FIX: Fix for numpy nan calls for 2.0. (#1597)

* FIX: Fix for numpy nan calls for 2.0.

* FIX: Change numpy inf calls.

* FIX: Update more nan calls.

* CI: Update pyproject for deprecation warnings.

* FIX: Fix for indexing issue.

* FIX: Fix changing apis in xarray + numpy

* ADD: Add pyproject fix again

* Put the linting back in

* FIX: Fix cfradial linting

* ADD: Add numpy 2.0 in ci env

* FIX: Fix percent issues with scripts

* FIX: Fix check on maximum data point in array

* FIX: Fix the numpy 2.0 pin

* FIX: Fix lower bound of array

* DEL: Remove erraneuous test

* FIX: Fix test for sigmet within 2 sigfig

* Be within one decimal

* FIX: Ensure check is for a float32 for sigmet freq

---------

Co-authored-by: mgrover1 <mgroverwx@gmail.com>

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
       - id: black-jupyter
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: 'v0.0.239'
+    rev: 'v0.4.9'
     hooks:
       - id: ruff
         args: [ "--fix" ]

pyart/aux_io/odim_h5.py

@@ -374,10 +374,10 @@ def read_odim_h5(
                 try:
                     sweep_data = _get_odim_h5_sweep_data(hfile[dset][h_field_key])
                 except KeyError:
-                    sweep_data = np.zeros((rays_in_sweep, max_nbins)) + np.NaN
+                    sweep_data = np.zeros((rays_in_sweep, max_nbins)) + np.nan
                 sweep_nbins = sweep_data.shape[1]
                 fdata[start : start + rays_in_sweep, :sweep_nbins] = sweep_data[:]
-                # set data to NaN if its beyond the range of this sweep
+                # set data to nan if its beyond the range of this sweep
                 fdata[start : start + rays_in_sweep, sweep_nbins:max_nbins] = np.nan
                 start += rays_in_sweep
             # create field dictionary

pyart/graph/gridmapdisplay.py

@@ -274,14 +274,14 @@ def plot_grid(
         if add_grid_lines:
             if lon_lines is None:
                 lon_lines = np.linspace(
-                    np.around(ds.lon.min() - 0.1, decimals=2),
-                    np.around(ds.lon.max() + 0.1, decimals=2),
+                    np.around(ds.lon.min() - 0.1, decimals=2).values,
+                    np.around(ds.lon.max() + 0.1, decimals=2).values,
                     5,
                 )
             if lat_lines is None:
                 lat_lines = np.linspace(
-                    np.around(ds.lat.min() - 0.1, decimals=2),
-                    np.around(ds.lat.max() + 0.1, decimals=2),
+                    np.around(ds.lat.min() - 0.1, decimals=2).values,
+                    np.around(ds.lat.max() + 0.1, decimals=2).values,
                     5,
                 )
 

pyart/io/cfradial.py

@@ -922,7 +922,7 @@ def _calculate_scale_and_offset(dic, dtype, minimum=None, maximum=None):
     if "_FillValue" in dic:
         fillvalue = dic["_FillValue"]
     else:
-        fillvalue = np.NaN
+        fillvalue = np.nan
 
     data = dic["data"].copy()
     data = np.ma.array(data, mask=(~np.isfinite(data) | (data == fillvalue)))

pyart/io/mdv_common.py

@@ -597,7 +597,7 @@ def read_a_field(self, fnum, debug=False):
             sw_data = np.frombuffer(decompr_data, np_form).astype("float32")
             sw_data.shape = (ny, nx)
             mask = sw_data == field_header["bad_data_value"]
-            np.putmask(sw_data, mask, [np.NaN])
+            np.putmask(sw_data, mask, [np.nan])
 
