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Merge branch 'main' into rajeeja/onefile_open_dataset
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‎.github/ISSUE_TEMPLATE/release_request.md‎

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---
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name: Release Request
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about: Request a release for this package
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title: '[Release]: <version-number>'
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labels: release, high-priority
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assignees: 'philipc2'
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title: "[Release]: <version-number>"
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labels: release
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assignees: rajeeja
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---
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Date of intended release:

‎.github/workflows/asv-benchmarking-pr.yml‎

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@@ -65,7 +65,7 @@ jobs:
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- name: Post or update result comment
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id: comment
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uses: actions/github-script@v8
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uses: actions/github-script@v9
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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script: |

‎.github/workflows/asv-benchmarking.yml‎

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@@ -38,7 +38,7 @@ jobs:
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path: uxarray-asv
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- name: Setup Miniforge
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uses: conda-incubator/setup-miniconda@v3
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uses: conda-incubator/setup-miniconda@v4
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with:
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miniforge-version: "24.1.2-0"
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activate-environment: asv

‎.github/workflows/ci.yml‎

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@@ -11,6 +11,8 @@ jobs:
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# github.repository == 'UXARRAY/uxarray'
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name: Python (${{ matrix.python-version }}, ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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env:
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MPLBACKEND: Agg
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defaults:
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run:
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shell: bash -l {0}
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token: ${{ github.token }}
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- name: conda_setup (x64)
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uses: conda-incubator/setup-miniconda@v3
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uses: conda-incubator/setup-miniconda@v4
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if: matrix.os != 'macos-14'
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with:
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activate-environment: uxarray_build
@@ -44,7 +46,7 @@ jobs:
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miniforge-version: latest
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- name: conda_setup (ARM64)
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uses: conda-incubator/setup-miniconda@v3
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uses: conda-incubator/setup-miniconda@v4
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if: matrix.os == 'macos-14'
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with:
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activate-environment: uxarray_build

‎.github/workflows/upstream-dev-ci.yml‎

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@@ -70,7 +70,7 @@ jobs:
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shell: bash -l {0}
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steps:
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- name: checkout
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uses: actions/checkout@v6.0.2
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uses: actions/checkout@v6
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- name: Create or update failure issue
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shell: bash

‎.github/workflows/yac-optional.yml‎

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name: YAC Optional CI
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on:
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pull_request:
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paths:
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- ".github/workflows/yac-optional.yml"
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- "uxarray/remap/**"
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- "test/test_remap_yac.py"
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workflow_dispatch:
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jobs:
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yac-optional:
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name: YAC core v3.14.0_p1 (Ubuntu)
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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env:
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YAC_VERSION: v3.14.0_p1
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YAXT_VERSION: v0.11.5.1
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MPIEXEC: /usr/bin/mpirun
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MPIRUN: /usr/bin/mpirun
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MPICC: /usr/bin/mpicc
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MPIFC: /usr/bin/mpif90
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MPIF90: /usr/bin/mpif90
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OMPI_ALLOW_RUN_AS_ROOT: 1
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OMPI_ALLOW_RUN_AS_ROOT_CONFIRM: 1
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steps:
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- name: checkout
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uses: actions/checkout@v6
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with:
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token: ${{ github.token }}
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- name: conda_setup
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uses: conda-incubator/setup-miniconda@v4
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with:
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activate-environment: uxarray_build
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channel-priority: strict
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python-version: "3.11"
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channels: conda-forge
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environment-file: ci/environment.yml
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miniforge-variant: Miniforge3
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miniforge-version: latest
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- name: Install build dependencies (apt)
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run: |
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sudo apt-get update
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sudo apt-get install -y \
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autoconf \
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automake \
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gawk \
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gfortran \
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libopenmpi-dev \
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libtool \
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make \
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openmpi-bin \
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pkg-config
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- name: Verify MPI tools
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run: |
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which mpirun
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which mpicc
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which mpif90
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mpirun --version
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mpicc --version
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mpif90 --version
66+
- name: Install Python build dependencies
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run: |
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python -m pip install --upgrade pip
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python -m pip install cython wheel
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- name: Build and install YAXT
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run: |
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set -euxo pipefail
73+
YAC_PREFIX="${GITHUB_WORKSPACE}/yac_prefix"
74+
echo "YAC_PREFIX=${YAC_PREFIX}" >> "${GITHUB_ENV}"
75+
git clone --depth 1 --branch "${YAXT_VERSION}" https://gitlab.dkrz.de/dkrz-sw/yaxt.git
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if [ ! -x yaxt/configure ]; then
77+
if [ -x yaxt/autogen.sh ]; then
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(cd yaxt && ./autogen.sh)
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else
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(cd yaxt && autoreconf -i)
81+
fi
82+
fi
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mkdir -p yaxt/build
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cd yaxt/build
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../configure \
86+
--prefix="${YAC_PREFIX}" \
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--without-regard-for-quality \
88+
CC="${MPICC}" \
89+
FC="${MPIF90}"
90+
make -j2
91+
make install
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- name: Build and install YAC
93+
run: |
94+
set -euxo pipefail
95+
git clone --depth 1 --branch "${YAC_VERSION}" https://gitlab.dkrz.de/dkrz-sw/yac.git
96+
if [ ! -x yac/configure ]; then
97+
if [ -x yac/autogen.sh ]; then
98+
(cd yac && ./autogen.sh)
99+
else
100+
(cd yac && autoreconf -i)
101+
fi
102+
fi
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mkdir -p yac/build
104+
cd yac/build
105+
../configure \
106+
--prefix="${YAC_PREFIX}" \
107+
--with-yaxt-root="${YAC_PREFIX}" \
108+
--disable-mci \
109+
--disable-utils \
110+
--disable-examples \
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--disable-tools \
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--disable-netcdf \
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--enable-python-bindings \
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CC="${MPICC}" \
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FC="${MPIF90}"
116+
make -j2
117+
make install
118+
- name: Configure YAC runtime paths
119+
run: |
120+
set -euxo pipefail
121+
PY_VER="$(python -c 'import sys; print(f"{sys.version_info.major}.{sys.version_info.minor}")')"
122+
echo "LD_LIBRARY_PATH=${YAC_PREFIX}/lib:${LD_LIBRARY_PATH:-}" >> "${GITHUB_ENV}"
123+
echo "PYTHONPATH=${YAC_PREFIX}/lib/python${PY_VER}/site-packages:${YAC_PREFIX}/lib/python${PY_VER}/dist-packages:${PYTHONPATH:-}" >> "${GITHUB_ENV}"
124+
- name: Verify YAC core Python bindings
125+
run: |
126+
python - <<'PY'
127+
from pathlib import Path
128+
import sys
129+
candidates = []
130+
for entry in sys.path:
131+
pkg = Path(entry) / "yac"
132+
candidates.extend(pkg.glob("core*.so"))
133+
candidates.extend(pkg.glob("core*.pyd"))
134+
assert candidates, "yac.core extension not found on sys.path"
135+
print("Found yac.core extension:", candidates[0])
136+
PY
137+
- name: Install uxarray
138+
run: |
139+
python -m pip install . --no-deps
140+
- name: Run tests (uxarray with YAC)
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run: |
142+
python -m pytest test/test_remap_yac.py

