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MNT make linkcheck run without errors #23775

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Jun 29, 2022
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MNT make linkcheck run without errors #23775

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MNT make linkcheck run without errors
lesteve Jun 28, 2022
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lesteve Jun 28, 2022
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2 changes: 1 addition & 1 deletion doc/about.rst
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Expand Up @@ -423,7 +423,7 @@ time of Joris van den Bossche (2017-2018).
.. image:: images/cds-logo.png
:width: 100pt
:align: center
:target: https://www.datascience-paris-saclay.fr/
:target: http://www.datascience-paris-saclay.fr/
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This is sad... I sent an email to the contact address to let them know that the TLS certificate has expired (in August 2020).

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I had the same feeling ;)


.. raw:: html

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12 changes: 8 additions & 4 deletions doc/conf.py
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Expand Up @@ -598,15 +598,19 @@ def setup(app):
# links falsely flagged as broken
"https://www.researchgate.net/publication/"
"233096619_A_Dendrite_Method_for_Cluster_Analysis",
"https://www.researchgate.net/publication/"
"221114584_Random_Fourier_Approximations_"
"https://www.researchgate.net/publication/221114584_Random_Fourier_Approximations_"
"for_Skewed_Multiplicative_Histogram_Kernels",
"https://www.researchgate.net/publication/4974606_"
"Hedonic_housing_prices_and_the_demand_for_clean_air",
"https://www.researchgate.net/profile/Anh-Huy-Phan/publication/220241471_Fast_"
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I grouped the researchgate links together here

"Local_Algorithms_for_Large_Scale_Nonnegative_Matrix_and_Tensor_Factorizations",
"https://doi.org/10.13140/RG.2.2.35280.02565",
"https://www.microsoft.com/en-us/research/uploads/prod/2006/01/"
"Bishop-Pattern-Recognition-and-Machine-Learning-2006.pdf",
"https://www.researchgate.net/publication/4974606_"
"Hedonic_housing_prices_and_the_demand_for_clean_air",
"https://www.microsoft.com/en-us/research/wp-content/uploads/2016/02/tr-99-87.pdf",
"https://microsoft.com/",
"https://www.jstor.org/stable/2984099",
"https://stat.uw.edu/sites/default/files/files/reports/2000/tr371.pdf",
# Broken links from testimonials
"http://www.bestofmedia.com",
"http://www.data-publica.com/",
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2 changes: 1 addition & 1 deletion doc/modules/decomposition.rst
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Expand Up @@ -956,7 +956,7 @@ is not readily available from the start, or when the data does not fit into memo

.. [4] `"SVD based initialization: A head start for nonnegative
matrix factorization"
<https://www.cb.uu.se/~milan/histo/before2011august/Boutsidis.pdf>`_
<https://www.boutsidis.org/Boutsidis_PRE_08.pdf>`_
C. Boutsidis, E. Gallopoulos, 2008

.. [5] `"Fast local algorithms for large scale nonnegative matrix and tensor
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2 changes: 1 addition & 1 deletion doc/modules/semi_supervised.rst
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Expand Up @@ -148,4 +148,4 @@ which can drastically reduce running times.

[3] Olivier Delalleau, Yoshua Bengio, Nicolas Le Roux. Efficient
Non-Parametric Function Induction in Semi-Supervised Learning. AISTAT 2005
https://research.microsoft.com/en-us/people/nicolasl/efficient_ssl.pdf
https://www.gatsby.ucl.ac.uk/aistats/fullpapers/204.pdf
6 changes: 3 additions & 3 deletions sklearn/cluster/_spectral.py
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Expand Up @@ -589,11 +589,11 @@ class SpectralClustering(ClusterMixin, BaseEstimator):
Stella X. Yu, Jianbo Shi
<https://www1.icsi.berkeley.edu/~stellayu/publication/doc/2003kwayICCV.pdf>`_

.. [4] `Toward the Optimal Preconditioned Eigensolver:
Locally Optimal Block Preconditioned Conjugate Gradient Method, 2001.
.. [4] :doi:`Toward the Optimal Preconditioned Eigensolver:
Locally Optimal Block Preconditioned Conjugate Gradient Method, 2001
A. V. Knyazev
SIAM Journal on Scientific Computing 23, no. 2, pp. 517-541.
<https://epubs.siam.org/doi/pdf/10.1137/S1064827500366124>`_
<10.1137/S1064827500366124>`
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I used the DOI for consistency with the links to the same article in this file. Also IIRC make linkcheck flag the epubs.siam.org link as broken

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Actually this DOI link does not lead to a downloadable PDF for me.

