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Commit74cc132

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Merge pull request#230 from bcgsc/Release/v2.2.8
Release/v2.2.8
2 parentse205d9e +b2798ce commit74cc132

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‎.github/CONTRIBUTING.md

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pytest tests
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```
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##Build theSphinxDocumentation
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##Build the Documentation
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```bash
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pip install .[docs]
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sphinx-build docs/source/ html
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markdown_refdocs mavis -o docs/package --link
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mkdocs build
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```
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The contents of the user manual can then be viewed by opening the build/html/index.html in any available
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web browser (i.e. google-chrome, firefox, etc.)
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The contents of the user manual can then be viewed by opening the build-docs/index.html
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in any availableweb browser (i.e. google-chrome, firefox, etc.)
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##Deploy to PyPi
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```
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###Reporting a Bug
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##Reporting a Bug
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Please make sure to search through the issues before reporting a bug to ensure there isn't already an open issue.
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Please make sure to search through the issues before reporting a bug to ensure there isn't
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already an open issue.
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###Coding Conventions
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##Conventions
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####Formatting/Style
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###Linting
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- In general, follow[pep8](https://www.python.org/dev/peps/pep-0008/) style guides (except maximum line width)
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- docstrings should follow[sphinx google code style](http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
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- any column name which may appear in any of the intermediate or final output files must be defined in``mavis.constants.COLUMNS``
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Use[black](https://github.com/psf/black) with strings off and line length 100
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```bash
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black mavis -S -l 100
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```
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###Docstrings
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#####Types in docstrings
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docstrings should follow[sphinx google code style](http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
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if you want to be more explicit with nested types, the following conventions are used throughout the code
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if you want to be more explicit with nested types, please follow the same format
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used by[python type annotations](https://docs.python.org/3/library/typing.html)
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- dictionary:``d = {<key>: <value>}`` becomes``dict of <value> by <key>``
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- list:``l = [1, 2, 3]`` becomes``list of int``
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- mixed:``d = {'a': [1, 2, 3], 'b': [4, 5, 6]}`` becomes``dict of list of int by str``
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- tuples:``('a', 1)`` becomes``tuple of str and int``
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```text
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arg1 (List[str]): a list of strings
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```
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However using proper type annotations is preferred for new code and then only including the
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description of the parameter in the docstring and not its type
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```python
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####Tests
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defsome_function(some_arg: List[str]) ->None:
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"""
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Args:
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some_arg: this arg does stuff
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"""
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```
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###Output Columns
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any column name which may appear in any of the intermediate or final output files must be defined in`mavis.constants.COLUMNS` as well as added to the[columns glossary](../outputs/columns)
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###Tests
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- all new code must have unit tests in the tests subdirectory
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- in general for assertEqual statements, the expected value is given first
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Tests can be run as follows
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```bash
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pytest tests
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```
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To run the tests with tox (multiple python installs tested). Note that you will need to have multiple python installs on your path
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###Branching Model
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If you are working on a large feature, create a base branch for the feature off develop. Generally
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these follow the naming pattern
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```bash
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tox
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git checkout -b integration/issue-<number>-<short-name>
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```
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If you are working on a smaller feature then simply make a feature branch off develop
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```bash
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git checkout -b feature/issue-<number>-<short-name>
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```
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Once ready, a PR should be made to develop and review should be requested from the other developers.
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Releases are done by creating a release branch off develop
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```bash
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git checkout -b release/vX.X.X
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```
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Updating the version number in setup.py in the release branch, and then making a PR to master.
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After the PR has been merged to master a tag/release should be created with the release notes
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and a PR to merge master back into develop should be made

‎.github/ISSUE_TEMPLATE.md

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‎.github/ISSUE_TEMPLATE/bug_report.md

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---
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name:Bug report
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about:Create a report to help us improve
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title:''
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labels:bug
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assignees:''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. run command '...'
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2. See error ...
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Input Data**
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If applicable, add the input data used when the bug was observed
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**Configuration**
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If applicable, include the mavis configuration file that was used to run the pipeline
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**Versions (please complete the following information):**
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- OS:[e.g. centos-07]
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- Python Version[e.g. 3.6.1]
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- MAVIS Version[e.g. 22]
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- Blat/BWA Version
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**Additional context**
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Add any other context about the problem here.
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---
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name:Feature request
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about:Suggest an idea for this project
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title:''
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labels:enhancement
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assignees:''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when[...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/workflows/build.yml

