Package health (#407)

xarray-contrib · Oct 30, 2023 · 683e1ed · 683e1ed
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diff --git a/.github/workflows/upstream-dev-ci.yml b/.github/workflows/upstream-dev-ci.yml
@@ -47,7 +47,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     outputs:
       artifacts_availability: ${{ steps.status.outputs.ARTIFACTS_AVAILABLE }}
     steps:

diff --git a/.github/workflows/xskillscore_installs.yml b/.github/workflows/xskillscore_installs.yml
@@ -38,7 +38,7 @@ jobs:
     - name: Setup python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

diff --git a/.github/workflows/xskillscore_testing.yml b/.github/workflows/xskillscore_testing.yml
@@ -34,7 +34,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ["3.9", "3.10", "3.11"]
     steps:
       - uses: actions/checkout@v2
       - name: Set up conda
@@ -78,7 +78,7 @@ jobs:
           channels: conda-forge
           mamba-version: "*"
           activate-environment: xskillscore-minimum-tests
-          python-version: 3.8
+          python-version: 3.9
       - name: Set up conda environment
         run: |
           mamba env update -f ci/minimum-tests.yml
@@ -109,7 +109,7 @@ jobs:
           channels: conda-forge
           mamba-version: "*"
           activate-environment: xskillscore-docs-notebooks
-          python-version: 3.8
+          python-version: 3.9
       - name: Set up conda environment
         run: |
           mamba env update -f ci/docs_notebooks.yml

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,47 +1,85 @@
+default_language_version:
+  python: python3
+
 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: quarterly
+    skip: []
+    submodules: false
 
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
-    hooks:
-      - id: trailing-whitespace
-      - id: no-commit-to-branch
+  -   repo: https://github.com/pre-commit/pre-commit-hooks
+      rev: v4.4.0
+      hooks:
+      - id: check-added-large-files
       - id: check-docstring-first
-      - id: end-of-file-fixer
+      - id: check-json
+        exclude: 'asv.conf.json'
       - id: check-merge-conflict
+      - id: check-toml
       - id: check-yaml
+        args: [ '--allow-multiple-documents' ]
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: no-commit-to-branch
+      - id: pretty-format-json
+        args: [ '--autofix', '--no-ensure-ascii', '--no-sort-keys' ]
+        exclude: '.ipynb|asv.conf.json'
+      - id: trailing-whitespace
 
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
-  - repo: https://github.com/psf/black
-    rev: 22.10.0
-    hooks:
+  -   repo: https://github.com/psf/black-pre-commit-mirror
+      rev: 23.10.1
+      hooks:
       - id: black
 
-  - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
-    hooks:
+  -   repo: https://github.com/PyCQA/flake8
+      rev: 6.1.0
+      hooks:
       - id: flake8
 
-  - repo: https://github.com/PyCQA/doc8
-    rev: v1.0.0
-    hooks:
+  -   repo: https://github.com/PyCQA/isort
+      rev: 5.12.0
+      hooks:
+      - id: isort
+
+  -   repo: https://github.com/keewis/blackdoc
+      rev: v0.3.8
+      hooks:
+      - id: blackdoc
+        additional_dependencies: [ 'black==23.10.1' ]
+
+  -   repo: https://github.com/PyCQA/doc8
+      rev: v1.0.0
+      hooks:
       - id: doc8
         args: ["--max-line-length", "100",
                "--allow-long-titles",
                "--ignore-path", "docs/source/api/"]
 
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
-    hooks:
+  -   repo: https://github.com/pre-commit/mirrors-mypy
+      rev: v0.982
+      hooks:
       - id: mypy
-        exclude: "asv_bench"
-        args:
-          - --ignore-missing-imports
-          - --follow-imports=silent
-          - --install-types
-          - --non-interactive
+        exclude: 'asv_bench'
+        additional_dependencies: [
+            # Type stubs
+            types-python-dateutil,
+            types-pkg_resources,
+            types-PyYAML,
+            types-pytz,
+            typing-extensions==3.10.0.0,
+            # Dependencies that are typed
+            numpy,
+          ]
+
+  -   repo: https://github.com/python-jsonschema/check-jsonschema
+      rev: 0.27.0
+      hooks:
+      - id: check-github-workflows
+      - id: check-readthedocs
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,7 +2,6 @@
 Changelog History
 =================
 
