Initial commit

.bumpversion.cfg

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+[bumpversion]
+current_version = 0.0.1
+commit = True
+tag = False
+tag_name = {new_version}
+
+[bumpversion:file:setup.py]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:README.md]
+search = Current version: {current_version}
+replace = Current version: {new_version}
+
+[bumpversion:file:src/carrot_cli/__main__.py]
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"

.coveragerc

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+[run]
+source = carrot_cli 
+branch = True
+
+[report]
+skip_covered = True
+exclude_lines =
+    no cov
+    no qa
+    noqa
+    pragma: no cover
+
+    # Don't complain if tests don't hit defensive assertion code:
+    raise AssertionError
+    raise NotImplementedError
+
+[html]
+directory = coverage_html_report

.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/
+*.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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+# PyCharm
+.idea

.isort.cfg

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+[settings]
+known_first_party=carrot_cli

.pylintrc

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+
+[TYPECHECK]
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E1101 when accessed. Python regular
+# expressions are accepted.
+generated-members=pysam*
+
+[MASTER]
+disable=
+    C0330,
+    C0114,
+    C0116,
+    E1136, # known bug in pylint 2.4.4

.readthedocs.yml

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+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2019, Broad Institute
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. 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.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND 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 THE COPYRIGHT HOLDER OR 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.

MANIFEST.in

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+graft tests
+graft src
+
+include README.rst
+include LICENSE.txt
+include tox.ini .travis.yml
+
+prune **/.hypothesis
+
+global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store

README.md

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+# Python CLI Project Template
+This template was created so that a new python3 CLI program could be quickly whipped up with a nice infrastructure. 
+
+## Acknowledgements
+This template is based on several projects that originated at or as part of collaborations involving The Broad Institute of MIT and Harvard.
+In particular, the following people were instrumental in those projects: 
+
+- Kiran Garimella (@kvg)
+- Winni Kretzschmar (@winni2k)
+- Karl Johan Westrin (@karljohanw)
+
+## Contents / Features
+Included in this template are the following features:
+- `click` for argument parsing with examples
+- an over-engineered logging module (ensures that all log messages have correct leading whitespace to be column-aligned)
+- `tox` setup (linting, black for code formatting, testing)
+- examples of tests (already connected to tox for quick starting)
+- `.gitignore` for most kinds of local files
+- include sort ordering defaults 
+- a `readthedocs` template
+- a `bumpversion` config file
+- a `pylint` config file
+
+If you check this out and run `tox` the tests will all pass.
+
+## Make It Your Own
+### Required Changes
+To make this project-specific, several placeholder values need to be replaced with your content.  
+
+| FIELD | DESCRIPTION |
+| ----- | ----------- |
+|  PROJECT\_NAME | The name of your new project / tool. |
+| \_SHORT\_PROJECT\_DESCRIPTION\_ | A concise description of your new project / tool. |
+| \_AUTHOR\_ | The name of the primary author / point of contact. |
+| \_AUTHOR\_EMAIL\_ | The email address of the primary author / point of contact. |
+
+This find/replace will be needed until github [implements template repo variables.](https://github.com/isaacs/github/issues/1716)
+
+However, fear not!  I have provided `initialize.sh` for this very purpose.  Run it with the following parameters after creating your repo to initialize your specific repository info:
+
+```
+./initialize.sh PROJECT_NAME "SHORT PROJECT DESCRIPTION" "AUTHOR NAME" AUTHOR_EMAIL
+```
+I quoted the fields that are likely to contain spaces - this will be necessary.
+
+### Optional Changes
+You may also need to do the following:
+- Update the LICENSE file - it defaults to the BSD 3-Clause License.
+
+When you add development dependencies, add them to `dev-requirements.txt`.
+
+When you add testing dependencies, add them to `test-requirements.txt`.
+
+When you add runtime dependencies, add them to `setup.py` in the `install_requires` section.
+
+## General Notes
+
+When running `tox`, you'll notice that the linter runs before black8.  This is intentional.  Rather than have it blindly reformat your code, I wanted to make sure you knew what you were doing wrong (i.e. against PEP 8 standards).  You can configure this order to suit your needs.
+
+Notable projects already using this template are:
+- [Cromshell 2.0](https://github.com/broadinstitute/cromshell/tree/cromshell_2.0)
+- [CARROT CLI](https://github.com/broadinstitute/carrot_cli)
+
+Lastly, it's worth double-checking everything to make sure you want what's included here.
+
+Below this line begins the project-specific portion of the README that should be modified after creating a new project:
+
+---
+
+# PROJECT\_NAME 
+\_SHORT\_PROJECT\_DESCRIPTION\_
+
+Current version: 0.0.1
+
+## Installation
+
+    pip install .
+
+## Development
+
+To do development in this codebase, the python3 development package must
+be installed.
+
+After installation the development environment can be set up by
+the following commands:
+
+    python3 -mvenv venv
+    . venv/bin/activate
+    pip install -r dev-requirements.txt
+    pip install -e .
+
+### Linting files
+
+    # run all linting commands
+    tox -e lint
+
+    # reformat all project files
+    black src tests setup.py
+
+    # sort imports in project files
+    isort -rc src tests setup.py
+
+    # check pep8 against all project files
+    flake8 src tests setup.py
+
+    # lint python code for common errors and codestyle issues
+    pylint src
+
+### Tests
+
+    # run all linting and test
+    tox
+
+    # run only (fast) unit tests
+    tox -e unit
+
+    # run only linting
+    tox -e lint
+
+Note: If you run into "module not found" errors when running tox for testing, verify the modules are listed in test-requirements.txt and delete the .tox folder to force tox to refresh dependencies.
+
+### Versioning
+
+We use `bumpversion` to maintain version numbers.
+*DO NOT MANUALLY EDIT ANY VERSION NUMBERS.*
+
+Our versions are specified by a 3 number semantic version system (https://semver.org/):
+
+	major.minor.patch
+
+To update the version with bumpversion do the following:
+
+`bumpversion PART` where PART is one of:
+- major
+- minor
+- patch
+
+This will increase the corresponding version number by 1.
+

dev-requirements.txt

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+isort==4.3.21
+tox
+wheel
+bumpversion
+twine
+black
+flake8
+pylint
+cython
+sphinx
+sphinx-rtd-theme
+mypy==0.770
+click