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Fix PyRosettaCluster environment reproduction unit tests and add PyRosettaCluster documentation (#4)
The aim of this PR is to: 1. Fix PyRosettaCluster environment reproduction unit tests using Conda, Mamba, uv, and Pixi 2. Add unit tests for Python 3.9, 3.10, 3.11, 3.12, 3.13, and 3.14 3. Add PyRosettaCluster documentation 4. Reorganize the repository structure to support future development
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‎.github/workflows/pyrosetta.yml‎

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‎.github/workflows/pyrosettacluster.yml‎

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name: PyRosettaCluster Tests
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on:
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push:
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branches: ['*']
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tags: ['*']
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pull_request:
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branches: ['*']
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schedule:
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# Run Every Monday 4 AM UTC
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- cron: '0 4 * * 1'
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env:
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CARGO_TERM_COLOR: always
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jobs:
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# ============================================================
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# PIXI JOB
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# ============================================================
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pixi:
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name: Pixi
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Pixi
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run: |
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curl -fsSL https://pixi.sh/install.sh | bash
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echo "$HOME/.pixi/bin" >> $GITHUB_PATH
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- name: Verify Pixi
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run: |
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export PATH="$HOME/.pixi/bin:$PATH"
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pixi --version
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- name: Add repo root to PYTHONPATH
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run: echo "PYTHONPATH=$PYTHONPATH:${{ github.workspace }}" >> $GITHUB_ENV
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- name: Run tests (pixi)
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shell: bash
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run: |
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export PATH="$HOME/.pixi/bin:$PATH"
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which python
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python --version
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python -u -m unittest actions.pyrosettacluster.test_env_reproducibility.TestEnvironmentReproducibility.test_recreate_environment_pixi -v
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# ============================================================
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# UV JOB
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# ============================================================
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uv:
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name: Uv
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install uv
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run: |
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curl -LsSf https://astral.sh/uv/install.sh | sh
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echo "$HOME/.local/bin" >> $GITHUB_PATH
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uv --version
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- name: Add repo root to PYTHONPATH
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run: echo "PYTHONPATH=$PYTHONPATH:${{ github.workspace }}" >> $GITHUB_ENV
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- name: Run tests (uv)
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shell: bash
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run: |
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which python
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python --version
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python -u -m unittest actions.pyrosettacluster.test_env_reproducibility.TestEnvironmentReproducibility.test_recreate_environment_uv -v
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# ============================================================
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# CONDA JOB
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# ============================================================
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conda:
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name: Conda
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Conda
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uses: conda-incubator/setup-miniconda@v3
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with:
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python-version: ${{ matrix.python-version }}
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auto-update-conda: true
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activate-environment: conda-job
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use-mamba: false
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channel-priority: strict
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- name: Add repo root to PYTHONPATH
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run: echo "PYTHONPATH=$PYTHONPATH:${{ github.workspace }}" >> $GITHUB_ENV
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- name: Run tests (conda)
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shell: bash
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run: |
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which python
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python --version
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python -u -m unittest actions.pyrosettacluster.test_env_reproducibility.TestEnvironmentReproducibility.test_recreate_environment_conda -v
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# ============================================================
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# MAMBA JOB
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# ============================================================
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mamba:
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name: Mamba
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: ["3.9", "3.10", "3.11", "3.12", "3.13", "3.14"]
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steps:
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- uses: actions/checkout@v4
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- name: Set up Conda
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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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activate-environment: ''
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channel-priority: strict
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- name: Install Mamba
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shell: bash -l {0}
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run: |
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conda install -y -n base -c conda-forge mamba
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- name: Set Mamba cache
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shell: bash -l {0}
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run: |
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mkdir -p $HOME/.conda/pkgs
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export CONDA_PKGS_DIRS="$HOME/.conda/pkgs"
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echo "CONDA_PKGS_DIRS=$CONDA_PKGS_DIRS"
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- name: Check Mamba
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shell: bash -l {0}
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run: |
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export PATH="/usr/share/miniconda/bin:$PATH"
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export CONDA_PKGS_DIRS="$HOME/.conda/pkgs"
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echo "PATH=$PATH"
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which mamba
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mamba --version
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- name: Add repo root to PYTHONPATH
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run: |
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export PATH="/usr/share/miniconda/bin:$PATH"
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export CONDA_PKGS_DIRS="$HOME/.conda/pkgs"
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echo "PYTHONPATH=$PYTHONPATH:${{ github.workspace }}" >> $GITHUB_ENV
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- name: Run tests (mamba)
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shell: bash -l {0}
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run: |
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export PATH="/usr/share/miniconda/bin:$PATH"
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export CONDA_PKGS_DIRS="$HOME/.conda/pkgs"
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which python
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python --version
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python -u -m unittest actions.pyrosettacluster.test_env_reproducibility.TestEnvironmentReproducibility.test_recreate_environment_mamba -v

‎README.md‎

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# ✨ PyRosetta Extras: a repository for PyRosetta scripts, tools, unit testing, and documentation
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# ✨ PyRosetta Extras: a repository for extra PyRosetta scripts, tools, unit testing, and documentation
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> [!IMPORTANT]
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> Scripts in this GitHub repository may require download and installation of [PyRosetta software](https://www.pyrosetta.org/downloads) to run properly.
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> Downloads of PyRosetta software are provided to academic and non-commercial users under the [PyRosetta Software Non-Commercial License Agreement](https://github.com/RosettaCommons/rosetta/blob/main/LICENSE.PyRosetta.md).

‎actions/__init__.py‎

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‎actions/pyrosettacluster/__init__.py‎

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