NAME loader fixes

docs/src/whatsnew/latest.rst

@@ -88,7 +88,6 @@ This document explains the changes made to Iris for this release
 🐛 Bugs Fixed
 =============
 
-
 #. `@rcomer`_ fixed :meth:`~iris.cube.Cube.intersection` for special cases where
    one cell's bounds align with the requested maximum and negative minimum, fixing
    :issue:`4221`. (:pull:`4278`)
@@ -110,6 +109,10 @@ This document explains the changes made to Iris for this release
    to indicate that the value of a scalar coordinate may be mismatched, rather than the metadata
    (:issue:`4096`, :pull:`4387`)
 
+#. `@bsherratt`_ fixed a regression to the NAME file loader introduced in 3.0.4,
+   as well as some long-standing bugs with vertical coordinates and number
+   formats. (:pull:`4411`)
+
 
 💣 Incompatible Changes
 =======================

lib/iris/fileformats/name_loaders.py

@@ -160,27 +160,37 @@ def _build_lat_lon_for_NAME_timeseries(column_headings):
     the provided column_headings dictionary.
 
     """
-    pattern = re.compile(r"\-?[0-9]*\.[0-9]*")
-    new_Xlocation_column_header = []
-    for t in column_headings["X"]:
-        if "Lat-Long" in t:
-            matches = pattern.search(t)
-            new_Xlocation_column_header.append(float(matches.group(0)))
-        else:
-            new_Xlocation_column_header.append(t)
-    column_headings["X"] = new_Xlocation_column_header
+    # Pattern to match a number
+    pattern = re.compile(
+        r"""
+        [-+]?          # Optional sign
+        (?:
+            \d+\.\d*   # Float: integral part required
+        |
+            \d*\.\d+   # Float: fractional part required
+        |
+            \d+        # Integer
+        )
+        (?![0-9.])     # Not followed by a numeric character
+        """,
+        re.VERBOSE,
+    )
+
+    # Extract numbers from the X and Y column headings, which are currently
+    # strings of the form "X = -1.9 Lat-Long"
+    for key in ("X", "Y"):
+        new_headings = []
+        for heading in column_headings[key]:
+            match = pattern.search(heading)
+            if match and "Lat-Long" in heading:
+                new_headings.append(float(match.group(0)))
+            else:
+                new_headings.append(heading)
+        column_headings[key] = new_headings
+
     lon = NAMECoord(
         name="longitude", dimension=None, values=column_headings["X"]
     )
-
-    new_Ylocation_column_header = []
-    for t in column_headings["Y"]:
-        if "Lat-Long" in t:
-            matches = pattern.search(t)
-            new_Ylocation_column_header.append(float(matches.group(0)))
-        else:
-            new_Ylocation_column_header.append(t)
-    column_headings["Y"] = new_Ylocation_column_header
     lat = NAMECoord(
         name="latitude", dimension=None, values=column_headings["Y"]
     )
@@ -387,6 +397,7 @@ def _cf_height_from_name(z_coord, lower_bound=None, upper_bound=None):
         standard_name=standard_name,
         long_name=long_name,
         bounds=bounds,
+        attributes={"positive": "up"},
     )
 
     return coord
@@ -478,7 +489,7 @@ def _generate_cubes(
                 coord_units = _parse_units("FL")
             if coord.name == "time":
                 coord_units = time_unit
-                pts = np.float_(time_unit.date2num(coord.values))
+                pts = time_unit.date2num(coord.values).astype(float)
 
             if coord.dimension is not None:
                 if coord.name == "longitude":
@@ -505,7 +516,7 @@ def _generate_cubes(
                 ):
                     dt = coord.values - field_headings["Av or Int period"]
                     bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
-                    icoord.bounds = np.float_(bnds)
+                    icoord.bounds = bnds.astype(float)
                 else:
                     icoord.guess_bounds()
                 cube.add_dim_coord(icoord, coord.dimension)
@@ -522,7 +533,7 @@ def _generate_cubes(
                 ):
                     dt = coord.values - field_headings["Av or Int period"]
                     bnds = time_unit.date2num(np.vstack((dt, coord.values)).T)
-                    icoord.bounds = np.float_(bnds[i, :])
+                    icoord.bounds = bnds[i, :].astype(float)
                 cube.add_aux_coord(icoord)
 
         # Headings/column headings which are encoded elsewhere.
@@ -1250,7 +1261,7 @@ def load_NAMEIII_trajectory(filename):
 
         long_name = units = None
         if isinstance(values[0], datetime.datetime):
-            values = np.float_(time_unit.date2num(values))
+            values = time_unit.date2num(values).astype(float)
             units = time_unit
             if name == "Time":
                 name = "time"

lib/iris/tests/results/name/NAMEIII_field.cml

@@ -51,7 +51,11 @@
         <dimCoord bounds="[[349215.0, 349219.0]]" id="cb784457" points="[349219.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>
@@ -112,7 +116,11 @@
         <dimCoord bounds="[[349218.0, 349219.0]]" id="cb784457" points="[349219.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>
@@ -172,7 +180,11 @@
         <dimCoord bounds="[[349215.0, 349219.0]]" id="cb784457" points="[349219.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>
@@ -232,7 +244,11 @@
         <dimCoord bounds="[[349215.0, 349219.0]]" id="cb784457" points="[349219.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>
@@ -292,7 +308,11 @@
         <dimCoord bounds="[[349215.0, 349219.0]]" id="cb784457" points="[349219.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>

