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Merge pull request #8 from OpenBioSim/release_2025.2.0
Release 2025.2.0
2 parents 193693e + 47abbc5 commit 8a8642f

20 files changed

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‎.github/workflows/devel.yaml‎

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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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branches: [devel]
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jobs:
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build:
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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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# Exclude all but the latest Python from macOS
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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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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: "3.11"
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environment:
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name: ghostly-build
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defaults:
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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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#
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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#
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- name: Compute version info
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shell: bash
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run: python actions/update_recipe.py
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#
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- name: Create sdist
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run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
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working-directory: ${{ github.workspace }}
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#
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- name: Install pixi
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uses: prefix-dev/setup-pixi@v0.9.4
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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 ${{ github.workspace }}/ghostly/actions/upload_package.py
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run-install: false
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#
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- name: Install rattler-build
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shell: bash
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run: pixi global install rattler-build
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#
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- name: Write Python variant config
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shell: bash
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run: printf 'python:\n - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Build package using rattler-build
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shell: bash
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run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Install anaconda-client
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shell: bash
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run: python -m pip install anaconda-client
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if: ${{ matrix.platform.name == 'linux' && matrix.python-version == '3.12' }}
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#
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- name: Upload package
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shell: bash
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run: python 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' }}
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if: ${{ matrix.platform.name == 'linux' && matrix.python-version == '3.12' }}

‎.github/workflows/main.yaml‎

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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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- 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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# No exclusions - release builds all combinations
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environment:
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name: ghostly-build
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defaults:
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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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#
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- uses: actions/checkout@v4
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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 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: 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: Upload Conda package
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run: python ${{ github.workspace }}/ghostly/actions/upload_package.py
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ref: main
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fetch-depth: 0
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#
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- name: Compute version info
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shell: bash
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run: python actions/update_recipe.py
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#
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- name: Create sdist
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run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
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working-directory: ${{ github.workspace }}
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#
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- name: Install pixi
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uses: prefix-dev/setup-pixi@v0.9.4
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with:
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run-install: false
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#
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- name: Install rattler-build
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shell: bash
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run: pixi global install rattler-build
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#
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- name: Write Python variant config
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shell: bash
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run: printf 'python:\n - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Build package using rattler-build
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shell: bash
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run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Install anaconda-client
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shell: bash
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run: python -m pip install anaconda-client
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if: github.event.inputs.upload_packages == 'true' && matrix.platform.name == 'linux' && matrix.python-version == '3.12'
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#
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- name: Upload package
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shell: bash
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run: python 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' && matrix.platform.name == 'linux' && matrix.python-version == '3.11'
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if: github.event.inputs.upload_packages == 'true' && matrix.platform.name == 'linux' && matrix.python-version == '3.12'

‎.github/workflows/pr.yaml‎

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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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# Exclude all but the latest Python from macOS
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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:
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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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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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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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#
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- uses: actions/checkout@v4
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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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fetch-depth: 0
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#
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- name: Compute version info
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shell: bash
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run: python actions/update_recipe.py
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#
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- name: Create sdist
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run: pip install build && python -m build --sdist && mv dist/*.tar.gz ghostly-source.tar.gz
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working-directory: ${{ github.workspace }}
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#
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- name: Install pixi
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uses: prefix-dev/setup-pixi@v0.9.4
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with:
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run-install: false
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#
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- name: Install rattler-build
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shell: bash
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run: pixi global install rattler-build
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#
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- name: Write Python variant config
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shell: bash
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run: printf 'python:\n - "${{ matrix.python-version }}"\n' > "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Build package using rattler-build (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 ${{ github.workspace }}/ghostly/recipes/ghostly
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#
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- name: Build Conda package using conda build using dev channel
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shell: bash
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run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/main --variant-config "${{ github.workspace }}/python_variant.yaml"
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#
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- name: Build package using rattler-build (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 ${{ github.workspace }}/ghostly/recipes/ghostly
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shell: bash
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run: rattler-build build --recipe "${{ github.workspace }}/recipes/ghostly" -c conda-forge -c openbiosim/label/dev --variant-config "${{ github.workspace }}/python_variant.yaml"

‎.gitignore‎

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dist/
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ghostly.egg-info
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src/ghostly/_version.py
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# Test output.
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output.yaml
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# VSCode config
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.vscode/
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# Conda recipe (it is auto-generated)
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recipes/ghostly/meta.yaml
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# Sire cache files.
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cache/
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# Auto-generated version file.
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src/ghostly/_version.py

‎.img/ghostly.png‎

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‎.pre-commit-config.yaml‎

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files: ^(src|tests)/
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exclude: ^tests/(input|output)/
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repos:
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# General file quality checks
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v5.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-added-large-files
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args: [--maxkb=1000] # Prevent files larger than 1MB
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- id: check-merge-conflict
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# Python formatting and linting
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- repo: https://github.com/astral-sh/ruff-pre-commit
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rev: v0.15.4
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hooks:
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# Run the formatter
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- id: ruff-format
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# Run the linter (optional - remove if too strict)
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- id: ruff
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args: [--fix, --exit-zero] # Auto-fix but don't block commits

‎CHANGELOG.md‎

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Changelog
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=========
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[2026.1.0](https://github.com/openbiosim/loch/compare/2025.2.0...2026.1.0) - ********
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-------------------------------------------------------------------------------------
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* Please add an item to this CHANGELOG for any new features or bug fixes when creating a PR.
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[2025.2.0](https://github.com/openbiosim/loch/compare/2025.1.0...2025.2.0) - Mar 2026
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-------------------------------------------------------------------------------------
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* Ensure that there are independent, per-state, physical neighbours. This removes the spurious cross-state ghost filter that resulted in a downgrading of junction types when multiple junctions were present in the molecule.
13+
* Added a fallback for failed angle optimisation to ensure that the original equilibrium value is preserved when convergence fails.
14+
* Added new ``--stiffen-ring-bridges`` option to control whether angle stiffening is applied to ring bridge atoms. (Default: False)
15+
* Added ``--stiffen-sp2-bridges`` to control whether angle stiffening is applied to SP2 bridge atoms. (Default: False)
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* Added ``--soften-anchors`` option to scale the force constants of surviving mixed ghost/physical dihedrals. (Default: 1.0, i.e. no softening)
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* Added rotamer anchor detection and options to stiffen the force constant using ``--stiffen-rotamers`` and ``--k-rotamer``. (Default: False, 50 kcal/mol)
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* Added scoring functionality to try to avoid anchoring through transmuting or bridge atoms where possible.
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* Handle edge cases for ring-breaking perturbations.
20+
* Fixed angle removal logic for ring and sp2 bridge atoms: when stiffening is skipped (``stiffen_ring_bridges=False`` or ``stiffen_sp2_bridges=False``), all ghost-containing angles are now preserved at their original force field values rather than removing the intraghost angles (dual junctions) or the sacrificial physical-bridge-ghost angle (triple junctions).
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* Changed the default for ``--optimise-angles`` to ``False``. Angle optimisation is conformer-dependent: different input geometries can yield different equilibrium angles for the same perturbation, adding variability to the resulting force field. The original force field theta0 is sufficient given the small ``k_soft`` value. Optimisation can still be enabled explicitly to follow Boresch et al. (JCTC 2021) strictly.
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[2025.1.0](https://github.com/OpenBioSim/loch/releases/tag/2025.1.0) - Nov 2025
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-------------------------------------------------------------------------------
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* Initial public release.

‎MANIFEST.in‎

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graft tests

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