Update dependency pins, fix typo (#1870)

### What kind of change does this PR introduce? * Synchronizes dependencies between `pyproject.toml` and `environment.yml` * Sets a few pins to their latest versions * Fixes a small typo in `cli.py` * Fixes an issue with the latest version of `dask` (2024.8.0) * Removed `poppler` from the list of Conda dependencies ### Does this PR introduce a breaking change? No. --------- Co-authored-by: Pascal Bourgault <bourgault.pascal@ouranos.ca>
Ouranosinc · Aug 7, 2024 · a2b34f5 · a2b34f5
1 parent 1407011
commit a2b34f5
Show file tree

Hide file tree

Showing 17 changed files with 130 additions and 232 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -103,6 +103,7 @@ jobs:
           python -m tox -- -m 'not slow'
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COVERALLS_PARALLEL: true
 
   test-pypi:
     needs: lint
@@ -192,7 +193,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_FLAG_NAME: run-${{ matrix.python-version }}-${{ matrix.os }}-${{ matrix.tox-env }}
           COVERALLS_PARALLEL: true
-          COVERALLS_SERVICE_NAME: github
       - name: Test with tox (specialized tests)
         if: ${{ matrix.tox-env != 'standard' }}
         run: |
@@ -201,7 +201,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_FLAG_NAME: run-${{ matrix.python-version }}-${{ matrix.os }}-${{ matrix.tox-env }}
           COVERALLS_PARALLEL: true
-          COVERALLS_SERVICE_NAME: github
 
   test-conda:
     needs: lint
@@ -278,7 +277,6 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           COVERALLS_FLAG_NAME: run-{{ matrix.python-version }}-conda
           COVERALLS_PARALLEL: true
-          COVERALLS_SERVICE_NAME: github
 
   finish:
     needs:
@@ -301,4 +299,3 @@ jobs:
           python -m coveralls --finish
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_SERVICE_NAME: github
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,27 +6,29 @@ v0.52.0 (unreleased)
 --------------------
 Contributors to this version: David Huard (:user:`huard`), Trevor James Smith (:user:`Zeitsperre`), Hui-Min Wang (:user:`Hem-W`), Éric Dupuis (:user:`coxipi`), Sarah Gammon (:user:`SarahG-579462`), Pascal Bourgault (:user:`aulemahal`), Juliette Lavoie (:user:`juliettelavoie`).
 
+Announcements
+^^^^^^^^^^^^^
+* `xclim` now supports both `numpy` versions `>=1.20` and `>=2.0`. (:issue:`1785`, :pull:`1814`, :pull:`1870`).
+* `xclim` now needs ``cf_xarray>=0.9.3`` but continues to support older versions of `pint` (`<0.24`) for compatibility reasons. (:pull:`1870`).
+
 New features and enhancements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 * ``xclim.sdba.nbutils.quantile`` and its child functions are now faster. If the module `fastnanquantile` is installed, it is used as the backend for the computation of quantiles and yields even faster results. This dependency is now listed in the `xclim[extras]` recipe. (:issue:`1255`, :pull:`1513`).
-* New multivariate bias adjustment class `MBCn`, giving a faster and more accurate implementation of the 'MBCn' algorithm (:issue:`1551`, :pull:`1580`).
+* New multivariate bias adjustment class ``MBCn``, giving a faster and more accurate implementation of the ``MBCn`` algorithm. (:issue:`1551`, :pull:`1580`).
 * `xclim` is now compatible with `pytest` versions `>=8.0.0`. (:pull:`1632`).
 
 Breaking changes
 ^^^^^^^^^^^^^^^^
-* As updated in ``cf_xarray>=0.9.3``, dimensionless quantities now use the "1" units attribute as specified by the CF conventions, previously an empty string was returned. (:pull:`1814`).
-
-Breaking changes
-^^^^^^^^^^^^^^^^
+* As of ``cf_xarray>=0.9.3``, dimensionless quantities now use the "1" units attribute as specified by the CF conventions, previously an empty string was returned. (:pull:`1814`).
 * The definitions of the ``frost_free_season_start`` and ``frost_free_season_end`` have been slightly changed to be coherent with the ``frost_free_season_length`` and `xclim`'s notion of `season` in general. Indicator and indices signature have changed. (:pull:`1845`).
 * Season length indicators have been modified to return ``0`` for all cases where a proper season was not found, but the data is valid. Previously, a ``nan`` was given if neither a start or an end were found, even if the data was valid, and a ``0`` was given if an end was found but no start. (:pull:`1845`).
 
