Repository: SciTools/iris (language: python)

Issue:
[CI Bot] environment lockfiles auto-update
Lockfiles updated to the latest resolvable environment.
### If the CI tasks fail, create a new branch based on this PR and add the required fixes to that branch.


Discussion / hints:
Looks like we might need #5098 for this one, as we just have more of Antarctica showing...

... though I'm not clear why or whether we _should_ be seeing more of Antarctica: the latitude coordinate doesn't go below 80S :thinking: 

![idiff](https://user-images.githubusercontent.com/10599679/208252556-68dec7f9-107a-436a-8bb2-298fa4d421ae.png)

> ... though I'm not clear why or whether we should be seeing more of Antarctica: the latitude coordinate doesn't go below 80S 🤔

Patch releases of Cartopy and PyProj seem like candidates for an unintended change. I'm not aware of any Minor/Major releases that might have deliberately changed behaviour.

Maybe Shapely? Maybe an interaction between Cartopy and Shapely? I know that was giving the Cartopy devs some grief.
Have proved during local testing that Shapely causes the change in `test_2d_coord_bounds_platecarree`:

- `v1.8.5` = pass
- `v2.0.0` = fail
The change in Shapely version has stumbled across a problem that already existed at different `central_longitude` settings: SciTools/cartopy#2121.

It is difficult to know how to address this. The behaviour already existed and the test was just getting lucky at avoiding it. Meanwhile the test has already set a precedent of using specific settings to avoid another known problem (see SciTools/cartopy#1421):

https://github.com/SciTools/iris/blob/34560a5c7352878086b2012e651472936916a19a/lib/iris/tests/integration/plot/test_plot_2d_coords.py#L39-L43

Possible ways forward:

- Pin Shapely until we/Cartopy can address the problem.
  - No guarantee of resource - could be a while
  - Pins are bad
- Accept this change in behaviour.
  - The test would then be knowingly asserting for an incorrect plot
- Pick a different `central_longitude` that behaves correctly.
  - Definitely feels like evasion, but the test was already doing that anyway
- Remove the test.
  - It's not really doing its job if we're willing to change it to hide problems
  - On the other hand it is still demonstrating other correct behaviours

Fix patch:
diff --git a/benchmarks/benchmarks/experimental/ugrid/__init__.py b/benchmarks/benchmarks/experimental/ugrid/__init__.py
index 2f9bb04e35..2e40c525a6 100644
--- a/benchmarks/benchmarks/experimental/ugrid/__init__.py
+++ b/benchmarks/benchmarks/experimental/ugrid/__init__.py
@@ -50,7 +50,7 @@ def time_create(self, *params):
 
 class Connectivity(UGridCommon):
     def setup(self, n_faces):
-        self.array = np.zeros([n_faces, 3], dtype=np.int)
+        self.array = np.zeros([n_faces, 3], dtype=int)
         super().setup(n_faces)
 
     def create(self):
diff --git a/docs/src/further_topics/metadata.rst b/docs/src/further_topics/metadata.rst
index de1afb15af..4c55047d4c 100644
--- a/docs/src/further_topics/metadata.rst
+++ b/docs/src/further_topics/metadata.rst
@@ -389,10 +389,10 @@ instances. Normally, this would cause issues. For example,
 
 .. doctest:: richer-metadata
 
-    >>> simply = {"one": np.int(1), "two": np.array([1.0, 2.0])}
+    >>> simply = {"one": np.int32(1), "two": np.array([1.0, 2.0])}
     >>> simply
     {'one': 1, 'two': array([1., 2.])}
-    >>> fruity = {"one": np.int(1), "two": np.array([1.0, 2.0])}
+    >>> fruity = {"one": np.int32(1), "two": np.array([1.0, 2.0])}
     >>> fruity
     {'one': 1, 'two': array([1., 2.])}
     >>> simply == fruity
@@ -419,7 +419,7 @@ However, metadata class equality is rich enough to handle this eventuality,
 
