feat: Add checkpoint update command

docs/cli/introduction.rst

@@ -19,3 +19,4 @@ The commands are:
 - :ref:`Validate Command <validate-command>`
 - :ref:`Patch Command <patch-command>`
 - :ref:`Requests Command <requests-command>`
+- :ref:`Redefine Command <redefine-command>`

docs/cli/redefine.rst

@@ -0,0 +1,160 @@
+.. _redefine-command:
+
+Redefine Command
+===============
+
+With this command, you can redefine the graph of a checkpoint file.
+This is useful when you want to change / reconfigure the local-domain of a model, or rebuild with a new graph.
+
+We should caution that such transfer of the model from one graph to
+another is not guaranteed to lead to good results. Still, it is a
+powerful tool to explore generalisability of the model or to test
+performance before starting fine tuning through transfer learning.
+
+This will create a new checkpoint file with the updated graph, and optionally save the graph to a file.
+
+Subcommands allow for a graph to be made from a lat/lon coordinate file, bounding box, or from a defined graph config.
+
+*********
+ Usage
+*********
+
+.. code-block:: bash
+
+    % anemoi-inference redefine --help
+
+    Redefine the graph of a checkpoint file.
+
+    positional arguments:
+      path                  Path to the checkpoint.
+
+    options:
+      -h, --help            show this help message and exit
+      -g GRAPH, --graph GRAPH
+                            Path to graph file to use
+      -y GRAPH_CONFIG, --graph_config GRAPH_CONFIG
+                            Path to graph config to use
+      -ll LATLON, --latlon LATLON
+                            Path to coordinate npy, should be of shape (N, 2) with latitudes and longitudes.
+      -c COORDS COORDS COORDS COORDS COORDS, --coords COORDS COORDS COORDS COORDS COORDS
+                            Coordinates, (North West South East Resolution).
+      -gr GLOBAL_RESOLUTION, --global_resolution GLOBAL_RESOLUTION
+                            Global grid resolution required with --coords, (e.g. n320, o96).
+      --save-graph SAVE_GRAPH
+                            Path to save the updated graph.
+      --output OUTPUT       Path to save the updated checkpoint.
+
+
+*********
+Examples
+*********
+
+Here are some examples of how to use the `redefine` command:
+
+#. Using a graph file:
+
+    .. code-block:: bash
+
+          anemoi-inference redefine path/to/checkpoint --graph path/to/graph
+
+#. Using a graph configuration:
+
+    .. code-block:: bash
+
+          anemoi-inference redefine path/to/checkpoint --graph_config path/to/graph_config
+
+    .. note::
+        The configuration of the existing graph can be found using:
+
+        .. code-block:: bash
+
+            anemoi-inference metadata path/to/checkpoint -get config.graph ----yaml
+
+#. Using latitude/longitude coordinates:
+    This lat lon file should be a numpy file of shape (N, 2) with latitudes and longitudes.
+
+    It can be easily made from a list of coordinates as follows:
+
+    .. code-block:: python
+
+          import numpy as np
+          coords = np.array(np.meshgrid(latitudes, longitudes)).T.reshape(-1, 2)
+          np.save('path/to/latlon.npy', coords)
+
+    Once created,
+
+    .. code-block:: bash
+
+          anemoi-inference redefine path/to/checkpoint --latlon path/to/latlon.npy
+
+#. Using bounding box coordinates:
+
+    .. code-block:: bash
+
+          anemoi-inference redefine path/to/checkpoint --coords North West South East Resolution
+
+    i.e.
+
+    .. code-block:: bash
+
+          anemoi-inference redefine path/to/checkpoint --coords 30.0 -10.0 20.0 0.0 0.1/0.1 --global_resolution n320
+
+
+All examples can optionally save the updated graph and checkpoint using the `--save-graph` and `--output` options.
+
+***************************
+Complete Inference Example
+***************************
+
+For this example we will redefine a checkpoint using a bounding box and then run inference
+
+
+Redefine the checkpoint
+-----------------------
+
+.. code-block:: bash
+
+    anemoi-inference redefine path/to/checkpoint --coords 30.0 -10.0 20.0 0.0 0.1/0.1 --global_resolution n320 --save-graph path/to/updated_graph --output path/to/updated_checkpoint
+
+Create the inference config
+---------------------------
+
+If you have an input file of the expected shape handy use it in place of the input block, here we will show
+how to use MARS to handle the regridding.
+
+.. note::
+    Using the `anemoi-plugins-ecmwf-inference <https://github.com/ecmwf/anemoi-plugins-ecmwf>`_ package, preprocessors are available which can handle the regridding for you from other sources.
+
+.. code-block:: yaml
+
+    checkpoint: path/to/updated_checkpoint
+    date: -2
+
+    input:
+        cutout:
+            lam_0:
+                mars:
+                    grid: 0.1/0.1 # RESOLUTION WE SET
+                    area: 30.0/-10.0/20.0/0.0 # BOUNDING BOX WE SET, N W S E
+            global:
+                mars:
+                    grid: n320 # GLOBAL RESOLUTION WE SET
+
+
+Run inference
+-----------------
+
+.. code-block:: bash
+
+    anemoi-inference run path/to/updated_checkpoint
+
+
+**********
+Reference
+**********
+
+.. argparse::
+    :module: anemoi.inference.__main__
+    :func: create_parser
+    :prog: anemoi-inference
+    :path: redefine

docs/index.rst

@@ -153,6 +153,7 @@ You may also have to install pandoc on MacOS:
    cli/inspect
    cli/patch
    cli/requests
+   cli/redefine
 
