Update tests

.github/workflows/main.yml

@@ -6,13 +6,18 @@ on:
       - main
   pull_request:
 
+concurrency:
+  # For a given workflow, if we push to the same branch, cancel all previous builds on that branch except on master.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+
 jobs:
   build:
     name: Conda Build with Python${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
     defaults:
       run:
         shell: bash -l {0}
@@ -21,7 +26,7 @@ jobs:
     - name: Install packages
       run: |
         sudo apt-get -y install pandoc
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
     - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
       uses: mamba-org/setup-micromamba@0dea6379afdaffa5d528b3d1dabc45da37f443fc # v2.0.4
       with:
@@ -41,4 +46,4 @@ jobs:
         python -m pytest -v tests
     - name: Build docs 🏗️
       run: make docs
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11

.pre-commit-config.yaml

@@ -3,46 +3,46 @@ default_language_version:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
       - id: debug-statements
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.19.0
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
         args: [ '--py310-plus' ]
         exclude: 'src/daops/utils/testing.py'
   - repo: https://github.com/psf/black
-    rev: 25.1.0
+    rev: 25.12.0
     hooks:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.0
+    rev: v0.14.9
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [ '--fix', '--show-fixes' ]
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
-#      - id: python-check-blanket-noqa
-#      - id: python-check-blanket-type-ignore
+      - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
       - id: python-no-eval
       - id: python-no-log-warn
       - id: python-use-type-annotations
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
       - id: text-unicode-replacement-char
   - repo: https://github.com/keewis/blackdoc
-    rev: v0.3.9
+    rev: v0.4.6
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==25.1.0' ]
+        additional_dependencies: [ 'black==25.12.0' ]
       - id: blackdoc-autoupdate-black
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.4
+    rev: 0.36.0
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs
@@ -54,10 +54,11 @@ repos:
 ci:
   autofix_commit_msg: |
     [pre-commit.ci] auto fixes from pre-commit.com hooks
+
     for more information, see https://pre-commit.ci
   autofix_prs: true
   autoupdate_branch: ''
   autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
-  autoupdate_schedule: weekly
+  autoupdate_schedule: quarterly
   skip: [ ]
   submodules: false

HISTORY.rst

@@ -1,6 +1,18 @@
 Version History
 ===============
 
+v0.16.0 (2025-12-16)
+--------------------
+
+Breaking Changes
+^^^^^^^^^^^^^^^^
+* ``clisops``>=0.16.2, ``numpy``>=1.26, and ``xesmf``>=0.9.2 are now required.
+* Dropped support for Python3.10. Added support for Python3.13.
+
+Fixes
+^^^^^
+* Addressed thousands of `DeprecationWarning` messages emitted from ``xarray`` in the testing suite.
+
 v0.15.0 (2025-03-24)
 --------------------
 
@@ -17,6 +29,7 @@ Breaking Changes
 * ``clisops``>=0.15.0 is now required.
 * ``roocs-utils`` has been rendered obsolete and removed from the dependencies (``roocs-utils`` functionality is now provided by ``clisops``).
 
+
 v0.13.0 (2025-02-07)
 --------------------
 

environment.yml

@@ -3,17 +3,24 @@ name: daops
 channels:
   - conda-forge
 dependencies:
-  - python >=3.10,<3.13
-  - pip >=25.0
+  - python >=3.11
+  - pip >=25.2
+  - flit >=3.11.0,<4.0
   - cftime
-  - clisops >=0.16.1
-  - dask
-  - elasticsearch>=8.0.1
-  - netcdf4
-  - numpy >=1.24.0,<2.0.0
+  - clisops >=0.17.0
+  - dask >=2024.12.0
+  - elasticsearch >=8.0.1,<9.0
+  - numpy >=1.26.0
   - roocs-grids >=0.1.2
-  - xarray >=2025.1.1,<2025.3.0
-  - xesmf >=0.8.2
+  - xarray >=2025.6.0
+  - xesmf >=0.9.2
+  # testing
+  - coverage >=7.6.0
+  - h5netcdf >=1.5.0
+  - pytest-loguru >=0.3.0
+  - pytest >=8.0.0
+  - pytest-cov >=6.0.0
+  - pytest-timeout >=2.4.0
   # logging
   - loguru >=0.5.3
   # catalog
@@ -24,3 +31,5 @@ dependencies:
   - aiohttp
   - zarr >=2.13.3
   - zstandard
+  # for versioning
+  - bump-my-version >=1.2.0

