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Add full CI, versioning, and packaging.
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‎.github/workflows/devel.yaml‎

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name: Release Devel
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on:
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workflow_dispatch:
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push:
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branches: [ devel ]
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jobs:
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build:
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name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
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runs-on: ${{ matrix.platform.os }}
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strategy:
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max-parallel: 9
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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platform:
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- { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
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- { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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exclude:
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# Exclude all but the latest Python from all
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# but Linux
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- platform:
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{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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python-version: "3.12" # MacOS can't run 3.12 yet... We want 3.10 and 3.11
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environment:
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name: ghostly-build
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defaults:
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run:
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shell: ${{ matrix.platform.shell }}
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env:
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SIRE_DONT_PHONEHOME: 1
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SIRE_SILENT_PHONEHOME: 1
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steps:
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: ghostly_build
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miniforge-version: latest
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#
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- name: Clone the devel branch
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run: git clone -b devel https://github.com/openbiosim/ghostly
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#
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- name: Setup Conda
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run: conda install -y -c conda-forge boa anaconda-client packaging
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#
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- name: Update Conda recipe
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run: python ${{ github.workspace }}/ghostly/actions/update_recipe.py
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#
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- name: Prepare build location
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run: mkdir ${{ github.workspace }}/build
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#
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- name: Build Conda package using conda build
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run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/ghostly/recipes/ghostly
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#
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- name: Upload Conda package
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run: python ${{ github.workspace }}/ghostly/actions/upload_package.py
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env:
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ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
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ANACONDA_LABEL: dev
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if: ${{ matrix.platform.name == 'linux' && matrix.python-version == '3.11' }}

‎.github/workflows/main.yaml‎

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name: Build and test
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name: Release Main
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on:
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workflow_dispatch:
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push:
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branches:
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- "**"
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pull_request:
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branches:
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- "main"
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inputs:
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upload_packages:
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required: true
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description: "Upload packages to anaconda?"
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type: boolean
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jobs:
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pre_job:
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runs-on: ubuntu-latest
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outputs:
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should_skip: ${{ steps.skip_check.outputs.should_skip }}
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steps:
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- id: skip_check
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uses: fkirc/skip-duplicate-actions@v5
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with:
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concurrent_skipping: 'same_content_newer'
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build:
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needs: pre_job
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if: needs.pre_job.outputs.should_skip != 'true'
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name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
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runs-on: ${{ matrix.platform.os }}
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strategy:
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max-parallel: 9
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fail-fast: false
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matrix:
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python-version: ["3.11"]
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python-version: ["3.10", "3.11", "3.12"]
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platform:
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#- { name: "windows", os: "windows-latest", shell: "pwsh" }
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- { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
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- { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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exclude:
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- platform:
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{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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python-version: "3.12" # MacOS can't run 3.12 yet...
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environment:
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name: ghostly-build
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defaults:
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run:
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shell: ${{ matrix.platform.shell }}
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env:
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SIRE_DONT_PHONEHOME: 1
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SIRE_SILENT_PHONEHOME: 1
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steps:
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#
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- name: Checkout the repository (commit)
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uses: actions/checkout@v4
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if: github.event_name != 'pull_request'
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#
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- name: Checkout the repository (PR)
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uses: actions/checkout@v4
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with:
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ref: ${{ github.event.pull_request.head.sha }}
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if: github.event_name == 'pull_request'
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#
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: somd2
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environment-file: environment.yaml
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activate-environment: ghostly_build
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miniforge-version: latest
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run-post: ${{ matrix.platform.name != 'windows' }}
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#
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- name: Install pytest
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run: conda install pytest
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- name: Clone the main branch
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run: git clone -b main https://github.com/openbiosim/ghostly
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#
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- name: Setup Conda
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run: conda install -y -c conda-forge boa anaconda-client packaging
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#
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- name: Update Conda recipe
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run: python ${{ github.workspace }}/ghostly/actions/update_recipe.py
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#
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- name: Prepare build location
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run: mkdir ${{ github.workspace }}/build
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#
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- name: Install the package
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run: pip install .
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- name: Build Conda package using conda build
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run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/ghostly/recipes/ghostly
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#
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- name: Run the tests
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run: python -m pytest -svvv --color=yes tests
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- name: Upload Conda package
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run: python ${{ github.workspace }}/ghostly/actions/upload_package.py
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env:
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ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
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ANACONDA_LABEL: main
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if: github.event.inputs.upload_packages == 'true' and ${{ matrix.platform.name == 'linux' && matrix.python-version == '3.11' }}

