propagate uv toml settings

src/groundhog_hpc/configuration/models.py

@@ -87,7 +87,9 @@ class UvMetadata(BaseModel, extra="allow", serialize_by_alias=True):
     exclude_newer: str | None = Field(
         default_factory=_default_exclude_newer, alias="exclude-newer"
     )
-    python_preference: str | None = Field(default="managed", alias="python-preference")
+    python_preference: str | None = Field(
+        default="only-managed", alias="python-preference"
+    )
     index_url: str | None = Field(default=None, alias="index-url")
     extra_index_url: list[str] | None = Field(default=None, alias="extra-index-url")
     python_downloads: str | None = Field(default=None, alias="python-downloads")

src/groundhog_hpc/templates/shell_command.sh.jinja

@@ -79,15 +79,31 @@ else
     fi
     {% endraw %}
 
-    "$UV_BIN" venv "$ENV_DIR"{% if requires_python %} --python "{{ requires_python }}"{% endif %}
+    {% if uv_config_toml %}
+
+    # Both `uv venv` and `uv pip install` will receive --config-file, then
+    # the file is moved into $ENV_DIR as a human-readable audit trail.
+    {% raw %}UV_TOML="${{ENV_DIR}}.uv.toml"{% endraw %}
+    mkdir -p "$(dirname "$UV_TOML")"
+
+    cat > "$UV_TOML" << 'UV_CONFIG_EOF'
+{{ uv_config_toml | escape_braces }}
+UV_CONFIG_EOF
+    {% endif %}
+
+    "$UV_BIN" venv "$ENV_DIR"{% if requires_python %} --python "{{ requires_python }}"{% endif %}{% if uv_config_toml %} --config-file "$UV_TOML"{% endif %}
+
+    {% if uv_config_toml %}
+    mv "$UV_TOML" "$ENV_DIR/uv.toml"
+    {% endif %}
 
     # Install dependencies
     "$UV_BIN" pip install --python "$ENV_DIR/bin/python" \
-        {% if exclude_newer %}--exclude-newer "{{ exclude_newer }}" {% endif %}\
+        {% if uv_config_toml %}--config-file "$ENV_DIR/uv.toml" {% endif %}\
         --exclude-newer-package groundhog-hpc={{ groundhog_timestamp }} \
         {% for dep in dependencies %}"{{ dep }}" {% endfor %}{{ version_spec }}
 
-    # Write metadata for debugging
+    # Write metadata for posterity
     cat > "$ENV_DIR/groundhog-meta.json" << 'META_EOF'
 {{ '{{' }}
     "created_at": "{{ groundhog_timestamp }}",

src/groundhog_hpc/templating.py

@@ -16,6 +16,7 @@
 from hashlib import sha1
 from pathlib import Path
 
+import tomlkit
 from jinja2 import Environment, FileSystemLoader
 
 from groundhog_hpc.configuration.models import Pep723Metadata
@@ -149,6 +150,8 @@ def template_shell_command(script_path: str, function_name: str, payload: str) -
         local_log_level = local_log_level.upper()
         logger.debug(f"Propagating log level to remote: {local_log_level}")
 
+    uv_config_toml = _serialize_uv_toml(metadata)
+
     # Render shell command
     shell_template = jinja_env.get_template("shell_command.sh.jinja")
     shell_command_string = shell_template.render(
@@ -165,16 +168,30 @@ def template_shell_command(script_path: str, function_name: str, payload: str) -
         groundhog_version=groundhog_version,
         requires_python=metadata.requires_python if metadata else "",
         dependencies=metadata.dependencies if metadata else [],
-        exclude_newer=metadata.tool.uv.exclude_newer
-        if metadata and metadata.tool and metadata.tool.uv
-        else None,
+        uv_config_toml=uv_config_toml,
     )
 
     logger.debug(f"Generated shell command ({len(shell_command_string)} chars)")
 
     return shell_command_string
 
 
+def _serialize_uv_toml(metadata: Pep723Metadata | None) -> str:
+    """Serialize [tool.uv] settings to uv.toml format for uv pip install.
+
+    Returns a TOML string containing all non-None settings from the user's
+    [tool.uv] block, or an empty string if there are no settings.
+    """
+    if not metadata or not metadata.tool or not metadata.tool.uv:
+        return ""
+
+    uv_dict = metadata.tool.uv.model_dump(by_alias=True, exclude_none=True)
+    if not uv_dict:
+        return ""
+
+    return tomlkit.dumps(uv_dict).strip()
+
+
 def _script_hash_prefix(contents: str, length: int = 8) -> str:
     return str(sha1(bytes(contents, "utf-8")).hexdigest()[:length])