 .. toctree::
    :maxdepth: 1

src/anemoi/inference/commands/redefine.py

@@ -0,0 +1,165 @@
+# (C) Copyright 2025- Anemoi contributors.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+
+
+import logging
+from argparse import ArgumentParser
+from argparse import Namespace
+from pathlib import Path
+
+from . import Command
+
+LOG = logging.getLogger(__name__)
+
+
+def check_redefine_imports():
+    """Check if required packages are installed."""
+    required_packages = ["anemoi.datasets", "anemoi.graphs", "anemoi.models"]
+    from importlib.util import find_spec
+
+    for package in required_packages:
+        if find_spec(package) is None:
+            raise ImportError(f"{package!r} is required for this command.")
+
+
+def format_namespace_as_str(namespace: Namespace) -> str:
+    """Format an argparse Namespace object as command-line arguments."""
+    args = []
+
+    for key, value in vars(namespace).items():
+        if key == "command":
+            continue
+        if value is None:
+            continue
+
+        # Convert underscores to hyphens for command line format
+        arg_name = f"--{key.replace('_', '-')}"
+
+        if isinstance(value, bool):
+            if value:
+                args.append(arg_name)
+        elif isinstance(value, list):
+            args.append(f"{arg_name} {' '.join(map(str, value))}")
+        else:
+            args.extend([arg_name, str(value)])
+
+    return " ".join(args)
+
+
+class RedefineCmd(Command):
+    """Redefine the graph of a checkpoint file."""
+
+    def add_arguments(self, command_parser: ArgumentParser) -> None:
+        """Add arguments to the command parser.
+
+        Parameters
+        ----------
+        command_parser : ArgumentParser
+            The argument parser to which the arguments will be added.
+        """
+        command_parser.description = "Redefine the graph of a checkpoint file. If using coordinate specifications, assumes the input to the local domain is already regridded."
+        command_parser.add_argument("path", help="Path to the checkpoint.")
+
+        group = command_parser.add_mutually_exclusive_group(required=True)
+
+        group.add_argument("-g", "--graph", type=Path, help="Path to graph file to use")
+        group.add_argument("-y", "--graph_config", type=Path, help="Path to graph config to use")
+        group.add_argument(
+            "-ll",
+            "--latlon",
+            type=Path,
+            help="Path to coordinate npy, should be of shape (N, 2) with latitudes and longitudes.",
+        )
+        group.add_argument("-c", "--coords", type=str, help="Coordinates, (North West South East Resolution).", nargs=5)
+
+        command_parser.add_argument(
+            "-gr",
+            "--global_resolution",
+            type=str,
+            help="Global grid resolution required with --coords, (e.g. n320, o96).",
+        )
+
+        command_parser.add_argument("--save-graph", type=str, help="Path to save the updated graph.", default=None)
+        command_parser.add_argument("--output", type=str, help="Path to save the updated checkpoint.", default=None)
+
+    def run(self, args: Namespace) -> None:
+        """Run the redefine command.
+
+        Parameters
+        ----------
+        args : Namespace
+            The arguments passed to the command.
+        """
+        from anemoi.inference.utils.redefine import create_graph_from_config
+        from anemoi.inference.utils.redefine import get_coordinates_from_file
+        from anemoi.inference.utils.redefine import get_coordinates_from_mars_request
+        from anemoi.inference.utils.redefine import load_graph_from_file
+        from anemoi.inference.utils.redefine import make_graph_from_coordinates
+        from anemoi.inference.utils.redefine import update_checkpoint
+
+        check_redefine_imports()
+
+        import torch
+        from anemoi.utils.checkpoints import load_metadata
+        from anemoi.utils.checkpoints import save_metadata
+
+        path = Path(args.path)
+
+        # Load checkpoint metadata and supporting arrays
+        metadata, supporting_arrays = load_metadata(str(path), supporting_arrays=True)
+
+        # Add command to history
+        metadata.setdefault("history", [])
+        metadata["history"].append(f"anemoi-inference redefine {format_namespace_as_str(args)}")
+
+        # Create or load the graph
+        if args.graph is not None:
+            graph = load_graph_from_file(args.graph)
+        elif args.graph_config is not None:
+            graph = create_graph_from_config(args.graph_config)
+        else:
+            # Generate graph from coordinates
+            LOG.info("Generating graph from coordinates...")
+
+            # Get coordinates based on input type
+            if args.latlon is not None:
+                local_lats, local_lons = get_coordinates_from_file(args.latlon)
+            elif args.coords is not None:
+                local_lats, local_lons = get_coordinates_from_mars_request(args.coords)
+            else:
+                raise ValueError("No valid coordinates found.")
+
+            metadata, supporting_arrays, graph = make_graph_from_coordinates(
+                local_lats, local_lons, args.global_resolution, metadata, supporting_arrays
+            )
+
+        # Save graph if requested
+        if args.save_graph is not None:
+            torch.save(graph, args.save_graph)
+            LOG.info("Saved updated graph to %s", args.save_graph)
+
+        # Update checkpoint
+        LOG.info("Updating checkpoint...")
+        model = torch.load(str(path), weights_only=False, map_location=torch.device("cpu"))
+        model = update_checkpoint(model, metadata, graph)
+
+        # Save updated checkpoint
+        model_path = args.output if args.output is not None else f"{path.stem}_updated{path.suffix}"
+        torch.save(model, model_path)
+
+        save_metadata(
+            model_path,
+            metadata=metadata,
+            supporting_arrays=supporting_arrays,
+        )
+
+        LOG.info("Updated checkpoint saved to %s", model_path)
+
+
+command = RedefineCmd