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Migrate to pyproject.toml and common workflows, update for numpy 2.0 (#35)
* move to pyproject file * remove setup.py * not needed anymore * using common workflows * switch to np.nan for numpy 2.0 compatibility * and bump patch version for release * and add to changelog * membership test should be 'not in' * not fstrings * update authors metadata as discussed
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‎.github/workflows/README.md

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# Continous Integration Workflows
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This package implements different workflows for CI.
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This package implements different workflows for CI, based on our organisation's common workflows.
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They are organised as follows.
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### Documentation
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The `documentation` workflow triggers on any push to master, builds the documentation and pushes it to the `gh-pages` branch (if the build is successful).
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It runs on `ubuntu-latest` and Python version, `Python 3.9`.
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### Testing Suite
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Tests are ensured in the `tests` workflow, which triggers on all pushes.
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It runs on a matrix of all supported operating systems (ubuntu-20.04, ubuntu-22.04, windows-latest and macos-latest) for all supported Python versions (currently `3.7`, `3.8`, `3.9` and `3.10`).
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It runs on a matrix of all supported operating systems for all supported Python versions.
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### Test Coverage
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Test coverage is calculated in the `coverage` wokflow, which triggers on pushes to `master` and any push to a `pull request`.
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It runs on `ubuntu-latest` & the Python version (`Python 3.9`), and reports the coverage results of the test suite to `CodeClimate`,
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It reports the coverage results of the test suite to `CodeClimate`.
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### Regular Testing
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A `cron` workflow triggers every Monday at 3am (UTC time) and runs the full testing suite, on all available operating systems and supported Python versions.
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It also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically detected.
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It also runs on `Python 3.x` so that newly released Python versions that would break tests are automatically included.
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### Publishing
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Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made of the Github repository.
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Publishing to `PyPI` is done through the `publish` workflow, which triggers anytime a `release` is made of the GitHub repository.
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It builds a `wheel`, checks it, and pushes to `PyPI` if checks are successful.

‎.github/workflows/coverage.yml

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# Runs all tests and pushes coverage report to codeclimate
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name: Coverage
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defaults:
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run:
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shell: bash
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on: # Runs on all push events to master branch and any push related to a pull request
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push:
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branches:
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jobs:
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coverage:
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name: ${{ matrix.os }} / ${{ matrix.python-version }}
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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: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: '**/setup.py'
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- name: Get full Python version
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id: full-python-version
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run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
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- name: Upgrade pip, setuptools and wheel
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run: python -m pip install --upgrade pip setuptools wheel
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- name: Install package
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run: python -m pip install '.[test]'
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- name: Set up env for CodeClimate (push)
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run: |
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echo "GIT_BRANCH=${GITHUB_REF/refs\/heads\//}" >> $GITHUB_ENV
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echo "GIT_COMMIT_SHA=$GITHUB_SHA" >> $GITHUB_ENV
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if: github.event_name == 'push'
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- name: Set up env for CodeClimate (pull_request)
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env:
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PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
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run: |
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echo "GIT_BRANCH=$GITHUB_HEAD_REF" >> $GITHUB_ENV
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echo "GIT_COMMIT_SHA=$PR_HEAD_SHA" >> $GITHUB_ENV
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if: github.event_name == 'pull_request'
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- name: Prepare CodeClimate binary
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env:
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CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
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run: |
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curl -LSs 'https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64' >./cc-test-reporter;
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chmod +x ./cc-test-reporter
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./cc-test-reporter before-build
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- name: Run all tests
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run: python -m pytest --cov-report xml --cov=optics_functions
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- name: Push Coverage to CodeClimate
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if: ${{ success() }} # only if tests were successful
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env:
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CC_TEST_REPORTER_ID: ${{ secrets.CC_TEST_REPORTER_ID }}
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run: ./cc-test-reporter after-build
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uses: pylhc/.github/.github/workflows/coverage.yml@master
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with:
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src-dir: optics_functions
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secrets: inherit

‎.github/workflows/cron.yml

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# Runs all tests on master everyday at 10 am (UTC time)
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# Runs all tests on master on Mondays at 3 am (UTC time)
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name: Cron Testing
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defaults:
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run:
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shell: bash
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on: # Runs on master branch on Mondays at 3am UTC time
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on:
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schedule:
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- cron: '* 3 * * mon'
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jobs:
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tests:
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name: ${{ matrix.os }} / ${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
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# Make sure to escape 3.10 with quotes so it doesn't get interpreted as float 3.1 by GA's parser
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python-version: [3.7, 3.8, 3.9, "3.10", "3.11", 3.x] # crons should always run latest python hence 3.x
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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: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: '**/setup.py'
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- name: Get full Python version
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id: full-python-version
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run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
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- name: Upgrade pip, setuptools and wheel
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run: python -m pip install --upgrade pip setuptools wheel
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- name: Install package
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run: python -m pip install '.[test]'
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- name: Run all tests
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run: python -m pytest
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tests:
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uses: pylhc/.github/.github/workflows/cron.yml@master