-
 xskillscore v0.0.25 (2021-xx-xx)
 --------------------------------
 

diff --git a/asv_bench/benchmarks/__init__.py b/asv_bench/benchmarks/__init__.py
@@ -56,7 +56,6 @@ class Generate:
     repeat = (2, 5, 20)
 
     def make_ds(self, nmember, nx, ny, chunks=None):
-
         # ds
         self.ds = xr.Dataset()
         self.nmember = nmember

diff --git a/ci/doc.yml b/ci/doc.yml
@@ -2,7 +2,7 @@ name: xskillscore-docs
 channels:
   - conda-forge
 dependencies:
-  - python=3.8
+  - python >=3.9
   - bottleneck
   - doc8
   - ipykernel

diff --git a/readthedocs.yml b/readthedocs.yml
@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   tools:
-    python: "mambaforge-4.10"
+    python: "mambaforge-22.9"
 
 conda:
     environment: ci/doc.yml
@@ -12,3 +12,8 @@ sphinx:
   fail_on_warning: false
 
 formats: []
+
+python:
+  install:
+    - method: pip
+      path: .
diff --git a/setup.cfg b/setup.cfg
@@ -1,6 +1,9 @@
 [tool:pytest]
 python_files = test_*.py
 testpaths = xskillscore/tests
+addopts =
+    --color=yes
+    --verbose
 markers =
     slow: marks tests as slow (deselect with '-m "not slow"')
 

diff --git a/setup.py b/setup.py
@@ -9,7 +9,7 @@
 URL = "https://github.com/xarray-contrib/xskillscore"
 with open("requirements.txt") as f:
     INSTALL_REQUIRES = f.read().strip().split("\n")
-PYTHON_REQUIRE = ">=3.8"
+PYTHON_REQUIRE = ">=3.9"
 
 EXTRAS_REQUIRE = {
     "accel": ["numba>=0.52", "bottleneck"],
@@ -24,7 +24,7 @@
     "matplotlib",
     "pytest-cov",
     "pytest-xdist",
-    "pytest-lazyfixures",
+    "pytest-lazy-fixures",
     "pre-commit",
 ]
 EXTRAS_REQUIRE["docs"] = EXTRAS_REQUIRE["complete"] + [

diff --git a/xskillscore/__init__.py b/xskillscore/__init__.py
@@ -1,5 +1,5 @@
 # flake8: noqa
-from pkg_resources import DistributionNotFound, get_distribution  # type: ignore
+from importlib.metadata import PackageNotFoundError, version as _get_version
 
 from .core import resampling
 from .core.accessor import XSkillScoreAccessor
@@ -40,7 +40,7 @@
 from .versioning.print_versions import show_versions
 
 try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
+    __version__ = _get_version("xskillscore")
+except PackageNotFoundError:  # pragma: no cover
     # package is not installed
     pass
diff --git a/xskillscore/core/comparative.py b/xskillscore/core/comparative.py
@@ -80,19 +80,17 @@ def sign_test(
 
     Examples
     --------
-    >>> f1 = xr.DataArray(np.random.normal(size=(30)),
-    ...                   coords=[('time', np.arange(30))])
+    >>> f1 = xr.DataArray(np.random.normal(size=(30)), coords=[("time", np.arange(30))])
     >>> f2 = f1 + 2
-    >>> o = xr.DataArray(np.random.normal(size=(30)),
-    ...                  coords=[('time', np.arange(30))])
+    >>> o = xr.DataArray(np.random.normal(size=(30)), coords=[("time", np.arange(30))])
     >>> significantly_different, walk, confidence = xs.sign_test(
-    ... f1, f2, o, time_dim='time', metric='mae', orientation='negative'
+    ...     f1, f2, o, time_dim="time", metric="mae", orientation="negative"
     ... )
-    >>> walk.plot() # doctest: +ELLIPSIS
+    >>> walk.plot()  # doctest: +ELLIPSIS
     [<matplotlib.lines.Line2D object at 0x...>]
-    >>> confidence.plot(color='gray') # doctest: +ELLIPSIS
+    >>> confidence.plot(color="gray")  # doctest: +ELLIPSIS
     [<matplotlib.lines.Line2D object at 0x...>]
-    >>> (-1 * confidence).plot(color='gray') # doctest: +ELLIPSIS
+    >>> (-1 * confidence).plot(color="gray")  # doctest: +ELLIPSIS
     [<matplotlib.lines.Line2D object at 0x...>]
     >>> walk
     <xarray.DataArray (time: 30)>
@@ -268,14 +266,11 @@ def halfwidth_ci_test(
 
