Merge back v3p0p1 (#3966)

bjlittle · tkknight · znicholls · web-flow · commit 40def237ecd2 · 2021-01-28T11:09:52.000Z
* Add release highlights and pin rc version (#3898) * Add release highlights and pin rc version * review actions * reorder release highlights (#3899) Tweak release highlights * Add whatsnew announcement (#3900) * Fix spelling (#3903) * Fix unit label handling (#3902) * Add failing test of plotting * Implement fix to pass test * Update idiff to ignore irrelevant hyphens in path * Update imagerepo (following docs) * Update after review by @trexfeathers * Add whatsnew entries * Move whatsnew entries into correct file * Release Docs Improvements (#3895) * Minor phrasing change in 'Release candidate'. * Before release deprecations. * Whatsnew highlights section. * Relax setup.py setup requirements (#3909) * Updated CF saver version in User Guide and docstring (#3925) * Updated CF saver version in User Guide and docstring * Remove references to CF version of the loader in docstrings * Added whatsnew * Pin cftime<1.3.0 * Migrate to cirrus-ci (#3928) * migrate from travis-ci to cirrus-ci * added whatsnew entries * ignore url for doc link check (#3929) * whatsnew for coord default units (#3924) * Cube._summary_coord_extra: efficiency and bugfix (#3922) * Add Documentation Title Case Capitalization (#3940) * Use Title Case Capitalisation for Documentation * add whatsnew enter * CI requirements drop pip packages (#3939) * requirements pip to conda * use pip install over develop * default PY_VER to python versions * update links (#3942) * update links * added s to http * Add support for 1-d weights in collapse. (#3943) * Remove warning for convert_units on lazy data (#3951) * drop stickler references in docs (#3953) * drop stickler references in docs * remove sticker from common links * update docs for travis-ci to cirrus-ci (#3954) * update docs for travis-ci to cirrus-ci * add 'travis-ci' reference locally to whatsnew * update whatsnew comment * docs for nox (#3955) * docs for nox * add titles, notices and additional detail * review actions * Resolve test coverage (#3947) * test coverage for __init__ and __call__ * test coverage for metadata resolve and coverage * partial test coverage for metadata mapping * python 3.6 workaround for deepcopy of mock.sentinel * test coverage for Resolve._free_mapping * test coverage for Resolve convenience methods * add test stub for Resolve._metadata_mapping * fix Test__tgt_cube_position * test coverage for shape * test coverage for _as_compatible_cubes * test coverage for Resolve._metadata_mapping * test coverage for Resolve._prepare_common_dim_payload * test coverage for Resolve._prepare_common_aux_payload * test coverage for Resolve._prepare_points_and_bounds * test coverage for Resolve._create_prepared_item * test coverage for Resolve._prepare_local_payload_dim * test coverage for Resolve._prepare_local_payload_aux * test coverage for Resolve._prepare_local_payload_scalar + docs URL skip * test coverage for Resolve._prepare_local_payload * test coverage for Resolve._metadata_prepare * added docs URL linkcheck skip * test coverage for Resolve._prepare_factory_payload * test coverage for Resolve._get_prepared_item * review actions * test coverage for Resolve.cube * pin v3.0.0 version and whatnew date (#3956) * update github ci checks image (#3957) * Promote unknown units to dimensionless in aux factories (#3965) * promote unknown to dimensionless units in aux factories * patch aux factories to promote unknown to dimensionless units for formula terms * add whatnew PR for entry Co-authored-by: tkknight <2108488+tkknight@users.noreply.github.com> Co-authored-by: Zeb Nicholls <zebedee.nicholls@climate-energy-college.org> Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> Co-authored-by: Jon Seddon <17068361+jonseddon@users.noreply.github.com> Co-authored-by: Ruth Comer <ruth.comer@metoffice.gov.uk> Co-authored-by: Patrick Peglar <patrick.peglar@metoffice.gov.uk>
diff --git a/docs/iris/src/conf.py b/docs/iris/src/conf.py
@@ -82,8 +82,8 @@ def autolog(message):
 if iris.__version__ == "dev":
     version = "dev"
 else:
-    # major.feature(.minor)-dev -> major.minor
-    version = ".".join(iris.__version__.split("-")[0].split(".")[:2])
+    # major.minor.patch-dev -> major.minor.patch
+    version = ".".join(iris.__version__.split("-")[0].split(".")[:3])
 # The full version, including alpha/beta/rc tags.
 release = iris.__version__
 