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["flit-core >=3.10.1,<4.0"]
+requires = ["flit-core >=3.11.0,<4.0"]
 build-backend = "flit_core.buildapi"
 
 [project]
@@ -11,10 +11,11 @@ maintainers = [
     {name = "Trevor James Smith", email = "smith.trevorj@ouranos.ca"},
     {name = "Carsten Ehbrecht", email = "ehbrecht@dkrz.de"}
 ]
-license = {text = "BSD"}
+license = "BSD-3-Clause"
+license-files = ["LICENSE"]
 readme = {file = "README.rst", content-type = "text/x-rst"}
 keywords = ["daops"]
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 classifiers = [
     "Development Status :: 4 - Beta",
     "Environment :: Console",
@@ -23,14 +24,13 @@ classifiers = [
     "Intended Audience :: Developers",
     "Intended Audience :: System Administrators",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Security",
     "Topic :: Internet",
     "Topic :: Scientific/Engineering",
@@ -41,13 +41,14 @@ classifiers = [
 dynamic = ["description", "version"]
 dependencies = [
   "cftime",
-  "clisops >=0.16.1",
-  "dask[complete]",
-  "elasticsearch >=8.0.1",
-  "numpy >=1.24.0,<2.0.0",
+  "clisops >=0.17.0",
+  "h5netcdf",
+  "dask[complete] >=2024.12.0",
+  "elasticsearch >=8.0.1,<9.0",
+  "numpy >=1.26.0",
   "roocs_grids >=0.1.2",
-  "xarray >=2025.1.1,<2025.3.0",
-  "xesmf >=0.8.2",
+  "xarray >=2025.6.0",
+  "xesmf >=0.9.2",
   # logging
   "loguru >=0.5.3",
   # catalog
@@ -62,16 +63,19 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-  "black >=25.1.0",
-  "bump-my-version >=0.28.0",
-  "coverage >=7.6.0",
+  "black >=25.12.0",
+  "bump-my-version >=1.2.0",
+  "coverage[toml] >=7.6.0",
+  "h5netcdf >=1.5.0",
   "jinja2",
   "packaging >=24.2",
+  "pip >=25.2",
   "pre-commit >=3.5.0",
   "pytest-loguru >=0.3.0",
   "pytest >=8.0.0",
   "pytest-cov >=6.0.0",
-  "ruff >=0.9.0",
+  "pytest-timeout >=2.4.0",
+  "ruff >=0.14.9",
   "tox >=4.18.1",
   "watchdog >=4.0",
 ]
@@ -100,10 +104,9 @@ daops = "daops.cli:main"
 
 [tool.black]
 target-version = [
-  "py39",
-  "py310",
   "py311",
-  "py312"
+  "py312",
+  "py313"
 ]
 
 [tool.bumpversion]
@@ -157,6 +160,7 @@ minversion = "8.0"
 addopts = [
   "--verbose",
   "--color=yes",
+  "--timeout=300",
   "--strict-config",
   "--strict-markers"
 ]
@@ -166,9 +170,10 @@ testpaths = [
   "tests"
 ]
 markers = [
-  "online: mark tests that require internet access (deselect with '-m \"not requires_internet\"')"
+  "online: mark tests that require internet access (deselect with '-m \"not requires_internet\"')",
+  "slow: mark tests that run quite long."
 ]
-xfail_strict = true
+xfail_strict = false
 
 [tool.ruff]
 src = ["src/daops"]

src/daops/__init__.py

@@ -24,7 +24,7 @@ def config_():
     return cfg
 
 
-from .utils.common import enable_logging  # noqa
+from .utils.common import enable_logging as enable_logging  # noqa: E402
 
 # Disable logging for daops and remove the logger that is instantiated on import
 logger.disable("daops")

src/daops/ops/regrid.py

@@ -58,7 +58,6 @@ def regrid(
     -------
     List of outputs in the selected type: a list of xarray Datasets or file paths.
 
-
     Examples
     --------
     | collection: ("cmip6.ukesm1.r1.gn.tasmax.v20200101",)

src/daops/utils/testing.py

@@ -2,7 +2,7 @@
 from pathlib import Path
 from typing import Optional
 
-from _pytest.logging import LogCaptureFixture  # noqa
+from _pytest.logging import LogCaptureFixture
 from clisops.utils.testing import ESGF_TEST_DATA_CACHE_DIR, ESGF_TEST_DATA_VERSION
 from jinja2 import Template