Add support for recreating uv environments from uv.lock files

actions/pyrosettacluster/test_env_reproducibility.py

@@ -123,7 +123,7 @@ def recreate_environment_test(
             )
         elif environment_manager == "uv":
             cmd = (
-                f"uv run --project {original_env_dir} python -u -m {module} "
+                f"uv run --locked --project {original_env_dir} python -u -m {module} "
                 f"--env_manager '{environment_manager}' "
                 f"--output_path '{original_output_path}' "
                 f"--scorefile_name '{original_scorefile_name}'"
@@ -174,7 +174,7 @@ def recreate_environment_test(
             )
         elif environment_manager == "uv":
             cmd = (
-                f"uv run --project {original_env_dir} python -u {dump_env_file_script} "
+                f"uv run --locked --project {original_env_dir} python -u {dump_env_file_script} "
                 f"--scorefile '{original_scorefile_path}' "
                 f"--decoy_name '{original_decoy_name}' "
                 f"--env_dir '{reproduce_env_dir}' "
@@ -230,7 +230,7 @@ def recreate_environment_test(
             )
         elif environment_manager == "uv":
             cmd = (
-                f"uv run --project {reproduce_env_dir} python -u -m {module} "
+                f"uv run --locked --project {reproduce_env_dir} python -u -m {module} "
                 f"--env_manager '{environment_manager}' "
                 f"--output_path '{reproduce_output_path}' "
                 f"--scorefile_name '{reproduce_scorefile_name}' "
@@ -310,7 +310,7 @@ def recreate_environment_test(
             )
         elif environment_manager == "uv":
             cmd = (
-                f"uv run --project {reproduce_env_dir} python -u -m {module} "
+                f"uv run --locked --project {reproduce_env_dir} python -u -m {module} "
                 f"--original_output_file '{original_output_file}' "
                 f"--reproduce_output_file '{reproduce_output_file}' "
                 f"--pyrosetta_init_flags '{pyrosetta_init_flags}'"

pyrosettacluster/README.md

@@ -105,7 +105,7 @@ Please see the [official PyRosettaCluster documentation](https://graylab.jhu.edu
 > If using the `uv` environment manager, please remember to set the `UV_PROJECT` environment variable to the `uv` project root directory, or run the `PyRosettaCluster` simulation from the `uv` project root directory, in order for `PyRosettaCluster` to automatically detect and cache the `uv` project's `pyproject.toml` file for environment reproducibility.
 
 > [!TIP]
-> If using the `uv` environment manager with custom/experimental libraries built from [source distributions (sdists)](https://packaging.python.org/en/latest/specifications/source-distribution-format/#source-distribution-file-format) instead of wheels, it may be helpful to cache the environment's `uv.lock` file contents for accounting or debugging purposes. The `uv.lock` file may be either committed to the GitHub repository before running the `PyRosettaCluster` simulation, or stored in the `system_info` keyword argument for persistent storage in the output decoys (and scorefile(s) if `simulation_records_in_scorefile=True`). Although very uncommon, if a `uv` project contains packages built from sdists, it may be necessary to reproduce the environment using `uv sync` from the `uv.lock` file rather than `uv pip sync` from the automatically exported and cached `requirements.txt` file. For example:
+> If using the `uv` environment manager with PyRosetta version `2026.3+releasequarterly.5e498f1409` and custom/experimental libraries built from [source distributions (sdists)](https://packaging.python.org/en/latest/specifications/source-distribution-format/#source-distribution-file-format) instead of wheels, it may be helpful to cache the environment's `uv.lock` file contents for accounting or debugging purposes. Note that subsequent quarterly releases of `pyrosetta` (and weekly releases `>2026.05` if using the PyPI `pyrosetta-installer` package for PyRosetta installation) automatically cache the `uv.lock` file. The `uv.lock` file may be either committed to the GitHub repository before running the `PyRosettaCluster` simulation, or stored in the `system_info` keyword argument for persistent storage in the output decoys (and scorefile(s) if `simulation_records_in_scorefile=True`). Although very uncommon, if a `uv` project contains packages built from sdists, it may be necessary to reproduce the environment using `uv sync` from the `uv.lock` file rather than `uv pip sync` from the automatically exported and cached `requirements.txt` file. For example:
 > ```
 > import sys
 > from pathlib import Path
@@ -239,3 +239,4 @@ if __name__ == "__main__":
 
