Merge branch 'master' into opt-dataset

.github/workflows/main.yml

@@ -84,6 +84,8 @@ jobs:
           disable-sudo: true
           egress-policy: block
           allowed-endpoints: >
+            api.github.com:443
+            dap.service.does.not.exist:443
             files.pythonhosted.org:443
             github.com:443
             pypi.org:443

.pre-commit-config.yaml

@@ -33,15 +33,15 @@ repos:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.12.1
+    rev: 24.1.0
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.13
+    rev: v0.1.14
     hooks:
       - id: ruff
   - repo: https://github.com/pylint-dev/pylint
@@ -61,7 +61,7 @@ repos:
       - id: nbqa-pyupgrade
         args: [ '--py38-plus' ]
       - id: nbqa-black
-        additional_dependencies: [ 'black==23.12.1' ]
+        additional_dependencies: [ 'black==24.1.0' ]
       - id: nbqa-isort
   - repo: https://github.com/kynan/nbstripout
     rev: 0.6.1
@@ -73,7 +73,7 @@ repos:
     rev: v0.3.9
     hooks:
       - id: blackdoc
-        additional_dependencies: [ 'black==23.12.1' ]
+        additional_dependencies: [ 'black==24.1.0' ]
         exclude: '(xclim/indices/__init__.py|docs/installation.rst)'
   - repo: https://github.com/gitleaks/gitleaks
     rev: v8.18.1

CHANGES.rst

@@ -11,6 +11,7 @@ Announcements
 * `xclim` now officially supports Python3.12 (requires `numba>=0.59.0`). (:pull:`1613`).
 * `xclim` now adheres to the `Semantic Versioning 2.0.0 <https://semver.org/>`_ specification. (:issue:`1556`, :pull:`1569`).
 * The `xclim` repository now uses `GitHub Discussions <https://github.com/Ouranosinc/xclim/discussions>`_ to offer help for users, coordinate translation efforts, and support general Q&A for the `xclim` community. The `xclim` `Gitter` room has been deprecated in favour of GitHub Discussions. (:issue:`1571`, :pull:`1572`).
+* For secure correspondence, `xclim` now offers a PGP key for users to encrypt sensitive communications. For more information, see the ``SECURITY.md``. (:issue:`1181`, :pull:`1604`).
 
 New features and enhancements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -26,6 +27,7 @@ Breaking changes
 * `xclim`'s units registry and units formatting are now extended from `cf-xarray`. The exponent sign "^" is now never added in the ``units`` attribute. For example, square meters are given as "m2" instead of "m^2" by xclim, both are still accepted as input. (:issue:`1010`, :pull:`1590`).
 * `yamale` is now listed as a core dependency (was previously listed in the `dev` installation recipe). (:issue:`1595`, :pull:`1596`).
 * Due to a licensing limitation, the calculation of empirical orthogonal function  based on `eofs` (``xclim.sdba.properties.first_eof``) has been removed from `xclim`. (:issue:`1620`, :pull:`1621`).
+* `black` formatting style has been updated to the 2024 stable conventions. `isort` has been added to the `dev` installation recipe. (:pull:`1626`).
 
 Bug fixes
 ^^^^^^^^^
@@ -48,6 +50,7 @@ Internal changes
     * A new GitHub Workflow (``workflow-warning.yml``) has been added to warn maintainers when a forked repository has been used to open a Pull Request that modifies GitHub Workflows.
     * `pylint` has been configured to provide some overhead checks of the `xclim` codebase as well as run as part of `xclim`'s `pre-commit` hooks.
     * Some small adjustments to code organization to address `pylint` errors.
+* `dev` formatting tools (`black`, `blackdoc`, `isort`) are now pinned to their `pre-commit` hook version equivalents in both `pyproject.toml` and `tox.ini`. (:pull:`1626`).
 
