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Merge pull request #149 from pyiron/main
Merge master
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‎.ci_support/environment.yml‎

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- coveralls
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- coverage
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- codacy-coverage
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- pandas =1.4.3
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- pandas =1.5.2
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- pyyaml =6.0
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- jinja2 =3.1.2
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- paramiko =2.11.0
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- tqdm =4.64.0
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- paramiko =2.12.0
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- tqdm =4.64.1

‎.github/delete-merged-branch-config.yml‎

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exclude:
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- master
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- main
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delete_closed_pr: false

‎.github/variables/cache_number.env‎

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CACHE_NUMBER=0

‎.github/workflows/UpdateDependabotPR.yml‎

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on:
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pull_request_target:
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branches: [ master ]
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branches: [ main ]
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jobs:
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build:

‎.github/workflows/black.yml‎

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push:
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branches: [ master ]
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branches: [ main ]
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pull_request:
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branches: [ master ]
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branches: [ main ]
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jobs:
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build:

‎.github/workflows/coverage.yml‎

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‎.github/workflows/format_black.yml‎

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# This workflow will checkout the branch of the PR, apply black formatting and commit the result to the PR. Does not work for forks.
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name: Format black
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on:
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pull_request:
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types: [labeled]
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jobs:
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build:
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if: contains(github.event.pull_request.labels.*.name, 'format_black' )
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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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with:
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token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
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ref: ${{ github.event.pull_request.head.ref }} # Check out the head of the actual branch, not the PR
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fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
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- name: format black
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uses: psf/black@stable
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with:
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options: ""
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src: "./pysqa"
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- name: commit
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run: |
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git config --local user.email "pyiron@mpie.de"
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git config --local user.name "pyiron-runner"
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git commit -m "Format black" -a
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- name: push
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uses: ad-m/github-push-action@master
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with:
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github_token: ${{ secrets.DEPENDABOT_WORKFLOW_TOKEN }}
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branch: ${{ github.event.pull_request.head.ref }}

‎.github/workflows/pypicheck.yml‎

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# This workflow is used to test, if the installation of the pypi package works
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name: Pip check
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branches: [ master ]
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branches: [ main ]
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pull_request:
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branches: [ master ]
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branches: [ main ]
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jobs:
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build:
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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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- uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: "3.10"
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mamba-version: "*"
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channels: conda-forge
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channel-priority: strict
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auto-update-conda: true
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environment-file: .ci_support/environment.yml
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- name: Setup
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shell: bash -l {0}
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run: |
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pip install --no-deps .
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pip check
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- uses: actions/checkout@v2
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- name: Setup environment
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run: cp .ci_support/environment.yml environment.yml
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- name: Setup Mambaforge
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uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: '3.10'
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miniforge-variant: Mambaforge
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channels: conda-forge
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channel-priority: strict
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activate-environment: my-env
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use-mamba: true
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- name: Set cache date and number
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run: |
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echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
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cat .github/variables/cache_number.env >> $GITHUB_ENV
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- uses: actions/cache@v2
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with:
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path: /usr/share/miniconda3/envs/my-env
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key: linux-64-py-3-10-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
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id: cache
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- name: Update environment
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run: mamba env update -n my-env -f environment.yml
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if: steps.cache.outputs.cache-hit != 'true'
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- name: Pip check
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shell: bash -l {0}
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run: |
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pip install --no-deps .
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pip check

