Move to numpy version 2

Changelog.rst

@@ -3,12 +3,19 @@ version 3.17.0
 
 **2025-??-??**
 
+* Set a new minimum version of `numpy`: ``2.0.0``
+  (https://github.com/NCAS-CMS/cf-python/issues/843)
 * Replace dataset aggregation functionality (CFA) with that imported
   from `cfdm` (https://github.com/NCAS-CMS/cf-python/issues/841)
 * New keyword parameter to `cf.Field.compute_vertical_coordinates`:
   ``key`` (https://github.com/NCAS-CMS/cf-python/issues/802)
-* Changed dependency: ``1.12.0.0<=cfdm<1.12.1.0``
-* Changed dependency: ``h5py>=3.12.0``
+* Changed dependency: ``Python>=3.9.0``
+* Changed dependency: ``numpy>=2.0.0``
+* Changed dependency: ``cfdm>=1.12.0.0, <1.12.1.0``
+* Changed optional dependency: ``esmpy>=8.7.0``
+* Removed dependency (now incorporated into ``cfdm``): ``h5py``
+* Removed dependency (now incorporated into ``cfdm``): ``h5netcdf``
+* Removed dependency (now incorporated into ``cfdm``): ``s3fs``
 
 ----
 
@@ -287,8 +294,8 @@ version 3.15.0
 * Handled the renaming of the ESMF Python interface from `ESMF` to
   `esmpy` at version 8.4.0. Both module names are accepted for now.
 * Changed dependency: ``1.10.1.0<=cfdm<1.10.2.0``
-* Changed (optional) dependency: ``8.0.0<=esmpy``
-* Changed (optional) dependency: ``1.10.0<=scipy``
+* Changed optional dependency: ``8.0.0<=esmpy``
+* Changed optional dependency: ``1.10.0<=scipy``
 
 ----
 

cf/__init__.py

@@ -80,7 +80,6 @@
 
 """
 
-__Conventions__ = "CF-1.11"
 __date__ = "2025-01-28"
 __version__ = "3.16.3"
 
@@ -95,154 +94,143 @@
     "packaging",
     "scipy",
 )
-
 x = ", ".join(_requires)
 _error0 = f"cf v{__version__} requires the modules {x}. "
 
+import importlib.util
+from platform import python_version
+
+_found_esmpy = bool(importlib.util.find_spec("esmpy"))
+
 try:
-    import cfdm
+    import packaging
+    from packaging.version import Version
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "20.0"
+    if Version(packaging.__version__) < Version(_minimum_vn):
+        raise RuntimeError(
+            f"Bad packaging version: cf requires packaging>={_minimum_vn}. "
+            f"Got {packaging.__version__} at {packaging.__file__}"
+        )
 
-__cf_version__ = cfdm.core.__cf_version__
-
-from packaging.version import Version
-import importlib.util
-import platform
-
-# ESMF renamed its Python module to `esmpy` at ESMF version 8.4.0. Allow
-# either for now for backwards compatibility.
-_found_esmpy = bool(
-    importlib.util.find_spec("esmpy") or importlib.util.find_spec("ESMF")
-)
+try:
+    import cfdm
+except ImportError as error1:
+    raise ImportError(_error0 + str(error1))
+else:
+    # Check the version of cfdm
+    _minimum_vn = "1.12.0.0"
+    _maximum_vn = "1.12.1.0"
+    _cfdm_version = Version(cfdm.__version__)
+    if (
+        _cfdm_version < Version(_minimum_vn) or
+        _cfdm_version >= Version(_maximum_vn)
+    ):
+        raise RuntimeError(
+            "Bad cfdm version: cf requires "
+            f"{_minimum_vn}<=cfdm<{_maximum_vn}. "
+            f"Got {cfdm.__version__} at {cfdm.__file__}"
+        )
+
+__cf_version__ = cfdm.__cf_version__
+__Conventions__ = f"CF-{__cf_version__}"
 
 try:
     import netCDF4
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "1.7.2"
+    if Version(netCDF4.__version__) < Version(_minimum_vn):
+        raise RuntimeError(
+            f"Bad netCDF4 version: cf requires netCDF4>={_minimum_vn}. "
+            f"Got {netCDF4.__version__} at {netCDF4.__file__}"
+        )
 
 try:
     import numpy as np
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "2.0.0"
+    if Version(np.__version__) < Version(_minimum_vn):
+        raise ValueError(
+            f"Bad numpy version: cf requires numpy>={_minimum_vn} "
+            f"Got {np.__version__} at {np.__file__}"
+        )
 
 try:
     import cftime
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "1.6.4"
+    if Version(cftime.__version__) < Version(_minimum_vn):
+        raise RuntimeError(
+            f"Bad cftime version: cf requires cftime>={_minimum_vn}. "
+            f"Got {cftime.__version__} at {cftime.__file__}"
+        )
 
