Merge branch 'v3.3.x' into mergeback_v3.3.1

* v3.3.x: Update whatsnew for 3.3.1 release (SciTools#5002) Port dependency fixes to `v3.3.x`. (SciTools#4992) Fix name loader problem (SciTools#4933) Reinstate CubeList._repr_html_() (SciTools#4976) # Conflicts: # .github/workflows/ci-tests.yml # requirements/ci/nox.lock/py310-linux-64.lock # requirements/ci/nox.lock/py38-linux-64.lock # requirements/ci/nox.lock/py39-linux-64.lock # requirements/ci/py310.yml # requirements/ci/py38.yml # requirements/ci/py39.yml # setup.cfg
stephenworsley · Sep 29, 2022 · c4781ec · c4781ec
2 parents da03d73 + 6829e61
commit c4781ec
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diff --git a/.github/workflows/ci-tests.yml b/.github/workflows/ci-tests.yml
@@ -46,7 +46,7 @@ jobs:
             session: "tests"
 
     env:
-      IRIS_TEST_DATA_VERSION: "2.16"
+      IRIS_TEST_DATA_VERSION: "2.17"
       ENV_NAME: "ci-tests"
 
     steps:

diff --git a/docs/src/whatsnew/3.3.rst b/docs/src/whatsnew/3.3.rst
@@ -31,6 +31,36 @@ This document explains the changes made to Iris for this release
    any issues or feature requests for improving Iris. Enjoy!
 
 
+v3.3.1 (29 Sep 2022)
+====================
+
+.. dropdown:: :opticon:`alert` v3.3.1 Patches
+   :container: + shadow
+   :title: text-primary text-center font-weight-bold
+   :body: bg-light
+   :animate: fade-in
+
+   The patches in this release of Iris include:
+
+    #. `@pp-mo`_ fixed the Jupyter notebook display of :class:`~iris.cube.CubeList`.
+       (:issue:`4973`, :pull:`4976`)
+
+    #. `@pp-mo`_ fixed a bug in NAME loaders where data with no associated statistic would
+       load as a cube with invalid cell-methods, which cannot be printed or saved to netcdf.
+       (:issue:`3288`, :pull:`4933`)
+
+    #. `@pp-mo`_ ensured that :data:`iris.cube.Cube.cell_methods` must always be an iterable
+       of :class:`iris.coords.CellMethod` objects (:pull:`4933`).
+
+    #. `@trexfeathers`_ advanced the Cartopy pin to ``>=0.21``, as Cartopy's
+       change to default Transverse Mercator projection affects an Iris test.
+       See `SciTools/cartopy@fcb784d`_ and `SciTools/cartopy@8860a81`_ for more
+       details. (:pull:`4992`)
+
+    #. `@trexfeathers`_ introduced the ``netcdf4!=1.6.1`` pin to avoid a
+       problem with segfaults. (:pull:`4992`)
+
+
 📢 Announcements
 ================
 
@@ -339,3 +369,5 @@ This document explains the changes made to Iris for this release
 .. _PyData Sphinx Theme: https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html
 .. _pytest: https://docs.pytest.org
 .. _setuptools-scm: https://github.com/pypa/setuptools_scm
+.. _SciTools/cartopy@fcb784d: https://github.com/SciTools/cartopy/commit/fcb784daa65d95ed9a74b02ca292801c02bc4108
+.. _SciTools/cartopy@8860a81: https://github.com/SciTools/cartopy/commit/8860a8186d4dc62478e74c83f3b2b3e8f791372e
diff --git a/lib/iris/cube.py b/lib/iris/cube.py
@@ -185,6 +185,12 @@ def _assert_is_cube(obj):
             )
             raise ValueError(msg)
 
+    def _repr_html_(self):
+        from iris.experimental.representation import CubeListRepresentation
+
+        representer = CubeListRepresentation(self)
+        return representer.repr_html()
+
     # TODO #370 Which operators need overloads?
 
     def __add__(self, other):
@@ -2293,10 +2299,23 @@ def cell_methods(self):
         return self._metadata_manager.cell_methods
 