‎ci/install-upstream.sh‎

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datashader \
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distributed \
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holoviews \
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numpy \
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pandas \
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scikit-learn \
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scipy \
@@ -33,7 +32,6 @@ python -m pip install \
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--no-deps \
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--pre \
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--upgrade \
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numpy \
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scikit-learn \
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scipy \
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xarray

‎docs/user-guide/remapping.ipynb‎

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"\n",
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"- **Nearest Neighbor** \n",
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"- **Inverse Distance Weighted**\n",
18-
"- **Bilinear**\n"
18+
"- **Bilinear**\n",
19+
"\n",
20+
"```{admonition} Optional YAC backend\n",
21+
":class: tip\n",
22+
"\n",
23+
"UXarray uses its native remapping backend by default. If [YAC](https://dkrz-sw.gitlab-pages.dkrz.de/yac/) is installed with its `yac.core` Python bindings, `.remap(...)`, `.remap.nearest_neighbor(...)`, and `.remap.bilinear(...)` can use `backend=\"yac\"` to route remapping through YAC.\n",
24+
"\n",
25+
"When `backend=\"yac\"`, the `yac_method` parameter selects the YAC interpolation method. Supported values are `nnn`, `average`, and `conservative`. `inverse_distance_weighted()` remains UXarray-only, and `bilinear(..., backend=\"yac\")` is a convenience wrapper for `yac_method=\"average\"`. For conservative face-centered remapping, use the generic `.remap(..., backend=\"yac\", yac_method=\"conservative\")` entrypoint.\n",
26+
"\n",
27+
"See the [YAC documentation](https://dkrz-sw.gitlab-pages.dkrz.de/yac/) and [YAC installation guide](https://dkrz-sw.gitlab-pages.dkrz.de/yac/d1/d9f/installing_yac.html) for build instructions, including enabling the Python bindings.\n",
28+
"```\n"
1929
]
2030
},
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{
@@ -132,6 +142,14 @@
132142
"- **remap_to** \n",
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" The grid element where values should be placed, one of `faces`, `edges`, or `nodes`.\n",
134144
"\n",
145+
"- **backend** \n",
146+
" The remapping backend to use. The default is `\"uxarray\"`; set `backend=\"yac\"` to route the remap through YAC.\n",
147+
"\n",
148+
"- **yac_method** \n",
149+
" Required only when `backend=\"yac\"`. Supported values are `nnn`, `average`, and `conservative`; `nearest_neighbor()` defaults to `nnn`.\n",
150+
"\n",
151+
"- **yac_options** \n",
152+
" Optional dictionary of method-specific keyword arguments forwarded to the selected YAC interpolation routine.\n",
135153
"\n",
136154
"```{warning}\n",
137155
"Nearest-neighbor remapping is fast and simple, but it does **not** conserve integrated quantities\n",
@@ -480,7 +498,9 @@
480498
"id": "6bec26ce-67b6-4300-a310-63cbac2b289a",
481499
"metadata": {},
482500
"source": [
483-
"Bilinear remapping breaks down the grid into triangles, and then finds the triangle that contains each point on the destinitation grid. It then uses the values stored at each vertex to bilinearly find a value for the point, depending on it's postion inside the triangle."
501+
"Bilinear remapping breaks down the grid into triangles, and then finds the triangle that contains each point on the destinitation grid. It then uses the values stored at each vertex to bilinearly find a value for the point, depending on it's postion inside the triangle.\n",
502+
"\n",
503+
"When `backend=\"yac\"`, `remap.bilinear()` delegates to YAC's `average` method. This is the only YAC method exposed through the bilinear convenience accessor; use `.remap(..., backend=\"yac\", yac_method=...)` if you need to select another YAC method explicitly."
484504
]
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},
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{

