From febfe36fbb5c2f947c4956eebfe6d4ce08768763 Mon Sep 17 00:00:00 2001
From: VNMabus <vnmabus@gmail.com>
Date: Thu, 12 Oct 2023 14:18:17 +0200
Subject: [PATCH 1/7] Fix some warnings.

---
 skfda/datasets/_real_datasets.py                            | 5 ++---
 skfda/exploratory/visualization/_boxplot.py                 | 5 ++---
 skfda/exploratory/visualization/_magnitude_shape_plot.py    | 3 +--
 skfda/ml/classification/_depth_classifiers.py               | 6 +++---
 .../dim_reduction/feature_extraction/__init__.py            | 1 +
 skfda/preprocessing/dim_reduction/projection/__init__.py    | 1 +
 skfda/preprocessing/smoothing/kernel_smoothers.py           | 1 +
 skfda/representation/basis/_bspline_basis.py                | 3 ++-
 skfda/representation/basis/_constant_basis.py               | 1 +
 skfda/representation/basis/_finite_element_basis.py         | 1 +
 skfda/representation/basis/_fourier_basis.py                | 1 +
 skfda/representation/basis/_monomial_basis.py               | 1 +
 skfda/representation/basis/_tensor_basis.py                 | 1 +
 skfda/representation/basis/_vector_basis.py                 | 1 +
 14 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/skfda/datasets/_real_datasets.py b/skfda/datasets/_real_datasets.py
index 28415c76c..d345ebdcf 100644
--- 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
index 19aae239b..e315a92f0 100644
--- 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
index bb5c56d51..6fc13fbdf 100644
--- 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
index 47e29e239..c258d608b 100644
--- 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
index 70fdefb97..d55d51315 100644
--- 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
index f028b2627..a56b0ff83 100644
--- 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/smoothing/kernel_smoothers.py b/skfda/preprocessing/smoothing/kernel_smoothers.py
index ae3b7ac85..fbe9d68ad 100644
--- 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
index 15059e49c..3c3981db4 100644
--- 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
index 6d7d6e24b..3305ba21a 100644
--- 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
index a2a64b0d1..6f8142b68 100644
--- 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
index c8d324330..cb7b737bd 100644
--- 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
index be6370398..35129ac3a 100644
--- 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
index f4f83dd2d..833395c2f 100644
--- 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
index 8c02af61b..ea5be4bb5 100644
--- 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,
         )

From adb1cd8a8b179a01c4ec8a375a4acfdfae81c89b Mon Sep 17 00:00:00 2001
From: VNMabus <vnmabus@gmail.com>
Date: Fri, 13 Oct 2023 10:16:31 +0200
Subject: [PATCH 2/7] Small fix in doc.

---
 skfda/preprocessing/missing/_interpolate.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skfda/preprocessing/missing/_interpolate.py b/skfda/preprocessing/missing/_interpolate.py
index d09ea07b2..d97dff0d8 100644
--- 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(

From 23d657102e47e1afd7b9ec42014f804f8b08dc79 Mon Sep 17 00:00:00 2001
From: VNMabus <vnmabus@gmail.com>
Date: Fri, 13 Oct 2023 10:21:28 +0200
Subject: [PATCH 3/7] Update version.

---
 skfda/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/skfda/__init__.py b/skfda/__init__.py
index f9434fa97..47a67be43 100644
--- a/skfda/__init__.py
+++ b/skfda/__init__.py
@@ -30,4 +30,4 @@
         concatenate as concatenate,
     )
 
-__version__ = "0.9.dev1"
+__version__ = "0.9"

From 8789db072bf5dbb1b971454574ef1807b2584396 Mon Sep 17 00:00:00 2001
From: VNMabus <vnmabus@gmail.com>
Date: Fri, 13 Oct 2023 11:23:54 +0200
Subject: [PATCH 4/7] Update version.

