Remove clip from cli

docs/api/cli.rst

@@ -20,11 +20,6 @@ Command Line Interface
    :prog: hydromt update
    :nested: full
 
-.. _clip_api:
-
-.. click:: hydromt.cli.main:clip
-   :prog: hydromt clip
-   :nested: full
 
 .. _export_api:
 

docs/guides/core_dev/contributing.rst

@@ -242,8 +242,8 @@ should be created with model-specific data readers, writers and setup methods as
   by arguments which end with ``_fn`` (short for filename) which refer to a source in the data catalog
   based on the source name or a file based on the (relative) path to the file. Within a model method the data is read
   by calling any ``DataCatalog.get_<data_type>`` method which work for both source and file names.
-- The Model class currently contains three high-level methods (:py:meth:`~hydromt.Model.build`,
-  :py:meth:`~hydromt.Model.update` and :py:meth:`~hydromt.Model.clip` which are common for all model plugins and
+- The Model class currently contains two high-level methods (:py:meth:`~hydromt.Model.build`,
+  :py:meth:`~hydromt.Model.update` is are common for all model plugins and
   exposed through the CLI. This list of methods might be extended going forward.
 - A Model child class implementation for a specific model kernel can be exposed to HydroMT as a plugin by specifying a
   ``hydromt.models`` `entry-point <https://packaging.python.org/en/latest/specifications/entry-points/>`_ in the pyproject.toml file of a package.

docs/guides/user_guide/hydromt_intro.rst

@@ -73,8 +73,7 @@ Finally user can interact with HydroMT through the following interfaces:
 - **Command Line Interface (CLI)**
 
   The :ref:`CLI <hydromt_cli>` is a high-level interface to HydroMT. It is used to run HydroMT commands such as
-  :ref:`build <model_build>`, :ref:`update <model_update>` or :ref:`clip <model_clip>`.
-
+  :ref:`build <model_build>`, :ref:`update <model_update>`
 - **Python Interface**
 
   While most common functionalities can be called through the CLI, the :ref:`Python interface <hydromt_python>` offers more flexibility for advanced users.

docs/guides/user_guide/model_overview.rst

@@ -10,10 +10,6 @@ HydroMT has the following high-level functionality for setting up models from ra
 
 * :ref:`building a model <model_build>`: building a model from scratch.
 * :ref:`updating a model <model_update>`: adding or changing model components of an existing model.
-* :ref:`clipping a model <model_clip>`: changing the spatial domain of an existing model (e.g. select subbasins from a larger model).
-
-The building and clipping methods required the user to provide a :ref:`region <region>` of interest. HydroMT provides
-several options to define a region based on a geospatial or hydrographic region.
 
 The exact process of building or updating a model can be configured in a single configuration :ref:`.yaml file <model_workflow>`.
 This file describes the full pipeline of model methods and their arguments. The methods vary for the

docs/guides/user_guide/terminology.rst

@@ -8,7 +8,7 @@ HydroMT and this documentation use a specific terminology to describe specific o
 ==============================  ======================================================================================
 Term                            Explanation
 ==============================  ======================================================================================
-Command Line Interface (CLI)    high-level interface to HydroMT *build*, *update*, *clip*, *check* and *export* methods.
+Command Line Interface (CLI)    high-level interface to HydroMT *build*, *update*, *check* and *export* methods.
 Configuration (HydroMT)         (.yaml) file describing the complete pipeline with all methods and their arguments to
                                 *build* or *update* a model.
 Data catalog                    A set of data sources available for HydroMT. It is build up from *yaml* files containing
@@ -33,6 +33,6 @@ Model plugin                    (Plugin) Package that links the HydroMT Model cl
                                 Plugins are installed separately from HydroMT and are not part of the HydroMT core package.
                                 Plugins are the most common way of using HydroMT to build and update specific models.
 Model kernel                    The model software to execute a model simulation. This is *not* part of any HydroMT plugin.
-Region                          Argument of the *build* and *clip* CLI methods that specifies the region of interest where
+Region                          Argument of the *build*CLI methods that specifies the region of interest where
                                 the model should be prepared / which spatial subregion should be clipped.
 ==============================  ======================================================================================

docs/overview/use_case_examples.rst

@@ -49,8 +49,7 @@ HydroMT was used to prepare the updated national hydrologic models for Indonesia
 Cooperation Program between the Netherlands and Indonesia. As this is a large scale domain, seven models corresponding
 to the different Indonesian regions (BaliNusaTenggara, Java, Kalimantan, Maluku, Papua, Sumatra, Sulawesi) were derived
 at three different resolutions and integrated to the IWRM Indonesia Instrument in Delft-FEWS (using a new export to FEWS
-function from HydroMT). The clipping functionality of HydroMT can also be used to prepare sub-models for use in specific
-projects and to connect to existing RIBASIM models (using RIBASIM components within HydroMT).
+function from HydroMT).
 