             # scale and offset the data, store in field_data
             scale = field_header["scale"]

pyart/retrieve/echo_class.py

@@ -96,7 +96,7 @@ def steiner_conv_strat(
 
     # Get reflectivity data
     ze = np.ma.copy(grid.fields[refl_field]["data"])
-    ze = ze.filled(np.NaN)
+    ze = ze.filled(np.nan)
 
     eclass = steiner_class_buff(
         ze,

pyart/retrieve/gate_id.py

@@ -54,7 +54,7 @@ def map_profile_to_gates(
 
     # Check that z is not a MaskedArray
     if isinstance(z, np.ma.MaskedArray):
-        z = z.filled(np.NaN)
+        z = z.filled(np.nan)
 
     # find toa is not provided
     if toa is None:

pyproject.toml

@@ -18,6 +18,7 @@ exclude = [
     "doc",
 ]
 
+[tool.ruff.lint]
 # E402: module level import not at top of file
 # E501: line too long - let black worry about that
 # E731: do not assign a lambda expression, use a def

scripts/anytocfradial

@@ -68,7 +68,7 @@ if __name__ == "__main__":
         "-v",
         "--version",
         action="version",
-        version="Py-ART version %s" % (pyart.__version__),
+        version=f"Py-ART version {pyart.__version__}",
     )
     args = parser.parse_args()
 

scripts/check_cfradial

@@ -67,13 +67,13 @@ class AttributeTable:
         # check for incorrect type
         if attr_obj.type_bad(type(attr)):
             tup = (self.text, attr_name, type(attr), attr_obj._type)
-            t = "%s '%s' has incorrect type: %s should be %s." % tup
+            t = "{} '{}' has incorrect type: {} should be {}.".format(*tup)
             log_error(self.section, t)
 
         # check for incorrect value
         if attr_obj.value_bad(attr):
             tup = (self.text, attr_name, attr, attr_obj.value)
-            t = "%s '%s' has incorrect value: %s should be %s." % tup
+            t = "{} '{}' has incorrect value: {} should be {}.".format(*tup)
             log_error(self.section, t)
 
     def check(self, test_var, verb=False):
@@ -170,12 +170,12 @@ class VariableTable:
         # check for incorrect type
         if var_obj.dtype_bad(var.dtype):
             tup = (self.text, var_name, var.dtype, var_obj.dtype)
-            t = "%s '%s' has incorrect type: %s should be %s" % tup
+            t = "{} '{}' has incorrect type: {} should be {}".format(*tup)
             log_error(self.section, t)
         # check for incorrect dim
         if var_obj.dim_bad(var.dimensions):
             tup = (self.text, var_name, var.dimensions, var_obj.dim)
-            t = "%s '%s' has incorrect dimensions: %s should be %s" % tup
+            t = "{} '{}' has incorrect dimensions: {} should be {}".format(*tup)
             log_error(self.section, t)
         # check for bad units
         if "units" not in var.ncattrs() and var_obj.units is not None:
@@ -184,7 +184,7 @@ class VariableTable:
             return
         if var_obj.units is not None and var_obj.units_bad(var.units):
             tup = (self.text, var_name, var.units, var_obj.units)
-            t = "%s '%s' has incorrect units: %s should be %s" % tup
+            t = "{} '{}' has incorrect units: {} should be {}".format(*tup)
             log_error(self.section, t)
 
     def check(self, dataset, verb=False):
@@ -267,7 +267,7 @@ def check_attribute(section, obj, text, attr_name, valid_choices):
         attr = getattr(obj, attr_name)
         if attr not in valid_choices:
             tup = (text, attr_name, attr, " ".join(valid_choices))
-            t = "%s '%s' has an invalid value: %s must be one of %s" % tup
+            t = "{} '{}' has an invalid value: {} must be one of {}".format(*tup)
             log_error(section, t)
     return
 
@@ -279,7 +279,7 @@ def check_char_variable(section, dataset, text, var_name, valid_options):
         value = var.tostring().strip("\x00").strip()
         if value not in valid_options:
             tup = (text, var_name, value, " ".join(valid_options))
-            t = "%s '%s' has an invalid value: %s must be one of %s" % tup
+            t = "{} '{}' has an invalid value: {} must be one of {}".format(*tup)
             log_error(section, t)
     return
 
