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

* v3.3.x: Update whatsnew for 3.3.1 release (#5002) Port dependency fixes to `v3.3.x`. (#4992) Fix name loader problem (#4933) Reinstate CubeList._repr_html_() (#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
SciTools · 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()