 Bug fixes
 ^^^^^^^^^
 * Fixed the indexer bug in the ``xclim.indices.standardized_index_fit_params`` when multiple or non-array indexers are specified and fitted parameters are reloaded from netCDF. (:issue:`1842`, :pull:`1843`).
 * Addressed a bug found in ``wet_spell_*`` indicators that was contributing to erroneous results. A new generic spell length statistic function ``xclim.indices.generic.spell_length_statistics`` is now used in wet and dry spells indicators. (:issue:`1834`, :pull:`1838`).
-* Syntax for ``nan`` and ``inf`` was adapted to support ``numpy>=2.0.0``. (:pull:`1814`, :issue:`1785`).
-* Force type in `jitter` to work with new version of dask. (:pull:`1864`)
+* Syntax for ``nan`` and ``inf`` was adapted to support `numpy>=2.0`. (:pull:`1814`, :issue:`1785`).
+* Force type in ``jitter`` to work with new version of `dask`. (:pull:`1864`).
 
 Internal changes
 ^^^^^^^^^^^^^^^^
@@ -39,7 +41,7 @@ CI changes
 * `pip-tools` (`pip-compile`) has been used to generate a lock file with hashes for the CI dependencies. (:pull:`1841`).
 * The ``main.yml`` workflow has been updated to use simpler trigger logic. (:pull:`1841`).
 * A workflow bug has been fixed that was causing multiple duplicate comments to be made on Pull Requests originating from forks. (:pull:`1841`).
-* The ``upstream.yml`` workflow was adapted to not install upstream Python dependencies using hashes (impossible to install directly from GitHub sources using --require-hashes). (:pull:`1859`).
+* The ``upstream.yml`` workflow was adapted to not install upstream Python dependencies using hashes (as it is impossible to install directly from GitHub sources using ``--require-hashes``). (:pull:`1859`).
 * The `tox-gh` configuration has been set to handle the environment configurations on GitHub Workflows. The tox.ini file is also a bit more organized/consistent. (:pull:`1859`).
 
 v0.51.0 (2024-07-04)