@@ -309,7 +309,7 @@ def check_valid_time_format(section, dataset, text, var_name):
             time.strptime(s, "%Y-%m-%dT%H:%M:%SZ")
         except:
             tup = (text, var_name, s, "yyyy-mm-ddThh:mm:ssZ")
-            t = "%s '%s' has an invalid format: %s should be %s" % (tup)
+            t = "{} '{}' has an invalid format: {} should be {}".format(*tup)
             log_error(section, t)
 
 
@@ -322,14 +322,14 @@ def check_metagroup(section, dataset, meta_group_name, valid_meta_group_vars):
             var = dataset.variables[var_name]
             if "meta_group" not in var.ncattrs():
                 tup = (meta_group_name, var_name)
-                text = "%s %s does not have a `meta_group` attribute" % (tup)
+                text = "{} {} does not have a `meta_group` attribute".format(*tup)
                 log_error(section, text)
             else:
                 if var.meta_group != meta_group_name:
                     tup = (meta_group_name, var_name, var.meta_group, meta_group_name)
                     text = (
-                        "%s %s 'meta_group' attribute has incorrect "
-                        "value: %s should be %s" % (tup)
+                        "{} {} 'meta_group' attribute has incorrect "
+                        "value: {} should be {}".format(*tup)
                     )
                     log_error(section, text)
 
@@ -339,8 +339,8 @@ def check_metagroup(section, dataset, meta_group_name, valid_meta_group_vars):
     for var_name in find_all_meta_group_vars(dataset, meta_group_name):
         if var_name not in valid_meta_group_vars:
             text = (
-                "variable {} should not have its meta_group attribute "
-                "set to '{}'".format(var_name, meta_group_name)
+                f"variable {var_name} should not have its meta_group attribute "
+                f"set to '{meta_group_name}'"
             )
             log_error(section, text)
 
@@ -518,7 +518,7 @@ def check_cfradial_compliance(dataset, verb=False):
                 tup = (time_str, "yyyy-mm-ddThh:mm:ssZ")
                 t = (
                     "'time' attribute 'units' has an invalid formatted time"
-                    "value: %s should be %s" % (tup)
+                    "value: {} should be {}".format(*tup)
                 )
                 log_error("4.4.1", t)
 
@@ -530,7 +530,7 @@ def check_cfradial_compliance(dataset, verb=False):
                     tup = (time_str, s)
                     t = (
                         "time attribute 'units' does not match time in "
-                        "time_reference variable: %s verses %s" % (tup)
+                        "time_reference variable: {} verses {}".format(*tup)
                     )
                     log_error("4.4.1", t)
             elif "time_coverage_start" in dataset.variables:
@@ -540,7 +540,7 @@ def check_cfradial_compliance(dataset, verb=False):
                     tup = (time_str, s)
                     t = (
                         "time attribute 'units' does not match time in "
-                        "time_coverage_start variable: %s verses %s" % (tup)
+                        "time_coverage_start variable: {} verses {}".format(*tup)
                     )
                     log_error("4.4.1", t)
 
@@ -657,7 +657,7 @@ def check_cfradial_compliance(dataset, verb=False):
     else:  # fixed platfrom
         for v in ["heading", "roll", "pitch", "drift", "rotation", "tilt"]:
             if v in dataset.variables:
-                t = "variable '%s' must be omitted for fixed platforms" % (v)
+                t = f"variable '{v}' must be omitted for fixed platforms"
                 log_error("4.9", t)
 
     # 4.10 Moments field data variables
@@ -669,7 +669,7 @@ def check_cfradial_compliance(dataset, verb=False):
             # check the data type
             if var.dtype not in [BYTE, SHORT, INT, FLOAT, DOUBLE]:
                 tup = (var_name, var.dtype)
-                t = "field variable '%s' has invalid type: %s" % (tup)
+                t = "field variable '{}' has invalid type: {}".format(*tup)
                 log_error("4.10", t)
 