‎.github/workflows/unittest.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: Python package
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name: Unittests
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branches: [ master ]
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branches: [ main ]
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pull_request:
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branches: [ master ]
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branches: [ main ]
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}
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jobs:
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runs-on: ${{ matrix.operating-system }}
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strategy:
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matrix:
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operating-system: [ubuntu-latest, windows-latest, macos-latest]
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python-version: ['3.10']
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include:
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- operating-system: ubuntu-latest
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python-version: 3.8
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- operating-system: ubuntu-latest
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python-version: 3.9
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- operating-system: macos-latest
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python-version: '3.11'
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label: osx-64-py-3-11
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prefix: /Users/runner/miniconda3/envs/my-env
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- operating-system: windows-latest
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python-version: '3.11'
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label: win-64-py-3-11
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prefix: C:\Miniconda3\envs\my-env
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- operating-system: ubuntu-latest
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python-version: '3.11'
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label: linux-64-py-3-11
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prefix: /usr/share/miniconda3/envs/my-env
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- operating-system: ubuntu-latest
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python-version: '3.10'
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label: linux-64-py-3-10
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prefix: /usr/share/miniconda3/envs/my-env
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- operating-system: ubuntu-latest
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python-version: 3.9
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label: linux-64-py-3-9
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prefix: /usr/share/miniconda3/envs/my-env
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- operating-system: ubuntu-latest
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python-version: 3.8
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label: linux-64-py-3-8
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prefix: /usr/share/miniconda3/envs/my-env
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steps:
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- uses: actions/checkout@v2
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- uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: ${{ matrix.python-version }}
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mamba-version: "*"
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channels: conda-forge
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channel-priority: strict
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auto-update-conda: true
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environment-file: .ci_support/environment.yml
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- name: Setup
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shell: bash -l {0}
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run: |
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pip install --no-deps .
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- name: Test
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shell: bash -l {0}
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run: coverage run --omit pysqa/_version.py -m unittest discover tests
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- uses: actions/checkout@v2
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- name: Setup environment
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run: cp .ci_support/environment.yml environment.yml
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- name: Setup Mambaforge
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uses: conda-incubator/setup-miniconda@v2
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with:
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python-version: ${{ matrix.python-version }}
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miniforge-variant: Mambaforge
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channels: conda-forge
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channel-priority: strict
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activate-environment: my-env
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use-mamba: true
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- name: Set cache date and number
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run: |
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echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV
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cat .github/variables/cache_number.env >> $GITHUB_ENV
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- uses: actions/cache@v2
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with:
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path: ${{ matrix.prefix }}
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key: ${{ matrix.label }}-conda-${{ hashFiles('environment.yml') }}-${{ env.DATE }}-${{ env.CACHE_NUMBER }}
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id: cache
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- name: Update environment
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run: mamba env update -n my-env -f environment.yml
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if: steps.cache.outputs.cache-hit != 'true'
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- name: Setup
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shell: bash -l {0}
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run: |
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pip install --no-deps .
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- name: Test
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shell: bash -l {0}
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run: coverage run --omit pysqa/_version.py -m unittest discover tests
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- name: Coverage
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if: matrix.label == 'linux-64-py-3-10'
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shell: bash -l {0}
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run: |
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coverage combine
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coveralls
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coverage xml
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python-codacy-coverage -r coverage.xml

‎README.md‎

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[![Codacy Badge](https://api.codacy.com/project/badge/Grade/9db80cb2477f46be870d1446540b4bf3)](https://www.codacy.com/app/pyiron-runner/pysqa?utm_source=github.com&utm_medium=referral&utm_content=pyiron/pysqa&utm_campaign=Badge_Grade_Dashboard)
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[![Python package](https://github.com/pyiron/pysqa/workflows/Python%20package/badge.svg)](https://github.com/pyiron/pysqa/actions)
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[![Coverage Status](https://coveralls.io/repos/github/pyiron/pysqa/badge.svg?branch=master)](https://coveralls.io/github/pyiron/pysqa?branch=master)
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[![Coverage Status](https://coveralls.io/repos/github/pyiron/pysqa/badge.svg?branch=main)](https://coveralls.io/github/pyiron/pysqa?branch=main)
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The goal of pysqa is to make submitting to an HPC cluster as easy as starting another subprocess. This is based on the assumption that even though modern queuing systems allow for an wide range of different configuration, most users submit the majority of their jobs with very similar parameters. Therefore pysqa allows the users to store their submission scripts as jinja2 templates for quick access. After the submission pysqa allows the users to track the progress of their jobs, delete them or enable reservations using the built-in functionality of the queuing system. The currently supported queuing systems are: LFS, MOAB, SGE (tested), SLURM (tested), TORQUE.
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# Usage
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pysqa requires the user to configure the type of queuing system as well as the available templates. Example configuration are available at:
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https://github.com/pyiron/pysqa/tree/master/tests/config
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https://github.com/pyiron/pysqa/tree/main/tests/config
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By default pysqa is searching for the queue configuration in `~/.queues/queue.yaml` and the corresponding jinja2 templates in the same folder.
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Sample configurations for the specific queuing systems are availabe in the tests:
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* lsf - https://github.com/pyiron/pysqa/tree/master/tests/config/lsf
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* moab - https://github.com/pyiron/pysqa/tree/master/tests/config/moab
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* SGE - https://github.com/pyiron/pysqa/tree/master/tests/config/sge
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* slurm - https://github.com/pyiron/pysqa/tree/master/tests/config/slurm
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* torque - https://github.com/pyiron/pysqa/tree/master/tests/config/torque
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* lsf - https://github.com/pyiron/pysqa/tree/main/tests/config/lsf
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* moab - https://github.com/pyiron/pysqa/tree/main/tests/config/moab
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* SGE - https://github.com/pyiron/pysqa/tree/main/tests/config/sge
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* slurm - https://github.com/pyiron/pysqa/tree/main/tests/config/slurm
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* torque - https://github.com/pyiron/pysqa/tree/main/tests/config/torque
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# License
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pysqa is released under the BSD license https://github.com/pyiron/pysqa/blob/master/LICENSE . It is a spin-off of the pyiron project https://github.com/pyiron/pyiron therefore if you use pysqa for your publication, please cite:
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pysqa is released under the BSD license https://github.com/pyiron/pysqa/blob/main/LICENSE . It is a spin-off of the pyiron project https://github.com/pyiron/pyiron therefore if you use pysqa for your publication, please cite:
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@article{pyiron-paper,
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title = {pyiron: An integrated development environment for computational materials science},

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