Refactor shape masking #6129

hsteptoe · 2024-08-22T14:35:28Z

🚀 Pull Request

Description

Fixes #6126 by exposing the shape geometry to the user. Adds to docs and docstrings to make it clearer how to use this.

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benchmark_this Request that this pull request be benchmarked to check if it introduces performance shifts

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pp-mo · 2024-08-28T09:16:41Z

From @SciTools/peloton : discussed what we are seeing here and in #6126.
We think this is looking useful, but the two of you seem to have it covered @hsteptoe @acchamber ?
Please shout if you need help.

hsteptoe · 2024-08-28T09:55:53Z

Discussion with @acchamber notes:

Don't move imports out of functions as this creates circular import errors
Check target_crs assignment for occasion when cube doesn't have a CRS
Re-write conversion of 0-360 -> -180-180 coords in case of degree based CRSs

hsteptoe · 2024-11-22T11:31:36Z

What are @SciTools/peloton (@pp-mo) thoughts about adding rasterio as a Iris dependency?

This would facilitate better handling of shapes to rasters (which is essentially the problem we're solving) with the added bonus that we could also mask to other shape types, like lines, to extract a trajectory from a Cube, for example.

acchamber · 2024-11-29T14:06:06Z

I've had a few other discussions with other users now where they can't use this function with OSGB shapefiles which this PR would fix. Where are we on being able to include it in the next release?

@hsteptoe @pp-mo

hsteptoe · 2024-12-02T09:56:12Z

I've had a few other discussions with other users now where they can't use this function with OSGB shapefiles which this PR would fix. Where are we on being able to include it in the next release?

@hsteptoe @pp-mo

I was planning on going to the AVD surgery this week to discuss some changes and/or make the case for rasterio

trexfeathers · 2024-12-02T15:28:12Z

Thanks for your patience everyone. It's sometimes a struggle to balance everything and we just haven't had an opportunity to discuss this. Coming to the Surgery (UK Met Office) is an ideal next step.

stephenworsley · 2024-12-04T12:57:19Z

@pp-mo, @trexfeathers and @stephenworsley have discussed this at the Surgery and agree in principle that we could consider adding rasterio as an optional dependency.

for more information, see https://pre-commit.ci

trexfeathers · 2025-02-05T10:42:50Z

From @SciTools/peloton: would @hsteptoe and @acchamber appreciate any more input from core devs at this point?

hsteptoe · 2025-02-05T12:07:07Z

From @SciTools/peloton: would @hsteptoe and @acchamber appreciate any more input from core devs at this point?

I just need to find more time, which is in short supply as we get near the end of FY...

for more information, see https://pre-commit.ci

hsteptoe · 2025-02-14T16:38:23Z

This is now ready for some initial (alpha?) testing 🎉. @acchamber are you available to try out the new features? (Updates to docs etc. will follow if this is successful) Tests are incomplete are should not be review yet.

This is a fairly substantial re-write. New/improved features include:

Automatic CRS transforms. Will handle situation where the cube and geometry have different CRSs by transforming the geometry.
Handles all shape types, including Points, Lines and MultiPolygons.

There are some breaking changes, principally moving away from having a minimum_weight keyword, replacing it with an all_touched keyword. The rational here is for consistency across shape types. Minimum weight doesn't make sense for Points and Lines. Instead, Line pixilation is based on Bresenham's line algorithm. Polygon pixilation is based on either: (a) pixel centres that intersect the polygon, or (b) all pixels touched by the polygon irrespective of the area of intersection.

My informal tests so far show working behaviour for iris test data from rotated_pole.nc, toa_brightness_stereographic.nc, E1_north_america.nc, air_temp.pp. Know limitation (not-working) for semi-structured model grids, such as orca2_votemper.nc. Some test shapefiles 👉test_shapefiles.zip

…bugfix-shape-masking

for more information, see https://pre-commit.ci

trexfeathers · 2025-08-29T10:07:35Z

pyproject.toml

+[project.optional-dependencies]
+RASTERIO = ["rasterio"]
+


@bjlittle I remember that we stopped doing PyPI optional dependencies during your tenure with Iris. Can you remember why? Would you anticipate problems if we started again?

Maybe it's just a problem with a single-source-of-truth?

