Merge branch 'develop' into docs/limited_area

ecmwf · Nov 12, 2024 · 3afbfe0 · 3afbfe0
2 parents 505d914 + 30f039f
commit 3afbfe0
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -59,11 +59,6 @@ repos:
   hooks:
   - id: rstfmt
     exclude: 'cli/.*' # Because we use argparse
-- repo: https://github.com/b8raoult/pre-commit-docconvert
-  rev: "0.1.5"
-  hooks:
-  - id: docconvert
-    args: ["numpy"]
 - repo: https://github.com/tox-dev/pyproject-fmt
   rev: "2.2.4"
   hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,17 +8,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Please add your functional changes to the appropriate section in the PR.
 Keep it human-readable, your future self will thank you!
 
-## [Unreleased](https://github.com/ecmwf/anemoi-graphs/compare/0.3.0...HEAD)
+## [Unreleased](https://github.com/ecmwf/anemoi-graphs/compare/0.4.0...HEAD)
 
-### Added
-
-- fix: bug in color when plotting isolated nodes
+## [0.4.0 - LAM and stretched graphs](https://github.com/ecmwf/anemoi-graphs/compare/0.3.0...0.4.0) - 2024-11-08
 
 ### Added
 
-- Add anemoi-transform link to documentation
-
-### Added
 - ci: hpc-config, CODEOWNERS (#49)
 - feat: New node builder class, CutOutZarrDatasetNodes, to create nodes from 2 datasets. (#30)
 - feat: New class, KNNAreaMaskBuilder, to specify Area of Interest (AOI) based on a set of nodes. (#30)
@@ -27,12 +22,24 @@ Keep it human-readable, your future self will thank you!
 - feat: New method update_graph(graph) in the GraphCreator class. (#60)
 - feat: New class StretchedTriNodes to create a stretched mesh. (#51)
 - feat: Expanded MultiScaleEdges to support multi-scale connections in stretched graphs. (#51)
+- fix: bug in color when plotting isolated nodes (#63)
+- Add anemoi-transform link to documentation (#59)
+- Added `CutOutMask` class to create a mask for a cutout. (#68)
+- Added `MissingZarrVariable` and `NotMissingZarrVariable` classes to create a mask for missing zarr variables. (#68)
 - feat: Add CONTRIBUTORS.md file. (#72)
 
 - Create package documentation.
 
 ### Changed
+
 - ci: small fixes and updates pre-commit, downsteam-ci (#49)
+- Update CODEOWNERS (#61)
+- ci: extened python versions to include 3.11 and 3.12 (#66)
+- Update copyright notice (#67)
+
+### Removed
+
+- Remove `CutOutZarrDatasetNodes` class. (#68)
 - Update CODEOWNERS
 - Fix pre-commit regex
 - ci: extened python versions to include 3.11 and 3.12

diff --git a/docs/conf.py b/docs/conf.py
@@ -29,15 +29,15 @@
 
 project = "Anemoi Graphs"
 
-author = "ECMWF"
+author = "Anemoi contributors"
 
 year = datetime.datetime.now().year
 if year == 2024:
     years = "2024"
 else:
     years = "2024-%s" % (year,)
 
-copyright = "%s, ECMWF" % (years,)
+copyright = "%s, Anemoi contributors" % (years,)
 
 try:
     from anemoi.graphs._version import __version__

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,14 +1,12 @@
-#!/usr/bin/env python
-# (C) Copyright 2024 ECMWF.
+# (C) Copyright 2024 Anemoi contributors.
 #
 # This software is licensed under the terms of the Apache Licence Version 2.0
 # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
 # In applying this licence, ECMWF does not waive the privileges and immunities
 # granted to it by virtue of its status as an intergovernmental organisation
 # nor does it submit to any jurisdiction.
 