     @cell_methods.setter
-    def cell_methods(self, cell_methods):
-        self._metadata_manager.cell_methods = (
-            tuple(cell_methods) if cell_methods else tuple()
-        )
+    def cell_methods(self, cell_methods: Iterable):
+        if not cell_methods:
+            # For backwards compatibility: Empty or null value is equivalent to ().
+            cell_methods = ()
+        else:
+            # Can supply any iterable, which is converted (copied) to a tuple.
+            cell_methods = tuple(cell_methods)
+            for cell_method in cell_methods:
+                # All contents should be CellMethods.  Requiring class membership is
+                # somewhat non-Pythonic, but simple, and not a problem for now.
+                if not isinstance(cell_method, iris.coords.CellMethod):
+                    msg = (
+                        f"Cube.cell_methods assigned value includes {cell_method}, "
+                        "which is not an iris.coords.CellMethod."
+                    )
+                    raise ValueError(msg)
+        self._metadata_manager.cell_methods = cell_methods
 
     def core_data(self):
         """

diff --git a/lib/iris/fileformats/name_loaders.py b/lib/iris/fileformats/name_loaders.py
@@ -571,7 +571,9 @@ def _generate_cubes(
                 cube.attributes[key] = value
 
         if cell_methods is not None:
-            cube.add_cell_method(cell_methods[i])
+            cell_method = cell_methods[i]
+            if cell_method is not None:
+                cube.add_cell_method(cell_method)
 
         yield cube
 
@@ -610,7 +612,7 @@ def _build_cell_methods(av_or_ints, coord):
             cell_method = None
             msg = "Unknown {} statistic: {!r}. Unable to create cell method."
             warnings.warn(msg.format(coord, av_or_int))
-        cell_methods.append(cell_method)
+        cell_methods.append(cell_method)  # NOTE: this can be a None
     return cell_methods
 
 

