Drop Python3.8, support Pandas v2.2, reduce Warnings

.github/workflows/main.yml

@@ -38,7 +38,7 @@ jobs:
     strategy:
       matrix:
         python-version:
-          - "3.8"
+          - "3.9"
     steps:
       - uses: actions/checkout@v4.1.1
       - name: Set up Python${{ matrix.python-version }}
@@ -93,9 +93,6 @@ jobs:
     strategy:
       matrix:
         include:
-          - tox-env: py38-coverage-eofs
-            python-version: "3.8"
-            markers: -m 'not slow'
           - tox-env: py39-coverage-sbck-eofs
             python-version: "3.9"
             markers: -m 'not slow'
@@ -143,8 +140,8 @@ jobs:
     strategy:
       matrix:
         include:
-          - tox-env: py310
-            python-version: "3.10"
+          - tox-env: py311
+            python-version: "3.11"
     defaults:
       run:
         shell: bash -l {0}

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
   rev: v3.15.0
   hooks:
   - id: pyupgrade
-    args: ['--py38-plus']
+    args: ['--py39-plus']
     exclude: 'xclim/core/indicator.py'
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
@@ -33,15 +33,15 @@ repos:
   - id: yamllint
     args: [ '--config-file=.yamllint.yaml' ]
 - repo: https://github.com/psf/black-pre-commit-mirror
-  rev: 23.11.0
+  rev: 23.12.0
   hooks:
   - id: black
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.1.6
+  rev: v0.1.8
   hooks:
   - id: ruff
 - repo: https://github.com/pycqa/flake8
@@ -54,9 +54,9 @@ repos:
   rev: 1.7.1
   hooks:
   - id: nbqa-black
-    additional_dependencies: [ 'black==23.11.0' ]
+    additional_dependencies: [ 'black==23.12.0' ]
   - id: nbqa-pyupgrade
-    args: [ '--py38-plus' ]
+    args: [ '--py39-plus' ]
   - id: nbqa-isort
 - repo: https://github.com/kynan/nbstripout
   rev: 0.6.1
@@ -69,9 +69,9 @@ repos:
   hooks:
   - id: blackdoc
     exclude: '(xclim/indices/__init__.py|docs/installation.rst)'
-    additional_dependencies: [ 'black==23.11.0' ]
+    additional_dependencies: [ 'black==23.12.0' ]
 - repo: https://github.com/python-jsonschema/check-jsonschema
-  rev: 0.27.2
+  rev: 0.27.3
   hooks:
   - id: check-github-workflows
   - id: check-readthedocs

CONTRIBUTING.rst

@@ -122,8 +122,8 @@ Ready to contribute? Here's how to set up `xclim` for local development.
 
 3. Create a development environment. We recommend using ``conda``::
 
-    $ conda create -n xclim python=3.8 --file=environment.yml
-    $ pip install -e .[dev]
+    $ conda create -n xclim python=3.9 --file=environment.yml
+    $ python -m pip install -e ".[dev]"
 
 4. Create a branch for local development::
 
@@ -163,10 +163,9 @@ Ready to contribute? Here's how to set up `xclim` for local development.
 
   Alternatively, one can use ``$ tox`` to run very specific testing configurations, as GitHub Workflows would do when a Pull Request is submitted and new commits are pushed::
 
-    $ tox -e py38  # run tests on Python 3.8
-    $ tox -e py39-upstream-doctest  # run tests on Python 3.9, including doctests, with upstream dependencies
-    $ tox -e py310 -- -m "not slow  # run tests on Python 3.10, excluding "slow" marked tests
-    $ tox -e py311  # run tests on Python 3.11
+    $ tox -e py39  # run tests on Python 3.9
+    $ tox -e py310-upstream-doctest  # run tests on Python 3.10, including doctests, with upstream dependencies
+    $ tox -e py311 -- -m "not slow  # run tests on Python 3.11, excluding "slow" marked tests
     $ tox -e notebooks_doctests  # run tests using the base Python on doctests and evaluate all notebooks
     $ tox -e offline  # run tests using the base Python, excluding tests requiring internet access
 
@@ -242,7 +241,7 @@ Before you submit a pull request, please follow these guidelines:
     If you aren't accustomed to writing documentation in reStructuredText (`.rst`), we encourage you to spend a few minutes going over the
     incredibly well-summarized `reStructuredText Primer`_ from the sphinx-doc maintainer community.
 
-5. The pull request should work for Python 3.8, 3.9, 3.10, and 3.11 as well as raise test coverage.
+5. The pull request should work for Python 3.9, 3.10, and 3.11 as well as raise test coverage.
    Pull requests are also checked for documentation build status and for `PEP8`_ compliance.
 
