Merge branch 'develop' into feature/541-add-standard-deviation-as-a-f…

…unction
eliegoudout · Oct 13, 2023 · 3115a6d · 3115a6d
2 parents bb5923d + 4fe909c
commit 3115a6d
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Showing 23 changed files with 49 additions and 43 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -11,7 +11,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9']
+        python-version: ['3.9', '3.10']
 
     steps:
     - uses: actions/checkout@v2

diff --git a/binder/requirements.txt b/binder/requirements.txt
@@ -1,4 +1,4 @@
--r ../readthedocs-requirements.txt
+scikit-fda[docs]
 jupytext
 sphinx-gallery<=0.7.0
 .
diff --git a/docs/_static/switcher.json b/docs/_static/switcher.json
@@ -5,7 +5,7 @@
         "url": "https://fda.readthedocs.io/en/latest/"
     },
     {
-    	"name": "0.8.1 (stable)",
+    	"name": "0.9 (stable)",
         "version": "stable",
         "url": "https://fda.readthedocs.io/en/stable/",
         "preferred": true

diff --git a/pyproject.toml b/pyproject.toml
@@ -2,7 +2,7 @@
 name = "scikit-fda"
 description = "Functional Data Analysis Python package."
 readme = "README.rst"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 license = {file = "LICENSE.txt"}
 keywords = [
 	"functional data",
@@ -20,7 +20,7 @@ classifiers = [
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
     "Topic :: Scientific/Engineering :: Mathematics",
     "Topic :: Software Development :: Libraries :: Python Modules",
     "Typing :: Typed",
@@ -45,6 +45,21 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
+docs = [
+  "basemap",
+  "basemap-data",
+  "basemap-data-hires",
+  "ipykernel",
+  "jupyter-sphinx",
+  "myst-parser",
+  "pillow",
+  "pydata-sphinx-theme",
+  "pytest",
+  "setuptools>=41.2",
+  "sphinx>=3",
+  "sphinx-gallery",
+  "sphinxcontrib-bibtex",
+]
 test = [
   "pytest",
   "pytest-env",

diff --git a/readthedocs-requirements.txt b/readthedocs-requirements.txt
diff --git a/readthedocs.yml b/readthedocs.yml
@@ -5,6 +5,11 @@
 # Required
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   builder: html
@@ -18,8 +23,8 @@ sphinx:
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: "3.8"
   install:
-    - requirements: readthedocs-requirements.txt
     - method: pip
-      path: .
+      path: .
+      extra_requirements:
+        - docs
diff --git a/requirements.txt b/requirements.txt
diff --git a/skfda/__init__.py b/skfda/__init__.py
@@ -30,4 +30,4 @@
         concatenate as concatenate,
     )
 
-__version__ = "0.9.dev1"
+__version__ = "0.9.1.dev1"
diff --git a/skfda/datasets/_real_datasets.py b/skfda/datasets/_real_datasets.py
@@ -5,12 +5,11 @@
 
 import numpy as np
 import pandas as pd
+import rdata
 from pandas import DataFrame, Series
 from sklearn.utils import Bunch
 from typing_extensions import Literal
 
-import rdata
-
 from ..representation import FDataGrid
 from ..typing._numpy import NDArrayFloat, NDArrayInt
 
@@ -180,7 +179,7 @@ def fetch_ucr(
     The UCR/UEA Time Series Classification repository, hosted at
     www.timeseriesclassification.com includes plenty of
     classification problems with univariate and multivariate time series
-    \ :footcite:p:`dau++_2019_ucr,bagnall++_2018_uea`.
+    :footcite:p:`dau++_2019_ucr,bagnall++_2018_uea`.
     They are widely used in the functional data classification literature.
 
     Args:

diff --git a/skfda/exploratory/visualization/_boxplot.py b/skfda/exploratory/visualization/_boxplot.py
@@ -11,7 +11,6 @@
 from typing import Sequence, Tuple
 
 import matplotlib
-import matplotlib.pyplot as plt
 import numpy as np
 from matplotlib.axes import Axes
 from matplotlib.colors import Colormap
@@ -376,7 +375,7 @@ def __init__(
 
         self._fdatagrid = fdatagrid
         self._prob = prob
-        self._colormap = plt.cm.get_cmap('RdPu')
+        self._colormap = matplotlib.colormaps['RdPu']
         self.barcol = "blue"
         self.outliercol = "red"
         self.mediancol = "black"
@@ -701,7 +700,7 @@ def __init__(
         self._non_outlying_envelope = _envelopes.compute_envelope(inliers)
 
         self._fdatagrid = fdatagrid
-        self.colormap = plt.cm.get_cmap('Greys')
+        self.colormap = matplotlib.colormaps['Greys']
         self._boxcol = 1.0
         self._outcol = 0.7
 

diff --git a/skfda/exploratory/visualization/_magnitude_shape_plot.py b/skfda/exploratory/visualization/_magnitude_shape_plot.py
@@ -10,7 +10,6 @@
 from typing import Any, Sequence
 
 import matplotlib
-import matplotlib.pyplot as plt
 import numpy as np
 from matplotlib.artist import Artist
 from matplotlib.axes import Axes
@@ -193,7 +192,7 @@ def __init__(
 
         self._fdata = fdata
         self._outliers = outliers
-        self._colormap = plt.cm.get_cmap('seismic')
+        self._colormap = matplotlib.colormaps['seismic']
         self._color = 0.2
         self._outliercol = 0.8
         self.xlabel = 'MO'

diff --git a/skfda/ml/classification/_depth_classifiers.py b/skfda/ml/classification/_depth_classifiers.py
@@ -71,7 +71,7 @@ class DDClassifier(
     Depth-versus-depth (DD) classifer for functional data.
 