diff --git a/lib/iris/tests/results/name/NAMEII_field__no_time_averaging.cml b/lib/iris/tests/results/name/NAMEII_field__no_time_averaging.cml
@@ -0,0 +1,47 @@
+<?xml version="1.0" ?>
+<cubes xmlns="urn:x-iris:cubeml-0.2">
+  <cube dtype="float32" long_name="VOLCANIC_ASH_AIR_CONCENTRATION" units="g/m2">
+    <attributes>
+      <attribute name="End of release" value="0000UTC 13/01/2011"/>
+      <attribute name="Forecast duration" value="6 hours"/>
+      <attribute name="Met data" value="NWP Flow.ECMWF ERAInt Regional"/>
+      <attribute name="NAME Version" value="NAME III (version 7.2)"/>
+      <attribute name="Quantity" value="Air Concentration"/>
+      <attribute name="Release height" value="Multiple Sources"/>
+      <attribute name="Release location" value="Multiple Sources"/>
+      <attribute name="Release rate" value="Multiple Sources"/>
+      <attribute name="Run time" value="1333UTC 07/12/2018"/>
+      <attribute name="Species" value="VOLCANIC_ASH"/>
+      <attribute name="Species Category" value="VOLCANIC"/>
+      <attribute name="Start of release" value="2200UTC 12/01/2011"/>
+      <attribute name="Time Av or Int" value="No time averaging"/>
+      <attribute name="Title" value="VA_Tutorial"/>
+    </attributes>
+    <coords>
+      <coord datadims="[0]">
+        <dimCoord bounds="[[29.9375, 30.0625],
+		[30.0625, 30.1875]]" id="77a50eb5" points="[30.0, 30.125]" shape="(2,)" standard_name="latitude" units="Unit('degrees')" value_type="float64">
+          <geogCS earth_radius="6371229.0"/>
+        </dimCoord>
+      </coord>
+      <coord datadims="[1]">
+        <dimCoord bounds="[[9.9375, 10.0625],
+		[10.0625, 10.1875]]" id="f913a8b3" points="[10.0, 10.125]" shape="(2,)" standard_name="longitude" units="Unit('degrees')" value_type="float64">
+          <geogCS earth_radius="6371229.0"/>
+        </dimCoord>
+      </coord>
+      <coord>
+        <dimCoord bounds="[[359686.0, 359686.0]]" id="cb784457" points="[359686.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='standard')" value_type="float64"/>
+      </coord>
+      <coord>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Vertical integral]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
+      </coord>
+    </coords>
+    <cellMethods/>
+    <data dtype="float32" shape="(2, 2)" state="loaded"/>
+  </cube>
+</cubes>
diff --git a/lib/iris/tests/results/name/NAMEII_field__no_time_averaging_0.cml b/lib/iris/tests/results/name/NAMEII_field__no_time_averaging_0.cml
@@ -0,0 +1,47 @@
+<?xml version="1.0" ?>
+<cubes xmlns="urn:x-iris:cubeml-0.2">
+  <cube dtype="float32" long_name="VOLCANIC_ASH_AIR_CONCENTRATION" units="g/m2">
+    <attributes>
+      <attribute name="End of release" value="0000UTC 13/01/2011"/>
+      <attribute name="Forecast duration" value="6 hours"/>
+      <attribute name="Met data" value="NWP Flow.ECMWF ERAInt Regional"/>
+      <attribute name="NAME Version" value="NAME III (version 7.2)"/>
+      <attribute name="Quantity" value="Air Concentration"/>
+      <attribute name="Release height" value="Multiple Sources"/>
+      <attribute name="Release location" value="Multiple Sources"/>
+      <attribute name="Release rate" value="Multiple Sources"/>
+      <attribute name="Run time" value="1333UTC 07/12/2018"/>
+      <attribute name="Species" value="VOLCANIC_ASH"/>
+      <attribute name="Species Category" value="VOLCANIC"/>
+      <attribute name="Start of release" value="2200UTC 12/01/2011"/>
+      <attribute name="Time Av or Int" value="No time averaging"/>
+      <attribute name="Title" value="VA_Tutorial"/>
+    </attributes>
+    <coords>
+      <coord datadims="[0]">
+        <dimCoord bounds="[[29.9375, 30.0625],
+		[30.0625, 30.1875]]" id="77a50eb5" points="[30.0, 30.125]" shape="(2,)" standard_name="latitude" units="Unit('degrees')" value_type="float64">
+          <geogCS earth_radius="6371229.0"/>
+        </dimCoord>
+      </coord>
+      <coord datadims="[1]">
+        <dimCoord bounds="[[9.9375, 10.0625],
+		[10.0625, 10.1875]]" id="f913a8b3" points="[10.0, 10.125]" shape="(2,)" standard_name="longitude" units="Unit('degrees')" value_type="float64">
+          <geogCS earth_radius="6371229.0"/>
+        </dimCoord>
+      </coord>
+      <coord>
+        <dimCoord bounds="[[359686.0, 359686.0]]" id="cb784457" points="[359686.0]" shape="(1,)" standard_name="time" units="Unit('hours since 1970-01-01 00:00:00', calendar='standard')" value_type="float64"/>
+      </coord>
+      <coord>
+        <auxCoord id="e92ff7b7" long_name="z" points="[Vertical integral]" shape="(1,)" units="Unit('no_unit')" value_type="string">
+          <attributes>
+            <attribute name="positive" value="up"/>
+          </attributes>
+        </auxCoord>
+      </coord>
+    </coords>
+    <cellMethods/>
+    <data checksum="0xecbb4b55" dtype="float32" shape="(2, 2)"/>
+  </cube>
+</cubes>
diff --git a/lib/iris/tests/test_name.py b/lib/iris/tests/test_name.py
@@ -8,6 +8,9 @@
 # import iris tests first so that some things can be initialised before
 # importing anything else
 import iris.tests as tests  # isort:skip
+
+import tempfile
+
 import iris
 
 
@@ -39,7 +42,7 @@ def test_NAMEIII_version2(self):
         )
         self.assertCMLApproxData(cubes, ("name", "NAMEIII_version2.cml"))
 
-    def test_NAMEII_trajectory(self):
+    def test_NAMEIII_trajectory(self):
         cubes = iris.load(
             tests.get_data_path(("NAME", "NAMEIII_trajectory.txt"))
         )
@@ -48,6 +51,32 @@ def test_NAMEII_trajectory(self):
             cubes, ("name", "NAMEIII_trajectory.cml"), checksum=False
         )
 
+    def test_NAMEII__no_time_averaging(self):
+        cubes = iris.load(
+            tests.get_data_path(("NAME", "NAMEII_no_time_averaging.txt"))
+        )
+
+        # Also check that it saves without error.
+        # This was previously failing, see https://github.com/SciTools/iris/issues/3288
+        with tempfile.TemporaryDirectory() as temp_dirpath:
+            iris.save(cubes, temp_dirpath + "/tmp.nc")
+
+        self.assertCML(
+            cubes[0],
+            (
+                "name",
+                "NAMEII_field__no_time_averaging_0.cml",
+            ),
+        )
+        self.assertCML(
+            cubes,
+            (
+                "name",
+                "NAMEII_field__no_time_averaging.cml",
+            ),
+            checksum=False,
+        )
+
 
 if __name__ == "__main__":
     tests.main()