 
 
+

pyrosettacluster/dump_env_file.py

@@ -17,6 +17,22 @@
 from typing import Optional
 
 
+def detect_uv_environment_format(environment: str) -> str:
+    """
+    Detect whether the PyRosettaCluster environment file string is in 'uv.lock' or 'requirements.txt' format.
+
+    Args:
+        environment: A `str` object representing the PyRosettaCluster environment file string.
+
+    Returns:
+        A `str` object of either 'uv.lock' or 'requirements.txt'.
+    """
+    for line in environment.splitlines():
+        if line.strip().startswith("[[package]]"):
+            return "uv.lock"
+    return "requirements.txt"
+
+
 def main(
     input_file: Optional[str],
     scorefile: Optional[str],
@@ -91,7 +107,8 @@ def main(
             )
 
     elif env_manager == "uv":
-        env_file = os.path.join(env_dir, "requirements.txt")
+        uv_environment_format = detect_uv_environment_format(environment)
+        env_file = os.path.join(env_dir, uv_environment_format)
         write_file(env_file, environment)
         if toml:
             toml_file = os.path.join(env_dir, toml_format)

pyrosettacluster/recreate_env.py

@@ -61,6 +61,13 @@ def run_subprocess(
         raise RuntimeError(cmd) from ex
 
 
+def uv_lock_package_present(lock_file: str, name: str) -> bool:
+    """Test if a package name is specified in an input 'uv.lock' file."""
+    with open(lock_file, "r") as f:
+        contents = f.read()
+    return bool(re.search(rf'^\[\[package\]\]\s*\n\s*name\s*=\s*"{name}"\s*$', contents, flags=re.MULTILINE))
+
+
 def requirement_present(req_file: str, name: str) -> bool:
     """Test if a package name is specified in an input 'requirements.txt' file."""
     with open(req_file, "r") as f:
@@ -94,16 +101,24 @@ def recreate_environment(env_dir: str, env_manager: str, timeout: float, mirror_
         env_create_cmd = "pixi install --frozen"
 
     elif env_manager == "uv":
-        req_file = os.path.join(env_dir, "requirements.txt")
-        if not os.path.isfile(req_file):
-            raise FileNotFoundError(
-                "Please ensure that the uv project 'requirements.txt' file "
-                "is in the uv project directory, then try again."
-            )
-        # Install packages strictly from requirements.txt
-        env_create_cmd = f"uv venv --project '{env_dir}' && uv pip sync --project '{env_dir}' '{req_file}'"
-        # Test if the 'pyrosetta-installer' package is specified
-        use_pyrosetta_installer = requirement_present(req_file, "pyrosetta-installer")
+        lock_file = os.path.join(env_dir, "uv.lock")
+        if os.path.isfile(lock_file):
+            # Install packages strictly from uv.lock
+            env_create_cmd = f"uv sync --frozen --project '{env_dir}'"
+            # Test if the 'pyrosetta-installer' package is specified
+            use_pyrosetta_installer = uv_lock_package_present(lock_file, "pyrosetta-installer")
+        else:
+            req_file = os.path.join(env_dir, "requirements.txt")
+            if os.path.isfile(req_file):
+                # Install packages strictly from requirements.txt
+                env_create_cmd = f"uv venv --project '{env_dir}' && uv pip sync --project '{env_dir}' '{req_file}' && uv lock"
+                # Test if the 'pyrosetta-installer' package is specified
+                use_pyrosetta_installer = requirement_present(req_file, "pyrosetta-installer")
+            else:
+                raise FileNotFoundError(
+                    "Please ensure that the uv project 'uv.lock' (or 'requirements.txt' file) "
+                    "is in the uv project directory, then try again."
+                )
 
     elif env_manager == "conda":
         yml_file = os.path.join(env_dir, "environment.yml")