     Transforms the data into a DD-plot and then classifies using a polynomial
-    of a chosen degree\ :footcite:p:`li++_2012_ddclassifier`.
+    of a chosen degree :footcite:p:`li++_2012_ddclassifier`.
     The polynomial passes through zero and maximizes the accuracy of the
     classification on the train dataset.
 
@@ -117,7 +117,7 @@ class DDClassifier(
     See also:
         :class:`~skfda.ml.classification.DDGClassifier`
         :class:`~skfda.ml.classification.MaximumDepthClassifier`
-        :class:`~skfda.preprocessing.dim_reduction.feature_extraction._ddg_transformer`
+        :class:`~skfda.preprocessing.dim_reduction.feature_construction._ddg_transformer`
 
     References:
         .. footbibliography::
@@ -307,7 +307,7 @@ class DDGClassifier(
     See also:
         :class:`~skfda.ml.classification.DDClassifier`
         :class:`~skfda.ml.classification.MaximumDepthClassifier`
-        :class:`~skfda.preprocessing.dim_reduction.feature_extraction._ddg_transformer`
+        :class:`~skfda.preprocessing.dim_reduction.feature_construction._ddg_transformer`
 
     References:
         .. footbibliography::

diff --git a/skfda/preprocessing/dim_reduction/feature_extraction/__init__.py b/skfda/preprocessing/dim_reduction/feature_extraction/__init__.py
@@ -8,4 +8,5 @@
     'Please use "dim_reduction" for FPCA'
     'or "feature_construction" for feature construction techniques',
     category=DeprecationWarning,
+    stacklevel=2,
 )
diff --git a/skfda/preprocessing/dim_reduction/projection/__init__.py b/skfda/preprocessing/dim_reduction/projection/__init__.py
@@ -5,4 +5,5 @@
 warnings.warn(
     'The module "projection" is deprecated. Please use "dim_reduction"',
     category=DeprecationWarning,
+    stacklevel=2,
 )
diff --git a/skfda/preprocessing/missing/_interpolate.py b/skfda/preprocessing/missing/_interpolate.py
@@ -134,7 +134,7 @@ class MissingValuesInterpolation(
 
         For multivariate functions, such as surfaces all dimensions are
         considered. This is currently done using
-        :external:class:`~scipy.interpolation.LinearNDInterpolator`, which
+        :external:class:`~scipy.interpolate.LinearNDInterpolator`, which
         triangulates the space and performs linear barycentric interpolation:
 
         >>> X = FDataGrid(

diff --git a/skfda/preprocessing/smoothing/kernel_smoothers.py b/skfda/preprocessing/smoothing/kernel_smoothers.py
@@ -18,6 +18,7 @@
     "The \"kernel_smoothers\" module is deprecated. "
     "Use the \"KernelSmoother\" class instead",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 

diff --git a/skfda/representation/basis/_bspline_basis.py b/skfda/representation/basis/_bspline_basis.py
@@ -460,6 +460,7 @@ def __init__(  # noqa: WPS238
             knots=knots,
         )
         warnings.warn(
-            "The BSplines class is deprecated. Use BSplineBasis instead.",
+            "The BSpline class is deprecated. Use BSplineBasis instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
diff --git a/skfda/representation/basis/_constant_basis.py b/skfda/representation/basis/_constant_basis.py
@@ -81,5 +81,6 @@ def __init__(self, domain_range: Optional[DomainRangeLike] = None) -> None:
         warnings.warn(
             "The Constant class is deprecated. Use ConstantBasis instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
         super().__init__(domain_range=domain_range)
diff --git a/skfda/representation/basis/_finite_element_basis.py b/skfda/representation/basis/_finite_element_basis.py
@@ -229,4 +229,5 @@ def __init__(
             "The FiniteElement class is deprecated. Use "
             "FiniteElementBasis instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
diff --git a/skfda/representation/basis/_fourier_basis.py b/skfda/representation/basis/_fourier_basis.py
@@ -319,6 +319,7 @@ def __init__(
         warnings.warn(
             "The Fourier class is deprecated. Use FourierBasis instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
         super().__init__(
             domain_range=domain_range,

diff --git a/skfda/representation/basis/_monomial_basis.py b/skfda/representation/basis/_monomial_basis.py
@@ -211,4 +211,5 @@ def __init__(
         warnings.warn(
             "The Monomial class is deprecated. Use MonomialBasis instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
diff --git a/skfda/representation/basis/_tensor_basis.py b/skfda/representation/basis/_tensor_basis.py
@@ -180,4 +180,5 @@ def __init__(self, basis_list: Iterable[Basis]):
         warnings.warn(
             "The Tensor class is deprecated. Use TensorBasis instead.",
             DeprecationWarning,
+            stacklevel=2,
         )
diff --git a/skfda/representation/basis/_vector_basis.py b/skfda/representation/basis/_vector_basis.py
@@ -245,4 +245,5 @@ def __init__(self, basis_list: Iterable[Basis]) -> None:
             "The VectorValued class is deprecated. "
             "Use VectorValuedBasis instead.",
             DeprecationWarning,
+            stacklevel=2,
         )