Maybe we should use https://www.researchgate.net/profile/Andrew-Knyazev/publication/2434555_Toward_The_Optimal_Preconditioned_Eigensolver_Locally_Optimal_Block_Preconditioned_Conjugate_Gradient_Method/links/5f1e060f299bf1720d67f9a7/Toward-The-Optimal-Preconditioned-Eigensolver-Locally-Optimal-Block-Preconditioned-Conjugate-Gradient-Method.pdf instead.

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The PDF link above those not directly link to the PDF. It redirects to an HTML page from which it's possible to download the PDF by clicking in a browser (probably with javascript enabled).

Maybe we should link to the HTML page then: https://www.researchgate.net/publication/2434555_Toward_The_Optimal_Preconditioned_Eigensolver_Locally_Optimal_Block_Preconditioned_Conjugate_Gradient_Method

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@ogrisel ogrisel Jun 28, 2022 •
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Actually, the following link directly leads to the PDF:

https://www.researchgate.net/profile/Andrew-Knyazev/publication/2434555_Toward_The_Optimal_Preconditioned_Eigensolver_Locally_Optimal_Block_Preconditioned_Conjugate_Gradient_Method/links/5f1e060f299bf1720d67f9a7/Toward-The-Optimal-Preconditioned-Eigensolver-Locally-Optimal-Block-Preconditioned-Conjugate-Gradient-Method.pdf?origin=publication_detail

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I suggest we have the DOI vs publically accessible PDF separately. This PR's goal is to get make linkcheck to run without errors.

Also this particular link (through the DOI) in used in multiple places:

❯ git grep 10.1137/S1064827500366124
sklearn/cluster/_spectral.py:           <10.1137/S1064827500366124>`
sklearn/cluster/_spectral.py:           <10.1137/S1064827500366124>`
sklearn/externals/_lobpcg.py:       pp. 517-541. :doi:`10.1137/S1064827500366124`
sklearn/externals/_lobpcg.py:           pp. 517-541. :doi:`10.1137/S1064827500366124`
sklearn/manifold/_spectral_embedding.py:      <10.1137/S1064827500366124>`


.. [5] :doi:`Simple, direct, and efficient multi-way spectral clustering, 2019
Anil Damle, Victor Minden, Lexing Ying
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2 changes: 1 addition & 1 deletion sklearn/cross_decomposition/_pls.py
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Expand Up @@ -170,7 +170,7 @@ class _PLS(

Main ref: Wegelin, a survey of Partial Least Squares (PLS) methods,
with emphasis on the two-block case
https://www.stat.washington.edu/research/reports/2000/tr371.pdf
https://stat.uw.edu/sites/default/files/files/reports/2000/tr371.pdf
"""

@abstractmethod
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4 changes: 2 additions & 2 deletions sklearn/decomposition/_kernel_pca.py
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Expand Up @@ -216,7 +216,7 @@ class KernelPCA(_ClassNamePrefixFeaturesOutMixin, TransformerMixin, BaseEstimato
.. [2] `Bakır, Gökhan H., Jason Weston, and Bernhard Schölkopf.
"Learning to find pre-images."
Advances in neural information processing systems 16 (2004): 449-456.
<https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.68.5164&rep=rep1&type=pdf>`_
<https://papers.nips.cc/paper/2003/file/ac1ad983e08ad3304a97e147f522747e-Paper.pdf>`_

.. [3] :arxiv:`Halko, Nathan, Per-Gunnar Martinsson, and Joel A. Tropp.
"Finding structure with randomness: Probabilistic algorithms for
Expand Down Expand Up @@ -532,7 +532,7 @@ def inverse_transform(self, X):
`Bakır, Gökhan H., Jason Weston, and Bernhard Schölkopf.
"Learning to find pre-images."
Advances in neural information processing systems 16 (2004): 449-456.
<https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.68.5164&rep=rep1&type=pdf>`_
<https://papers.nips.cc/paper/2003/file/ac1ad983e08ad3304a97e147f522747e-Paper.pdf>`_
"""
if not self.fit_inverse_transform:
raise NotFittedError(
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