‎.github/workflows/pr.yaml‎

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name: Pull-Request
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on:
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pull_request:
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branches: [devel, main]
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jobs:
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build:
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name: build (${{ matrix.python-version }}, ${{ matrix.platform.name }})
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runs-on: ${{ matrix.platform.os }}
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strategy:
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max-parallel: 9
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fail-fast: false
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matrix:
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python-version: ["3.10", "3.11", "3.12"]
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platform:
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- { name: "windows", os: "windows-latest", shell: "pwsh" }
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- { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
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- { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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exclude:
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# Exclude all but the latest Python from all
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# but Linux
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- platform:
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{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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python-version: "3.10"
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- platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
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python-version: "3.10"
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- platform:
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{ name: "macos", os: "macos-latest", shell: "bash -l {0}" }
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python-version: "3.12" # MacOS can't run 3.12 yet...
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- platform: { name: "windows", os: "windows-latest", shell: "pwsh" }
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python-version: "3.11"
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environment:
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name: ghostly-build
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defaults:
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run:
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shell: ${{ matrix.platform.shell }}
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env:
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SIRE_DONT_PHONEHOME: 1
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SIRE_SILENT_PHONEHOME: 1
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REPO: "${{ github.event.pull_request.head.repo.full_name || github.repository }}"
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steps:
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- uses: conda-incubator/setup-miniconda@v3
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with:
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auto-update-conda: true
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python-version: ${{ matrix.python-version }}
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activate-environment: ghostly_build
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miniforge-version: latest
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#
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- name: Clone the feature branch
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run: git clone -b ${{ github.head_ref }} --single-branch https://github.com/${{ env.REPO }} ghostly
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#
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- name: Setup Conda
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run: conda install -y -c conda-forge boa anaconda-client packaging
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#
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- name: Update Conda recipe
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run: python ${{ github.workspace }}/ghostly/actions/update_recipe.py
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#
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- name: Prepare build location
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run: mkdir ${{ github.workspace }}/build
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#
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- name: Build Conda package using conda build using main channel
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if: ${{ github.base_ref == 'main' }}
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run: conda build -c conda-forge -c openbiosim/label/main ${{ github.workspace }}/ghostly/recipes/ghostly
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#
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- name: Build Conda package using conda build using dev channel
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if: ${{ github.base_ref != 'main' }}
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run: conda build -c conda-forge -c openbiosim/label/dev ${{ github.workspace }}/ghostly/recipes/ghostly

‎README.md‎

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# Ghostly
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[![GitHub Actions](https://github.com/openbiosim/ghostly/actions/workflows/main.yaml/badge.svg)](https://github.com/openbiosim/ghostly/actions/workflows/main.yaml)
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[![Conda Version](https://anaconda.org/openbiosim/ghostly/badges/downloads.svg)](https://anaconda.org/openbiosim/ghostly)
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[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
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Ghostly is a package to perform modification of ghost (dummy) atom bonded

