Merge remote-tracking branch 'upstream/main' into pymc_dev

sktime · Nov 7, 2024 · 7844e7c · 7844e7c
2 parents 6c32481 + 5849045
commit 7844e7c
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -29,20 +29,23 @@ concurrency:
 
 jobs:
   code-quality:
+    name: code-quality
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-      - id: file_changes
-        uses: trilom/[email protected]
-        with:
-          output: " "
-      - name: List changed files
-        run: echo '${{ steps.file_changes.outputs.files}}'
-      - uses: pre-commit/[email protected]
+      - name: repository checkout step
+        uses: actions/checkout@v4
+      - name: python environment step
+        uses: actions/setup-python@v5
         with:
-          extra_args: --files ${{ steps.file_changes.outputs.files}}
-      - name: Check for missing init files
+          python-version: "3.11"
+      - name: install pre-commit
+        run: python3 -m pip install pre-commit
+      - id: changed-files
+        name: identify modified files
+        uses: tj-actions/changed-files@v45
+      - name: run pre-commit hooks on modified files
+        run: pre-commit run --color always --files ${{ steps.changed-files.outputs.all_changed_files }} --show-diff-on-failure
+      - name: check missing __init__ files
         run: build_tools/fail_on_missing_init_files.sh
         shell: bash
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -88,7 +88,7 @@ docs = [
     "pydata-sphinx-theme",
     "sphinx!=7.2.0,<9.0.0",
     "sphinx-design<0.7.0",
-    "sphinx-issues<5.0.0",
+    "sphinx-issues<6.0.0",
     "sphinx-gallery<0.19.0",
     "sphinx-panels",
     "tabulate",

diff --git a/setup.cfg b/setup.cfg
@@ -11,7 +11,6 @@ addopts =
     --ignore build_tools
     --ignore examples
     --ignore docs
-    --doctest-modules
     --durations 10
     --timeout 600
     --cov skpro

diff --git a/skpro/distributions/alpha.py b/skpro/distributions/alpha.py
@@ -38,8 +38,8 @@ class Alpha(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions import Alpha
 
     >>> distr = Alpha(a=[[1, 2], [3, 4]])

diff --git a/skpro/distributions/beta.py b/skpro/distributions/beta.py
@@ -29,8 +29,8 @@ class Beta(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.beta import Beta
 
     >>> d = Beta(beta=[[1, 1], [2, 3], [4, 5]], alpha=2)

diff --git a/skpro/distributions/binomial.py b/skpro/distributions/binomial.py
@@ -26,8 +26,8 @@ class Binomial(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.binomial import Binomial
 
     >>> d = Binomial(n=[[10, 10], [20, 30], [40, 50]], p=0.5)

diff --git a/skpro/distributions/chi_squared.py b/skpro/distributions/chi_squared.py
@@ -19,8 +19,8 @@ class ChiSquared(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.chi_squared import ChiSquared
     >>> chi = ChiSquared(dof=[[1, 2], [3, 4], [5, 6]])
     """

diff --git a/skpro/distributions/compose/_iid.py b/skpro/distributions/compose/_iid.py
@@ -28,8 +28,8 @@ class IID(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> import pandas as pd
     >>> from skpro.distributions.compose import IID
     >>> from skpro.distributions.normal import Normal

diff --git a/skpro/distributions/delta.py b/skpro/distributions/delta.py
@@ -30,8 +30,8 @@ class Delta(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.delta import Delta
 
     >>> delta = Delta(c=[[0, 1], [2, 3], [4, 5]])

diff --git a/skpro/distributions/empirical.py b/skpro/distributions/empirical.py
@@ -42,8 +42,8 @@ class Empirical(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> import pandas as pd
     >>> from skpro.distributions.empirical import Empirical
 

diff --git a/skpro/distributions/fisk.py b/skpro/distributions/fisk.py
@@ -29,8 +29,8 @@ class Fisk(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.fisk import Fisk
 
     >>> d = Fisk(beta=[[1, 1], [2, 3], [4, 5]], alpha=2)

diff --git a/skpro/distributions/gamma.py b/skpro/distributions/gamma.py
@@ -32,8 +32,8 @@ class Gamma(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.gamma import Gamma
 