---
 docs/_static/switcher.json | 2 +-
 skfda/__init__.py          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/_static/switcher.json b/docs/_static/switcher.json
index 71b626e80..f4e362095 100644
--- 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/skfda/__init__.py b/skfda/__init__.py
index 47a67be43..f9434fa97 100644
--- a/skfda/__init__.py
+++ b/skfda/__init__.py
@@ -30,4 +30,4 @@
         concatenate as concatenate,
     )
 
-__version__ = "0.9"
+__version__ = "0.9.dev1"

From 02bee403f1c1111284b24b9ed6654460f796ca5b Mon Sep 17 00:00:00 2001
From: VNMabus <vnmabus@gmail.com>
Date: Fri, 13 Oct 2023 11:47:57 +0200
Subject: [PATCH 5/7] Remove Python 3.8 support.

---
 .github/workflows/tests.yml | 2 +-
 pyproject.toml              | 4 ++--
 skfda/__init__.py           | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f08ec8d3f..a3cfcd644 100644
--- 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/pyproject.toml b/pyproject.toml
index dc5ea6708..97247f3b5 100644
--- 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",
diff --git a/skfda/__init__.py b/skfda/__init__.py
index f9434fa97..ac12bc7f5 100644
--- a/skfda/__init__.py
+++ b/skfda/__init__.py
@@ -30,4 +30,4 @@
         concatenate as concatenate,
     )
 
-__version__ = "0.9.dev1"
+__version__ = "0.9.1.dev1"

From 4ebf2b65e02efd2192c06d5dfa9c4bbc8c4d3e92 Mon Sep 17 00:00:00 2001
From: VNMabus <vnmabus@gmail.com>
Date: Fri, 13 Oct 2023 12:00:01 +0200
Subject: [PATCH 6/7] Update readthedocs config.

---
 readthedocs.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/readthedocs.yml b/readthedocs.yml
index 2c148156d..47b68f8d7 100644
--- 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
@@ -18,7 +23,6 @@ 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

From d9228519dedc5750b2020fd465309bc1b28baab8 Mon Sep 17 00:00:00 2001
From: VNMabus <vnmabus@gmail.com>
Date: Fri, 13 Oct 2023 13:22:19 +0200
Subject: [PATCH 7/7] Remove useless requirement files.

Optional dependences for building the docs live now in pyproject.toml.
---
 binder/requirements.txt      |  2 +-
 pyproject.toml               | 15 +++++++++++++++
 readthedocs-requirements.txt | 14 --------------
 readthedocs.yml              |  5 +++--
 requirements.txt             |  7 -------
 5 files changed, 19 insertions(+), 24 deletions(-)
 delete mode 100644 readthedocs-requirements.txt
 delete mode 100644 requirements.txt

diff --git a/binder/requirements.txt b/binder/requirements.txt
index b913cb3e4..9ee80ec8d 100644
--- 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
 .
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 97247f3b5..edf05d3ba 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -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
deleted file mode 100644
index f646304da..000000000
--- a/readthedocs-requirements.txt
+++ /dev/null
@@ -1,14 +0,0 @@
--r ./requirements.txt
-basemap
-basemap-data
-basemap-data-hires
-ipykernel
-Sphinx>=3
-pydata-sphinx-theme
-sphinx-gallery
-pillow
-setuptools>=41.2
-jupyter-sphinx
-myst-parser
-pytest
-sphinxcontrib-bibtex
\ No newline at end of file
diff --git a/readthedocs.yml b/readthedocs.yml
index 47b68f8d7..46689c30d 100644
--- a/readthedocs.yml
+++ b/readthedocs.yml
@@ -24,6 +24,7 @@ sphinx:
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: readthedocs-requirements.txt
     - method: pip
-      path: .
\ No newline at end of file
+      path: .
+      extra_requirements:
+        - docs
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 2a806336a..000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-matplotlib
-numpy
-scipy
-setuptools
-scikit-learn
-multimethod>=1.2
-findiff