-# https://packaging.python.org/en/latest/guides/writing-pyproject-toml/
-
 [build-system]
 requires = [ "setuptools>=60", "setuptools-scm>=8" ]
 

diff --git a/src/anemoi/graphs/__init__.py b/src/anemoi/graphs/__init__.py
@@ -1,6 +1,8 @@
-# (C) Copyright 2023 European Centre for Medium-Range Weather Forecasts.
+# (C) Copyright 2024 Anemoi contributors.
+#
 # This software is licensed under the terms of the Apache Licence Version 2.0
 # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
 # In applying this licence, ECMWF does not waive the privileges and immunities
 # granted to it by virtue of its status as an intergovernmental organisation
 # nor does it submit to any jurisdiction.

diff --git a/src/anemoi/graphs/__main__.py b/src/anemoi/graphs/__main__.py
@@ -1,12 +1,11 @@
-#!/usr/bin/env python
-# (C) Copyright 2024 ECMWF.
+# (C) Copyright 2024 Anemoi contributors.
 #
 # This software is licensed under the terms of the Apache Licence Version 2.0
 # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
 # In applying this licence, ECMWF does not waive the privileges and immunities
 # granted to it by virtue of its status as an intergovernmental organisation
 # nor does it submit to any jurisdiction.
-#
 
 from anemoi.utils.cli import cli_main
 from anemoi.utils.cli import make_parser

diff --git a/src/anemoi/graphs/commands/__init__.py b/src/anemoi/graphs/commands/__init__.py
@@ -1,12 +1,11 @@
-#!/usr/bin/env python
-# (C) Copyright 2024 ECMWF.
+# (C) Copyright 2024 Anemoi contributors.
 #
 # This software is licensed under the terms of the Apache Licence Version 2.0
 # which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
 # In applying this licence, ECMWF does not waive the privileges and immunities
 # granted to it by virtue of its status as an intergovernmental organisation
 # nor does it submit to any jurisdiction.
-#
 
 import os
 

diff --git a/src/anemoi/graphs/edges/__init__.py b/src/anemoi/graphs/edges/__init__.py
@@ -1,3 +1,12 @@
+# (C) Copyright 2024 Anemoi contributors.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+
 from .builder import CutOffEdges
 from .builder import KNNEdges
 from .builder import MultiScaleEdges

diff --git a/src/anemoi/graphs/generate/__init__.py b/src/anemoi/graphs/generate/__init__.py
@@ -0,0 +1,8 @@
+# (C) Copyright 2024 Anemoi contributors.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
diff --git a/src/anemoi/graphs/generate/tri_icosahedron.py b/src/anemoi/graphs/generate/tri_icosahedron.py
@@ -175,8 +175,8 @@ def add_edges_to_nx_graph(
 
         # Limit area of mesh points.
         if area_mask_builder is not None:
-            aoi_mask = area_mask_builder.get_mask(r_vertices_rad)
-            valid_nodes = np.where(aoi_mask)[0]
+            area_mask = area_mask_builder.get_mask(r_vertices_rad)
+            valid_nodes = np.where(area_mask)[0]
         else:
             valid_nodes = None
 

diff --git a/src/anemoi/graphs/nodes/__init__.py b/src/anemoi/graphs/nodes/__init__.py
@@ -1,4 +1,12 @@
-from .builders.from_file import CutOutZarrDatasetNodes
+# (C) Copyright 2024 Anemoi contributors.
+#
+# This software is licensed under the terms of the Apache Licence Version 2.0
+# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# In applying this licence, ECMWF does not waive the privileges and immunities
+# granted to it by virtue of its status as an intergovernmental organisation
+# nor does it submit to any jurisdiction.
+
 from .builders.from_file import LimitedAreaNPZFileNodes
 from .builders.from_file import NPZFileNodes
 from .builders.from_file import ZarrDatasetNodes
@@ -17,7 +25,6 @@
     "HexNodes",
     "HEALPixNodes",
     "LimitedAreaHEALPixNodes",
-    "CutOutZarrDatasetNodes",
     "LimitedAreaNPZFileNodes",
     "LimitedAreaTriNodes",
     "LimitedAreaHexNodes",