     >>> d = Gamma(beta=[[1, 1], [2, 3], [4, 5]], alpha=2)

diff --git a/skpro/distributions/halfcauchy.py b/skpro/distributions/halfcauchy.py
@@ -39,8 +39,8 @@ class HalfCauchy(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.halfcauchy import HalfCauchy
 
     >>> hc = HalfCauchy(beta=1)

diff --git a/skpro/distributions/halflogistic.py b/skpro/distributions/halflogistic.py
@@ -40,8 +40,8 @@ class HalfLogistic(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.halflogistic import HalfLogistic
 
     >>> hl = HalfLogistic(beta=1)

diff --git a/skpro/distributions/halfnormal.py b/skpro/distributions/halfnormal.py
@@ -35,8 +35,8 @@ class HalfNormal(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.halfnormal import HalfNormal
 
     >>> hn = HalfNormal(sigma=1)

diff --git a/skpro/distributions/histogram.py b/skpro/distributions/histogram.py
@@ -622,5 +622,19 @@ def get_test_params(cls, parameter_set="default"):
             "index": pd.Index(np.arange(3)),
             "columns": pd.Index(np.arange(2)),
         }
+        params2 = {
+            "bins": [
+                [[0, 1.5, 2, 3, 4], [5, 5.5, 5.8, 6.5, 7, 7.5]],
+                [(2, 12, 5), [0, 1, 2, 3, 4]],
+                [[1.5, 2.5, 3.1, 4, 5.4], [-4, -2, -1.5, 5, 10]],
+            ],
+            "bin_mass": [
+                [[0.1, 0.2, 0.3, 0.4], [0.25, 0.1, 0, 0.4, 0.25]],
+                [[0.1, 0.2, 0.4, 0.2, 0.1], [0.4, 0.3, 0.2, 0.1]],
+                [[0.06, 0.15, 0.09, 0.7], [0.4, 0.15, 0.325, 0.125]],
+            ],
+            "index": pd.Index(np.arange(3)),
+            "columns": pd.Index(np.arange(2)),
+        }
 
-        return [params1]
+        return [params1, params2]
diff --git a/skpro/distributions/inversegamma.py b/skpro/distributions/inversegamma.py
@@ -31,8 +31,8 @@ class InverseGamma(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.inversegamma import InverseGamma
 
     >>> d = InverseGamma(beta=[[1, 1], [2, 3], [4, 5]], alpha=2)

diff --git a/skpro/distributions/laplace.py b/skpro/distributions/laplace.py
@@ -36,8 +36,8 @@ class Laplace(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions import Laplace
 
     >>> n = Laplace(mu=[[0, 1], [2, 3], [4, 5]], scale=1)

diff --git a/skpro/distributions/logistic.py b/skpro/distributions/logistic.py
@@ -29,8 +29,8 @@ class Logistic(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.logistic import Logistic
 
     >>> l = Logistic(mu=[[0, 1], [2, 3], [4, 5]], scale=1)

diff --git a/skpro/distributions/loglaplace.py b/skpro/distributions/loglaplace.py
@@ -39,8 +39,8 @@ class LogLaplace(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.loglaplace import LogLaplace
 
     >>> ll = LogLaplace(scale=1)

diff --git a/skpro/distributions/lognormal.py b/skpro/distributions/lognormal.py
@@ -27,8 +27,8 @@ class LogNormal(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.lognormal import LogNormal
 
     >>> n = LogNormal(mu=[[0, 1], [2, 3], [4, 5]], sigma=1)

diff --git a/skpro/distributions/meanscale.py b/skpro/distributions/meanscale.py
@@ -35,8 +35,8 @@ class MeanScale(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.normal import Normal
 
