remove deprecated dependency group and associated code (#467)

* remove deprecated dependency group and associated code

* update chagnelog

docs/api.rst

@@ -780,16 +780,6 @@ Vector
    gis_utils.nearest_merge
 
 
-PCRaster I/O
-============
-
-.. autosummary::
-   :toctree: _generated
-
-   gis_utils.write_map
-   gis_utils.write_clone
-
-
 .. _statistics:
 
 =====================================

docs/changelog.rst

@@ -31,7 +31,7 @@ Fixed
 
 Deprecated
 ----------
--
+- the dependencies ``pcraster`` and ``pygeos`` are no longer used and were removed. (PR #467)
 
 
 v0.8.0 (2023-07-18)

hydromt/__init__.py

@@ -3,12 +3,6 @@
 # version number without 'v' at start
 __version__ = "0.8.1.dev0"
 
-# Set environment variables (this will be temporary)
-# to use shapely 2.0 in favor of pygeos (if installed)
-import os
-
-os.environ["USE_PYGEOS"] = "0"
-
 # pkg_resource deprication warnings originate from dependencies
 # so silence them for now
 import warnings

hydromt/_compat.py

@@ -3,10 +3,8 @@
 __all__ = []
 
 HAS_XUGRID = False
-HAS_PCRASTER = False
 HAS_SHAPELY20 = False
 HAS_PYET = False
-HAS_PYGEOS = False
 HAS_GCSFS = False
 HAS_S3FS = False
 HAS_OPENPYXL = False
@@ -26,21 +24,6 @@
 except ImportError:
     False
 
-try:
-    import pygeos
-
-    HAS_PYGEOS = True
-except ImportError:
-    pass
-
-try:
-    import pcraster
-
-    HAS_PCRASTER = True
-except ImportError:
-    pass
-
-
 try:
     import xugrid
 

hydromt/gis_utils.py

@@ -6,14 +6,12 @@
 import logging
 import os
 import subprocess
-from os.path import dirname, isfile, join
+from os.path import dirname, join
 from typing import Optional, Tuple
 
 import geopandas as gpd
 import numpy as np
-import rasterio
 import xarray as xr
-from pyflwdir import core_conversion, core_d8, core_ldd
 from pyflwdir import gis_utils as gis
 from pyproj import CRS
 from rasterio.transform import Affine
@@ -76,7 +74,6 @@
     "jpg": "JPEG",
     "kro": "KRO",
     "lcp": "LCP",
-    "map": "PCRaster",
     "mbtiles": "MBTiles",
     "mpr/mpl": "ILWIS",
     "ntf": "NITF",
@@ -498,121 +495,6 @@ def spread2d(
     return ds_out
 