@trexfeathers @bjlittle Did you come to a conclusion about this?

We didn't. However we are attempting to standardise across our repositories and we don't have an agreed way to handle optional dependencies, so please remove this entry.

CLAassistant · 2025-10-06T07:55:06Z

All committers have signed the CLA.

hsteptoe · 2025-10-07T13:28:28Z

@stephenworsley @trexfeathers Can you advise on apparently nox related errors that I'm seeing in the current CI failures, giving an error message: CondaHTTPError: HTTP 401 CONNECTION FAILED for url...

And, do you know why my local pre-commit version of numpydoc-validation might pass, but the github action one fails?

trexfeathers · 2025-10-14T14:54:35Z

@stephenworsley @trexfeathers Can you advise on apparently nox related errors that I'm seeing in the current CI failures, giving an error message: CondaHTTPError: HTTP 401 CONNECTION FAILED for url...

And, do you know why my local pre-commit version of numpydoc-validation might pass, but the github action one fails?

@hsteptoe really sorry for missing this. There is a MO-specific step you will need to do for the lockfiles, will message you offline.

I'm less sure about pre-commit. There is some nuance about only testing files which have been edited; perhaps the merge from main means that your PR is changing more than your local branch was.

hsteptoe · 2025-10-15T13:09:40Z

@stephenworsley @trexfeathers Can you advise on apparently nox related errors that I'm seeing in the current CI failures, giving an error message: CondaHTTPError: HTTP 401 CONNECTION FAILED for url...
And, do you know why my local pre-commit version of numpydoc-validation might pass, but the github action one fails?

@hsteptoe really sorry for missing this. There is a MO-specific step you will need to do for the lockfiles, will message you offline.

I'm less sure about pre-commit. There is some nuance about only testing files which have been edited; perhaps the merge from main means that your PR is changing more than your local branch was.

pre-commit related errors may have been something wrong going on with my pre-commit cache. Did a pre-commit clean and re-ran and that seemed to resolve the inconsistency issues.

trexfeathers

Still left to review:

_shapefiles.py
tests
lock files

trexfeathers · 2025-10-15T10:41:17Z

docs/src/whatsnew/latest.rst

+#. `@hsteptoe <https://github.com/hsteptoe>`_ added `rasterio <https://rasterio.readthedocs.io/en/stable/index.html>`_ 
+   and `affiine <https://affine.readthedocs.io/en/latest/>`_ as a dependency for :func:`iris.util.mask_cube_from_shapefile`. 
+   This is to support the new functionality of handling additional shapefiles and projections. (:issue:`6126`, :pull:`6129`)


Very important to emphasise that this is an optional dependency.

trexfeathers · 2025-10-15T11:06:02Z

pyproject.toml

+[project.optional-dependencies]
+RASTERIO = ["rasterio"]
+


We didn't. However we are attempting to standardise across our repositories and we don't have an agreed way to handle optional dependencies, so please remove this entry.

trexfeathers · 2025-10-15T11:06:29Z

docs/src/whatsnew/latest.rst

   horizontal grid.
   (:issue:`5770`, :pull:`6581`)

+#. `@hsteptoe <https://github.com/hsteptoe>`_ and `@...`_ (reviewer) extended :func:`iris.util.mask_cube_from_shapefile`


Suggested change

#. `@hsteptoe <https://github.com/hsteptoe>`_ and `@...`_ (reviewer) extended :func:`iris.util.mask_cube_from_shapefile`

#. `@hsteptoe <https://github.com/hsteptoe>`_ and `@trexfeathers`_ (reviewer) extended :func:`iris.util.mask_cube_from_shapefile`

trexfeathers · 2025-10-15T11:22:29Z

lib/iris/util.py

+    cube: iris.cube.Cube,
+    shape: shapely.Geometry,
+    shape_crs: cartopy.crs | pyproj.CRS,
+    in_place: bool = False,
+    minimum_weight: float = 0.0,
+    **kwargs,


You've changed the order of parameters. Anyone calling this without using keywords e.g. mask_cube_from_shapefile(my_cube, my_shape, 0.5, True) will get a failure.