‎test/core/test_dataset.py‎

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@@ -99,3 +99,16 @@ def test_sel_method_forwarded(gridpath, datasetpath):
9999
nearest["time"].values,
100100
np.array(uxds["time"].values[2], dtype="datetime64[ns]"),
101101
)
102+
103+
def test_uxdataset_init_from_xarray_dataset():
104+
ds = xr.Dataset(
105+
data_vars={"a": ("x", [1, 2])},
106+
coords={"x": [10, 20]},
107+
attrs={"source": "testing"},
108+
)
109+
110+
uxds = ux.UxDataset(ds)
111+
112+
assert "a" in uxds.data_vars
113+
assert "x" in uxds.coords
114+
assert uxds.attrs["source"] == "testing"

‎test/io/test_utils.py‎

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1+
import numpy as np
2+
import pytest
3+
import xarray as xr
4+
5+
from uxarray.io.utils import _parse_grid_type
6+
7+
8+
@pytest.mark.parametrize(
9+
("path_args", "expected_spec"),
10+
[
11+
(("exodus", "outCSne8", "outCSne8.g"), "Exodus"),
12+
(("scrip", "outCSne8", "outCSne8.nc"), "Scrip"),
13+
(("ugrid", "outCSne30", "outCSne30.ug"), "UGRID"),
14+
(("mpas", "QU", "mesh.QU.1920km.151026.nc"), "MPAS"),
15+
(("esmf", "ne30", "ne30pg3.grid.nc"), "ESMF"),
16+
(("geos-cs", "c12", "test-c12.native.nc4"), "GEOS-CS"),
17+
(("icon", "R02B04", "icon_grid_0010_R02B04_G.nc"), "ICON"),
18+
(("fesom", "soufflet-netcdf", "grid.nc"), "FESOM2"),
19+
],
20+
)
21+
def test_parse_grid_type_detects_supported_formats(gridpath, path_args, expected_spec):
22+
with xr.open_dataset(gridpath(*path_args)) as ds:
23+
source_grid_spec, lon_name, lat_name = _parse_grid_type(ds)
24+
25+
assert source_grid_spec == expected_spec
26+
assert lon_name is None
27+
assert lat_name is None
28+
29+
30+
def test_parse_grid_type_detects_structured_grid():
31+
lon = xr.DataArray(
32+
np.array([0.0, 1.0, 2.0]),
33+
dims=["lon"],
34+
attrs={"standard_name": "longitude"},
35+
)
36+
lat = xr.DataArray(
37+
np.array([-1.0, 0.0, 1.0]),
38+
dims=["lat"],
39+
attrs={"standard_name": "latitude"},
40+
)
41+
ds = xr.Dataset(coords={"lon": lon, "lat": lat})
42+
43+
source_grid_spec, lon_name, lat_name = _parse_grid_type(ds)
44+
45+
assert source_grid_spec == "Structured"
46+
assert lon_name == "lon"
47+
assert lat_name == "lat"
48+
49+
50+
@pytest.mark.parametrize(
51+
"dataset",
52+
[
53+
xr.Dataset({"grid_center_lon": xr.DataArray([0.0], dims=["grid_size"])}),
54+
xr.Dataset(
55+
{
56+
"coordx": xr.DataArray([0.0, 1.0], dims=["num_nodes"]),
57+
"coordy": xr.DataArray([0.0, 1.0], dims=["num_nodes"]),
58+
}
59+
),
60+
xr.Dataset({"verticesOnCell": xr.DataArray([[1, 2, 3]], dims=["nCells", "nVert"])}),
61+
],
62+
)
63+
def test_parse_grid_type_rejects_incomplete_format_signals(dataset):
64+
with pytest.raises(RuntimeError, match="Could not recognize dataset format"):
65+
_parse_grid_type(dataset)

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