 
-## PCRASTER
-
-
-def write_clone(tmpdir, gdal_transform, wkt_projection, shape):
-    """Write pcraster clone file to a tmpdir using gdal."""
-    from osgeo import gdal
-
-    gdal.AllRegister()
-    driver1 = gdal.GetDriverByName("GTiff")
-    driver2 = gdal.GetDriverByName("PCRaster")
-    fn = join(tmpdir, "clone.map")
-    # create temp tif file
-    fn_temp = join(tmpdir, "clone.tif")
-    TempDataset = driver1.Create(fn_temp, shape[1], shape[0], 1, gdal.GDT_Float32)
-    TempDataset.SetGeoTransform(gdal_transform)
-    if wkt_projection is not None:
-        TempDataset.SetProjection(wkt_projection)
-    # TODO set csr
-    # copy to pcraster format
-    driver2.CreateCopy(fn, TempDataset, 0)
-    # close and cleanup
-    TempDataset = None
-    return fn
-
-
-def write_map(
-    data,
-    raster_path,
-    nodata,
-    transform,
-    crs=None,
-    clone_path=None,
-    pcr_vs="scalar",
-    **kwargs,
-):
-    """Write pcraster map files using pcr.report functionality.
-
-    A PCRaster clone map is written to a temporary directory if not provided.
-    For PCRaster types see https://www.gdal.org/frmt_various.html#PCRaster
-
-    Parameters
-    ----------
-    data : ndarray
-        Raster data
-    raster_path : str
-        Path to output map
-    nodata : int, float
-        no data value
-    transform : affine transform
-        Two dimensional affine transform for 2D linear mapping
-    clone_path : str, optional
-        Path to PCRaster clone map, by default None
-    pcr_vs : str, optional
-        pcraster type, by default "scalar"
-    **kwargs:
-        not used in this function, mainly here for compatability reasons.
-    crs:
-        The coordinate reference system of the data.
-
-
-    Raises
-    ------
-    ImportError
-        pcraster package is required
-    ValueError
-        if invalid ldd
-    """
-    if not _compat.HAS_PCRASTER:
-        raise ImportError("The pcraster package is required to write map files")
-    import tempfile
-
-    import pcraster as pcr
-
-    with tempfile.TemporaryDirectory() as tmpdir:
-        # deal with pcr clone map
-        if clone_path is None:
-            clone_path = write_clone(
-                tmpdir,
-                gdal_transform=transform.to_gdal(),
-                wkt_projection=None if crs is None else CRS.from_user_input(crs).wkt,
-                shape=data.shape,
-            )
-        elif not isfile(clone_path):
-            raise IOError(f'clone_path: "{clone_path}" does not exist')
-        pcr.setclone(clone_path)
-        if nodata is None and pcr_vs != "ldd":
-            raise ValueError("nodata value required to write PCR map")
-        # write to pcrmap
-        if pcr_vs == "ldd":
-            # if d8 convert to ldd
-            data = data.astype(np.uint8)  # force dtype
-            if core_d8.isvalid(data):
-                data = core_conversion.d8_to_ldd(data)
-            elif not core_ldd.isvalid(data):
-                raise ValueError("LDD data not understood")
-            mv = int(core_ldd._mv)
-            ldd = pcr.numpy2pcr(pcr.Ldd, data.astype(int), mv)
-            # make sure it is pcr sound
-            # NOTE this should not be necessary
-            pcrmap = pcr.lddrepair(ldd)
-        elif pcr_vs == "bool":
-            pcrmap = pcr.numpy2pcr(pcr.Boolean, data.astype(bool), np.bool_(nodata))
-        elif pcr_vs == "scalar":
-            pcrmap = pcr.numpy2pcr(pcr.Scalar, data.astype(float), float(nodata))
-        elif pcr_vs == "ordinal":
-            pcrmap = pcr.numpy2pcr(pcr.Ordinal, data.astype(int), int(nodata))
-        elif pcr_vs == "nominal":
-            pcrmap = pcr.numpy2pcr(pcr.Nominal, data.astype(int), int(nodata))
-        pcr.report(pcrmap, raster_path)
-        # set crs (pcrmap ignores this info from clone ??)
-        if crs is not None:
-            with rasterio.open(raster_path, "r+") as dst:
-                dst.crs = crs
-
-
 def create_vrt(
     vrt_path: str,
     file_list_path: str = None,

hydromt/raster.py

@@ -12,7 +12,7 @@
 import os
 import tempfile
 from itertools import product
-from os.path import basename, dirname, isdir, join
+from os.path import isdir, join
 from typing import Any, Optional, Union
 