    The build statuses and build errors for pull requests can be found at: https://github.com/Ouranosinc/xclim/actions

docs/explanation.rst

@@ -5,11 +5,6 @@ Why use xclim?
 Purpose
 =======
 
-.. important::
-
-    The content of this section is actively being developed in the forthcoming paper submission to JOSS.
-    This section will be updated and finalized when the wording has been agreed upon in :pull:`250`
-
 `xclim` aims to position itself as a climate services tool for any researchers interested in using Climate and Forecast Conventions (`CF-Conventions <https://cfconventions.org/>`_) compliant datasets to perform climate analyses. This tool is optimized for working with Big Data in the climate science domain and can function as an independent library for one-off analyses in *Jupyter Notebooks* or as a backend engine for performing climate data analyses via **Web Processing Services** (`WPS <https://www.ogc.org/standard/wps/>`_; e.g. `Finch <https://github.com/bird-house/finch>`_). It was primarily developed targeting Earth and Environmental Science audiences and researchers, originally for calculating climate indicators for the Canadian government web service `ClimateData.ca <https://climatedata.ca/>`_.
 
 The primary domains that `xclim` is built for are in calculating climate indicators, performing statistical correction / bias adjustment of climate model output variables or simulations, and in performing climate model simulation ensemble statistics.

docs/installation.rst

@@ -11,7 +11,7 @@ To install `xclim` via `pip`, run this command in your terminal:
 
 .. code-block:: shell
 
-    $ pip install xclim
+    $ python -m pip install xclim
 
 If you don't have `pip`_ installed, this `Python installation guide`_ can guide you through the process.
 
@@ -55,7 +55,7 @@ Both of these libraries are available on PyPI and conda-forge:
 
 .. code-block:: shell
 
-    $ pip install flox clisops
+    $ python -m pip install flox clisops
     # Or, alternatively:
     $ conda install -c conda-forge flox clisops
 
@@ -70,7 +70,7 @@ For convenience, these libraries can be installed alongside `xclim` using the fo
 
 .. code-block:: shell
 
-    $ pip install -r requirements_upstream.txt
+    $ python -m pip install -r requirements_upstream.txt
 
 Or, alternatively:
 
@@ -105,13 +105,13 @@ Afterwards, `SBCK` can be installed from PyPI using `pip`:
 
 .. code-block:: shell
 
-    $ pip install SBCK
+    $ python -m pip install SBCK
 
 Another experimental function :py:indicator:`xclim.sdba.property.first_eof` makes use of the `eofs`_ library, which is available on both PyPI and conda-forge:
 
 .. code-block:: shell
 
-    $ pip install eofs
+    $ python -m pip install eofs
     # or alternatively,
     $ conda install -c conda-forge eofs
 
@@ -145,7 +145,7 @@ Once you have extracted a copy of the source, you can install it with pip:
 
 .. code-block:: shell
 
-    $ pip install -e ".[dev]"
+    $ python -m pip install -e ".[dev]"
 
 Alternatively, you can also install a local development copy via `flit`_:
 
@@ -166,4 +166,4 @@ To create a conda environment including `xclim`'s dependencies and several optio
 
     $ conda env create -n my_xclim_env python=3.8 --file=environment.yml
     $ conda activate my_xclim_env
-    (my_xclim_env) $ pip install -e .
+    (my_xclim_env) $ python -m pip install -e .

environment.yml

@@ -3,27 +3,26 @@ channels:
     - conda-forge
     - defaults
 dependencies:
-    - python >=3.8
+    - python >=3.9,<3.12
     - astroid
     - boltons >=20.1
     - bottleneck >=1.3.1
     - cf_xarray >=0.6.1
     - cftime >=1.4.1
     - Click >=8.1
     - dask >=2.6.0
-    - importlib-resources  # For Python3.8
     - jsonpickle
     - lmoments3
     - numba
     - numpy >=1.16
-    - pandas >=0.23,<2.2
+    - pandas >=2.1  # This should be raised to Pandas 2.2 when released
     - pint >=0.9
     - poppler >=0.67
     - pyyaml
     - scikit-learn >=0.21.3
     - scipy >=1.2
     - statsmodels
-    - xarray >=2022.06.0,<2023.11.0
+    - xarray >=2023.11.0
     # Extras
     - eofs
     - flox