 try:
     import cfunits
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "3.3.7"
+    if Version(cfunits.__version__) < Version(_minimum_vn):
+        raise RuntimeError(
+            f"Bad cfunits version: cf requires cfunits>={_minimum_vn}. "
+            f"Got {cfunits.__version__} at {cfunits.__file__}"
+        )
 
 try:
     import psutil
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "0.6.0"
+    if Version(psutil.__version__) < Version(_minimum_vn):
+        raise RuntimeError(
+            f"Bad psutil version: cf requires psutil>={_minimum_vn}. "
+            f"Got {psutil.__version__} at {psutil.__file__}"
+        )
 
 try:
     import dask
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
-
-try:
-    import packaging
-except ImportError as error1:
-    raise ImportError(_error0 + str(error1))
+else:
+    _minimum_vn = "2024.6.1"
+    _maximum_vn = "2024.7.1"
+    if (
+        Version(dask.__version__) < Version(_minimum_vn) or
+        Version(dask.__version__) > Version(_maximum_vn)
+    ):
+        raise ValueError(
+            "Bad dask version: cf requires "
+            f"{_minimum_vn}<=dask<={_maximum_vn}. "
+            f"Got {dask.__version__} at {dask.__file__}"
+        )
 
 try:
     import scipy
 except ImportError as error1:
     raise ImportError(_error0 + str(error1))
-
-# Check the version of packaging
-_minimum_vn = "20.0"
-if Version(packaging.__version__) < Version(_minimum_vn):
-    raise RuntimeError(
-        f"Bad packaging version: cf requires packaging>={_minimum_vn}. "
-        f"Got {packaging.__version__} at {packaging.__file__}"
-    )
-
-# Check the version of psutil
-_minimum_vn = "0.6.0"
-if Version(psutil.__version__) < Version(_minimum_vn):
-    raise RuntimeError(
-        f"Bad psutil version: cf requires psutil>={_minimum_vn}. "
-        f"Got {psutil.__version__} at {psutil.__file__}"
-    )
-
-# Check the version of netCDF4
-_minimum_vn = "1.6.5"
-if Version(netCDF4.__version__) < Version(_minimum_vn):
-    raise RuntimeError(
-        f"Bad netCDF4 version: cf requires netCDF4>={_minimum_vn}. "
-        f"Got {netCDF4.__version__} at {netCDF4.__file__}"
-    )
-
-# Check the version of cftime
-_minimum_vn = "1.6.2"
-if Version(cftime.__version__) < Version(_minimum_vn):
-    raise RuntimeError(
-        f"Bad cftime version: cf requires cftime>={_minimum_vn}. "
-        f"Got {cftime.__version__} at {cftime.__file__}"
-    )
-
-# Check the version of numpy
-_minimum_vn = "1.22"
-_maximum_vn = "2.0"
-if not Version(_minimum_vn) <= Version(np.__version__) < Version(_maximum_vn):
-    raise ValueError(
-        "Bad numpy version: cf requires _minimum_vn}<=numpy<{_maximum_vn}. "
-        f"Got {np.__version__} at {np.__file__}"
-    )
-
-# Check the version of cfunits
-_minimum_vn = "3.3.7"
-if Version(cfunits.__version__) < Version(_minimum_vn):
-    raise RuntimeError(
-        f"Bad cfunits version: cf requires cfunits>={_minimum_vn}. "
-        f"Got {cfunits.__version__} at {cfunits.__file__}"
-    )
-
-# Check the version of cfdm
-_minimum_vn = "1.12.0.0"
-_maximum_vn = "1.12.1.0"
-_cfdm_version = Version(cfdm.__version__)
-if not Version(_minimum_vn) <= _cfdm_version < Version(_maximum_vn):
-    raise RuntimeError(
-        f"Bad cfdm version: cf requires {_minimum_vn}<=cfdm<{_maximum_vn}. "
-        f"Got {cfdm.__version__} at {cfdm.__file__}"
-    )
-
-# Check the version of dask
-
-_minimum_vn = "2024.6.1"
-_maximum_vn = "2024.7.1"
-if (
-    not Version(_minimum_vn)
-    <= Version(dask.__version__)
-    <= Version(_maximum_vn)
-):
+else:
+    _minimum_vn = "1.10.0"
+    if Version(scipy.__version__) < Version(_minimum_vn):
+        raise RuntimeError(
+            f"Bad scipy version: cf requires scipy>={_minimum_vn}. "
+            f"Got {scipy.__version__} at {scipy.__file__}"
+        )
+
+_minimum_vn = "3.9.0"
+if Version(python_version()) < Version(_minimum_vn):
     raise ValueError(
-        "Bad dask version: cf requires {_minimum_vn}<=dask<={_maximum_vn}. "
-        f"Got {dask.__version__} at {dask.__file__}"
-    )
-
-# Check the version of Python
-_minimum_vn = "3.8.0"
-if Version(platform.python_version()) < Version(_minimum_vn):
-    raise ValueError(
-        f"Bad python version: cf requires python version {_minimum_vn} "
-        f"or later. Got {platform.python_version()}"
-    )
-
-# Check the version of scipy
-_minimum_vn = "1.10.0"
-if Version(scipy.__version__) < Version(_minimum_vn):
-    raise RuntimeError(
-        f"Bad scipy version: cf requires scipy>={_minimum_vn}. "
-        f"Got {scipy.__version__} at {scipy.__file__}"
+        f"Bad python version: cf requires python>={_minimum_vn}. "
+        f"Got {python_version()}"
     )
 
