Issue #1320 Add CopyFiles package (#1321)

Fixes #1320

# Description
The iMOD5 projectfile contains an "EXTRA" section, with files to copy.
These files usually contain settings and lookup tables for MetaSWAP,
which have no direct relation to cell data.

This PR adds CopyFiles package to copy these files.

# Checklist
- [x] Links to correct issue
- [x] Update changelog, if changes affect users
- [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737``
- [x] Unit tests were added
- [ ] **If feature added**: Added/extended example

docs/api/changelog.rst

@@ -14,6 +14,8 @@ Added
 
 - :class:`imod.msw.MeteoGridCopy` to copy existing `mete_grid.inp` files, so
   ASCII grids in large existing meteo databases do not have to be read.
+- :class:`imod.msw.CopyFiles` to copy settings and lookup tables in existing
+  ``.inp`` files.
 - :meth:`imod.mf6.LayeredWell.from_imod5_cap_data` to construct a
   :class:`imod.mf6.LayeredWell` package from iMOD5 data in the CAP package (for
   MetaSWAP). Currently only griddata (IDF) is supported.

imod/msw/__init__.py

@@ -1,3 +1,4 @@
+from imod.msw.copy_files import FileCopier
 from imod.msw.coupler_mapping import CouplerMapping
 from imod.msw.grid_data import GridData
 from imod.msw.idf_mapping import IdfMapping

imod/msw/copy_files.py

@@ -0,0 +1,55 @@
+from pathlib import Path
+from shutil import copy2
+from typing import cast
+
+import numpy as np
+import xarray as xr
+
+from imod.logging import logger
+from imod.logging.loglevel import LogLevel
+from imod.msw.pkgbase import MetaSwapPackage
+from imod.typing import Imod5DataDict
+
+_LOG_MESSAGE_TEMPLATE = """\
+Will not copy files {filtered}, these will be generated by iMOD Python
+instead."""
+
+
+class FileCopier(MetaSwapPackage):
+    def __init__(self, paths: list[str]):
+        super().__init__()
+        paths_da = xr.DataArray(
+            paths, coords={"file_nr": np.arange(len(paths))}, dims=("file_nr",)
+        )
+        self.dataset["paths"] = paths_da
+
+    @classmethod
+    def from_imod5_data(cls, imod5_data: Imod5DataDict):
+        paths = cast(list[list[str]], imod5_data["extra"]["paths"])
+        paths_unpacked = {Path(p[0]) for p in paths}
+        files_to_filter = (
+            "mete_grid.inp",
+            "para_sim.inp",
+            "svat2precgrid.inp",
+            "svat2etrefgrid.inp",
+        )
+        paths_included = [
+            str(p) for p in paths_unpacked if p.name.lower() not in files_to_filter
+        ]
+        paths_excluded = {str(p) for p in paths_unpacked} - set(paths_included)
+        if paths_excluded:
+            log_message = _LOG_MESSAGE_TEMPLATE.format(filtered=paths_excluded)
+            logger.log(
+                loglevel=LogLevel.INFO,
+                message=log_message,
+            )
+        return cls(paths_included)
+
+    def write(self, directory: str | Path, *_):
+        directory = Path(directory)
+
+        src_paths = [Path(p) for p in self.dataset["paths"].to_numpy()]
+        dst_paths = [directory / p.name for p in src_paths]
+
+        for src_path, dst_path in zip(src_paths, dst_paths):
+            copy2(src_path, dst_path)

imod/tests/test_msw/test_copy_files.py

@@ -0,0 +1,69 @@
+from pytest_cases import parametrize_with_cases
+
+from imod.msw.copy_files import FileCopier
+
+
+def write_test_files(directory, filenames):
+    paths = [directory / filename for filename in filenames]
+    for p in paths:
+        with open(p, mode="w") as f:
+            f.write("test")
+    return paths
+
+
+def case_simple_files(tmp_path_factory):
+    directory = tmp_path_factory.mktemp("simple_files")
+    filenames = [
+        "a.inp",
+        "b.inp",
+        "c.inp",
+    ]
+    return write_test_files(directory, filenames)
+
+
+def case_imod5_extra_files(tmp_path_factory):
+    directory = tmp_path_factory.mktemp("imod5_extra_files")
+    filenames = [
+        "a.inp",
+        "b.inp",
+        "c.inp",
+        "mete_grid.inp",
+        "para_sim.inp",
+        "svat2precgrid.inp",
+        "svat2etrefgrid.inp",
+    ]
+    return write_test_files(directory, filenames)
+
+
+@parametrize_with_cases("src_files", cases=".")
+def test_copyfile_init(src_files):
+    # Act
+    copyfiles = FileCopier(src_files)
+    # Arrange
+    assert "paths" in copyfiles.dataset.keys()
+    assert len(copyfiles.dataset["paths"]) == len(src_files)
+
+
+@parametrize_with_cases("src_files", cases=".")
+def test_copyfile_write(src_files, tmp_path):
+    # Arrange
+    expected_filenames = {f.name for f in src_files}
+    # Act
+    copyfiles = FileCopier(src_files)
+    copyfiles.write(tmp_path)
+    # Assert
+    actual_filepaths = tmp_path.glob("*.inp")
+    actual_filenames = {f.name for f in actual_filepaths}
+    diff = expected_filenames ^ actual_filenames
+    assert len(diff) == 0
+
+
+@parametrize_with_cases("src_files", cases=".")
+def test_from_imod5_data(src_files):
+    # Arrange
+    imod5_ls = [[p] for p in src_files]
+    imod5_data = {"extra": {"paths": imod5_ls}}
+    # Act
+    copyfiles = FileCopier.from_imod5_data(imod5_data)
+    # Assert
+    len(copyfiles.dataset["paths"]) == 3