lib/iris/tests/results/name/NAMEIII_timeseries.cml

@@ -61,7 +61,11 @@
 		358354.0, 358355.0, 358356.0, 358357.0]" shape="(72,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods/>
@@ -128,7 +132,11 @@
 		358354.0, 358355.0, 358356.0, 358357.0]" shape="(72,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer average]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods/>
@@ -194,7 +202,11 @@
 		358354.0, 358355.0, 358356.0, 358357.0]" shape="(72,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods/>
@@ -260,7 +272,11 @@
 		358354.0, 358355.0, 358356.0, 358357.0]" shape="(72,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods/>
@@ -326,7 +342,11 @@
 		358354.0, 358355.0, 358356.0, 358357.0]" shape="(72,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods/>

lib/iris/tests/results/name/NAMEII_field.cml

@@ -19,7 +19,11 @@
     </attributes>
     <coords>
       <coord>
-        <dimCoord bounds="[[0.0, 100.0]]" id="c87e380b" long_name="height above ground level" points="[50.0]" shape="(1,)" standard_name="height" units="Unit('m')" value_type="float64"/>
+        <dimCoord bounds="[[0.0, 100.0]]" id="1a539915" long_name="height above ground level" points="[50.0]" shape="(1,)" standard_name="height" units="Unit('m')" value_type="float64">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </dimCoord>
       </coord>
       <coord datadims="[0]">
         <dimCoord bounds="[[52.36655, 52.3676555276],
@@ -76,7 +80,11 @@
     </attributes>
     <coords>
       <coord>
-        <dimCoord bounds="[[0.0, 100.0]]" id="c87e380b" long_name="height above ground level" points="[50.0]" shape="(1,)" standard_name="height" units="Unit('m')" value_type="float64"/>
+        <dimCoord bounds="[[0.0, 100.0]]" id="1a539915" long_name="height above ground level" points="[50.0]" shape="(1,)" standard_name="height" units="Unit('m')" value_type="float64">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </dimCoord>
       </coord>
       <coord datadims="[0]">
         <dimCoord bounds="[[52.36655, 52.3676555276],
@@ -161,7 +169,11 @@
         <dimCoord bounds="[[351249.0, 351252.0]]" id="cb784457" points="[351252.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>
@@ -218,7 +230,11 @@
         <dimCoord bounds="[[351249.0, 351252.0]]" id="cb784457" points="[351252.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>
@@ -275,7 +291,11 @@
         <dimCoord bounds="[[351249.0, 351252.0]]" id="cb784457" points="[351252.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods>

lib/iris/tests/results/name/NAMEII_timeseries.cml

@@ -39,7 +39,11 @@
 		370475.0, 370476.0]" shape="(132,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods/>
@@ -84,7 +88,11 @@
 		370475.0, 370476.0]" shape="(132,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='gregorian')" value_type="float64"/>
       </coord>
       <coord>
-        <auxCoord id="457ac36d" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string"/>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Boundary layer]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
       </coord>
     </coords>
     <cellMethods/>

lib/iris/tests/unit/fileformats/name_loaders/test__build_lat_lon_for_NAME_timeseries.py

@@ -0,0 +1,52 @@
+# Copyright Iris contributors
+#
+# This file is part of Iris and is released under the LGPL license.
+# See COPYING and COPYING.LESSER in the root of the repository for full
+# licensing details.
+"""
+Unit tests for :func:`iris.analysis.name_loaders._build_lat_lon_for_NAME_timeseries`.
+
+"""
+
+# Import iris.tests first so that some things can be initialised before
+# importing anything else.
+import iris.tests as tests  # isort:skip
+
+from iris.fileformats.name_loaders import (
+    NAMECoord,
+    _build_lat_lon_for_NAME_timeseries,
+)
+
+
+class TestCellMethods(tests.IrisTest):
+    def test_float(self):
+        column_headings = {
+            "X": ["X = -.100 Lat-Long", "X = -1.600 Lat-Long"],
+            "Y": ["Y = 52.450 Lat-Long", "Y = 51. Lat-Long"],
+        }
+        lat, lon = _build_lat_lon_for_NAME_timeseries(column_headings)
+        self.assertIsInstance(lat, NAMECoord)
+        self.assertIsInstance(lon, NAMECoord)
+        self.assertEqual(lat.name, "latitude")
+        self.assertEqual(lon.name, "longitude")
+        self.assertIsNone(lat.dimension)
+        self.assertIsNone(lon.dimension)
+        self.assertArrayEqual(lat.values, [52.45, 51.0])
+        self.assertArrayEqual(lon.values, [-0.1, -1.6])
+
+    def test_int(self):
+        column_headings = {
+            "X": ["X = -1 Lat-Long", "X = -2 Lat-Long"],
+            "Y": ["Y = 52 Lat-Long", "Y = 51 Lat-Long"],
+        }
+        lat, lon = _build_lat_lon_for_NAME_timeseries(column_headings)
+        self.assertIsInstance(lat, NAMECoord)
+        self.assertIsInstance(lon, NAMECoord)
+        self.assertEqual(lat.name, "latitude")
+        self.assertEqual(lon.name, "longitude")
+        self.assertIsNone(lat.dimension)
+        self.assertIsNone(lon.dimension)
+        self.assertArrayEqual(lat.values, [52.0, 51.0])
+        self.assertArrayEqual(lon.values, [-1.0, -2.0])
+        self.assertIsInstance(lat.values[0], float)
+        self.assertIsInstance(lon.values[0], float)