68 new env

environment.yml

@@ -4,21 +4,24 @@ channels:
 dependencies:
   - black
   - cftime
-  - dask=2023.11.0
-  - esmf=8.4.2=mpi_mpich_h2a0de38_103
-  - esmpy=8.4.2
+  - dask
+  - esmf=*=nompi_*
+  - esmpy
   - f90nml
   - flake8
-  - gdal=3.9.1
+  - gdal
   - geovista
-  - iris-esmf-regrid>=0.9
+  - hdf5=*=nompi_*
+  - iris-esmf-regrid=0.15
   - iris-sample-data
-  - iris=3.7.1
+  - iris
   - isort
+  - libnetcdf!=4.9.1=nompi_*
   - mo_pack
   - nccmp
+  - netcdf-fortran=*=nompi_*
   - numba
-  - numpy=1.26.0
+  - numpy=2.3.5
   - pre-commit
   - pydata-sphinx-theme
   - pyflakes
@@ -27,11 +30,11 @@ dependencies:
   - pytest-cov
   - pytest-xdist
   - python-stratify
-  - python=3.10.13
+  - python=3.12.12
   - ruff
   - setuptools
   - setuptools-scm
-  - sphinx=7.2.6
+  - sphinx
   - sphinx-argparse
   - sphinx-copybutton
   - sphinx-sitemap

lib/ants/_constraints.py

@@ -110,7 +110,7 @@ def _bounding_box(target_x, target_y, src_crs):
     src_crs = source_x.coord_system.as_ants_crs()
     box = _bounding_box(target_x, target_y, src_crs)
 
-    (minx, miny, maxx, maxy) = box.bounds
+    minx, miny, maxx, maxy = box.bounds
     slices = utils.cube.get_slices(source, [miny, maxy], [minx, maxx], pad_width)
 
     if len(slices) > 2:

lib/ants/_version.py

@@ -3,4 +3,5 @@
 # This file is part of ANTS and is released under the BSD 3-Clause license.
 # See LICENSE.txt in the root of the repository for full licensing details.
 """Define the fallback version to be used when ANTS is not installed into an environment."""  # noqa: E501
+
 FALLBACK_VERSION = "3.2.0dev"

lib/ants/analysis/__init__.py

@@ -29,6 +29,7 @@
 <https://scitools-iris.readthedocs.io/en/latest/userguide/merge_and_concat.html>`_.
 
 """
+
 import warnings
 
 import ants
@@ -251,7 +252,7 @@ def merge(primary_cube, alternate_cube, validity_polygon=None):
 def _flood_fill_neighbour_identify(
     shape, coords, seed_point, extended_neighbourhood, wraparound
 ):
-    (yy, xx) = seed_point
+    yy, xx = seed_point
     if yy > 0:
         coords.add((yy - 1, xx))
     if yy < (shape[0] - 1):
@@ -320,7 +321,7 @@ def flood_fill(
         When True, support wraparound in 'x', otherwise stop at the boundary.
 
     """
-    (y, x) = seed_point
+    y, x = seed_point
     if array.ndim != 2:
         msg = "The provided array should be 2D but that provided is {}D"
         raise ValueError(msg.format(array.ndim))
@@ -473,7 +474,7 @@ def find_similar_region(
         identified as similar.
 
     """
-    (y, x) = seed_point
+    y, x = seed_point
     if array.ndim != 2:
         msg = "The provided array should be 2D but that provided is {}D"
         raise ValueError(msg.format(array.ndim))

lib/ants/analysis/_merge.py

@@ -7,6 +7,7 @@
 The metadata is also updated to reflect the analysis made.
 
 """
+
 import abc
 import logging
 import warnings

lib/ants/cli/ancil_2anc.py

@@ -30,6 +30,7 @@
 <https://code.metoffice.gov.uk/doc/um/latest/papers/umdp_F03.pdf>`_
 
 """
+
 import warnings
 
 import ants

lib/ants/cli/ancil_create_shapefile.py

@@ -10,6 +10,7 @@
 Creates and saves a shapefile from a list of pairs of longitude, latitude
 points defining a single polygon in a specified polygon file.
 """
+
 import argparse
 import json
 

lib/ants/cli/ancil_fill_n_merge.py

@@ -11,6 +11,7 @@
 missing values.
 
 """
+
 import ants
 import ants.io.save as save
 import cartopy

lib/ants/cli/ancil_general_regrid.py

@@ -28,6 +28,7 @@
 is produced, regardless of the number of longitude
 points in the regrid target.
 """
+
 import ants
 import ants.decomposition as decomp
 import ants.io.save as save

lib/ants/config.py

@@ -49,6 +49,7 @@
   see different results). This environment variable is read by cartopy directly.
 