 import dask
@@ -2311,53 +2311,35 @@ def to_raster(
             count = da_out[dim0].size
             da_out = da_out.sortby(dim0)
         # write
-        if driver.lower() == "pcraster" and _compat.HAS_PCRASTER:
-            for i in range(count):
-                if dim0:
-                    bname = basename(raster_path).split(".")[0]
-                    bname = f"{bname[:8]:8s}".replace(" ", "0")
-                    raster_path = join(dirname(raster_path), f"{bname}.{i+1:03d}")
-                    data = da_out.isel({dim0: i}).load().squeeze().data
+        profile = dict(
+            driver=driver,
+            height=da_out.raster.height,
+            width=da_out.raster.width,
+            count=count,
+            dtype=str(da_out.dtype),
+            crs=da_out.raster.crs,
+            transform=da_out.raster.transform,
+            nodata=nodata,
+            **profile_kwargs,
+        )
+        with rasterio.open(raster_path, "w", **profile) as dst:
+            if windowed:
+                window_iter = dst.block_windows(1)
+            else:
+                window_iter = [(None, None)]
+            for _, window in window_iter:
+                if window is not None:
+                    row_slice, col_slice = window.toslices()
+                    sel = {self.x_dim: col_slice, self.y_dim: row_slice}
+                    data = da_out.isel(sel).load().values
                 else:
-                    data = da_out.load().data
-                gis_utils.write_map(
-                    data,
-                    raster_path,
-                    crs=da_out.raster.crs,
-                    transform=da_out.raster.transform,
-                    nodata=nodata,
-                    **profile_kwargs,
-                )
-        else:
-            profile = dict(
-                driver=driver,
-                height=da_out.raster.height,
-                width=da_out.raster.width,
-                count=count,
-                dtype=str(da_out.dtype),
-                crs=da_out.raster.crs,
-                transform=da_out.raster.transform,
-                nodata=nodata,
-                **profile_kwargs,
-            )
-            with rasterio.open(raster_path, "w", **profile) as dst:
-                if windowed:
-                    window_iter = dst.block_windows(1)
+                    data = da_out.load().values
+                if data.ndim == 2:
+                    dst.write(data, 1, window=window)
                 else:
-                    window_iter = [(None, None)]
-                for _, window in window_iter:
-                    if window is not None:
-                        row_slice, col_slice = window.toslices()
-                        sel = {self.x_dim: col_slice, self.y_dim: row_slice}
-                        data = da_out.isel(sel).load().values
-                    else:
-                        data = da_out.load().values
-                    if data.ndim == 2:
-                        dst.write(data, 1, window=window)
-                    else:
-                        dst.write(data, window=window)
-                if tags is not None:
-                    dst.update_tags(**tags)
+                    dst.write(data, window=window)
+            if tags is not None:
+                dst.update_tags(**tags)
 
     def vectorize(self, connectivity=8):
         """Return geometry of grouped pixels with the same value in a DataArray object.

pyproject.toml

@@ -87,10 +87,6 @@ examples = [
     "matplotlib-base", # plotting
     "notebook",        # jupyter integration
 ]
-deprecated = [
-    "pcraster", # Old Wflow model was build on this
-    "pygeos",   # Supersceded by shapely 2
-]
 
 full = ["hydromt[io,extra,dev,test,doc,examples]"]
 slim = ["hydromt[io,extra,examples]"]

tests/conftest.py

@@ -1,6 +1,3 @@
-import os
-
-os.environ["USE_PYGEOS"] = "0"
 import geopandas as gpd
 import numpy as np
 import pandas as pd

tests/test_io.py

@@ -206,30 +206,3 @@ def test_rasterio_errors(tmpdir, rioda):
         da0.raster.to_raster(str(tmpdir.join("test2.tif")), count=3)
     with pytest.raises(ValueError, match="Extension unknown for driver"):
         da0.to_dataset().raster.to_mapstack(root=str(tmpdir), driver="unknown")
-
-
-@pytest.mark.skipif(not _compat.HAS_PCRASTER, reason="PCRaster not installed.")
-def test_io_pcr(tmpdir):
-    # test write ldd with clone
-    da = raster.full_from_transform(
-        [0.5, 0.0, 3.0, 0.0, -0.5, -9.0], (4, 6), nodata=247, dtype=np.uint8, name="ldd"
-    )
-    fn_ldd = str(tmpdir.join("test_ldd.map"))
-    da.raster.to_raster(fn_ldd, driver="PCRaster", pcr_vs="ldd")
-    assert os.path.isfile(fn_ldd)
-    # test ordinal
-    da.raster.to_raster(fn_ldd, driver="PCRaster", pcr_vs="ordinal", clone_path=fn_ldd)
-    assert os.path.isfile(fn_ldd)
-    da.expand_dims("time").raster.to_raster(
-        tmpdir.join("testldd.map"), driver="PCRaster"
-    )
-    assert os.path.isfile(tmpdir.join("testldd0.001"))
-    ds_in = hydromt.open_mfraster(
-        str(tmpdir.join("testldd*")), concat=True, mask_nodata=True
-    )
-    assert "dim0" in ds_in.coords
-    # mapstack
-    prefix = "test_"
-    root = str(tmpdir)
-    assert np.all([np.isnan(ds_in[n].raster.nodata) for n in ds_in.raster.vars])
-    ds_in.raster.to_mapstack(join(root, "pcr"), prefix=prefix, driver="PCRaster")