 v0.47.0 (2023-12-01)
 --------------------

CODE_OF_CONDUCT.md

@@ -60,7 +60,7 @@ representative at an online or offline event.
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-[email protected].
+[github-[email protected]](mailto:[email protected]).
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

SECURITY.md

@@ -0,0 +1,38 @@
+# Security Policy
+
+## Supported Versions
+
+`xclim` is in rapid development and receives regular updates every four to six (4-6) weeks. In the event of a security-related bug discovery soon after the release of an `xclim` version, the last supported version will receive a patch release.
+
+## Reporting a Vulnerability
+
+If you believe you have found a security vulnerability in `xclim`, we encourage you to let us know right away. We take all security vulnerabilities seriously and appreciate your efforts to responsibly disclose them.
+
+Please follow these steps to report a security vulnerability:
+
+1. **Email**: Email [[email protected]](mailto:[email protected]) with a detailed description of the vulnerability. If applicable, please include any steps or a proof-of-concept to help us understand and reproduce the issue.
+
+2. **Encryption (Optional)**: If you are concerned about the sensitivity of the information you are sharing, you can use the PGP key found below to encrypt your communication.
+
+3. **Response**: We will acknowledge your email within 48 hours and work with you to understand and confirm the vulnerability.
+
+4. **Fix and Disclosure**: Once the vulnerability is confirmed, we will work to address it promptly. We appreciate your patience as we investigate and implement a fix. Once resolved, we will coordinate the disclosure and provide credit to the reporter unless they prefer to remain anonymous.
+
+## PGP Encryption Key
+
+You can use the following PGP key to encrypt your communications with us:
+
+    -----BEGIN PGP PUBLIC KEY BLOCK-----
+
+    mDMEZamQrhYJKwYBBAHaRw8BAQdA+saPvmvr1MYe1nQy3n3QDcRE9T7UzTJ1XH31
+    EI4Zb6u0Mk91cmFub3MgR2l0SHViIFN1cHBvcnQgPGdpdGh1Yi1zdXBwb3J0QG91
+    cmFub3MuY2E+iJkEExYKAEEWIQSeAu+Cbjupx79jy9VeVFD6o5TVcwUCZamQrgIb
+    AwUJCWYBgAULCQgHAgIiAgYVCgkICwIEFgIDAQIeBwIXgAAKCRBeVFD6o5TVc4ho
+    AQDXjDkx0b3A7yl6PQ4hBJ2uYzw0UWbml7mUwVdhMmdZkQD/VJZQNWrCQeOtYEM8
+    icZJYwR/OsKFOWqlDytusGGtjwa4OARlqZCuEgorBgEEAZdVAQUBAQdAa41Zabjz
+    P9O+p6tI69Cnft6U5om3+qCcMo8amTqauH0DAQgHiH4EGBYKACYWIQSeAu+Cbjup
+    x79jy9VeVFD6o5TVcwUCZamQrgIbDAUJCWYBgAAKCRBeVFD6o5TVcwmaAQClDxW6
+    2gir7lhRXAcO+vmRImpGd29TrkcQVh+ak7VlwQEA706d7Kusiorlf/h8pLSoNMmS
+    kuLGmHpUJ8NVGppU+wo=
+    =wuxr
+    -----END PGP PUBLIC KEY BLOCK-----

docs/autodoc_indicator.py

@@ -4,6 +4,7 @@
 
 Based on https://github.com/powerline/powerline/blob/83d855d3d73498c47553afeba212415990d95c54/docs/source/powerline_autodoc.py
 """
+
 from __future__ import annotations
 
 from sphinx.domains.python import PyFunction, PyXRefRole

docs/conf.py

@@ -103,6 +103,7 @@
     "sphinx_autodoc_typehints",
     "sphinx_codeautolink",
     "sphinx_copybutton",
+    "sphinx_mdinclude",
     "sphinx_rtd_theme",
 ]
 