     >>> n = Normal(mu=[[0, 1], [2, 3], [4, 5]], sigma=2)

diff --git a/skpro/distributions/mixture.py b/skpro/distributions/mixture.py
@@ -31,8 +31,8 @@ class Mixture(BaseMetaObject, BaseDistribution):
     index : pd.Index, optional, default = inferred from component distributions
     columns : pd.Index, optional, default = inferred from component distributions
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.mixture import Mixture
     >>> from skpro.distributions.normal import Normal
 

diff --git a/skpro/distributions/normal.py b/skpro/distributions/normal.py
@@ -19,7 +19,7 @@ class Normal(BaseDistribution):
     The normal distribution is parametrized by mean :math:`\mu` and
     standard deviation :math:`\sigma`, such that the pdf is
 
-    .. math:: f(x) = \frac{1}{\sigma \sqrt{2\pi}} \exp\left(-\frac{(x - \mu)^2}{2\sigma^2}\right)  # noqa E501
+    .. math:: f(x) = \frac{1}{\sigma \sqrt{2\pi}} \exp\left(-\frac{(x - \mu)^2}{2\sigma^2}\right)
 
     The mean :math:`\mu` is represented by the parameter ``mu``,
     and the standard deviation :math:`\sigma` by the parameter ``sigma``.
@@ -33,12 +33,12 @@ class Normal(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.normal import Normal
 
     >>> n = Normal(mu=[[0, 1], [2, 3], [4, 5]], sigma=1)
-    """
+    """  # noqa E501
 
     _tags = {
         "capabilities:approx": ["pdfnorm"],

diff --git a/skpro/distributions/pareto.py b/skpro/distributions/pareto.py
@@ -16,7 +16,8 @@ class Pareto(BaseDistribution):
     and the Pareto index (or shape parameter) :math:`\alpha`
     by the parameter ``alpha``.
 
-    The CDF can be represented as,
+    The CDF can be represented as
+
     :math:`F(x) = 1-\left(\frac{\text{scale}}{x}\right)^\alpha
     \text{ if } x>0, 0 \text{ if } x<0`
 
@@ -29,8 +30,8 @@ class Pareto(BaseDistribution):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.pareto import Pareto
 
     >>> n = Pareto(scale=[[1, 1.5], [2, 2.5], [3, 4]], alpha=3)

diff --git a/skpro/distributions/poisson.py b/skpro/distributions/poisson.py
@@ -21,8 +21,8 @@ class Poisson(_ScipyAdapter):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions import Poisson
 
     >>> distr = Poisson(mu=[[1, 1], [2, 3], [4, 5]])

diff --git a/skpro/distributions/qpd.py b/skpro/distributions/qpd.py
@@ -53,8 +53,8 @@ class QPD_Johnson(_DelegatedDistribution):
     base_dist: str, one of ``'normal'`` (default), ``'logistic'``
         options are ``'normal'`` (default) or ``'logistic'``
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.qpd import QPD_Johnson  # doctest: +SKIP
 
     >>> qpd = QPD_Johnson(
@@ -193,8 +193,8 @@ class QPD_S(BaseDistribution):
     base_dist: str, one of ``'normal'`` (default), ``'logistic'``
         options are ``'normal'`` (default) or ``'logistic'``
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.qpd import QPD_S  # doctest: +SKIP
 
     >>> qpd = QPD_S(
@@ -371,8 +371,8 @@ class QPD_B(BaseDistribution):
     base_dist: str, one of ``'normal'`` (default), ``'logistic'``
         options are ``'normal'`` (default) or ``'logistic'``
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.qpd import QPD_B  # doctest: +SKIP
 
     >>> qpd = QPD_B(
@@ -555,8 +555,8 @@ class QPD_U(BaseDistribution):
     base_dist: str, one of ``'normal'`` (default), ``'logistic'``
         options are ``'normal'`` (default) or ``'logistic'``
 
-    Example
-    -------
+    Examples
+    --------
     >>> from skpro.distributions.qpd import QPD_U  # doctest: +SKIP
 
     >>> qpd = QPD_U(

diff --git a/skpro/distributions/qpd_empirical.py b/skpro/distributions/qpd_empirical.py
@@ -57,8 +57,8 @@ class QPD_Empirical(Empirical):
     index : pd.Index, optional, default = RangeIndex
     columns : pd.Index, optional, default = RangeIndex
 
-    Example
-    -------
+    Examples
+    --------
     >>> import pandas as pd
     >>> from skpro.distributions import QPD_Empirical