 """
+
 import argparse
 import configparser
 import copy

lib/ants/coord_systems.py

@@ -18,6 +18,7 @@
  * :func:`ants.regrid.rectilinear`
 
 """
+
 import copy
 import re
 from abc import ABCMeta, abstractmethod

lib/ants/decomposition.py

@@ -24,6 +24,7 @@
 See :func:`ants.utils.cube.defer_cube`.
 
 """
+
 import itertools
 import logging
 import os
@@ -172,8 +173,8 @@ def _guess_split(sources, target=None):
         if not isinstance(target, iris.cube.Cube):
             target = target[0]
         dtype = np.promote_types(dtype, target.dtype)
-        if (np.prod(target.shape) * np.nbytes[dtype]) > (
-            np.prod(source.shape) * np.nbytes[dtype]
+        if (np.prod(target.shape) * np.dtype(dtype).itemsize) > (
+            np.prod(source.shape) * np.dtype(dtype).itemsize
         ):
             largest_array = target
 
@@ -186,7 +187,7 @@ def _guess_split(sources, target=None):
     z_elements = np.prod(rem_shape)
 
     # Number of points which amount to size_bytes footprint.
-    n_elements = int((size_bytes) / np.nbytes[dtype])
+    n_elements = int((size_bytes) / np.dtype(dtype).itemsize)
 
     # Split such that ~square extracts occur for likely optimisation of saving.
     shape = np.array(largest_array.shape)

lib/ants/fileformats/__init__.py

@@ -7,6 +7,7 @@
 ancillary generation. These include those supported by iris and additional
 formats such as grid namelists and raster files.
 """
+
 import warnings
 
 import ants

lib/ants/fileformats/_grid_extract.py

@@ -7,6 +7,7 @@
 grid via the ants.io.load.load_grid interface.
 
 """
+
 import ants
 import dask.array as da
 import iris

lib/ants/fileformats/ancil/__init__.py

@@ -21,6 +21,7 @@
    cube.attributes['grid_staggering'].
 
 """
+
 import warnings
 
 import ants

lib/ants/fileformats/ancil/preprocessing.py

@@ -17,6 +17,7 @@
 #. Create a metadata.ini file for climatology time information (write_metadata_file)
 
 """
+
 import configparser
 import numbers
 from collections import Counter

lib/ants/fileformats/ancil/template.py

@@ -7,6 +7,7 @@
 Tools for generating the template required for saving ancillary files.
 
 """
+
 import itertools
 import re
 
@@ -136,7 +137,7 @@ def _set_grid_definition(headers, grid, field):
     headers["fixed_length_header"]["horiz_grid_type"] = horiz_grid_type
 
     # REAL CONSTANTS
-    (regular_x, regular_y) = field.is_regular
+    regular_x, regular_y = field.is_regular
     if regular_x:
         headers["real_constants"]["col_spacing"] = field.bdx
         # Longitude of first column in degrees (longitudes in range 0-360)

lib/ants/fileformats/ancil/time_headers.py

@@ -7,6 +7,7 @@
 This module provides functions related to time handling for ancillary files.
 
 """
+
 import itertools
 
 import ants

lib/ants/fileformats/namelist/__init__.py

@@ -6,6 +6,7 @@
 Module for reading Fortran namelist files and constructing Python or Iris
 objects, as appropriate, from the contents.
 """
+
 import warnings
 
 import ants

lib/ants/fileformats/namelist/umgrid.py

@@ -22,6 +22,7 @@
 definition specification.
 
 """
+
 from abc import ABCMeta, abstractproperty
 from collections import namedtuple
 
@@ -642,7 +643,7 @@ def __init__(self, namelist_dict):
         _eta_rho.insert(0, 0.0)
         # rho level above model top not in namelist.  Instead, derived after
         # conversion to self._brlev, so use NAN as a placeholder:
-        _eta_rho.append(np.NAN)
+        _eta_rho.append(np.nan)
 
         self._eta_rho = np.array(_eta_rho, dtype=np.float64)
         # brlev defines level_height.lower bounds

lib/ants/fileformats/netcdf/__init__.py

@@ -3,6 +3,7 @@
 # This file is part of ANTS and is released under the BSD 3-Clause license.
 # See LICENSE.txt in the root of the repository for full licensing details.
 """The entry point for netCDF saving is via :func:`ants.io.save.netcdf`."""
+
 from . import cf, ukca
 
 __all__ = [

lib/ants/fileformats/pp/__init__.py

@@ -15,6 +15,7 @@
 1. Pseudo-level order from the PP file is preserved.
 
 """
+
 import collections
 import itertools
 

lib/ants/fileformats/raster.py

@@ -9,6 +9,7 @@
 information.
 