     >>> metadata1
     CubeMetadata(standard_name='air_temperature', long_name=None, var_name='air_temperature', units=Unit('K'), attributes={'one': 1, 'two': array([1., 2.])}, cell_methods=(CellMethod(method='mean', coord_names=('time',), intervals=('6 hour',), comments=()),))
-    >>> metadata2 = cube.metadata._replace(attributes={"one": np.int(1), "two": np.array([1000.0, 2000.0])})
+    >>> metadata2 = cube.metadata._replace(attributes={"one": np.int32(1), "two": np.array([1000.0, 2000.0])})
     >>> metadata2
     CubeMetadata(standard_name='air_temperature', long_name=None, var_name='air_temperature', units=Unit('K'), attributes={'one': 1, 'two': array([1000., 2000.])}, cell_methods=(CellMethod(method='mean', coord_names=('time',), intervals=('6 hour',), comments=()),))
     >>> metadata1 == metadata2
diff --git a/requirements/ci/nox.lock/py310-linux-64.lock b/requirements/ci/nox.lock/py310-linux-64.lock
index 81a1661c1e..75ec1e5579 100644
--- a/requirements/ci/nox.lock/py310-linux-64.lock
+++ b/requirements/ci/nox.lock/py310-linux-64.lock
@@ -1,6 +1,6 @@
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 # platform: linux-64
-# input_hash: 65e8c3d4ababc804f8d3715a14ce94c3f564a37860525f35ea1aed69efd67be8
+# input_hash: 234b47d943728b5abe70fba0fd74c6adc10e4f1e2a14b919344f8a693b5b3e6f
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diff --git a/requirements/ci/nox.lock/py38-linux-64.lock b/requirements/ci/nox.lock/py38-linux-64.lock
index 0836e3d018..77cd6b8962 100644
--- a/requirements/ci/nox.lock/py38-linux-64.lock
+++ b/requirements/ci/nox.lock/py38-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: dc794a12a2155d2a605b34fc34ece8039a0f0d43fbf7d304366cf8c33cf94cd1
+# input_hash: 0543fd9bbb31e9f896ccf547f3b155d68bb748634268c28dde6ff3ac77aa74d3
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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@@ -36,18 +36,20 @@ https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h166bdaf_2.tar.bz2#ee8b8
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@@ -67,7 +69,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.t
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@@ -118,8 +120,9 @@ https://conda.anaconda.org/conda-forge/linux-64/xcb-util-wm-0.4.1-h166bdaf_0.tar
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+https://conda.anaconda.org/conda-forge/noarch/imagehash-4.3.1-pyhd8ed1ab_0.tar.bz2#132ad832787a2156be1f1b309835001a
diff --git a/requirements/ci/nox.lock/py39-linux-64.lock b/requirements/ci/nox.lock/py39-linux-64.lock
index f3f071da34..cc896e6989 100644
--- a/requirements/ci/nox.lock/py39-linux-64.lock
+++ b/requirements/ci/nox.lock/py39-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 8720b47771aff1b233330a6562a535e5ad3a153a023d02d4dc71b383a25796a3
+# input_hash: de178c2d53980747bafc10c4a4387eeb8c700311af7b35a2fcb49f1b441b960b
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080
@@ -37,18 +37,20 @@ https://conda.anaconda.org/conda-forge/linux-64/jpeg-9e-h166bdaf_2.tar.bz2#ee8b8
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+https://conda.anaconda.org/conda-forge/linux-64/libaec-1.0.6-h9c3ff4c_0.tar.bz2#c77f5e4e418fa47d699d6afa54c5d444
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-https://conda.anaconda.org/conda-forge/linux-64/libtool-2.4.6-h9c3ff4c_1008.tar.bz2#16e143a1ed4b4fd169536373957f6fee
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@@ -68,7 +70,7 @@ https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.t
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+https://conda.anaconda.org/conda-forge/linux-64/xxhash-0.8.1-h0b41bf4_0.conda#e9c3bcf0e0c719431abec8ca447eee27
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+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hff17c54_0.conda#dd682f0b6d65e75b2bc868fc8e93d87e
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@@ -99,14 +101,14 @@ https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.2-h6239696_4.tar.bz2#ad
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+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78
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+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.5.0-h82bc61c_0.conda#a01611c54334d783847879ee40109657
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@@ -119,8 +121,9 @@ https://conda.anaconda.org/conda-forge/linux-64/xcb-util-wm-0.4.1-h166bdaf_0.tar
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+https://conda.anaconda.org/conda-forge/noarch/appdirs-1.4.4-pyh9f0ad1d_0.tar.bz2#5f095bc6454094e96f146491fd03633b
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-https://conda.anaconda.org/conda-forge/noarch/attrs-22.1.0-pyh71513ae_1.tar.bz2#6d3ccbc56256204925bfa8378722792f
+https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9
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@@ -132,12 +135,12 @@ https://conda.anaconda.org/conda-forge/noarch/cycler-0.11.0-pyhd8ed1ab_0.tar.bz2
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@@ -145,21 +148,20 @@ https://conda.anaconda.org/conda-forge/noarch/imagesize-1.4.1-pyhd8ed1ab_0.tar.b
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Test patch:
diff --git a/lib/iris/tests/integration/plot/test_plot_2d_coords.py b/lib/iris/tests/integration/plot/test_plot_2d_coords.py
index b8fbc5e31a..1b95899803 100644
--- a/lib/iris/tests/integration/plot/test_plot_2d_coords.py
+++ b/lib/iris/tests/integration/plot/test_plot_2d_coords.py
@@ -38,10 +38,17 @@ def simple_cube_w_2d_coords():
 class Test(tests.GraphicsTest):
     def test_2d_coord_bounds_platecarree(self):
         # To avoid a problem with Cartopy smearing the data where the
-        # longitude wraps, we set the central_longitude
+        #  longitude wraps, we set the central_longitude.
+        #  SciTools/cartopy#1421
         cube = simple_cube_w_2d_coords()[0, 0]
         ax = plt.axes(projection=ccrs.PlateCarree(central_longitude=180))
         qplt.pcolormesh(cube)
+
+        # Cartopy can't reliably set y-limits with curvilinear plotting.
+        #  SciTools/cartopy#2121
+        y_lims = [m(cube.coord("latitude").points) for m in (np.min, np.max)]
+        ax.set_ylim(*y_lims)
+
         ax.coastlines(resolution="110m", color="red")
         self.check_graphic()
 
diff --git a/lib/iris/tests/unit/analysis/maths/__init__.py b/lib/iris/tests/unit/analysis/maths/__init__.py
index 311da8a0e6..558a6fccfe 100644
--- a/lib/iris/tests/unit/analysis/maths/__init__.py
+++ b/lib/iris/tests/unit/analysis/maths/__init__.py
@@ -247,7 +247,7 @@ def test_partial_mask_second_lazy_not_in_place(self):
 
     def test_in_place_introduces_mask(self):
         # If second cube is masked, result should also be masked.
-        data1 = np.arange(4, dtype=np.float)
+        data1 = np.arange(4, dtype=float)
         data2 = ma.array([2.0, 2.0, 2.0, 2.0], mask=[1, 1, 0, 0])
         cube1 = Cube(data1)
         cube2 = Cube(data2)