@@ -248,7 +249,7 @@ class XCStyle(AlphaStyle):
 # the built documents.
 #
 # The short X.Y version.
-version = xclim.__version__
+version = xclim.__version__.split("-")[0]
 # The full version, including alpha/beta/rc tags.
 release = xclim.__version__
 
@@ -267,6 +268,7 @@ class XCStyle(AlphaStyle):
     "Thumbs.db",
     ".DS_Store",
     "notebooks/xclim_training",
+    "paper/paper.md",
     "**.ipynb_checkpoints",
 ]
 

docs/index.rst

@@ -41,6 +41,7 @@ Leveraging xarray and dask, users can easily bias-adjust climate simulations ove
 
    authors
    changes
+   security
    references
 
 .. toctree::

docs/security.rst

@@ -0,0 +1 @@
+.. mdinclude:: ../SECURITY.md

environment.yml

@@ -29,9 +29,9 @@ dependencies:
   # Extras
   - flox
   # Testing and development dependencies
-  - black >=22.12
-  - blackdoc
-  - bump-my-version
+  - black ==24.1.0
+  - blackdoc ==0.3.9
+#  - bump-my-version  # The conda package is not as up-to-date as the PyPI package.
   - cairosvg
   - codespell
   - coverage
@@ -43,6 +43,7 @@ dependencies:
   - h5netcdf
   - ipykernel
   - ipython
+  - isort ==5.13.2
   - matplotlib
   - mypy
   - nbqa
@@ -65,14 +66,16 @@ dependencies:
   - sphinx-autodoc-typehints
   - sphinx-codeautolink
   - sphinx-copybutton
+  - sphinx-mdinclude
   - sphinx-rtd-theme >=1.0
   - sphinxcontrib-bibtex
   - tokenize-rt
-  - tox
+  - tox >=4.0
 #  - tox-conda  # Will be added when a [email protected]+ compatible plugin is released.
   - xdoctest
   - yamllint
   - pip
   - pip:
+    - bump-my-version >=0.17.1  # The conda package is not as up-to-date as the PyPI package.
     - flake8-alphabetize
     - sphinxcontrib-svg2pdfconverter

pyproject.toml

@@ -59,16 +59,17 @@ dependencies = [
 [project.optional-dependencies]
 dev = [
   # Dev tools and testing
-  "black >=23.3.0",
-  "blackdoc",
-  "bump-my-version",
+  "black ==24.1.0",
+  "blackdoc ==0.3.9",
+  "bump-my-version >=0.17.1",
   "codespell",
   "coverage[toml]",
   "flake8",
   "flake8-alphabetize",
   "flake8-rst-docstrings",
   "h5netcdf",
   "ipython",
+  "isort ==5.13.2",
   "mypy",
   "nbqa",
   "nbval",
@@ -83,7 +84,7 @@ dev = [
   "pytest-xdist[psutil] >=3.2",
   "ruff >=0.1.0",
   "tokenize-rt",
-  "tox",
+  "tox >=4.0",
   # "tox-conda",  # Will be added when a [email protected]+ compatible plugin is released.
   "xdoctest",
   "yamllint",
@@ -98,6 +99,7 @@ dev = [
   "sphinx-autodoc-typehints",
   "sphinx-codeautolink",
   "sphinx-copybutton",
+  "sphinx-mdinclude",
   "sphinx-rtd-theme >=1.0",
   "sphinxcontrib-bibtex",
   "sphinxcontrib-svg2pdfconverter[Cairosvg]"
@@ -124,7 +126,7 @@ target-version = [
 ]
 
