Add helper function for setting --nthreads

This will be useful in Snakemake workflows to prevent
over/under-allocating threads.

Author: victorlin

CHANGES.md

@@ -2,13 +2,18 @@
 
 ## __NEXT__
 
+### Features
+
+* A helper function – `augur.subsample.get_parallelism` – has been added to optimize usage of `augur subsample` in Snakemake workflows. This is experimental and not yet part of the public API. [#1963][] (@victorlin)
+
 ### Bug fixes
 
 * filter, merge: Fixed formatting of the error message shown when there are duplicate sequence ids. [#1954][] @victorlin
 * filter: Adjusted the error message shown when there are missing weights to mention the option of updating values in metadata. [#1956][] @victorlin
 
 [#1954]: https://github.com/nextstrain/augur/pull/1954
 [#1956]: https://github.com/nextstrain/augur/pull/1956
+[#1963]: https://github.com/nextstrain/augur/pull/1963
 
 ## 33.0.0 (26 January 2026)
 

augur/subsample.py

@@ -233,6 +233,39 @@ def run(args: argparse.Namespace) -> None:
                 sample.remove_output_strains()
 
 
+def get_parallelism(
+    config_file: str,
+    config_section: Optional[List[str]] = None,
+    limit: int = None
+) -> int:
+    """Compute the degree of parallelism (i.e., optimal value for ``--nthreads``).
+
+    Inspects the subsample config file to return the degree of parallelism that
+    should be used for ``--nthreads``. Higher values will underutilize
+    resources, while lower values will underallocate resources and not fully use
+    available parallelism.
+
+    Parameters
+    ----------
+    config_file
+        Path to the subsample config file.
+
+    config_section
+        Optional list of keys to navigate to a specific section of the config file.
+
+    limit
+        Upper bound for return value.
+
+    Returns
+    -------
+    int
+        Degree of parallelism.
+    """
+    schema_validator = load_json_schema("schema-subsample-config.json")
+    config = _parse_config(config_file, config_section, schema_validator)
+    return max(1, min(limit, len(config["samples"])))
+
+
 def get_referenced_files(
     config_file: str,
     config_section: Optional[List[str]] = None,