` or other packages with native code, try setting the following and re-running `poetry install`:
+```bash
+export CFLAGS="-stdlib=libc++"
+``` 
+
+[poetry-link]: https://github.com/python-poetry/poetry
+[conda-link]:  https://docs.conda.io/en/latest/miniconda.html

ci/check.sh

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+#!/bin/bash
+
+function banner() {
+    echo
+    echo "================================================================================"
+    echo $*
+    echo "================================================================================"
+    echo
+}
+
+#####################################################################
+# Takes two parameters, a "name" and a "command".
+# Runs the command and prints out whether it succeeded or failed, and
+# also tracks a list of failed steps in $failures.
+#####################################################################
+function run() {
+    local name=$1
+    local cmd=$2
+
+    banner "Running $name [$cmd]"
+    set +e
+    $cmd
+    exit_code=$?
+    set -e
+
+    if [[ $exit_code == 0 ]]; then
+        echo Passed $name: "[$cmd]"
+    else
+        echo Failed $name: "[$cmd]"
+        if [ -z "$failures" ]; then
+            failures="$failures $name"
+        else
+            failures="$failures, $name"
+        fi
+    fi
+}
+
+parent=$(cd $(dirname $0) && pwd -P)
+
+# If the script is invoked with --check only have black check, otherwise have it fix!
+black_extra_args=""
+if [[ "$1" == "--check" ]]; then
+    black_extra_args="--check"
+fi
+
+banner "Executing in conda environment ${CONDA_DEFAULT_ENV} in directory ${root}"
+run "Unit Tests"     "python -m pytest -vv -r sx pybedlite"
+run "Style Checking" "black --line-length 99 $black_extra_args pybedlite"
+run "Linting"        "flake8 --config=$parent/flake8.cfg pybedlite"
+run "Type Checking"  "mypy -p pybedlite --config $parent/mypy.ini"
+
+if [ -z "$failures" ]; then
+    banner "Checks Passed"
+else
+    banner "Checks Failed with failures in: $failures"
+    exit 1
+fi

ci/flake8.cfg

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+# flake8 config file
+
+[flake8]
+max_line_length = 100
+show-source = true
+ignore = E701 W504 W503
+extend-ignore = E203

ci/mypy.ini

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+[mypy]
+strict_optional = False
+ignore_missing_imports = True
+disallow_untyped_decorators = False
+follow_imports = silent
+disallow_untyped_defs = True