Add core library to package

.flake8

@@ -11,6 +11,7 @@ ignore =
 	E,
 	F,
 	RST210,
+	RST213,
 	W503
 per-file-ignores =
 rst-roles =

.github/workflows/main.yml

@@ -62,7 +62,7 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ "3.10", "3.11", "3.12", "3.13", "3.14" ]
+        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
     steps:
       - name: Harden Runner
         uses: step-security/harden-runner@0634a2670c59f64b4a01f0f96f84700a4088b9f0 # v2.12.0
@@ -101,7 +101,7 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ 3.10", "3.11", "3.12", "3.13", "3.14" ]
+        python-version: [ "3.11", "3.12", "3.13", "3.14" ]
     defaults:
       run:
         shell: bash -l {0}
@@ -139,6 +139,7 @@ jobs:
           parallel: true
 
   finish:
+    name: Finish
     needs:
       - test-pypi
       - test-conda

.pre-commit-config.yaml

@@ -46,7 +46,7 @@ repos:
       - id: rst-inline-touching-normal
       - id: text-unicode-replacement-char
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.15.12
     hooks:
       - id: ruff-check
         args: [ '--fix', '--show-fixes' ]
@@ -61,10 +61,10 @@ repos:
     rev: v2.16
     hooks:
       - id: vulture
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
-    hooks:
-      - id: mypy
+  # - repo: https://github.com/pre-commit/mirrors-mypy
+  #   rev: v1.20.2
+  #   hooks:
+  #     - id: mypy
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.2
     hooks:
@@ -82,12 +82,12 @@ repos:
       - id: check-github-workflows
       - id: check-readthedocs
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.23.1
+    rev: v1.24.1
     hooks:
       - id: zizmor
         args: [ '--config=.zizmor.yml' ]
   - repo: https://github.com/gitleaks/gitleaks
-    rev: v8.30.0
+    rev: v8.30.1
     hooks:
       - id: gitleaks
   - repo: meta

AUTHORS.rst

@@ -10,9 +10,17 @@ Development Lead
 Co-Developers
 -------------
 
-None yet. Why not be the first?
+* Ag Stephens <ag.stephens@stfc.ac.uk> `@agstephens <https://github.com/agstephens>`_
+* Carsten Ehbrecht <ehbrecht@dkrz.de> `@cehbrecht <https://github.com/cehbrecht>`_
+* Martin Schupfner <schupfner@dkrz.de> `@sol1105 <https://github.com/sol1105>`_
+* Pascal Bourgault <bourgault.pascal@ouranos.ca> `@aulemahal <https://github.com/aulemahal>`_
 
 Contributors
 ------------
 
-None yet. Why not be the first?
+* Marco Braun <braun.marco@ouranos.ca> `@vindelico <https://github.com/vindelico>`_
+* Charles Gauthier <gauthier.charles@ouranos.ca> `@charlesgauthier-udm <https://github.com/charlesgauthier-udm>`_
+* David Huard <huard.david@ouranos.ca> `@huard <https://github.com/huard>`_
+* Travis Logan <logan.travis@ouranos.ca> `@tlogan2000 <https://github.com/tlogan2000>`_
+* Gabriel Rondeau-Genesse <rondeau-genesse.gabriel@ouranos.ca> `@RondeauG <https://github.com/RondeauG>`_
+* Eleanor Smith `@ellesmith88 <https://github.com/ellesmith88>`_

CITATION.cff

@@ -18,6 +18,6 @@ contact:
     email: 'smith.trevorj@ouranos.ca'
     orcid: "https://orcid.org/0000-0001-5393-8359"
 repository-code: "https://github.com/roocs/clisops-core"
-abstract: "A Python package for peforming core subsetting and spatial operations in clisops"
+abstract: "A Python package for performing core subsetting and spatial operations in clisops."
 license: "BSD-3-Clause"
 version: "0.1.0"

README.rst

@@ -14,7 +14,7 @@ clisops-core
 | Development Status         | |status| |build| |coveralls|                        |
 +----------------------------+-----------------------------------------------------+
 
-A Python package for peforming core subsetting and spatial operations in clisops
+A Python package for performing core subsetting and spatial operations in clisops.
 