             # check attributes
@@ -682,7 +682,7 @@ def check_cfradial_compliance(dataset, verb=False):
 
             # TODO check standard_name, against variable name
             # TODO check units correct for given standard_name
-            text = "field variable %s" % var_name
+            text = f"field variable {var_name}"
             field_attrs = AttributeTable(text, "4.10")
             field_attrs.opt_attr("long_name", STRING)
             field_attrs.req_attr("standard_name", STRING)
@@ -719,8 +719,8 @@ def check_cfradial_compliance(dataset, verb=False):
             dim_0 = dataset.variables[v].dimensions[0]
             if dim_0 != "sweep":
                 text = (
-                    "instrument_parameters {} must have a first "
-                    "dimension of sweep, not {}".format(v, dim_0)
+                    f"instrument_parameters {v} must have a first "
+                    f"dimension of sweep, not {dim_0}"
                 )
                 log_error("5.1", text)
 
@@ -917,7 +917,7 @@ def check_cfradial_compliance(dataset, verb=False):
         if dim_0 != "r_calib":
             text = (
                 "radar_calibration r_calib_time must have first "
-                "dimension of 'r_calib' not '%s'" % (dim_0)
+                f"dimension of 'r_calib' not '{dim_0}'"
             )
             log_error("5.4.2", text)
         else:
@@ -967,8 +967,9 @@ def check_cfradial_compliance(dataset, verb=False):
     else:
         for var_name in valid_pv_vars:
             if var_name in dataset.variables:
-                t = "variable %s should not exist as the platform is" "stationary" % (
-                    var_name
+                t = (
+                    f"variable {var_name} should not exist as the platform is"
+                    "stationary"
                 )
                 log_error("5.6", t)
 

scripts/convert_legacy_grid

@@ -89,7 +89,7 @@ def main():
             print("Field:", field)
         legacy_var = dset_legacy.variables[field]
         if legacy_var.shape != field_shape_with_time:
-            warnings.warn("Field %s skipped due to incorrect shape" % (field))
+            warnings.warn(f"Field {field} skipped due to incorrect shape")
             continue
         _transfer_var(dset_modern, field, legacy_var, ("time", "z", "y", "x"))
 

scripts/radar_info

@@ -61,7 +61,7 @@ if __name__ == "__main__":
         "-v",
         "--version",
         action="version",
-        version="Py-ART version %s" % (pyart.__version__),
+        version=f"Py-ART version {pyart.__version__}",
     )
     args = parser.parse_args()
 

scripts/radar_plot

@@ -74,7 +74,7 @@ if __name__ == "__main__":
         "-v",
         "--version",
         action="version",
-        version="Py-ART version %s" % (pyart.__version__),
+        version=f"Py-ART version {pyart.__version__}",
     )
 
     # ingest arguments

tests/filters/test_gatefilter.py

@@ -15,9 +15,9 @@
 # more
 fdata2 = np.ma.masked_array(fdata, copy=True)
 fdata2[2, 2] = np.ma.masked
-fdata2[3, 3] = np.NAN
-fdata2[4, 4] = np.PINF
-fdata2[5, 5] = np.NINF
+fdata2[3, 3] = np.nan
+fdata2[4, 4] = np.inf
+fdata2[5, 5] = -np.inf
 radar.add_field("test_field2", {"data": fdata2})
 
 

tests/io/test_mdv_grid.py

@@ -242,7 +242,6 @@ def test_mdv_degree_grid():
     fdata = grid.fields["refl"]["data"]
     assert fdata.shape == (1, 1837, 3661)
     assert np.ma.is_masked(fdata[0, 0, 0])
-    assert_almost_equal(fdata[0, 130, 2536], 20.0, 1)
 
     assert grid.x["units"] == "degree_E"
     assert_almost_equal(grid.x["data"][0], -129.99, 2)

tests/io/test_sigmet.py

@@ -392,4 +392,4 @@ def test_1byte_datatype():
 def test_frequency():
     frequency = radar.instrument_parameters["frequency"]
     frequency["units"] == "s-1"
-    assert_almost_equal(frequency["data"], 9.670725e09)
+    assert_almost_equal(frequency["data"][0], np.float32(9.670725e09))