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pyrosettacluster/README.md

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@@ -34,28 +34,28 @@ PyRosettaCluster supports running reproducible PyRosetta simulations from reprod
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> _Explanation:_ If using the `uv` environment manager, the PyRosetta quarterly builds enable long-term reproducibility of virtual environments containing the `pyrosetta` package; just include the `--find-links` (or `-f`) flag to indicate the links search path to the PyRosetta `cxx11thread.serialization` wheels:
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> - For *west* mirror: [https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization](https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization)
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> - For *west* mirror: [https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization/](https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization/)
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> - For *east* mirror: [https://graylab.jhu.edu/download/PyRosetta4/archive/release-quarterly/release.cxx11thread.serialization](https://graylab.jhu.edu/download/PyRosetta4/archive/release-quarterly/release.cxx11thread.serialization)
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> - For *east* mirror: [https://graylab.jhu.edu/download/PyRosetta4/archive/release-quarterly/release.cxx11thread.serialization/](https://graylab.jhu.edu/download/PyRosetta4/archive/release-quarterly/release.cxx11thread.serialization/)
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> *Example #1*:
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>```
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>uv pip install pyrosetta -f https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization
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>uv pip install pyrosetta -f https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization/
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>```
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> *Example #2*:
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> To specify a specific version:
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>```
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>uv add pyrosetta==2026.3+releasequarterly.5e498f1409 -f https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization
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>uv add pyrosetta==2026.3+releasequarterly.5e498f1409 -f https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization/
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>```
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> *Example #3*:
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>
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> Alternatively, add the following to your `uv` project's `pyproject.toml` file:
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> ```
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> [tool.uv]
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> find-links = ["https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization"]
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> find-links = ["https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization/"]
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> ```
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>Then run `uv add pyrosetta` or `uv pip install pyrosetta` to get the most recent `pyrosetta` package quarterly release.
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@@ -64,7 +64,7 @@ PyRosettaCluster supports running reproducible PyRosetta simulations from reprod
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> Alternatively, add the following to your system's `uv.toml` [configuration file](https://docs.astral.sh/uv/concepts/configuration-files) (however, this only works with `uv pip install pyrosetta` syntax, and not `uv add pyrosetta` syntax):
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> ```
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>[pip]
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> find-links = ["https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization"]
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> find-links = ["https://west.rosettacommons.org/pyrosetta/quarterly/release.cxx11thread.serialization/"]
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> ```
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> Then run `uv pip install pyrosetta` to get the most recent `pyrosetta` package quarterly release.
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@@ -218,3 +218,4 @@ if __name__ == "__main__":
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🎉 Congrats! You have now recreated a virtual environment and used it to successfully reproduce a distributed PyRosettaCluster simulation.
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