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SarahAlidoostSarahAlidoost
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Merge pull request #9 from EcoExtreML/use_python_template
Use python template to restructure the repo
2 parents 2767265 + 3ddb272 commit 647e8c1

32 files changed

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‎.bumpversion.cfg‎

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[bumpversion]
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current_version = 0.1.0
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[comment]
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comment = The contents of this file cannot be merged with that of setup.cfg until https://github.com/c4urself/bump2version/issues/185 is resolved
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[bumpversion:file:PyStemmusScope/__init__.py]
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search = __version__ = "{current_version}"
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replace = __version__ = "{new_version}"
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[bumpversion:file:setup.cfg]
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search = version = {current_version}
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replace = version = {new_version}
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[bumpversion:file:CITATION.cff]
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search = version: "{current_version}"
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replace = version: "{new_version}"
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[bumpversion:file:docs/conf.py]
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search = version = "{current_version}"
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replace = version = "{new_version}"

‎.editorconfig‎

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# EditorConfig is awesome: http://EditorConfig.org
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# top-most EditorConfig file
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root = true
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# Unix-style newlines with a newline ending every file
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[*]
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end_of_line = lf
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insert_final_newline = true
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trim_trailing_whitespace = true
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charset = utf-8
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# 4 space indentation
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[*.{py,java,r,R}]
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indent_style = space
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indent_size = 4
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# 2 space indentation
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[*.{js,json,y{a,}ml,html,cwl}]
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indent_style = space
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indent_size = 2
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[*.{md,Rmd,rst}]
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trim_trailing_whitespace = false
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indent_style = space
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indent_size = 2

‎.githooks/pre-commit‎

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#!/bin/sh
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echo "Script $0 triggered ..."
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# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
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echo "Starting prospector analysis using configuration from .prospector.yml..."
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# quietly run prospector
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prospector 1>/dev/null
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# use return code to abort commit if necessary
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if [ $? != "0" ]; then
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echo "Commit aborted. Run 'prospector' to see the errors."
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exit 1
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fi
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# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
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echo "Starting isort analysis using configuration from setup.cfg..."
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# recursively run isort on PyStemmusScope/ directory, don't try to automatically fix anything
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isort --recursive --check-only PyStemmusScope
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if [ $? != "0" ]; then
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echo "Commit aborted."
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echo " Run 'isort --recursive --check-only --diff PyStemmusScope' to see what's wrong."
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echo " Run 'isort --recursive PyStemmusScope' to let isort fix problems automatically."
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exit 1
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fi
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echo "Pre-commit checks completed successfully."
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exit 0

‎.github/workflows/build.yml‎

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name: Python package
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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jobs:
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build:
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name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
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python-version: ['3.7', '3.8', '3.9']
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Python info
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shell: bash -l {0}
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run: |
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which python3
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python3 --version
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- name: Upgrade pip and install dependencies
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run: |
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python3 -m pip install --upgrade pip setuptools
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python3 -m pip install .[dev,publishing]
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- name: Run unit tests
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run: pytest -v
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- name: Verify that we can build the package
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run: python3 setup.py sdist bdist_wheel
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lint:
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name: Linting build
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python 3.9
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uses: actions/setup-python@v3
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with:
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python-version: 3.9
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- name: Python info
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shell: bash -l {0}
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run: |
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which python3
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python3 --version
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- name: Upgrade pip and install dependencies
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run: |
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python3 -m pip install --upgrade pip setuptools
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python3 -m pip install .[dev,publishing]
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- name: Check style against standards using prospector
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run: prospector
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- name: Check import order
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run: isort --check-only PyStemmusScope --diff

‎.github/workflows/cffconvert.yml‎

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name: cffconvert
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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jobs:
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verify:
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name: "cffconvert"
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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name: Check out a copy of the repository
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- uses: citation-file-format/cffconvert-github-action@main
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name: Check whether the citation metadata from CITATION.cff is equivalent to that in .zenodo.json

‎.github/workflows/documentation.yml‎

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name: documentation
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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jobs:
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build-documentation:
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name: Build documentation
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python 3.9
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Python info
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shell: bash -l {0}
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run: |
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which python3
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python3 --version
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- name: Upgrade pip and install dependencies
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run: |
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python3 -m pip install --upgrade pip setuptools
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python3 -m pip install .[dev,publishing]
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- name: Install pandoc using apt
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run: sudo apt install pandoc
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- name: Build documentation
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run: make coverage doctest html
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working-directory: docs

‎.github/workflows/markdown-link-check.yml‎

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name: markdown-link-check
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on:
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push:
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branches:
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- main
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pull_request:
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branches:
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- main
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jobs:
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markdown-link-check:
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name: Check markdown links
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: gaurav-nelson/github-action-markdown-link-check@v1
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with:
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config-file: '.mlc-config.json'

‎.github/workflows/sonarcloud.yml‎

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name: sonarcloud
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on:
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push:
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branches:
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- main
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pull_request:
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types: [opened, synchronize, reopened]
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branches:
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- main
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jobs:
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sonarcloud:
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name: SonarCloud
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0 # Shallow clones should be disabled for a better relevancy of analysis
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- name: Set up Python
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uses: actions/setup-python@v3
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with:
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python-version: 3.9
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- name: Python info
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shell: bash -l {0}
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run: |
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which python3
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python3 --version
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- name: Install dependencies
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run: python3 -m pip install .[dev]
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- name: Check style against standards using prospector
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run: prospector --zero-exit --output-format grouped --output-format pylint:pylint-report.txt
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- name: Run unit tests with coverage
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run: pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml tests/
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- name: Correct coverage paths
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run: sed -i "s+$PWD/++g" coverage.xml
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- name: SonarCloud Scan
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uses: SonarSource/sonarcloud-github-action@master
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env:
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GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
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SONAR_TOKEN: ${{secrets.SONAR_TOKEN }}

‎.gitignore‎

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# output file
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out/
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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]

‎.mlc-config.json‎

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{
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"_comment": "Markdown Link Checker configuration, see https://github.com/gaurav-nelson/github-action-markdown-link-check and https://github.com/tcort/markdown-link-check",
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"ignorePatterns": [
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{
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"pattern": "^http://localhost"
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},
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{
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"pattern": "^https://doi.org/<replace-with-created-DOI>"
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},
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{
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"pattern": "^https://github.com/.*/settings/secrets/actions$"
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},
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{
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"pattern": "^https://github.com/organizations/.*/repositories/new"
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},
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{
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"pattern": "^https://test.pypi.org"
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},
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{
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"pattern": "^https://bestpractices.coreinfrastructure.org/projects/<replace-with-created-project-identifier>"
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},
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{
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"pattern": "^https://readthedocs.org/dashboard/import.*"
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}
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],
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"replacementPatterns": [
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],
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"retryOn429": true,
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"timeout": "20s"
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}

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