     Examples
     --------
-    >>> f1 = xr.DataArray(np.random.normal(size=(30)),
-    ...                   coords=[('time', np.arange(30))])
-    >>> f2 = xr.DataArray(np.random.normal(size=(30)),
-    ...                   coords=[('time', np.arange(30))])
-    >>> o = xr.DataArray(np.random.normal(size=(30)),
-    ...                  coords=[('time', np.arange(30))])
+    >>> f1 = xr.DataArray(np.random.normal(size=(30)), coords=[("time", np.arange(30))])
+    >>> f2 = xr.DataArray(np.random.normal(size=(30)), coords=[("time", np.arange(30))])
+    >>> o = xr.DataArray(np.random.normal(size=(30)), coords=[("time", np.arange(30))])
     >>> significantly_different, diff, hwci = xs.halfwidth_ci_test(
-    ...    f1, f2, o, "mae", time_dim='time', dim=[], alpha=0.05
+    ...     f1, f2, o, "mae", time_dim="time", dim=[], alpha=0.05
     ... )
     >>> significantly_different
     <xarray.DataArray ()>
@@ -290,7 +285,7 @@ def halfwidth_ci_test(
     >>> # confidence interval, therefore not significant at level alpha=0.05
     >>> # now comparing against an offset f2, the difference in MAE is significant
     >>> significantly_different, diff, hwci = xs.halfwidth_ci_test(
-    ... f1, f2 + 2., o, "mae", time_dim='time', dim=[], alpha=0.05
+    ...     f1, f2 + 2.0, o, "mae", time_dim="time", dim=[], alpha=0.05
     ... )
     >>> significantly_different
     <xarray.DataArray ()>

diff --git a/xskillscore/core/contingency.py b/xskillscore/core/contingency.py
@@ -74,15 +74,17 @@ class Contingency:
 
     Examples
     --------
-    >>> da = xr.DataArray(np.random.normal(size=(3, 3)),
-    ...                   coords=[("x", np.arange(3)), ("y", np.arange(3))])
+    >>> da = xr.DataArray(
+    ...     np.random.normal(size=(3, 3)),
+    ...     coords=[("x", np.arange(3)), ("y", np.arange(3))],
+    ... )
     >>> o = xr.Dataset({"var1": da, "var2": da})
     >>> f = o * 1.1
     >>> o_category_edges = np.linspace(-2, 2, 5)
     >>> f_category_edges = np.linspace(-3, 3, 5)
-    >>> xs.Contingency(o, f,
-    ...                o_category_edges, f_category_edges,
-    ...                dim=['x', 'y']) # doctest: +SKIP
+    >>> xs.Contingency(
+    ...     o, f, o_category_edges, f_category_edges, dim=["x", "y"]
+    ... )  # doctest: +SKIP
     <xskillscore.Contingency>
     Dimensions:                       (forecasts_category: 4, observations_category: 4)
     Coordinates:
@@ -774,7 +776,7 @@ def _gerrity_s(table):
             a = (1.0 - p_sum) / p_sum
             k = a.shape[-1]
             s = np.zeros(table.shape, dtype=float)
-            for (i, j) in np.ndindex(*s.shape[-2:]):
+            for i, j in np.ndindex(*s.shape[-2:]):
                 if i == j:
                     s[..., i, j] = (
                         1.0