‎.github/workflows/documentation.yml

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# The build is published to github pages if the triggering event is a push to the master branch (PR merge)
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name: Build and upload documentation
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defaults:
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run:
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shell: bash
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on: # Runs on any push event in a PR or any push event to master
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pull_request:
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push:
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jobs:
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documentation:
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name: ${{ matrix.os }} / ${{ matrix.python-version }}
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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: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: '**/setup.py'
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- name: Get full Python version
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id: full-python-version
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run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
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- name: Upgrade pip, setuptools and wheel
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run: python -m pip install --upgrade pip setuptools wheel
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- name: Install package
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run: python -m pip install '.[doc]'
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- name: Build documentation
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run: python -m sphinx -b html doc ./doc_build -d ./doc_build
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- name: Upload build artifacts # upload artifacts so reviewers can have a quick look without building documentation from the branch locally
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uses: actions/upload-artifact@v3
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if: success() && github.event_name == 'pull_request' # only for pushes in PR
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with:
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name: site-build
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path: doc_build
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retention-days: 5
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- name: Upload documentation to gh-pages
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if: success() && github.ref == 'refs/heads/master' # only for pushes to master
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uses: JamesIves/github-pages-deploy-action@v4
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with:
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folder: doc_build
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uses: pylhc/.github/.github/workflows/documentation.yml@master

‎.github/workflows/publish.yml

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# Publishes to PyPI upon creation of a release
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name: Upload Package to PyPI
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defaults:
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run:
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shell: bash
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on: # Runs everytime a release is added to the repository
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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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name: ${{ matrix.os }} / ${{ matrix.python-version }}
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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: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: '**/setup.py'
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- name: Get full Python version
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id: full-python-version
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run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
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- name: Upgrade pip, setuptools, wheel, build and twine
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run: python -m pip install --upgrade pip setuptools wheel build twine
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- name: Build and check build
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run: |
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python -m build
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twine check dist/*
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- name: Publish
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if: ${{ success() }}
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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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twine upload dist/*
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uses: pylhc/.github/.github/workflows/publish.yml@master
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secrets: inherit

‎.github/workflows/tests.yml

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# Runs all tests not flagged as "extended" with a pytest marker
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name: Tests
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# Runs all tests
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name: All Tests
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defaults:
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run:
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shell: bash
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on: [push] # Runs on all push events to any branch
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on: # Runs on any push event to any branch except master (the coverage workflow takes care of that)
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push:
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branches-ignore:
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- 'master'
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jobs:
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tests:
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name: ${{ matrix.os }} / ${{ matrix.python-version }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-20.04, ubuntu-22.04, macos-latest, windows-latest]
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# Make sure to escape 3.10 with quotes so it doesn't get interpreted as float 3.1 by GA's parser
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python-version: [3.7, 3.8, 3.9, "3.10", "3.11"]
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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: ${{ matrix.python-version }}
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cache: 'pip'
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cache-dependency-path: '**/setup.py'
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- name: Get full Python version
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id: full-python-version
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run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
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- name: Upgrade pip, setuptools and wheel
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run: python -m pip install --upgrade pip setuptools wheel
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- name: Install package
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run: python -m pip install '.[test]'
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- name: Run basic tests
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run: python -m pytest
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uses: pylhc/.github/.github/workflows/tests.yml@master

‎CHANGELOG.md

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# optics_functions Changelog
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## Version 0.1.3
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- Fixed use of `np.NaN` to ensure compatibility with `numpy 2.0`.
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## Version 0.1.2
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- Fixed:
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- an issue that could lead to an indexing error in the closest tune approach calculation for some of the available methods.
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## Version 0.1.1
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A patch for some closest tune approach methods, and the addition of new methods.
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- Fixed:

‎optics_functions/__init__.py

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__title__ = "optics_functions"
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__description__ = "Calculate optics parameters from TWISS outputs."
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__url__ = "https://github.com/pylhc/optics_functions"
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__version__ = "0.1.2"
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__version__ = "0.1.3"
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__author__ = "pylhc"
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__author_email__ = "pylhc@github.com"
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__license__ = "MIT"

‎optics_functions/coupling.py

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"of the data points |F1001| < |F1010|. Your closest tune "
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"approach estimates might not be accurate.")
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if to_nan:
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df.loc[condition_not_fulfilled, COUPLING_RDTS] = np.NaN
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df.loc[condition_not_fulfilled, COUPLING_RDTS] = np.nan
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return df

‎optics_functions/rdt.py

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if ((order in orders) # check for order
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and not (x[0] == x[1] and x[2] == x[3]) # rdt index rule
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and ((skew and sum(x[2:4]) % 2) or (normal and not sum(x[2:4]) % 2)) # skew or normal
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and (complex_conj or not((x[1], x[0], x[3], x[2]) in permut[order])) # filter conj
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and (complex_conj or (x[1], x[0], x[3], x[2]) not in permut[order]) # filter conj
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):
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permut[order].append(x)
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return permut

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