 .. image:: ../_static/wflow_indonesia.png
 

examples/working_with_models_basics.ipynb

@@ -17,7 +17,6 @@
     "\n",
     "- **building** a model: building a model from scratch.\n",
     "- **updating** a model: adding or changing model components of an existing model.\n",
-    "- **clipping** a model: changing the spatial domain of an existing model (e.g. select subbasins from a larger model).\n",
     "\n",
     "Here we show how to build and update a hypothetical distributed model from the command line interface (CLI) based on the generic HydroMT **Model**."
    ]
@@ -32,79 +31,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Usage: hydromt [OPTIONS] COMMAND [ARGS]...\n",
-      "\n",
-      "  Command line interface for hydromt models.\n",
-      "\n",
-      "Options:\n",
-      "  --version     Show the version and exit.\n",
-      "  --models      Print available model plugins and exit.\n",
-      "  --components  Print available component plugins and exit.\n",
-      "  --plugins     Print available component plugins and exit.\n",
-      "  --help        Show this message and exit.\n",
-      "\n",
-      "Commands:\n",
-      "  build   Build models\n",
-      "  check   Validate config / data catalog / region\n",
-      "  clip    Clip models.\n",
-      "  export  Export data\n",
-      "  update  Update models\n",
-      "\u001b[0m"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "!hydromt --help"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Model plugins:\n",
-      "\t- model (hydromt 1.0.0a0)\n",
-      "\u001b[0m"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "!hydromt --models"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Component plugins:\n",
-      "\t- ConfigComponent (hydromt 1.0.0a0)\n",
-      "\t- DatasetsComponent (hydromt 1.0.0a0)\n",
-      "\t- GeomsComponent (hydromt 1.0.0a0)\n",
-      "\t- GridComponent (hydromt 1.0.0a0)\n",
-      "\t- MeshComponent (hydromt 1.0.0a0)\n",
-      "\t- SpatialDatasetsComponent (hydromt 1.0.0a0)\n",
-      "\t- TablesComponent (hydromt 1.0.0a0)\n",
-      "\t- VectorComponent (hydromt 1.0.0a0)\n",
-      "\u001b[0m"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "!hydromt --components"
    ]
@@ -142,7 +89,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.9.19"
   },
   "vscode": {
    "interpreter": {

hydromt/cli/main.py

@@ -598,72 +598,5 @@ def export(
         log._wait_and_remove_file_handlers(logger)  # Release locks on logs
 
 
-## CLIP
-
-
-@main.command(short_help="Clip models.")
-@click.argument(
-    "MODEL",
-    type=str,
-)
-@arg_root
-@click.argument(
-    "MODEL_DESTINATION",
-    type=click.Path(resolve_path=True, dir_okay=True, file_okay=False),
-)
-@click.argument(
-    "REGION",
-    type=str,
-    callback=_utils.parse_json,
-)
-@quiet_opt
-@verbose_opt
-@click.pass_context
-def clip(ctx, model, model_root, model_destination, region, quiet, verbose):
-    """Create a new model based on clipped region of an existing model.
-
-    If the existing model contains forcing, they will also be clipped to the new model.
-
-    Example usage:
-    --------------
-
-    Example usage to clip a wflow model for a subbasin derived from point coordinates
-    snapped to cells with upstream area >= 50 km2
-    hydromt clip wflow /path/to/model_root /path/to/model_destination "{'subbasin': [-7.24, 62.09], 'wflow_uparea': 50}"
-
-    Example usage basin based on ID from model_root basins map
-    hydromt clip wflow /path/to/model_root /path/to/model_destination "{'basin': 1}"
-
-    Example usage basins whose outlets are inside a geometry
-    hydromt clip wflow /path/to/model_root /path/to/model_destination "{'outlet': 'geometry.geojson'}"
-
-    All available option in the clip_grid function help.
-
-    """  # noqa: E501
-    log_level = max(10, 30 - 10 * (verbose - quiet))
-    log._setuplog(join(model_destination, "hydromt-clip.log"), log_level=log_level)
-    logger.info(f"Clipping instance of {model} model.")
-    logger.info(f"Region: {region}")
-
-    if model != "wflow":
-        raise NotImplementedError("Clip function only implemented for wflow model.")
-    try:
-        mod = PLUGINS.model_plugins[model](root=model_root, mode="r")
-        logger.info("Reading model to clip")
-        mod.read()
-        mod.root.set(model_destination, mode="w")
-        logger.info("Clipping grid")
-        mod.clip_grid(region)
-        logger.info("Clipping forcing")
-        mod.clip_forcing()
-        logger.info("Writting clipped model")
-        mod.write()
-    except Exception as e:
-        logger.exception(e)  # catch and log errors
-        raise
-    finally:
-        log._wait_and_remove_file_handlers(logger)  # Release locks on logs
-
-
 if __name__ == "__main__":
     main()

tests/cli/test_cli.py

@@ -55,14 +55,6 @@ def test_cli_update_help():
     assert r.output.startswith("Usage: main update [OPTIONS] MODEL MODEL_ROOT")
 
 
-def test_cli_clip_help():
-    r = CliRunner().invoke(hydromt_cli, ["clip", "--help"])
-    assert r.exit_code == 0
-    assert r.output.startswith(
-        "Usage: main clip [OPTIONS] MODEL MODEL_ROOT MODEL_DESTINATION"
-    )
-
-
 @pytest.fixture()
 def _reset_log_level() -> Generator[None, None, None]:
     yield
@@ -116,16 +108,6 @@ def test_cli_update_unknown_model(tmpdir):
         )
 
 
-@pytest.mark.usefixtures("_reset_log_level")
-def test_cli_clip_unknown_model(tmpdir):
-    with pytest.raises(NotImplementedError):
-        _ = CliRunner().invoke(
-            hydromt_cli,
-            ["clip", "test_model", str(tmpdir), str(tmpdir), "{'bbox': [1,2,3,4]}"],
-            catch_exceptions=False,
-        )
-
-
 @pytest.mark.usefixtures("_reset_log_level")
 def test_export_cli_deltares_data(tmpdir):
     r = CliRunner().invoke(