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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name:build
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on:[push, pull_request]
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jobs:
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build:
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runs-on:ubuntu-latest
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strategy:
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matrix:
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python-version:[3.6, 3.7, 3.8]
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steps:
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-uses:actions/checkout@v2
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-name:Set up Python ${{ matrix.python-version }}
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uses:actions/setup-python@v2
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with:
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python-version:${{ matrix.python-version }}
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-name:Install dependencies
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run:|
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python -m pip install --upgrade pip setuptools
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pip install .[test]
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-name:Lint with flake8
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run:|
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pip install flake8
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# stop the build if there are Python syntax errors or undefined names
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flake8 mavis --count --select=E9,F63,F7,F82 --show-source --statistics
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-name:Lint with black
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run:|
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pip install black
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# stop the build if black needs to be run
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black mavis -S -l 100 --check
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-name:install bwa
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run:|
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git clone https://github.com/lh3/bwa.git
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cd bwa
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git checkout v0.7.17
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make
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cd ..
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-name:install blat
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run:|
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wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
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chmod a+x blat
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-name:run short tests with pytest
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run:|
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export PATH=$PATH:$(pwd):$(pwd)/bwa
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pytest tests -v --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov mavis --cov-report term --cov-report xml --durations=10
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env:
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RUN_FULL:0
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if:github.event_name != 'pull_request'
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-name:run full tests with pytest
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run:|
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export PATH=$PATH:$(pwd):$(pwd)/bwa
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pytest tests -v --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov mavis --cov-report term --cov-report xml --durations=10
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env:
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RUN_FULL:1
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if:github.event_name == 'pull_request'
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-name:Upload pytest test results
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uses:actions/upload-artifact@master
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with:
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name:pytest-results-${{ matrix.python-version }}
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path:junit/test-results-${{ matrix.python-version }}.xml
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# Use always() to always run this step to publish test results when there are test failures
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if:always()
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-name:Update code coverage report to CodeCov
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uses:codecov/codecov-action@v1
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with:
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token:${{ secrets.CODECOV_TOKEN }}
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file:./coverage.xml
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flags:unittests
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env_vars:OS,PYTHON
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name:codecov-umbrella
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fail_ci_if_error:true
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if:matrix.python-version == 3.8

‎.github/workflows/publish.yml

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# This workflows will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name:publish
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on:
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release:
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types:[created]
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jobs:
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deploy:
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runs-on:ubuntu-latest
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steps:
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-uses:actions/checkout@v2
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-name:Set up Python
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uses:actions/setup-python@v2
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with:
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python-version:'3.x'
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-name:Install dependencies
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run:|
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python -m pip install --upgrade pip
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pip install setuptools wheel twine
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-name:Build and publish
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env:
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TWINE_USERNAME:${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD:${{ secrets.PYPI_PASSWORD }}
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run:|
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python setup.py sdist bdist_wheel install
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twine check dist/*
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twine upload dist/*

‎.gitignore

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/*/*/tmp
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# python generated files
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/.eggs
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/tmp
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# /
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*.~lock*
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*.noseids
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/cytoBand.txt
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/temp*
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/coverage
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/test*svg
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/venv
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/.coverage
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*.pyc
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*__pycache__
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/*.bed
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/*.fa
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/docs/build
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/docs/source/auto
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/output
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/hg19_masked_regions.tsv
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*.fai
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POG*
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build-docs
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*.egg-info*
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build
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dist
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src
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/docs/source/config_settings_glossary.rst
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*coverage*
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*.tgf
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analysis_scripts
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.vscode
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*.nfs*
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*eggs/
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html
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dist
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junit
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.pytest*
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.tox
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*eggs/
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.mypy_cache
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# aligners
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blat
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bwa
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*.fai
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# user editing generated files
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*.~lock*
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.vscode
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*.nfs*
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junit
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# generated documentation
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/docs/package/mavis/*.md
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/docs/package/mavis/*/*.md
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# don't ignore subpackage summary files
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!/docs/package/mavis/*/index.md

‎.readthedocs.yml

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# Required
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version:2
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# Build documentation in the docs/ directory with Sphinx
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sphinx:
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configuration:docs/source/conf.py
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# Build documentation with MkDocs
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#mkdocs:
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# configuration: mkdocs.yml
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mkdocs:
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configuration:mkdocs.yml
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fail_on_warning:false
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# Optionally build your docs in additional formats such as PDF and ePub
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formats:all

‎.travis.yml

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