 * Free software: BSD license
 * Documentation: https://clisops-core.readthedocs.io.

environment-dev.yml

@@ -3,7 +3,23 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python >=3.10,<3.15
+  - python >=3.11,<3.15
+  - bottleneck >=1.3.1
+  - cftime >=1.4.1
+  - cf-xarray
+  - filelock >=3.15.4
+  - geopandas >=1.0.0
+  - loguru >=0.5.3
+  - numpy >=2.2
+  - packaging >=23.2
+  - pandas >=2.0
+  - pooch >=1.8.0
+  - xarray >=2025.6.0
+  # Performance
+  - dask >=2024.12
+  # Extras
+  - roocs-grids >=0.1.2
+  - xesmf >=0.9.2
   # Dev tools and testing
   - pip >=26.0.1
   - bump-my-version >=1.3.0
@@ -18,6 +34,8 @@ dependencies:
   - prek >=0.3.0
   - pytest >=9.0.2
   - pytest-cov >=7.0.0
+  - pytest-loguru >=0.4.1
+  - pytest-xdist >=3.2.0
   - ruff >=0.15.9
   - tox >=4.52.0
   - tox-gh >=1.7.1

environment-docs.yml

@@ -5,7 +5,8 @@ channels:
 dependencies:
   - python >=3.12,<3.13
   # Docs
-  - sphinx >=8.2
+  - nbsphinx >=0.9.8
+  - sphinx >=9.0
   - sphinx-codeautolink >=0.16.2
   - sphinx-copybutton >=0.5.2
   - sphinx-intl

pyproject.toml

@@ -16,19 +16,26 @@ lint = [
   "vulture >=2.14",
   "yamllint >=1.38.0"
 ]
+io = [
+  "h5netcdf >=1.5.0",
+  "h5py>=3.12.1"
+]
 test = [
   # Base testing support
   "coverage[toml] >=7.13.4",
   "pytest >=9.0.2",
-  "pytest-cov >=7.0.0"
+  "pytest-cov >=7.0.0",
+  "pytest-loguru >=0.4.1",
+  "pytest-xdist >=3.2.0",
+  {include-group = "io"}
 ]
 docs = [
   # Documentation and example support
   "ipykernel",
   "ipython >=8.10.0",
   "jupyter_client",
   "nbsphinx >=0.9.8",
-  "sphinx >=8.2.0",
+  "sphinx >=9.0.0",
   "sphinx-codeautolink >=0.16.2",
   "sphinx-copybutton >=0.5.2",
   "sphinx-intl",
@@ -59,7 +66,7 @@ maintainers = [
   {name = "Trevor James Smith", email = "smith.trevorj@ouranos.ca"}
 ]
 readme = {file = "README.rst", content-type = "text/x-rst"}
-requires-python = ">=3.10.0"
+requires-python = ">=3.11.0"
 keywords = ["clisops-core"]
 license = "BSD-3-Clause"
 license-files = ["LICENSE"]
@@ -70,7 +77,6 @@ classifiers = [
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
@@ -80,12 +86,28 @@ classifiers = [
 ]
 dynamic = ["description", "version"]
 dependencies = [
+  "bottleneck >=1.3.1",
+  "cftime >=1.4.1",
+  "cf-xarray",
+  "filelock >=3.15.4",
+  "geopandas >=1.0.0",
+  "loguru >=0.5.3",
+  "numpy >=2.2",
+  "packaging >=23.2",
+  "pandas >=2.0",
+  "pooch >=1.8.0",
+  "pyproj",
+  "scipy",
+  "shapely",
+  "xarray >=2025.6.0"
 ]
 
 [project.optional-dependencies]
-extras = []
-
-
+performance = ["dask >=2024.12"]
+regrid = [
+  "roocs_grids >=0.1.2",
+  "xesmf >=0.9.2"
+]
 
 [project.urls]
 # "Homepage" = "https://clisops-core.readthedocs.io/"
@@ -145,7 +167,7 @@ regex = true
 replace = "version: \"{new_version}\""
 
