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Merge pull request #9 from katehyerinjeon/hw5
hw5
2 parents 93d7440 + 1404c73 commit 0ede6be

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‎.bumpversion.cfg‎

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[bumpversion]
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current_version = 0.1.0
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commit = True
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tag = True
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[bumpversion:file:pynrm/_version.py]
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search = __version__ = "{current_version}"
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replace = __version__ = "{new_version}"
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[bumpversion:file:pyproject.toml]
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search = version="{current_version}"
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replace = version="{new_version}"
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[bumpversion:file:setup.py]
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search = version="{current_version}"
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replace = version="{new_version}"

‎.gitattributes‎

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*.ipynb linguist-documentation
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* text=auto eol=lf

‎.github/dependabot.yml‎

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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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interval: "weekly"

‎.github/workflows/build.yml‎

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name: Build Status
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on:
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push:
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branches:
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- hw4
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tags:
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- v*
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paths-ignore:
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- CONTRIBUTING.md
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- LICENSE
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- README.md
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pull_request:
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workflow_dispatch:
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: [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@v4
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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cache-dependency-path: 'pyproject.toml'
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- name: Install dependencies
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run: |
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make develop
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- name: Build
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run: |
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make build
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- name: Lint
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run: |
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make lint
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- name: Checks
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run: |
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make checks
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- name: Test
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run: |
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make coverage
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- name: Upload test results
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uses: actions/upload-artifact@v3
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with:
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name: pytest-results-${{ matrix.os }}-${{ matrix.python-version }}
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path: python_junit.xml
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if: ${{ always() }}
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- name: Upload coverage
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uses: codecov/codecov-action@v3

‎.gitignore‎

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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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*.py,cover
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.hypothesis/
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.pytest_cache/
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lib-cov
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coverage
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python_junit.xml
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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# Documentation
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docs/_build/
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/site
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# Linting
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.eslintcache
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# Mac
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.DS_Store
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# VS Code
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.vscode

‎MANIFEST.in‎

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graft pynrm
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graft pynrm/tests
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include LICENSE
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include README.md
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include CONTRIBUTING.md
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include .bumpversion.cfg
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include pyproject.toml
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include Makefile
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prune .vscode
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prune .github
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exclude .gitignore
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exclude .gitattributes
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# Patterns to exclude from any directory
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global-exclude *~
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global-exclude *.pyc
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global-exclude *.pyo
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global-exclude .git
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global-exclude .ipynb_checkpoints
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global-exclude .DS_Store

‎Makefile‎

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#########
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# BUILD #
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#########
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develop: ## install dependencies and build library
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python -m pip install -e .[develop]
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build: ## build the python library
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python setup.py build build_ext --inplace
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install: ## install library
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python -m pip install .
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#########
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# LINTS #
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#########
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lint: ## run static analysis with flake8
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python -m black --check pynrm setup.py
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python -m flake8 --max-line-length=120 --extend-ignore=E203 pynrm setup.py
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# Alias
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lints: lint
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format: ## run autoformatting with black
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python -m black pynrm/ setup.py
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# alias
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fix: format
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check: ## check assets for packaging
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check-manifest -v
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# Alias
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checks: check
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annotate: ## run type checking
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python -m mypy ./pynrm
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#########
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# TESTS #
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#########
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test: ## clean and run unit tests
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python -m pytest -v pynrm/tests
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coverage: ## clean and run unit tests with coverage
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python -m pytest -v pynrm/tests --cov=pynrm --cov-branch --cov-fail-under=75 --cov-report term-missing
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# Alias
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tests: test
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###########
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# VERSION #
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###########
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show-version:
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bump2version --dry-run --allow-dirty setup.py --list | grep current | awk -F= '{print $2}'
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patch:
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bump2version patch
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minor:
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bump2version minor
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major:
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bump2version major
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########
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# DIST #
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########
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dist-build: # Build python dist
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python setup.py sdist bdist_wheel
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dist-check:
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python -m twine check dist/*
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dist: clean build dist-build dist-check ## Build dists
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publish: # Upload python assets
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echo "would usually run python -m twine upload dist/* --skip-existing"
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#########
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# CLEAN #
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#########
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deep-clean: ## clean everything from the repository
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git clean -fdx
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clean: ## clean the repository
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rm -rf .coverage coverage cover htmlcov logs build dist *.egg-info .pytest_cache
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############################################################################################
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# Thanks to Francoise at marmelab.com for this
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.DEFAULT_GOAL := help
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help:
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@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-30s\033[0m %s\n", $$1, $$2}'
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print-%:
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@echo '$*=$($*)'
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.PHONY: develop build install lint lints format fix check checks annotate test coverage show-coverage tests show-version patch minor major dist-build dist-check dist publish deep-clean clean help

‎README.md‎

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# pynrm
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`pynrm` is a lightweight and extensible animal breeding simulation library for Python.
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[![Build Status](https://github.com/katehyerinjeon/pynrm/workflows/Build%20Status/badge.svg?branch=main)](https://github.com/katehyerinjeon/pynrm/actions?query=workflow%3A%22Build+Status%22)
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[![codecov](https://codecov.io/gh/katehyerinjeon/pynrm/branch/main/graph/badge.svg)](https://codecov.io/gh/katehyerinjeon/pynrm)
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![GitHub](https://img.shields.io/github/license/katehyerinjeon/pynrm)
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![GitHub issues](https://img.shields.io/github/issues/katehyerinjeon/pynrm)
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Numerous evaluation-selection systems have been devised to produce populations with favorable genetic responses while maintaining moderate to low rates of inbreeding.
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`pynrm` provides a simple yet powerful simulation tool to forecast the stochastic impacts of these systems.
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One major bottleneck to running these simulations is that as the number of animals bred increases, the size of the matrix grows exponentially.
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`pynrm` efficiently solves for the numerator relationship matrix values by tracing up the pedigree for only the relevant ancestors, thereby minimizing computational overhead.
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`pynrm` efficiently solves for the numerator relationship matrix values by tracing up the pedigree for only the relevant ancestors, thereby minimizing computational overhead.

‎nrm.py‎

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