trexfeathers · 2025-10-15T11:30:45Z

lib/iris/util.py

+        A number between 0-1 describing what % of a cube cell area must the shape overlap to be masked.
+        Only applied to polygon shapes.  If the shape is a line or point then this is ignored.
+
+    Other Parameters


How did you decide which ones were kwargs and which ones were named parameters?

trexfeathers · 2025-10-15T12:49:14Z

lib/iris/util.py

+    For best masking results, both the cube _and_ masking geometry should have a
+    coordinate reference system (CRS) defined. Masking results will be most reliable


Clarify that the masking geometry CRS comes from the function parameter (as opposed to being part of the shape object itself)?

trexfeathers · 2025-10-15T12:52:50Z

lib/iris/util.py

+
+    Mask a :class:`~iris.cube.Cube` with any shape object, (e.g. Natural Earth Shapefiles via cartopy).
+    Finds the overlap between the `shape` and the :class:`~iris.cube.Cube` and
+    masks out any cells that __do not__ intersect the shape.


Suggested change

masks out any cells that __do not__ intersect the shape.

masks out any cells that _do not_ intersect the shape.

This is rendering weird.

trexfeathers · 2025-10-15T12:54:24Z

lib/iris/util.py

+    By default, all cells touched by geometries are kept (equivalent to `minimum_weight=0`). This behaviour
+    can be changed by increasing the `minimum_weight` keyword argument or setting `all_touched=False`,
+    then only the only cells whose center is within the polygon or that are selected by Bresenham’s line algorithm
+    (for line type shapes) are kept.   For points, the `minimum_weight` is ignored, and the cell that intersects the point
+    is kept.


Suggested change

By default, all cells touched by geometries are kept (equivalent to `minimum_weight=0`). This behaviour

can be changed by increasing the `minimum_weight` keyword argument or setting `all_touched=False`,

then only the only cells whose center is within the polygon or that are selected by Bresenham’s line algorithm

(for line type shapes) are kept. For points, the `minimum_weight` is ignored, and the cell that intersects the point

is kept.

By default, all cells touched by geometries are kept (equivalent to ``minimum_weight=0``). This behaviour

can be changed by increasing the ``minimum_weight`` keyword argument or setting ``all_touched=False``,

then only the only cells whose center is within the polygon or that are selected by Bresenham’s line algorithm

(for line type shapes) are kept. For points, the `minimum_weight` is ignored, and the cell that intersects the point

is kept.

If you want monospace: it's double-backtick.

If you want to refer to a parameter: I believe the standard recommends single-backtick.

There are a few more examples elsewhere in this docstring.

trexfeathers · 2025-10-15T13:02:42Z

lib/iris/util.py

+    >>> admin1 = shpreader.natural_earth(resolution='110m',
+                                         category='cultural',
+                                         name='admin_1_states_provinces_lakes')


Suggested change

>>> admin1 = shpreader.natural_earth(resolution='110m',

category='cultural',

name='admin_1_states_provinces_lakes')

>>> admin1 = shpreader.natural_earth(resolution='110m',

... category='cultural',

... name='admin_1_states_provinces_lakes')

trexfeathers · 2025-10-15T13:11:21Z

lib/iris/util.py

+
+    Extract a rectangular region covering the UK from a stereographic projection cube:
+
+    >>> cube = iris.load_cube(iris.sample_data_path("toa_brightness_stereographic.nc"))


It would be great to print some one line Cube summaries to demonstrate the effect that masking is having.

Example:

Suggested change

>>> cube = iris.load_cube(iris.sample_data_path("toa_brightness_stereographic.nc"))

>>> cube = iris.load_cube(iris.sample_data_path("toa_brightness_stereographic.nc"))

>>> print(cube.summary(shorten=True))

toa_brightness_temperature / (K) (projection_y_coordinate: 160; projection_x_coordinate: 256)

trexfeathers · 2025-10-15T13:17:34Z

lib/iris/util.py

+import cartopy
 import cf_units
 from dask import array as da
 import numpy as np
 import numpy.ma as ma
+import pyproj
+import shapely


Imports that are exclusively for type-hinting should be moved into the TYPE_CHECKING code block:

iris/lib/iris/util.py

Lines 38 to 39 in 8333991

if TYPE_CHECKING:

from iris.cube import Cube, CubeList

trexfeathers · 2025-10-15T13:19:35Z

lib/iris/util.py

 from iris._deprecation import warn_deprecated
 from iris._lazy_data import is_lazy_data, is_lazy_masked_data
-from iris._shapefiles import create_shapefile_mask
+from iris._shapefiles import create_shape_mask


This needs to be moved within mask_cube_from_shape(), since it invokes an optional dependency. Otherwise anyone who wants to use ANYTHING in iris.util needs to have Rasterio and Affine installed!

