Update docstrings and README.md

pyrosettacluster/README.md

@@ -153,7 +153,7 @@ Please refer to the following table to select _one_ environment file extraction
 > Also note the `record["instance"]["sha1"]` nested key value holding the GitHub commit SHA1 required to [reproduce the PyRosettaCluster simulation](#clone-original-repository)!
 
 > [!NOTE]  
-> **Extraction method #2:** If running `dump_env_file.py`, the `pyrosetta` package (with version >=2025.47) must be installed in any existing virtual environment, and that virtual environment's python interpreter used to run the script.
+> **Extraction method #2:** If running `dump_env_file.py`, the `pyrosetta` package (with version `>=2025.47`) and the [PyPI pyrosetta-distributed](https://pypi.org/project/pyrosetta-distributed/) package (for the `pyrosetta.distributed` framework dependencies) must be installed in any existing virtual environment, and that virtual environment's python interpreter used to run the script.
 >
 > Also note the printed GitHub commit SHA1 required to [reproduce the PyRosettaCluster simulation](#clone-original-repository)!
 
@@ -238,3 +238,4 @@ if __name__ == "__main__":
 
 
 
+

pyrosettacluster/dump_env_file.py

@@ -1,7 +1,7 @@
 """
-Extract and write a PyRosettaCluster environment file based on
-metadata from a PyRosettaCluster result. This script requires PyRosetta version >=2025.47
-to be installed for the PyRosettaCluster environment file extraction.
+Extract and write a PyRosettaCluster environment file based on metadata from a PyRosettaCluster
+output decoy file or PyRosettaCluster output scorefile. This script requires PyRosetta version
+`>=2025.47` and `pyrosetta.distributed` framework dependencies to be installed.
 """
 
 __author__ = "Jason C. Klima"
@@ -68,7 +68,10 @@ def main(
     env_manager = metadata_kwargs.get("environment_manager")  # may be `None` in legacy cases
 
     sha1 = instance_kwargs.get("sha1")
+    print("[INFO] " + "-" * 72)
+    print("[INFO] Please note the GitHub SHA1 from which the original simulation was run!")
     print(f"[INFO] GitHub SHA1: {sha1}")
+    print("[INFO] " + "-" * 72)
 
     # Determine output files based on manager
     if env_manager == "pixi":
@@ -152,12 +155,7 @@ def ensure_env_dir(path: Optional[str]) -> str:
 
 
 if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description=(
-            "Dump a PyRosettaCluster environment file using metadata contained in a "
-            "PyRosettaCluster output decoy file or PyRosettaCluster output scorefile."
-        )
-    )
+    parser = argparse.ArgumentParser(description=__doc__)
 
     # -------------------------------------------------------------------------
     # Inputs for `pyrosetta.distributed.cluster.get_instance_kwargs`
@@ -204,7 +202,7 @@ def ensure_env_dir(path: Optional[str]) -> str:
     # -------------------------------------------------------------------------
     parser.add_argument(
         "--env_dir",
-        type=ensure_env_dir,
+        type=str,
         required=False,
         default=None,
         help=(
@@ -247,6 +245,7 @@ def ensure_env_dir(path: Optional[str]) -> str:
     )
 
     args = parser.parse_args()
+    args.env_dir = ensure_env_dir(args.env_dir)
 
     main(
         input_file=args.input_file,

pyrosettacluster/recreate_env.py

@@ -14,7 +14,7 @@
 The environment manager used (i.e., either 'conda', 'mamba', 'uv', or 'pixi') is
 automatically determined from the operating system environment variable
 'PYROSETTACLUSTER_ENVIRONMENT_MANAGER' if exported, or otherwise it must be
-provided using the `--env_manager` flag. Run `./recreate_env.py --help` for more details.
+provided using the `--env_manager` flag.
 """
 
 __author__ = "Jason C. Klima"
@@ -217,7 +217,7 @@ def validate_env_manager(manager: str) -> str:
     parser = argparse.ArgumentParser(
         description=(
             "Recreate a PyRosettaCluster environment using one of the supported "
-            "environment managers ('pixi', 'uv', 'conda', 'mamba')."
+            f"environment managers ('pixi', 'uv', 'conda', 'mamba').\n{__doc__}"
         )
     )
 
@@ -261,8 +261,10 @@ def validate_env_manager(manager: str) -> str:
         type=int,
         default=[0, 1],
         help=(
-            "Optionally specify the PyRosetta installer mirror order to try, e.g. `--mirror_order 0 1`. "
-            "See the PyPI 'pyrosetta-installer' package website for details."
+            "Optionally, if using the `uv` environment manager and the `pyrosetta-installer` package "
+            "is specified as a dependency in the `requirements.txt` file, then this option sets the "
+            "PyRosetta installer mirror order to try, e.g. `--mirror_order 0 1`. If not using `uv`, "
+            "this option is ignored. See the PyPI 'pyrosetta-installer' package website for details."
         ),
     )