pyproject.toml

@@ -12,7 +12,7 @@ maintainers = [
   {name = "Pascal Bourgault", email = "bourgault.pascal@ouranos.ca"}
 ]
 readme = {file = "README.rst", content-type = "text/x-rst"}
-requires-python = ">=3.8.0"
+requires-python = ">=3.9.0"
 keywords = ["xclim", "xarray", "climate", "climatology", "bias correction", "ensemble", "indicators", "analysis"]
 license = {file = "LICENSE"}
 classifiers = [
@@ -23,41 +23,39 @@ classifiers = [
   "Natural Language :: English",
   "Operating System :: OS Independent",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  # "Programming Language :: Python :: 3.12",
   "Topic :: Scientific/Engineering :: Atmospheric Science"
 ]
 dynamic = ["description", "version"]
 dependencies = [
   "boltons>=20.1",
   "bottleneck>=1.3.1",
   # cf-xarray is differently named on conda-forge
-  "cf-xarray>=0.6.1,<0.8.5; python_version == '3.8'",
-  "cf-xarray>=0.6.1; python_version >= '3.9'",
+  "cf-xarray>=0.6.1",
   "cftime>=1.4.1",
   "Click>=8.1",
   "dask[array]>=2.6",
-  "importlib-resources; python_version == '3.8'",
   "jsonpickle",
   "lmoments3>=1.0.5",
   "numba",
   "numpy>=1.16",
-  "pandas>=0.23,<2.0; python_version == '3.8'",
-  "pandas>=0.23,<2.2; python_version >= '3.9'",
+  # This should be raised to Pandas 2.2 when released
+  "pandas>=2.1",
   "pint>=0.10",
   "pyyaml",
   "scikit-learn>=0.21.3",
   "scipy>=1.2",
   "statsmodels",
-  "xarray>=2022.06.0,<2023.11.0"
+  "xarray>=2023.11.0"
 ]
 
 [project.optional-dependencies]
 dev = [
   # Dev tools and testing
-  "black >=23.3.0",
+  "black >=23.12.0",
   "blackdoc",
   "bump2version",
   "coverage[toml]",
@@ -67,6 +65,7 @@ dev = [
   "h5netcdf",
   "ipython",
   "mypy",
+  "nbconvert",
   "nbqa",
   "nbval",
   "netCDF4 >=1.4",
@@ -115,10 +114,10 @@ xclim = "xclim.cli:cli"
 
 [tool.black]
 target-version = [
-  "py38",
   "py39",
   "py310",
-  "py311"
+  "py311",
+  "py312"
 ]
 
 [tool.coverage.run]
@@ -165,12 +164,12 @@ exclude = [
 
 [tool.isort]
 profile = "black"
-py_version = 38
+py_version = 39
 append_only = true
 add_imports = "from __future__ import annotations"
 
 [tool.mypy]
-python_version = 3.8
+python_version = 3.9
 show_error_codes = true
 warn_return_any = true
 warn_unused_configs = true
@@ -218,13 +217,12 @@ markers = [
 [tool.ruff]
 src = ["xclim"]
 line-length = 150
-target-version = "py38"
+target-version = "py39"
 exclude = [
   ".git",
   "docs",
   "build",
-  ".eggs",
-  "tests"
+  ".eggs"
 ]
 ignore = [
   "D205",

tests/test_calendar.py

@@ -396,7 +396,7 @@ def test_convert_calendar_360_days_random():
     [
         ("standard", "noleap", "D"),
         ("noleap", "default", "4H"),
-        ("noleap", "all_leap", "M"),
+        ("noleap", "all_leap", "M"),  # Do we want "MS" or "ME"?
         ("360_day", "noleap", "D"),
         ("noleap", "360_day", "D"),
     ],
@@ -416,6 +416,7 @@ def test_convert_calendar_missing(source, target, freq):
         np.linspace(0, 1, src.size), dims=("time",), coords={"time": src}
     )
     out = convert_calendar(da_src, target, missing=0, align_on="date")
+    # FIXME: Do we want to raise an error here for "M"? Do we want "ME" or "MS"?
     assert xr.infer_freq(out.time) == freq
     if source == "360_day":
         assert out.time[-1].dt.day == 31

tests/test_checks.py

@@ -197,6 +197,7 @@ def test_common_time(self, tas_series, date_range, random):
         db["time"] = db.time + pd.Timedelta(30, "min")
         with pytest.raises(
             ValidationError,
-            match=r"All inputs have the same frequency \(H\), but they are not anchored on the same minutes",
+            # FIXME: Do we want to emit warnings when frequency code is changed within the function?
+            match=r"All inputs have the same frequency \(h\), but they are not anchored on the same minutes",
         ):
             datachecks.check_common_time([db, da])

tests/test_indicators.py

@@ -5,7 +5,7 @@
 import gc
 import json
 from inspect import signature
-from typing import Tuple, Union
+from typing import Union
 
 import dask
 import numpy as np
@@ -487,7 +487,7 @@ def test_signature():
     assert sig.return_annotation == xr.DataArray
 
     sig = signature(xclim.atmos.wind_speed_from_vector)
-    assert sig.return_annotation == Tuple[xr.DataArray, xr.DataArray]
+    assert sig.return_annotation == tuple[xr.DataArray, xr.DataArray]
 
 
 def test_doc():