feat(models): add copy command (#295)

this was already in the python API just needed a CLI command too

Author: wpbonelli

autotest/test_models.py

@@ -514,6 +514,127 @@ def test_cli_clear(self, capsys):
         captured = capsys.readouterr()
         assert "Cleared 1 cached registry" in captured.out
 
+    def test_cli_copy(self, tmp_path):
+        """Test 'copy' command."""
+        # Sync a registry first
+        _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
+        source = ModelSourceRepo(
+            repo=TEST_MODELS_REPO,
+            name=TEST_MODELS_SOURCE_NAME,
+            refs=[TEST_MODELS_REF],
+        )
+        result = source.sync(ref=TEST_MODELS_REF)
+        assert len(result.synced) == 1
+
+        # Load registry and get first model name
+        registry = _DEFAULT_CACHE.load(TEST_MODELS_SOURCE_NAME, TEST_MODELS_REF)
+        assert len(registry.models) > 0
+        model_name = next(iter(registry.models.keys()))
+
+        # Create workspace
+        workspace = tmp_path / "test-workspace"
+
+        # Copy model
+        import argparse
+
+        from modflow_devtools.models.__main__ import cmd_copy
+
+        args = argparse.Namespace(model=model_name, workspace=str(workspace), verbose=True)
+        cmd_copy(args)
+
+        # Verify workspace was created and contains files
+        assert workspace.exists()
+        assert len(list(workspace.rglob("*"))) > 0
+
+    def test_cli_copy_nonexistent_model(self, tmp_path, capsys):
+        """Test 'copy' command with nonexistent model."""
+        # Sync a registry first
+        _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
+        source = ModelSourceRepo(
+            repo=TEST_MODELS_REPO,
+            name=TEST_MODELS_SOURCE_NAME,
+            refs=[TEST_MODELS_REF],
+        )
+        result = source.sync(ref=TEST_MODELS_REF)
+        assert len(result.synced) == 1
+
+        # Try to copy nonexistent model
+        import argparse
+
+        from modflow_devtools.models.__main__ import cmd_copy
+
+        workspace = tmp_path / "test-workspace"
+        args = argparse.Namespace(
+            model="nonexistent-model-12345", workspace=str(workspace), verbose=False
+        )
+
+        with pytest.raises(SystemExit):
+            cmd_copy(args)
+
+        captured = capsys.readouterr()
+        assert "not in registry" in captured.err.lower()
+
+    def test_cli_cp_alias(self, tmp_path):
+        """Test 'cp' alias for 'copy' command."""
+        # Sync a registry first
+        _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
+        source = ModelSourceRepo(
+            repo=TEST_MODELS_REPO,
+            name=TEST_MODELS_SOURCE_NAME,
+            refs=[TEST_MODELS_REF],
+        )
+        result = source.sync(ref=TEST_MODELS_REF)
+        assert len(result.synced) == 1
+
+        # Load registry and get first model name
+        registry = _DEFAULT_CACHE.load(TEST_MODELS_SOURCE_NAME, TEST_MODELS_REF)
+        assert len(registry.models) > 0
+        model_name = next(iter(registry.models.keys()))
+
+        # Create workspace
+        workspace = tmp_path / "test-workspace-cp"
+
+        # Test that cp alias works via command parsing
+        import argparse
+
+        from modflow_devtools.models.__main__ import cmd_copy
+
+        # Simulate args as if 'cp' command was used (argparse will set command to 'cp')
+        args = argparse.Namespace(model=model_name, workspace=str(workspace), verbose=False)
+        cmd_copy(args)
+
+        # Verify workspace was created and contains files
+        assert workspace.exists()
+        assert len(list(workspace.rglob("*"))) > 0
+
+    def test_python_cp_alias(self, tmp_path):
+        """Test Python API cp() alias for copy_to()."""
+        # Sync a registry first
+        _DEFAULT_CACHE.clear(source=TEST_MODELS_SOURCE_NAME, ref=TEST_MODELS_REF)
+        source = ModelSourceRepo(
+            repo=TEST_MODELS_REPO,
+            name=TEST_MODELS_SOURCE_NAME,
+            refs=[TEST_MODELS_REF],
+        )
+        result = source.sync(ref=TEST_MODELS_REF)
+        assert len(result.synced) == 1
+
+        # Load registry and get first model name
+        registry = _DEFAULT_CACHE.load(TEST_MODELS_SOURCE_NAME, TEST_MODELS_REF)
+        assert len(registry.models) > 0
+        model_name = next(iter(registry.models.keys()))
+
+        # Test cp() function
+        from modflow_devtools.models import cp
+
+        workspace = tmp_path / "test-workspace-python-cp"
+        result_path = cp(str(workspace), model_name, verbose=False)
+
+        # Verify workspace was created and contains files
+        assert result_path is not None
+        assert workspace.exists()
+        assert len(list(workspace.rglob("*"))) > 0
+
 