diff --git a/environment.yml b/environment.yml
@@ -6,77 +6,77 @@ dependencies:
   - python >=3.9
   - boltons >=20.1
   - bottleneck >=1.3.1
-  - cf_xarray >=0.6.1
+  - cf_xarray >=0.9.3
   - cftime >=1.4.1
   - click >=8.1
   - dask >=2.6.0
-  - jsonpickle
-  - numba
+  - filelock >=3.14.0
+  - jsonpickle >=3.1.0
+  - numba >=0.54.1
   - numpy >=1.20.0
+  - packaging >=24.0
   - pandas >=2.2.0
   - pint >=0.18.0
-  - poppler >=0.67
-  - pyarrow  # Strongly encouraged for Pandas v2.2.0+
-  - pyyaml
+  - pyarrow >=15.0.0  # Strongly encouraged for Pandas v2.2.0+
+  - pyyaml >=6.0.1
   - scikit-learn >=0.21.3
   - scipy >=1.9.0
-  - statsmodels
+  - statsmodels >=0.14.2
   - xarray >=2023.11.0
-  - yamale
+  - yamale >=5.0.0
   # Extras
   - flox
   - lmoments3  # Required for some Jupyter notebooks
   # Testing and development dependencies
   - black ==24.4.2
   - blackdoc ==0.3.9
-  - bump-my-version >=0.23.0
+  - bump-my-version >=0.24.3
   - cairosvg
   - codespell ==2.3.0
   - coverage >=7.5.0
   - coveralls >=4.0.0
-  - deptry ==0.16.1
+  - deptry ==0.18.0
   - distributed >=2.0
-  - filelock
-  - flake8 >=7.0.0
-  - flake8-rst-docstrings
+  - flake8 >=7.1.1
+  - flake8-rst-docstrings >=0.3.0
   - flit >=3.9.0
   - furo >=2023.9.10
   - h5netcdf >=1.3.0
   - ipykernel
   - ipython
   - isort ==5.13.2
   - matplotlib
-  - mypy
+  - mypy >=1.10.0
   - nbconvert <7.14  # Pinned due to directive errors in sphinx. See: https://github.com/jupyter/nbconvert/issues/2092
-  - nbqa
+  - nbqa >=1.8.2
   - nbsphinx
   - nbval >=0.11.0
-  - nc-time-axis
+  - nc-time-axis >=1.4.1
   - notebook
-  - pandas-stubs
-  - platformdirs
-  - pooch
+  - pandas-stubs >=2.2
+  - platformdirs >=3.2
+  - pooch >=1.8.0
   - pre-commit >=3.7
   - pybtex >=0.24.0
   - pylint >=3.1
   - pytest >=8.0.0
-  - pytest-cov
-  - pytest-socket
+  - pytest-cov >=5.0.0
+  - pytest-socket >=0.6.0
   - pytest-xdist >=3.2
-  - ruff >=0.4.10
+  - ruff >=0.5.6
   - sphinx >=7.0.0
   - sphinx-autobuild >=2024.4.16
   - sphinx-autodoc-typehints
   - sphinx-codeautolink
   - sphinx-copybutton
   - sphinx-mdinclude
   - sphinxcontrib-bibtex
-  - tokenize-rt
+  - tokenize-rt >=5.2.0
   - tox >=4.16.0
   # - tox-conda  # Will be added when a tox@v4.0+ compatible plugin is released.
   - vulture # ==2.11  # The conda-forge version is out of date.
   - xdoctest >=1.1.5
-  - yamllint
-  - pip
+  - yamllint >=1.35.1
+  - pip >=24.0
   - pip:
     - sphinxcontrib-svg2pdfconverter
diff --git a/pyproject.toml b/pyproject.toml
@@ -27,32 +27,35 @@ classifiers = [
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
-  "Topic :: Scientific/Engineering :: Atmospheric Science"
+  "Programming Language :: Python :: 3 :: Only",
+  "Topic :: Scientific/Engineering :: Atmospheric Science",
+  "Topic :: Scientific/Engineering :: Hydrology",
+  "Typing :: Typed"
 ]
 dynamic = ["description", "version"]
 dependencies = [
-  "boltons>=20.1",
-  "bottleneck>=1.3.1",
+  "boltons >=20.1",
+  "bottleneck >=1.3.1",
   # cf-xarray is differently named on conda-forge
-  "cf-xarray>=0.6.1",
-  "cftime>=1.4.1",
-  "click>=8.1",
-  "dask[array]>=2.6",
-  "filelock",
-  "jsonpickle",
-  "numba",
-  "numpy>=1.20.0",
-  "packaging",
-  "pandas>=2.2",
-  "pint>=0.18",
+  "cf-xarray >=0.9.3",
+  "cftime >=1.4.1",
+  "click >=8.1",
+  "dask[array] >=2.6",
+  "filelock >=3.14.0",
+  "jsonpickle >=3.1.0",
+  "numba >=0.54.1",
+  "numpy >=1.20.0",
+  "packaging >=24.0",
+  "pandas >=2.2",
+  "pint >=0.18",
   "platformdirs >=3.2",
-  "pyarrow", # Strongly encouraged for pandas v2.2.0+
-  "pyyaml",
-  "scikit-learn>=0.21.3",
-  "scipy>=1.9.0",
-  "statsmodels",
-  "xarray>=2023.11.0",
-  "yamale"
+  "pyarrow >=15.0.0", # Strongly encouraged for pandas v2.2.0+
+  "pyyaml >=6.0.1",
+  "scikit-learn >=0.21.3",
+  "scipy >=1.9.0",
+  "statsmodels >=0.14.2",
+  "xarray >=2023.11.0",
+  "yamale >=5.0.0"
 ]
 