diff --git a/docs/iris/src/whatsnew/3.0.1.rst b/docs/iris/src/whatsnew/3.0.1.rst
diff --git a/docs/iris/src/whatsnew/index.rst b/docs/iris/src/whatsnew/index.rst
@@ -11,6 +11,7 @@ Iris versions.
    :maxdepth: 1
 
    latest.rst
+   3.0.1.rst
    3.0.rst
    2.4.rst
    2.3.rst
diff --git a/lib/iris/aux_factory.py b/lib/iris/aux_factory.py
@@ -11,6 +11,7 @@
 from abc import ABCMeta, abstractmethod
 import warnings
 
+import cf_units
 import dask.array as da
 import numpy as np
 
@@ -619,6 +620,10 @@ def _check_dependencies(delta, sigma, surface_air_pressure):
             warnings.warn(msg, UserWarning, stacklevel=2)
 
         # Check units.
+        if sigma is not None and sigma.units.is_unknown():
+            # Be graceful, and promote unknown to dimensionless units.
+            sigma.units = cf_units.Unit("1")
+
         if sigma is not None and not sigma.units.is_dimensionless():
             raise ValueError("Invalid units: sigma must be dimensionless.")
         if (
@@ -863,6 +868,10 @@ def _check_dependencies(sigma, eta, depth, depth_c, nsigma, zlev):
             )
             raise ValueError(msg)
 
+        if sigma is not None and sigma.units.is_unknown():
+            # Be graceful, and promote unknown to dimensionless units.
+            sigma.units = cf_units.Unit("1")
+
         if sigma is not None and not sigma.units.is_dimensionless():
             msg = (
                 "Invalid units: sigma coordinate {!r} "
@@ -1127,6 +1136,10 @@ def _check_dependencies(sigma, eta, depth):
                 warnings.warn(msg, UserWarning, stacklevel=2)
 
         # Check units.
+        if sigma is not None and sigma.units.is_unknown():
+            # Be graceful, and promote unknown to dimensionless units.
+            sigma.units = cf_units.Unit("1")
+
         if sigma is not None and not sigma.units.is_dimensionless():
             msg = (
                 "Invalid units: sigma coordinate {!r} "
@@ -1335,6 +1348,10 @@ def _check_dependencies(s, c, eta, depth, depth_c):
         # Check units.
         coords = ((s, "s"), (c, "c"))
         for coord, term in coords:
+            if coord is not None and coord.units.is_unknown():
+                # Be graceful, and promote unknown to dimensionless units.
+                coord.units = cf_units.Unit("1")
+
             if coord is not None and not coord.units.is_dimensionless():
                 msg = (
                     "Invalid units: {} coordinate {!r} "
@@ -1551,6 +1568,10 @@ def _check_dependencies(s, eta, depth, a, b, depth_c):
                 raise ValueError(msg)
 
         # Check units.
+        if s is not None and s.units.is_unknown():
+            # Be graceful, and promote unknown to dimensionless units.
+            s.units = cf_units.Unit("1")
+
         if s is not None and not s.units.is_dimensionless():
             msg = (
                 "Invalid units: s coordinate {!r} "
@@ -1776,6 +1797,10 @@ def _check_dependencies(s, c, eta, depth, depth_c):
         # Check units.
         coords = ((s, "s"), (c, "c"))
         for coord, term in coords:
+            if coord is not None and coord.units.is_unknown():
+                # Be graceful, and promote unknown to dimensionless units.
+                coord.units = cf_units.Unit("1")
+
             if coord is not None and not coord.units.is_dimensionless():
                 msg = (
                     "Invalid units: {} coordinate {!r} "
diff --git a/lib/iris/fileformats/netcdf.py b/lib/iris/fileformats/netcdf.py
@@ -719,6 +719,9 @@ def coord_from_term(term):
                         warnings.warn(msg)
                     coord_a = coord_from_term("a")
                     if coord_a is not None:
+                        if coord_a.units.is_unknown():
+                            # Be graceful, and promote unknown to dimensionless units.
+                            coord_a.units = "1"
                         delta = coord_a * coord_p0.points[0]
                         delta.units = coord_a.units * coord_p0.units
                         delta.rename("vertical pressure")
diff --git a/lib/iris/tests/unit/aux_factory/test_HybridPressureFactory.py b/lib/iris/tests/unit/aux_factory/test_HybridPressureFactory.py
@@ -113,6 +113,15 @@ def test_factory_metadata(self):
         self.assertIsNone(factory.coord_system)
         self.assertEqual(factory.attributes, {})
 
+    def test_promote_sigma_units_unknown_to_dimensionless(self):
+        sigma = mock.Mock(units=cf_units.Unit("unknown"), nbounds=0)
+        factory = HybridPressureFactory(
+            delta=self.delta,
+            sigma=sigma,
+            surface_air_pressure=self.surface_air_pressure,
+        )
+        self.assertEqual("1", factory.dependencies["sigma"].units)
+
 
 class Test_dependencies(tests.IrisTest):
     def setUp(self):
diff --git a/lib/iris/tests/unit/aux_factory/test_OceanSFactory.py b/lib/iris/tests/unit/aux_factory/test_OceanSFactory.py
@@ -137,6 +137,12 @@ def test_depth_incompatible_units(self):
         with self.assertRaises(ValueError):
             OceanSFactory(**self.kwargs)
 
+    def test_promote_s_units_unknown_to_dimensionless(self):
+        s = mock.Mock(units=Unit("unknown"), nbounds=0)
+        self.kwargs["s"] = s
+        factory = OceanSFactory(**self.kwargs)
+        self.assertEqual("1", factory.dependencies["s"].units)
+
 
 class Test_dependencies(tests.IrisTest):
     def setUp(self):
diff --git a/lib/iris/tests/unit/aux_factory/test_OceanSg1Factory.py b/lib/iris/tests/unit/aux_factory/test_OceanSg1Factory.py
@@ -121,6 +121,15 @@ def test_depth_incompatible_units(self):
         with self.assertRaises(ValueError):
             OceanSg1Factory(**self.kwargs)
 
+    def test_promote_c_and_s_units_unknown_to_dimensionless(self):
+        c = mock.Mock(units=Unit("unknown"), nbounds=0)
+        s = mock.Mock(units=Unit("unknown"), nbounds=0)
+        self.kwargs["c"] = c
+        self.kwargs["s"] = s
+        factory = OceanSg1Factory(**self.kwargs)
+        self.assertEqual("1", factory.dependencies["c"].units)
+        self.assertEqual("1", factory.dependencies["s"].units)
+
 
 class Test_dependencies(tests.IrisTest):
     def setUp(self):
diff --git a/lib/iris/tests/unit/aux_factory/test_OceanSg2Factory.py b/lib/iris/tests/unit/aux_factory/test_OceanSg2Factory.py
@@ -121,6 +121,15 @@ def test_depth_incompatible_units(self):
         with self.assertRaises(ValueError):
             OceanSg2Factory(**self.kwargs)
 
+    def test_promote_c_and_s_units_unknown_to_dimensionless(self):
+        c = mock.Mock(units=Unit("unknown"), nbounds=0)
+        s = mock.Mock(units=Unit("unknown"), nbounds=0)
+        self.kwargs["c"] = c
+        self.kwargs["s"] = s
+        factory = OceanSg2Factory(**self.kwargs)
+        self.assertEqual("1", factory.dependencies["c"].units)
+        self.assertEqual("1", factory.dependencies["s"].units)
+
 
 class Test_dependencies(tests.IrisTest):
     def setUp(self):
diff --git a/lib/iris/tests/unit/aux_factory/test_OceanSigmaFactory.py b/lib/iris/tests/unit/aux_factory/test_OceanSigmaFactory.py
@@ -59,6 +59,12 @@ def test_depth_incompatible_units(self):
         with self.assertRaises(ValueError):
             OceanSigmaFactory(**self.kwargs)
 