 [[tool.bumpversion.files]]
-filename = "src/clisops_core/__init__.py"
+filename = "src/clisops_core/_version.py"
 search = "__version__ = \"{current_version}\""
 replace = "__version__ = \"{new_version}\""
 
@@ -170,7 +192,8 @@ values = [
 ]
 
 [tool.codespell]
-ignore-words-list = "astroid,socio-economic,thirdparty"
+ignore-words-list = "astroid,scrip,socio-economic,thirdparty"
+skip = "docs/_build"
 
 [tool.coverage.paths]
 source = ["src/clisops_core/", "*/site-packages/clisops_core/"]
@@ -182,7 +205,10 @@ source = ["clisops_core"]
 
 [tool.deptry]
 extend_exclude = ["extras"]
-pep621_dev_dependency_groups = ["extras"]
+
+[tool.deptry.per_rule_ignores]
+DEP001 = ["dask"]
+DEP002 = ["bottleneck"]
 
 [tool.flit.sdist]
 include = [
@@ -193,6 +219,7 @@ include = [
   "LICENSE",
   "Makefile",
   "README.rst",
+  "clisops_core/**/*.py",
   "environment-dev.yml",
   "environment-docs.yml",
   "docs/_static/_images/*.gif",
@@ -267,12 +294,21 @@ minversion = "9.0"
 addopts = [
   "-ra",
   "--color=yes",
-  "--verbose"
+  "--numprocesses=0",
+  "--maxprocesses=8",
+  "--dist=worksteal",
+  "--strict-config",
+  "--strict-markers"
 ]
 filterwarnings = ["ignore::UserWarning"]
 testpaths = [
   "tests"
 ]
+markers = [
+  "online: mark test to need internet connection",
+  "slow: mark test to be slow",
+  "thread_unsafe: mark test to be thread unsafe"
+]
 
 [tool.ruff]
 src = ["clisops_core"]
@@ -335,7 +371,7 @@ lines-after-imports = 2
 no-lines-before = ["future", "standard-library"]
 
 [tool.ruff.lint.mccabe]
-max-complexity = 15
+max-complexity = 30
 
 [tool.ruff.lint.per-file-ignores]
 "docs/**" = ["E402"]

src/clisops_core/__init__.py

@@ -1,4 +1,4 @@
-"""A Python package for peforming core subsetting and spatial operations in clisops"""
+"""A Python package for performing core subsetting and spatial operations in clisops."""
 
 ###################################################################################
 # BSD 3-Clause License
@@ -32,6 +32,33 @@
 # OF THE POSSIBILITY OF SUCH DAMAGE.
 ###################################################################################
 
-__author__ = """Trevor James Smith"""
-__email__ = "smith.trevorj@ouranos.ca"
-__version__ = "0.1.0"
+import warnings
+
+from loguru import logger
+
+from clisops_core._version import __version__ as __version__
+from clisops_core.subset import (
+    create_mask,
+    subset_bbox,
+    subset_gridpoint,
+    subset_level,
+    subset_level_by_values,
+    subset_shape,
+    subset_time,
+    subset_time_by_components,
+    subset_time_by_values,
+)
+
+
+def showwarning(message, *args, **kwargs):  # numpydoc ignore=PR01
+    """Inject warnings from `warnings.warn` into `loguru`."""
+    logger.warning(message)
+    showwarning_(message, *args, **kwargs)
+
+
+showwarning_ = warnings.showwarning
+warnings.showwarning = showwarning
+
+# Disable logging for clisops_core and remove the logger that is instantiated on import
+logger.disable("clisops_core")
+logger.remove()

src/clisops_core/_version.py

@@ -0,0 +1,10 @@
+"""The version information for the CLISOPS-core package."""
+# This information is located in its own file so that it can be loaded
+# without importing the main package when its dependencies are not installed.
+# See: https://packaging.python.org/guides/single-sourcing-package-version
+
+__author__ = """Trevor James Smith"""
+__email__ = "smith.trevorj@ouranos.ca"
+__copyright__ = "Copyright 2026. United Kingdom Research and Innovation and Ouranos Inc."
+__license__ = "BSD-3-Clause"
+__version__ = "0.1.0"