‎actions/update_recipe.py‎

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import sys
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import os
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import subprocess
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# Get the name of the script.
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script = os.path.abspath(sys.argv[0])
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# we want to import the 'get_requirements' package from this directory
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sys.path.insert(0, os.path.dirname(script))
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# go up one directories to get the source directory
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# (this script is in BioSimSpace/actions/)
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srcdir = os.path.dirname(os.path.dirname(script))
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condadir = os.path.join(srcdir, "recipes", "ghostly")
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print(f"conda recipe in {condadir}")
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# Store the name of the recipe and template YAML files.
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recipe = os.path.join(condadir, "meta.yaml")
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template = os.path.join(condadir, "template.yaml")
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gitdir = os.path.join(srcdir, ".git")
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def run_cmd(cmd):
27+
p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE)
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return str(p.stdout.read().decode("utf-8")).lstrip().rstrip()
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# Get the remote.
32+
remote = run_cmd(
33+
f"git --git-dir={gitdir} --work-tree={srcdir} config --get remote.origin.url"
34+
)
35+
print(remote)
36+
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# Get the branch.
38+
branch = run_cmd(
39+
f"git --git-dir={gitdir} --work-tree={srcdir} rev-parse --abbrev-ref HEAD"
40+
)
41+
print(branch)
42+
43+
lines = open(template, "r").readlines()
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45+
with open(recipe, "w") as FILE:
46+
for line in lines:
47+
line = line.replace("GHOSTLY_REMOTE", remote)
48+
line = line.replace("GHOSTLY_BRANCH", branch)
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FILE.write(line)

‎actions/upload_package.py‎

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import os
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import sys
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import glob
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script = os.path.abspath(sys.argv[0])
6+
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# go up one directories to get the source directory
8+
# (this script is in ghostly/actions/)
9+
srcdir = os.path.dirname(os.path.dirname(script))
10+
11+
print(f"Ghostly source is in {srcdir}\n")
12+
13+
# Get the anaconda token to authorise uploads
14+
if "ANACONDA_TOKEN" in os.environ:
15+
conda_token = os.environ["ANACONDA_TOKEN"]
16+
else:
17+
conda_token = "TEST"
18+
19+
# Get the anaconda channel labels.
20+
if "ANACONDA_LABEL" in os.environ:
21+
conda_label = os.environ["ANACONDA_LABEL"]
22+
else:
23+
conda_label = "dev"
24+
25+
# get the root conda directory
26+
conda = os.environ["CONDA"]
27+
28+
# Set the path to the conda-bld directory.
29+
conda_bld = os.path.join(conda, "envs", "ghostly_build", "conda-bld")
30+
31+
print(f"conda_bld = {conda_bld}")
32+
33+
# Find the packages to upload
34+
ghostly_pkg = glob.glob(os.path.join(conda_bld, "noarch", "ghostly-*.tar.bz2"))
35+
36+
if len(ghostly_pkg) == 0:
37+
print("No ghostly packages to upload?")
38+
sys.exit(-1)
39+
40+
packages = ghostly_pkg
41+
42+
print(f"Uploading packages:")
43+
print(" * ", "\n * ".join(packages))
44+
45+
packages = " ".join(packages)
46+
47+
48+
def run_cmd(cmd):
49+
import subprocess
50+
51+
p = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE)
52+
return str(p.stdout.read().decode("utf-8")).lstrip().rstrip()
53+
54+
55+
gitdir = os.path.join(srcdir, ".git")
56+
57+
tag = run_cmd(f"git --git-dir={gitdir} --work-tree={srcdir} tag --contains")
58+
59+
# Upload the packages to the openbiosim channel on Anaconda Cloud.
60+
cmd = f"anaconda --token {conda_token} upload --user openbiosim --label {conda_label} --force {packages}"
61+
62+
print(f"\nUpload command:\n\n{cmd}\n")
63+
64+
if conda_token == "TEST":
65+
print("Not uploading as the ANACONDA_TOKEN is not set!")
66+
sys.exit(-1)
67+
68+
output = run_cmd(cmd)
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print(output)
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print("Package uploaded!")

‎pyproject.toml‎

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[build-system]
2-
requires = ["setuptools", "setuptools-scm"]
2+
requires = ["setuptools", "versioningit"]
33
build-backend = "setuptools.build_meta"
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55
[project]
@@ -25,5 +25,10 @@ repository = "https://github.com/OpenBioSim/ghostly"
2525
[tool.setuptools.packages.find]
2626
where = ["src"]
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28-
[tool.setuptools_scm]
29-
write_to = "src/ghostly/_version.py"
28+
[tool.versioningit.format]
29+
distance = "{base_version}+{distance}.{vcs}{rev}"
30+
dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
31+
distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
32+
33+
[tool.versioningit.write]
34+
file = "src/ghostly/_version.py"

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