 @pytest.mark.xdist_group("registry_cache")
 class TestIntegration:

docs/md/dev/models.md

@@ -7,6 +7,7 @@ This is a living document which will be updated as development proceeds. As the
 <!-- START doctoc generated TOC please keep comment here to allow auto update -->
 <!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
 
+
 - [Background](#background)
 - [Objective](#objective)
 - [Motivation](#motivation)
@@ -43,6 +44,8 @@ This is a living document which will be updated as development proceeds. As the
     - [Show Registry Status](#show-registry-status)
     - [Sync Registries](#sync-registries)
     - [List Available Models](#list-available-models)
+    - [Clear Cached Registries](#clear-cached-registries)
+    - [Copy Models to Workspace](#copy-models-to-workspace)
   - [Registry Creation Tool](#registry-creation-tool)
   - [User Config Overlay for Fork Testing](#user-config-overlay-for-fork-testing)
   - [Upstream CI Workflow Examples](#upstream-ci-workflow-examples)
@@ -328,6 +331,7 @@ The simplest approach would be a single such script/command, e.g. `python -m mod
 - `sync`: synchronize registries for all configured source model repositories, or a specific repo
 - `info`: show configured registries and their sync status, or a particular registry's sync status
 - `list`: list available models for all registries, or for a particular registry
+- `copy` (or `cp`): copy a model's input files to a workspace directory
 
 ```bash
 # Show configured registries and status
@@ -345,6 +349,10 @@ mf models sync --repo MODFLOW-ORG/modflow6-examples --ref current
 # For a repo with models under version control
 mf models sync --repo MODFLOW-ORG/modflow6-testmodels --ref develop
 mf models sync --repo MODFLOW-ORG/modflow6-testmodels --ref f3df630  # commit hash works too
+
+# Copy a model to a workspace (cp is an alias for copy)
+mf models copy mf6/test/test001a_Tharmonic ./my-workspace
+mf models cp mf6/example/ex-gwf-twri01 /path/to/workspace --verbose
 ```
 
 CLI commands are available in two forms:
@@ -544,7 +552,7 @@ The Models, Programs, and DFNs APIs share a consistent design for ease of use an
 7. **Unified CLI operations**:
    - Sync all APIs: `python -m modflow_devtools sync --all`
    - Clean all caches: `python -m modflow_devtools clean --all`
-   - Individual API operations: `python -m modflow_devtools.{api} sync|info|list|clean`
+   - Individual API operations: `python -m modflow_devtools.{api} sync|info|list|copy|clean`
 
 8. **MergedRegistry pattern**: Only used where needed
    - Models: Yes (essential for multi-source/multi-ref unified view)
@@ -723,6 +731,19 @@ $ mf models clear --source mf6/test --ref develop
 $ mf models clear --force
 ```
 
+#### Copy Models to Workspace
+
+```bash
+# Copy a model to a workspace directory
+$ mf models copy mf6/test/test001a_Tharmonic ./my-workspace
+
+# Copy with verbose output (cp is an alias for copy)
+$ mf models cp mf6/example/ex-gwf-twri01 /path/to/workspace --verbose
+
+# Works with absolute or relative paths
+$ mf models copy mf6/large/prudic2004t2 ../workspace
+```
+
 ### Registry Creation Tool
 
 The `make_registry` tool uses a mode-based interface with **remote-first operation** by default:

docs/md/models.md

@@ -131,14 +131,37 @@ python -m modflow_devtools.models list --source mf6/test --verbose
 
 ### Copying models to a workspace
 
+Models can be copied to a workspace programmatically:
+
 ```python
 from tempfile import TemporaryDirectory
-from modflow_devtools.models import copy_to
+from modflow_devtools.models import copy_to, cp  # cp is an alias
 