+    def test_promote_sigma_units_unknown_to_dimensionless(self):
+        sigma = mock.Mock(units=Unit("unknown"), nbounds=0)
+        self.kwargs["sigma"] = sigma
+        factory = OceanSigmaFactory(**self.kwargs)
+        self.assertEqual("1", factory.dependencies["sigma"].units)
+
 
 class Test_dependencies(tests.IrisTest):
     def setUp(self):
diff --git a/lib/iris/tests/unit/aux_factory/test_OceanSigmaZFactory.py b/lib/iris/tests/unit/aux_factory/test_OceanSigmaZFactory.py
@@ -138,6 +138,12 @@ def test_depth_incompatible_units(self):
         with self.assertRaises(ValueError):
             OceanSigmaZFactory(**self.kwargs)
 
+    def test_promote_sigma_units_unknown_to_dimensionless(self):
+        sigma = mock.Mock(units=Unit("unknown"), nbounds=0)
+        self.kwargs["sigma"] = sigma
+        factory = OceanSigmaZFactory(**self.kwargs)
+        self.assertEqual("1", factory.dependencies["sigma"].units)
+
 
 class Test_dependencies(tests.IrisTest):
     def setUp(self):
diff --git a/lib/iris/tests/unit/fileformats/netcdf/test__load_aux_factory.py b/lib/iris/tests/unit/fileformats/netcdf/test__load_aux_factory.py
@@ -53,8 +53,44 @@ def test_formula_terms_ap(self):
         self.assertEqual(factory.surface_air_pressure, self.ps)
 
     def test_formula_terms_a_p0(self):
-        coord_a = DimCoord(np.arange(5), units="Pa")
-        coord_p0 = DimCoord(10, units="1")
+        coord_a = DimCoord(np.arange(5), units="1")
+        coord_p0 = DimCoord(10, units="Pa")
+        coord_expected = DimCoord(
+            np.arange(5) * 10,
+            units="Pa",
+            long_name="vertical pressure",
+            var_name="ap",
+        )
+        self.cube_parts["coordinates"].extend(
+            [(coord_a, "a"), (coord_p0, "p0")]
+        )
+        self.requires["formula_terms"] = dict(a="a", b="b", ps="ps", p0="p0")
+        _load_aux_factory(self.engine, self.cube)
+        # Check cube.coord_dims method.
+        self.assertEqual(self.cube.coord_dims.call_count, 1)
+        args, _ = self.cube.coord_dims.call_args
+        self.assertEqual(len(args), 1)
+        self.assertIs(args[0], coord_a)
+        # Check cube.add_aux_coord method.
+        self.assertEqual(self.cube.add_aux_coord.call_count, 1)
+        args, _ = self.cube.add_aux_coord.call_args
+        self.assertEqual(len(args), 2)
+        self.assertEqual(args[0], coord_expected)
+        self.assertIsInstance(args[1], mock.Mock)
+        # Check cube.add_aux_factory method.
+        self.assertEqual(self.cube.add_aux_factory.call_count, 1)
+        args, _ = self.cube.add_aux_factory.call_args
+        self.assertEqual(len(args), 1)
+        factory = args[0]
+        self.assertEqual(factory.delta, coord_expected)
+        self.assertEqual(factory.sigma, mock.sentinel.b)
+        self.assertEqual(factory.surface_air_pressure, self.ps)
+
+    def test_formula_terms_a_p0__promote_a_units_unknown_to_dimensionless(
+        self,
+    ):
+        coord_a = DimCoord(np.arange(5), units="unknown")
+        coord_p0 = DimCoord(10, units="Pa")
         coord_expected = DimCoord(
             np.arange(5) * 10,
             units="Pa",
@@ -71,6 +107,7 @@ def test_formula_terms_a_p0(self):
         args, _ = self.cube.coord_dims.call_args
         self.assertEqual(len(args), 1)
         self.assertIs(args[0], coord_a)
+        self.assertEqual("1", args[0].units)
         # Check cube.add_aux_coord method.
         self.assertEqual(self.cube.add_aux_coord.call_count, 1)
         args, _ = self.cube.add_aux_coord.call_args