(this would fix the benchmarking CI by the way)

trexfeathers

Still left to review:

tests
lock files
confirm stable behaviour given the heavy refactor

trexfeathers · 2025-10-15T13:40:12Z

lib/iris/_shapefiles.py

+# to "OFF" in the environment. Having PROJ_NETWORK = "ON"
+# can lead to some coordinate transformations resulting in Inf values.


What a pointless feature! I'd be interested to know why.

trexfeathers · 2025-10-15T13:41:42Z

lib/iris/_shapefiles.py

+if "iris.cube" in sys.modules:
+    import iris.cube
+if "iris.analysis.cartography" in sys.modules:
+    import iris.analysis.cartography


This is unprecedented. Something larger is wrong if these modules are not available.

trexfeathers · 2025-10-15T14:06:36Z

lib/iris/_shapefiles.py

+    minimum_weight : float, optional
+        The minimum weight of the geometry to be included in the mask.
+        If the weight is less than this value, the geometry will not be
+        included in the mask. Defaults to 0.0.
+    all_touched : bool, optional
+        If True, all pixels touched by the geometry will be included in the mask.
+        If False, only pixels fully covered by the geometry will be included in the mask.
+        Defaults to True.
+    invert : bool, optional
+        If True, the mask will be inverted, so that pixels not covered by the geometry
+        will be included in the mask. Defaults to False.


I'm confused about the defaults.

Stating optional is the correct way to say that something defaults to None. So that's correct for geometry_crs/all_touched/invert, but minimum_weight should say: float, default=0.0.

However: all_touched and invert incorrectly state that they have other default values. If this should be the case, then some changes are needed and optional needs to be replaced with default=. If this should NOT be the case, then the docstring needs correcting.

trexfeathers · 2025-10-15T14:19:47Z

lib/iris/_shapefiles.py

+    Examples
+    --------
+    >>> from shapely.geometry import box
+    >>> from pyproj import CRS
+    >>> from iris._shapefiles import is_geometry_valid
+
+    Create a valid geometry covering Canada, and check
+    its validity for the WGS84 coordinate system:
+
+    >>> canada = box(-143.5,42.6,-37.8,84.0)
+    >>> wgs84 = CRS.from_epsg(4326)
+    >>> is_geometry_valid(canada, wgs84)
+
+    The function returns silently if the geometry is valid.
+
+    Now create an invalid geometry covering the Bering Sea,
+    and check its validity for the WGS84 coordinate system.
+
+    >>> bering_sea = box(148.42,49.1,-138.74,73.12)
+    >>> wgs84 = CRS.from_epsg(4326)
+    >>> is_geometry_valid(bering_sea, wgs84) # doctest: +IGNORE_EXCEPTION_DETAIL
+    Traceback (most recent call last)
+    ValueError: Geometry crossing the 180th meridian is not supported.


This is admirable, but I should make you aware that by default no private modules - those named beginning with _ - are rendered in the documentation.

Still useful for future developers, or if we ever choose to make this public.

trexfeathers · 2025-10-15T14:26:45Z

lib/iris/_shapefiles.py

+        # Make pyproj transformer
+        # Transforms the input geometry to the WGS84 coordinate system
+        t = Transformer.from_crs(geometry_crs, WGS84_crs, always_xy=True).transform
+        geometry = shapely.ops.transform(t, geometry)


Should be calling _transform_geometry() here - an ideal way to ensure D.R.Y.

trexfeathers · 2025-10-15T16:22:58Z

lib/iris/_shapefiles.py

+    for xy in mask_xy:
+        weighted_mask_template[xy] = False


If you're concerned about performance, I believe there are ways to refactor this to assign False in a single NumPy operation instead of a loop.

