Merge branch 'dev' of github.com:gwmod/nlmod into dev

Author: OnnoEbbens

docs/advanced_stress_packages/01_lake.ipynb

@@ -181,7 +181,7 @@
     "mask = lak_grid.area > 0.5 * ds[\"area\"].sel(icell2d=lak_grid.index)\n",
     "lak_grid = lak_grid[mask]\n",
     "# set the geometry to the entire cell\n",
-    "gi = flopy.utils.GridIntersect(nlmod.grid.modelgrid_from_ds(ds), method=\"vertex\")\n",
+    "gi = flopy.utils.GridIntersect(nlmod.grid.modelgrid_from_ds(ds))\n",
     "lak_grid.geometry = gi.geoms[lak_grid.index]\n",
     "\n",
     "# remove drains that overlap with the lake\n",

docs/getting_started.rst

@@ -111,7 +111,6 @@ On top of that there are some optional dependecies:
 - scikit-image (used in nlmod.read.rws.calculate_sea_coverage)
 - py7zr (used in nlmod.read.bofek.download_bofek_gdf)
 - joblib (used in nlmod.cache)
-- colorama (used in nlmod.util.get_color_logger)
 - tqdm (used for showing progress in long-running methods)
 - hydropandas (used in nlmod.read.knmi and nlmod.read.bro)
 - owslib (used in nlmod.read.ahn.get_latest_ahn_from_wcs)

nlmod/dims/grid.py

@@ -1347,12 +1347,12 @@ def polygon_to_area(modelgrid, polygon, da, gridtype="structured"):
     df = ix.intersect(polygon, geo_dataframe=True)
 
     if gridtype == "structured":
-        area_array = util.get_da_from_da_ds(da, dims=("y", "x"), data=0)
+        area_array = util.get_da_from_da_ds(da, dims=("y", "x"), data=0.0)
         for row, col, area in zip(df["row"], df["col"], df["areas"]):
             area_array[row, col] = area
     elif gridtype == "vertex":
-        area_array = util.get_da_from_da_ds(da, dims=("icell2d",), data=0)
-        area_array[df["cellid"]] = df["areas"]
+        area_array = util.get_da_from_da_ds(da, dims=("icell2d",), data=0.0)
+        area_array[df["cellid"].values] = df["areas"]
 
     return area_array
 
@@ -2443,6 +2443,22 @@ def get_extent_polygon(ds, rotated=True):
 
 
 def get_extent_gdf(ds, rotated=True, crs="EPSG:28992"):
+    """Get the model extent as a GeoDataFrame with a polygon.
+
+    Parameters
+    ----------
+    ds : xr.Dataset
+        model dataset.
+    rotated : bool, optional
+        if True, the extent is corrected for angrot. The default is True.
+    crs : str, optional
+        Coordinate reference system. The default is "EPSG:28992".
+
+    Returns
+    -------
+    gdf : geopandas.GeoDataFrame
+        GeoDataFrame containing the model extent as a polygon geometry.
+    """
     polygon = get_extent_polygon(ds, rotated=rotated)
     return gpd.GeoDataFrame(geometry=[polygon], crs=crs)
 

nlmod/dims/time.py

@@ -394,7 +394,7 @@ def set_ds_time_numeric(
 
 
 def set_time_variables(ds, start, time, steady, steady_start, time_units, nstp, tsmult):
-    """Add data variables: steady, nstp and tsmult, set attributes: start, time_units
+    """Add data variables: steady, nstp and tsmult, set attributes: start, time_units.
 
     Parameters
     ----------

nlmod/prt/prt.py

@@ -144,6 +144,8 @@ def prp(ds, prt, packagedata, perioddata, pname="prp", **kwargs):
     """
     logger.info("creating mf6 PRP")
     prp_track_file = kwargs.pop("prp_track_file", f"{ds.model_name}.prp.trk")
+    # the default value in flopy for coordinate_check_method of 'eager' gives an error
+    # in MODFLOW verion 6.6.3
     prp = fp.mf6.ModflowPrtprp(
         prt,
         pname=pname,
@@ -156,6 +158,7 @@ def prp(ds, prt, packagedata, perioddata, pname="prp", **kwargs):
         boundnames=kwargs.pop("boundnames", False),
         exit_solve_tolerance=kwargs.pop("exit_solve_tolerance", 1e-5),
         extend_tracking=kwargs.pop("extend_tracking", True),
+        coordinate_check_method=kwargs.pop("coordinate_check_method", None),
         **kwargs,
     )
     return prp

nlmod/util.py

@@ -878,13 +878,7 @@ def __init__(
     def format(self, record) -> str:
         """Format the specified record as text."""
         record.color = self.colors.get(record.levelname, "")
-        try:
-            from colorama import Style
-
-            record.reset = Style.RESET_ALL
-
-        except ImportError:
-            record.reset = ""
+        record.reset = "\x1b[0m"
 
         return super().format(record)
 
@@ -907,19 +901,13 @@ def get_color_logger(level="INFO", logger_name=None):
     else:
         FORMAT = "{color}{levelname}:{name}.{funcName}:{message}{reset}"
 
-    try:
-        from colorama import Back, Fore, Style
-
-        colors = {
-            "DEBUG": Fore.CYAN,
-            "INFO": Fore.GREEN,
-            "WARNING": Fore.YELLOW,
-            "ERROR": Fore.RED,
-            "CRITICAL": Fore.RED + Back.WHITE + Style.BRIGHT,
-        }
-    except ImportError:
-        logger.warning("colorama package not found, colored logging is disabled.")
-        colors = {}
+    colors = {
+        "DEBUG": "\x1b[36m",
+        "INFO": "\x1b[32m",
+        "WARNING": "\x1b[33m",
+        "ERROR": "\x1b[31m",
+        "CRITICAL": "\x1b[31m" + "\x1b[47m" + "\x1b[1m",
+    }
 
     formatter = ColoredFormatter(
         FORMAT,

nlmod/version.py

@@ -1,7 +1,7 @@
 from importlib import metadata
 from platform import python_version
 
-__version__ = "0.11.2dev"
+__version__ = "0.11.2"
 
 
 def show_versions() -> None:

pyproject.toml

@@ -20,7 +20,7 @@ maintainers = [
 ]
 requires-python = ">= 3.10"
 dependencies = [
-    "flopy>=3.3.6",
+    "flopy>=3.10.0",
     "xarray>=0.16.1",
     "netcdf4>=1.7.2",
     "rasterio>=1.1.0",
@@ -63,7 +63,6 @@ full = [
     "scikit-image",
     "py7zr",
     "joblib",
-    "colorama",
     "tqdm",
     "hydropandas>=0.9.2",
     "owslib>=0.24.1",