 with TemporaryDirectory() as workspace:
     model_path = copy_to(workspace, "mf6/example/ex-gwf-twri01", verbose=True)
+    # Or use the shorter alias
+    model_path = cp(workspace, "mf6/example/ex-gwf-twri01", verbose=True)
+```
+
+Or via CLI (both forms are equivalent):
+
+```bash
+# Using the mf command
+mf models copy mf6/test/test001a_Tharmonic ./my-workspace
+mf models cp mf6/example/ex-gwf-twri01 /path/to/workspace --verbose  # cp is an alias
+
+# Or using the module form
+python -m modflow_devtools.models copy mf6/test/test001a_Tharmonic ./my-workspace
+python -m modflow_devtools.models cp mf6/example/ex-gwf-twri01 /path/to/workspace --verbose
 ```
 
+The copy command:
+- Automatically attempts to sync registries before copying (unless `MODFLOW_DEVTOOLS_NO_AUTO_SYNC=1`)
+- Creates the workspace directory if it doesn't exist
+- Copies all input files for the specified model
+- Preserves subdirectory structure within the workspace
+- Use `--verbose` or `-v` flag to see detailed progress
+
 ### Using the default registry
 
 The module provides explicit access to the default registry used by `get_models()` etc.

modflow_devtools/cli.py

@@ -5,6 +5,8 @@
     mf models sync
     mf models info
     mf models list
+    mf models copy <model> <workspace>
+    mf models cp <model> <workspace>  # cp is an alias for copy
     mf programs sync
     mf programs info
     mf programs list

modflow_devtools/models/__init__.py

@@ -1362,6 +1362,15 @@ def copy_to(workspace: str | PathLike, model_name: str, verbose: bool = False) -
     return get_default_registry().copy_to(workspace, model_name, verbose=verbose)
 
 
+def cp(workspace: str | PathLike, model_name: str, verbose: bool = False) -> Path | None:
+    """
+    Alias for copy_to().
+    Copy the model's input files to the given workspace.
+    The workspace will be created if it does not exist.
+    """
+    return copy_to(workspace, model_name, verbose=verbose)
+
+
 def __getattr__(name: str):
     """
     Lazy module attribute access for backwards compatibility.

modflow_devtools/models/__main__.py

@@ -5,6 +5,8 @@
     python -m modflow_devtools.models sync
     python -m modflow_devtools.models info
     python -m modflow_devtools.models list
+    python -m modflow_devtools.models copy <model> <workspace>
+    python -m modflow_devtools.models cp <model> <workspace>  # cp is an alias for copy
     python -m modflow_devtools.models clear
 """
 
@@ -280,6 +282,26 @@ def cmd_clear(args):
     )
 
 
+def cmd_copy(args):
+    """Copy command handler."""
+    # Attempt auto-sync before copying (unless disabled)
+    if not os.environ.get("MODFLOW_DEVTOOLS_NO_AUTO_SYNC"):
+        _try_best_effort_sync()
+
+    from . import copy_to
+
+    try:
+        workspace = copy_to(args.workspace, args.model, verbose=args.verbose)
+        if workspace:
+            print(f"\nSuccessfully copied model '{args.model}' to: {workspace}")
+        else:
+            print(f"Error: Model '{args.model}' not found in registry", file=sys.stderr)
+            sys.exit(1)
+    except Exception as e:
+        print(f"Error copying model: {e}", file=sys.stderr)
+        sys.exit(1)
+
+
 def main():
     """Main CLI entry point."""
     parser = argparse.ArgumentParser(
@@ -352,6 +374,23 @@ def main():
         help="Skip confirmation prompt",
     )
 
+    # Copy command (with cp alias)
+    copy_parser = subparsers.add_parser("copy", aliases=["cp"], help="Copy model to workspace")
+    copy_parser.add_argument(
+        "model",
+        help="Name of the model to copy (e.g., mf6/test/test001a_Tharmonic)",
+    )
+    copy_parser.add_argument(
+        "workspace",
+        help="Destination workspace directory",
+    )
+    copy_parser.add_argument(
+        "--verbose",
+        "-v",
+        action="store_true",
+        help="Print detailed progress messages",
+    )
+
     args = parser.parse_args()
 
     if not args.command:
@@ -367,6 +406,8 @@ def main():
             cmd_list(args)
         elif args.command == "clear":
             cmd_clear(args)
+        elif args.command in ("copy", "cp"):
+            cmd_copy(args)
     except Exception as e:
         print(f"Error: {e}", file=sys.stderr)
         sys.exit(1)