If you're not worried then I'm not worried.

trexfeathers · 2025-10-15T16:36:35Z

lib/iris/_shapefiles.py

+    if not cube.coord(axis="X", dim_coords=True).has_bounds():
+        cube.coord(axis="X", dim_coords=True).guess_bounds()
+    if not cube.coord(axis="Y", dim_coords=True).has_bounds():
+        cube.coord(axis="Y", dim_coords=True).guess_bounds()
+    # Get the shape of the cube
+    w = len(cube.coord(axis="X", dim_coords=True).points)
+    h = len(cube.coord(axis="Y", dim_coords=True).points)
+    # Get the bounds of the cube
+    # x_bounds = _get_mod_rebased_coord_bounds(cube.coord(x_name))
+    # y_bounds = _get_mod_rebased_coord_bounds(cube.coord(y_name))
+    x_bounds = cube.coord(axis="X", dim_coords=True).bounds
+    y_bounds = cube.coord(axis="Y", dim_coords=True).bounds


I had trouble reading this section. Also calling cube.coord() is expensive.

Suggested change

if not cube.coord(axis="X", dim_coords=True).has_bounds():

cube.coord(axis="X", dim_coords=True).guess_bounds()

if not cube.coord(axis="Y", dim_coords=True).has_bounds():

cube.coord(axis="Y", dim_coords=True).guess_bounds()

# Get the shape of the cube

w = len(cube.coord(axis="X", dim_coords=True).points)

h = len(cube.coord(axis="Y", dim_coords=True).points)

# Get the bounds of the cube

# x_bounds = _get_mod_rebased_coord_bounds(cube.coord(x_name))

# y_bounds = _get_mod_rebased_coord_bounds(cube.coord(y_name))

x_bounds = cube.coord(axis="X", dim_coords=True).bounds

y_bounds = cube.coord(axis="Y", dim_coords=True).bounds

x_coord, y_coord = [cube.coord(axis=a, dim_coords=True) for a in ("X", "Y")]

w, h = [len(c.points) for c in (x_coord, y_coord)]

for coord in (x_coord, y_coord):

if not coord.has_bounds():

coord.guess_bounds()

x_bounds, y_bounds = [c.bounds() for c in (x_coord, y_coord)]

trexfeathers · 2025-10-15T16:46:44Z

lib/iris/_shapefiles.py

+    w = len(x_coord.points)
+    h = len(y_coord.points)
+    # Mask by weight if minimum_weight > 0.0
+    if minimum_weight > 0:


We discussed preserving existing behaviour with minimum_weight - #6129 (comment) - to avoid breaking changes. I'm having a hard time confirming this:

The code for this behaviour has been heavily refactored

The existing tests have been rewritten and can no longer be run in their original form due to API changes

Can you help? Do you have anything 'ready-made' that I can use to confirm stable behaviour? Otherwise I'll write something myself. Thanks

trexfeathers · 2025-10-15T17:06:32Z

lib/iris/_shapefiles.py

+    x_points = cube.coord(axis="X", dim_coords=True).points
+    y_points = cube.coord(axis="Y", dim_coords=True).points


Please assign the coords to variables to avoid running Cube.coord() more than you need to (it's slow)

trexfeathers · 2025-10-15T17:11:35Z

lib/iris/_shapefiles.py

+        # Define raster transform based on cube
+        # This maps the geometry domain onto the cube domain
+        tr = _make_raster_cube_transform(cube)
+        # Generate mask from geometry
+        mask_template = rfeatures.geometry_mask(
+            geometries=shapely.get_parts(geometry),
+            out_shape=(h, w),
+            transform=tr,
+            all_touched=all_touched,
+        )


Would you be up for giving me a 5 minute lesson about this?

hsteptoe and others added 3 commits August 22, 2024 15:05

Updates to allow varying shape crs

ebee977

Ruff fixes

e32f911

[pre-commit.ci] auto fixes from pre-commit.com hooks

76eae38

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Merge branch 'SciTools:main' into bugfix-shape-masking

bcdca30

hsteptoe and others added 11 commits December 6, 2024 13:37

Merge branch 'SciTools:main' into bugfix-shape-masking

9dab7c6

Adding rasterio as optional dependency

ebaa1ee

Adding rasterio functionality

103e3d7

First working version with rasterio

3c65dab

Add further shape geometry checks

25de18d

Update shapefile tests

10e4413

Reorganise test fixtures

cd5cf99

Reorganise test fixtures

edc25cc

Fix fixture fetching

789c98d

Merge branch 'SciTools:main' into bugfix-shape-masking

27a9025

[pre-commit.ci] auto fixes from pre-commit.com hooks

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hsteptoe and others added 4 commits February 7, 2025 08:26