 del _minimum_vn, _maximum_vn

cf/data/collapse/dask_collapse.py

@@ -858,9 +858,17 @@ def cf_sample_size_chunk(x, dtype="i8", computing_meta=False, **kwargs):
         return x
 
     x = cfdm_to_memory(x)
-
     if np.ma.isMA(x):
-        N = chunk.sum(np.ones_like(x, dtype=dtype), **kwargs)
+        # Note: We're not using `np.ones_like` here (like we used to)
+        #       because numpy currently (numpy==2.2.3) has a bug that
+        #       produces a RuntimeWarning: "numpy/ma/core.py:502:
+        #       RuntimeWarning: invalid value encountered in cast
+        #       fill_value = np.asarray(fill_value,
+        #       dtype=ndtype)". See
+        #       https://github.com/numpy/numpy/issues/28255 for more
+        #       details.
+        x = np.ma.array(np.ones((x.shape), dtype=x.dtype), mask=x.mask)
+        N = chunk.sum(x, **kwargs)
     else:
         if dtype:
             kwargs["dtype"] = dtype

cf/functions.py

@@ -2755,6 +2755,7 @@ def dirname(path, normalise=False, uri=None, isdir=False, sep=False):
 dirname.__doc__ = cfdm.dirname.__doc__.replace("cfdm.", "cf.")
 
 from functools import partial
+
 dirname2 = partial(cfdm.dirname)
 dirname2.__doc__ = cfdm.dirname.__doc__.replace("cfdm.", "cf.")
 

cf/mixin/fielddomain.py

@@ -692,8 +692,7 @@ def _point_not_in_cell(nodes_x, nodes_y, point):
             if ind is not None:
                 mask_component_shape = []
                 masked_subspace_size = 1
-                # TODONUMPY2: https://numpy.org/devdocs/numpy_2_0_migration_guide.html#adapting-to-changes-in-the-copy-keyword
-                ind = np.array(ind, copy=False)
+                ind = np.array(ind)
 
                 for i, (axis, start, stop) in enumerate(
                     zip(canonical_axes, ind.min(axis=1), ind.max(axis=1))

cf/mixin/propertiesdata.py

@@ -49,14 +49,6 @@ class PropertiesData(Properties):
 
     _special_properties = ("units", "calendar")
 
-    def __array__(self, *dtype):
-        """Returns a numpy array representation of the data."""
-        data = self.get_data(None)
-        if data is not None:
-            return data.__array__(*dtype)
-
-        raise ValueError(f"{self.__class__.__name__} has no data")
-
     def __contains__(self, value):
         """Called to implement membership test operators.
 

cf/regrid/regrid.py

@@ -2186,7 +2186,7 @@ def create_esmpy_mesh(grid, mask=None):
     # esmpy.
     min_id = node_ids.min()
     if min_id < 1:
-        node_ids += min_id + 1
+        node_ids = node_ids + min_id + 1
 
     # Add nodes. This must be done before `add_elements`.
     esmpy_mesh.add_nodes(

cf/test/test_Data.py

@@ -2621,7 +2621,7 @@ def test_Data_percentile_median(self):
                     a1 = np.nanpercentile(filled, q, keepdims=keepdims)
                     mask = np.isnan(a1)
                     if mask.any():
-                        a1 = np.ma.masked_where(mask, a1, copy=False)
+                        a1 = np.ma.masked_where(mask, a1)
 
                     b1 = d.percentile(q, squeeze=not keepdims)
                     self.assertEqual(b1.shape, a1.shape)
@@ -3613,6 +3613,7 @@ def test_Data_sample_size(self):
             b = np.ma.asanyarray(b)
 
             e = d.sample_size(axes=axis, squeeze=True)
+
             e = np.ma.array(e.array)
 
             self.assertTrue((e.mask == b.mask).all())