 [tool.bumpversion]
-current_version = "0.47.5-dev.9"
+current_version = "0.47.5-dev.11"
 commit = true
 commit_args = "--no-verify"
 tag = false

tests/test_generic.py

@@ -1,4 +1,5 @@
 """Tests for generic indices."""
+
 from __future__ import annotations
 
 import numpy as np

tests/test_land.py

@@ -1,4 +1,5 @@
 """Tests for indicators in `land` realm."""
+
 from __future__ import annotations
 
 import numpy as np

tests/test_stats.py

@@ -1,4 +1,5 @@
 """Tests for statistical indices."""
+
 from __future__ import annotations
 
 import numpy as np

tox.ini

@@ -21,13 +21,15 @@ description = Run code quality compliance tests under {basepython}
 skip_install = True
 extras =
 deps =
+    codespell
     flake8
+    flake8-alphabetize
     flake8-rst-docstrings
-    black[jupyter]
-    blackdoc
-    isort
+    black[jupyter]==24.1.0
+    blackdoc==0.3.9
+    isort==5.13.2
     nbqa
-    ruff
+    ruff>=0.1.0
     yamllint
 commands_pre =
 commands =
@@ -38,6 +40,7 @@ commands =
     nbqa black --check docs
     blackdoc --check --exclude=xclim/indices/__init__.py xclim
     blackdoc --check docs
+    codespell xclim tests docs
     yamllint --config-file=.yamllint.yaml xclim
 commands_post =
 

xclim/__init__.py

@@ -1,4 +1,5 @@
 """Climate indices computation package based on Xarray."""
+
 from __future__ import annotations
 
 try:
@@ -15,7 +16,7 @@
 
 __author__ = """Travis Logan"""
 __email__ = "[email protected]"
-__version__ = "0.47.5-dev.9"
+__version__ = "0.47.5-dev.11"
 
 
 _module_data = _files("xclim.data")

xclim/analog.py

@@ -1,4 +1,5 @@
 """Spatial Analogues module."""
+
 # TODO: Hellinger distance
 # TODO: Mahalanobis distance
 # TODO: Comment on "significance" of results.

xclim/cli.py

@@ -3,6 +3,7 @@
 Command Line Interface module
 =============================
 """
+
 from __future__ import annotations
 
 import sys

xclim/core/__init__.py

@@ -1,4 +1,5 @@
 """Core module."""
+
 from __future__ import annotations
 
 from . import missing

xclim/core/bootstrapping.py

@@ -1,4 +1,5 @@
 """Module comprising the bootstrapping algorithm for indicators."""
+
 from __future__ import annotations
 
 import warnings

xclim/core/calendar.py

@@ -4,6 +4,7 @@
 
 Helper function to handle dates, times and different calendars with xarray.
 """
+
 from __future__ import annotations
 
 import datetime as pydt
@@ -1013,12 +1014,14 @@ def resample_doy(doy: xr.DataArray, arr: xr.DataArray | xr.Dataset) -> xr.DataAr
 
 
 def time_bnds(  # noqa: C901
-    time: xr.DataArray
-    | xr.Dataset
-    | CFTimeIndex
-    | pd.DatetimeIndex
-    | DataArrayResample
-    | DatasetResample,
+    time: (
+        xr.DataArray
+        | xr.Dataset
+        | CFTimeIndex
+        | pd.DatetimeIndex
+        | DataArrayResample
+        | DatasetResample
+    ),
     freq: str | None = None,
     precision: str | None = None,
 ):
@@ -1768,9 +1771,11 @@ def stack_periods(
         periods.append(
             slice(
                 strd_slc.start + win_slc.start,
-                (strd_slc.start + win_slc.stop)
-                if win_slc.stop is not None
-                else da.time.size,
+                (
+                    (strd_slc.start + win_slc.stop)
+                    if win_slc.stop is not None
+                    else da.time.size
+                ),
             )
         )
 

xclim/core/cfchecks.py

@@ -4,6 +4,7 @@
 
 Utilities designed to verify the compliance of metadata with the CF-Convention.
 """
+
 from __future__ import annotations
 
 import fnmatch

xclim/core/datachecks.py

@@ -4,6 +4,7 @@
 
 Utilities designed to check the validity of data inputs.
 """
+
 from __future__ import annotations
 
 from typing import Sequence