Merge branch 'SciTools:main' into bugfix-shape-masking

5b1054b

Recording Affine transform trials

8948ce6

Working masking

a77c628

[pre-commit.ci] auto fixes from pre-commit.com hooks

1793e1f

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bjlittle added this to the v3.13 milestone Feb 17, 2025

hsteptoe and others added 5 commits August 27, 2025 13:25

Merge branch 'SciTools:main' into bugfix-shape-masking

9787b6a

Merge branch 'bugfix-shape-masking' of github.com:hsteptoe/iris into …

73e6113

…bugfix-shape-masking

Minor function call name change

7311dac

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pre-commit fixes

b455a26

trexfeathers reviewed Aug 29, 2025

View reviewed changes

Merge branch 'main' into bugfix-shape-masking

e0a4eaf

stephenworsley added this to 🦌 Iris 3.14 Sep 2, 2025

scitools-ci bot removed this from 🚴 Peloton Sep 24, 2025

scitools-ci bot added this to 🚴 Peloton Sep 25, 2025

hsteptoe added 6 commits October 7, 2025 09:01

Merge branch 'main' into bugfix-shape-masking

4bba208

Resolve lock files with added rasterio and affine

84fd9c2

Sync branches

bb8ba7f

Resolve lock files with added rasterio and affine

6f42579

Test consistency updates

d17a4d5

Merge branch 'main' into bugfix-shape-masking

c4a7b63

hsteptoe added 4 commits October 15, 2025 10:06

Update lock file urls

1536638

Merge branch 'SciTools:main' into bugfix-shape-masking

3d2d60b

Trying to fix numpy-doc error

3a10a0e

Update lockfiles

1b2b0b3

trexfeathers moved this to 👀 In Review in 🦌 Iris 3.14 Oct 15, 2025

trexfeathers changed the title ~~Bugfix shape masking~~ Refactor shape masking Oct 15, 2025

Merge branch 'main' into bugfix-shape-masking

8333991

trexfeathers requested changes Oct 15, 2025

View reviewed changes

	#. `@hsteptoe <https://github.com/hsteptoe>`_ and `@...`_ (reviewer) extended :func:`iris.util.mask_cube_from_shapefile`
	#. `@hsteptoe <https://github.com/hsteptoe>`_ and `@trexfeathers`_ (reviewer) extended :func:`iris.util.mask_cube_from_shapefile`

		For best masking results, both the cube _and_ masking geometry should have a
		coordinate reference system (CRS) defined. Masking results will be most reliable

	masks out any cells that __do not__ intersect the shape.
	masks out any cells that _do not_ intersect the shape.


		Extract a rectangular region covering the UK from a stereographic projection cube:

		>>> cube = iris.load_cube(iris.sample_data_path("toa_brightness_stereographic.nc"))

		# to "OFF" in the environment. Having PROJ_NETWORK = "ON"
		# can lead to some coordinate transformations resulting in Inf values.

		x_points = cube.coord(axis="X", dim_coords=True).points
		y_points = cube.coord(axis="Y", dim_coords=True).points

		[project.optional-dependencies]
		RASTERIO = ["rasterio"]

		[project.optional-dependencies]
		RASTERIO = ["rasterio"]

Refactor shape masking #6129

Are you sure you want to change the base?

Refactor shape masking #6129

Conversation

hsteptoe commented Aug 22, 2024

🚀 Pull Request

Description

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pp-mo commented Aug 28, 2024

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hsteptoe commented Aug 28, 2024

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hsteptoe commented Nov 22, 2024

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acchamber commented Nov 29, 2024

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hsteptoe commented Dec 2, 2024

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trexfeathers commented Dec 2, 2024

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stephenworsley commented Dec 4, 2024

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trexfeathers commented Feb 5, 2025

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hsteptoe commented Feb 14, 2025 •

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CLAassistant commented Oct 6, 2025 •

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