 """
+
 import copy
 import warnings
 
@@ -64,7 +65,16 @@ def __init__(self, shape, dtype, path, raster_band_index, fill_value):
         #       the saving of netcdf3 output properly (auto type-casting etc.)
         dtype = np.dtype(dtype)
         if dtype.name.startswith("uint"):
-            dtype = np.dtype(np.sctypeDict[dtype.num + 1])
+            if (dtype.name) == "uint8":
+                dtype = np.dtype("int16")
+            elif (dtype.name) == "uint16":
+                dtype = np.dtype("int32")
+            elif (dtype.name) == "uint32":
+                dtype = np.dtype("int64")
+            elif (dtype.name) == "uint64":
+                dtype = np.dtype("int128")
+            else:
+                raise TypeError(f"Cannot cast {dtype.name} from unsigned to signed int")
         self.dtype = dtype
         self.path = path
         self.raster_band_index = raster_band_index

lib/ants/io/load.py

@@ -55,6 +55,7 @@
 :func:`ants.fileformats.namelist.load_um_vertical`
 
 """
+
 import copy
 import warnings
 from contextlib import contextmanager

lib/ants/io/save.py

@@ -20,6 +20,7 @@
 specifying ``saver='ukca'`` (see :func:`ants.io.save.ukca_netcdf`).
 
 """
+
 import os
 import sys
 import warnings

lib/ants/regrid/__init__.py

@@ -17,6 +17,7 @@
 For further details see the user guide.
 
 """
+
 import logging
 import sys
 

lib/ants/regrid/esmf.py

@@ -412,33 +412,27 @@ def __init__(self, src_cube, target_cube, **kwargs):
         if keywarg_diff:
             msg = "unexpected keyword argument {}"
             raise ValueError(msg.format(keywarg_diff))
-
         if esmpy is None:
             raise _ESMPY_IMPORT_ERROR
         _supported_cube_check(src_cube)
         _supported_cube_check(target_cube)
-
         # Set some parameters.
         self.handle = None
         self.coordSystem = esmpy.api.constants.CoordSys.SPH_DEG
         self.method = esmpy.api.constants.RegridMethod.CONSERVE
         self.stagger = esmpy.StaggerLoc.CENTER
-
         method = kwargs.get("method", "areaweighted")
         if method.lower() != "areaweighted":
             raise ValueError("Currently only area weighted regridding " "supported.")
-
         # Simply return if the src and tgt grids are identical.
         if (src_cube.coord(axis="x") == target_cube.coord(axis="x")) and (
             src_cube.coord(axis="y") == target_cube.coord(axis="y")
         ):
             return
         _source_cube_sanity_check(src_cube)
-
         # Build the 2D esmf grid and field objects.
         self.esmpy_src_grid, self.esmpy_src_field = self._build_field(src_cube)
         self.esmpy_tgt_grid, self.esmpy_tgt_field = self._build_field(target_cube)
-
         # Compute/read the weights following ESMPy weights tutorial.  See
         # ESMPy docs for details of arguments.
         self._cache_fnme = self._gen_cache_filename([src_cube, target_cube])
@@ -872,7 +866,6 @@ def _build_field(self, cube):
         #
         # Build the esmpy field object.
         #
-
         staggering = "corner"
         if self.method != esmpy.api.constants.RegridMethod.CONSERVE:
             # Need to pass corner coordinates in all cases. When the field is
@@ -884,20 +877,16 @@ def _build_field(self, cube):
         extractor = _LatLonExtractor(cube, staggering)
         lats = extractor.get_latitude()
         lons = extractor.get_longitude()
-
         # Create the grid.
         cellDims = np.array([lons.shape[0] - 1, lats.shape[1] - 1])
         grid = esmpy.Grid(max_index=cellDims, coord_sys=self.coordSystem)
-
         # Allocate space for the vertices, esmpy wants the first coordinate to
         # be longitudes.
         grid.add_coords(staggerloc=esmpy.StaggerLoc.CORNER, coord_dim=0)
         # No need to add lats, it will be added automatically with lons
-
         # Get pointers to the esmf coordinates.
         lonPoint = grid.get_coords(coord_dim=0, staggerloc=esmpy.StaggerLoc.CORNER)
         latPoint = grid.get_coords(coord_dim=1, staggerloc=esmpy.StaggerLoc.CORNER)
-
         # When esmpy runs in parallel, the start/end indices may be other than
         # 0,-1.
         # CP: Is esmpy running in parallel being tested??  I suggest just
@@ -909,7 +898,6 @@ def _build_field(self, cube):
         iend0 = grid.upper_bounds[esmpy.StaggerLoc.CORNER][0]
         ibeg1 = grid.lower_bounds[esmpy.StaggerLoc.CORNER][1]
         iend1 = grid.upper_bounds[esmpy.StaggerLoc.CORNER][1]
-
         lonPoint[...] = lons[ibeg0:iend0, ibeg1:iend1]
         latPoint[...] = lats[ibeg0:iend0, ibeg1:iend1]