 [project.optional-dependencies]
@@ -65,27 +68,28 @@ dev = [
   "coverage[toml] >=7.5.0",
   "coveralls >=4.0.0",
   "deptry ==0.18.0",
-  "flake8 >=7.1.0",
-  "flake8-rst-docstrings",
+  "flake8 >=7.1.1",
+  "flake8-rst-docstrings >=0.3.0",
   "h5netcdf>=1.3.0",
   "ipython",
   "isort ==5.13.2",
-  "mypy",
+  "mypy >=1.10.0",
   "nbconvert <7.14", # Pinned due to directive errors in sphinx. See: https://github.com/jupyter/nbconvert/issues/2092
   "nbqa >=1.8.2",
   "nbval >=0.11.0",
   "pandas-stubs >=2.2",
+  "pip >=24.0",
   "platformdirs >=3.2",
-  "pooch",
+  "pooch >=1.8.0",
   "pre-commit >=3.7",
   "pylint >=3.2.4",
   "pytest >=8.0.0",
-  "pytest-cov",
-  "pytest-socket",
+  "pytest-cov >=5.0.0",
+  "pytest-socket >=0.6.0",
   "pytest-xdist[psutil] >=3.2",
-  "ruff >=0.4.10",
-  "tokenize-rt",
-  "tox >=4.16.0",
+  "ruff >=0.5.6",
+  "tokenize-rt >=5.2.0",
+  "tox >=4.17.0",
   # "tox-conda",  # Will be added when a tox@v4.0+ compatible plugin is released.
   "vulture ==2.11",
   "xdoctest >=1.1.5",
@@ -98,8 +102,8 @@ docs = [
   "ipykernel",
   "matplotlib",
   "nbsphinx",
-  "nc-time-axis",
-  "pooch",
+  "nc-time-axis >=1.4.1",
+  "pooch >=1.8.0",
   "pybtex >=0.24.0",
   "sphinx >=7.0.0",
   "sphinx-autobuild >=2024.4.16",
@@ -110,7 +114,7 @@ docs = [
   "sphinxcontrib-bibtex",
   "sphinxcontrib-svg2pdfconverter[Cairosvg]"
 ]
-extras = ["fastnanquantile"]
+extras = ["fastnanquantile >=0.0.2"]
 all = ["xclim[dev]", "xclim[docs]", "xclim[extras]"]
 
 [project.scripts]

diff --git a/tests/test_atmos.py b/tests/test_atmos.py
@@ -4,8 +4,6 @@
 
 import numpy as np
 import xarray as xr
-from cf_xarray import __version__ as __cfxr_version__
-from packaging.version import Version
 
 from xclim import atmos, set_options
 
@@ -262,11 +260,7 @@ def test_wind_profile(atmosds):
 
 def test_wind_power_potential(atmosds):
     out = atmos.wind_power_potential(wind_speed=atmosds.sfcWind)
-
-    if Version(__cfxr_version__) < Version("0.9.3"):
-        assert out.attrs["units"] == ""
-    else:
-        assert out.attrs["units"] == "1"
+    assert out.attrs["units"] == "1"
     assert (out >= 0).all()
     assert (out <= 1).all()
 

diff --git a/tests/test_generic.py b/tests/test_generic.py
@@ -5,8 +5,6 @@
 import numpy as np
 import pytest
 import xarray as xr
-from cf_xarray import __version__ as __cfxr_version__
-from packaging.version import Version
 
 from xclim.core.calendar import doy_to_days_since, select_time
 from xclim.indices import generic
@@ -104,10 +102,7 @@ def test_doyminmax(self, q_series):
             for attr in ["units", "is_dayofyear", "calendar"]:
                 assert attr in da.attrs.keys()
 
-            if Version(__cfxr_version__) < Version("0.9.3"):
-                assert da.attrs["units"] == ""
-            else:
-                assert da.attrs["units"] == "1"
+            assert da.attrs["units"] == "1"
             assert da.attrs["is_dayofyear"] == 1
 
 

diff --git a/tests/test_hydrology.py b/tests/test_hydrology.py
@@ -1,8 +1,6 @@
 from __future__ import annotations
 
 import numpy as np
-from cf_xarray import __version__ as __cfxr_version__
-from packaging.version import Version
 
 from xclim import indices as xci
 
@@ -42,11 +40,7 @@ def test_simple(self, snw_series):
         snw = snw_series(a, start="1999-01-01")
         out = xci.snw_max_doy(snw, freq="YS")
         np.testing.assert_array_equal(out, [11, np.nan])
-
-        if Version(__cfxr_version__) < Version("0.9.3"):
-            assert out.attrs["units"] == ""
-        else:
-            assert out.attrs["units"] == "1"
+        assert out.attrs["units"] == "1"
 
 
 class TestSnowMeltWEMax: