Broken Hyperlinks on Website

[hectormz]

I ran https://docs.pymc.io/ through a dead link checker and found a number of broken links on the website. Some should be fixed from the pymc-examples repo and some are in the main pymc3 repo, so I'm posting in both. Some hyperlinks just need to be updated (and images to bayesian book covers), but others may point to entities or resources that don't exist anymore.

This doesn't seem to be exhaustive because the link from the GLM Logistic Regression by @springcoil and @jbencook to @jbencook 's original blog post is definitely broken

Error	URL	Anchor Text	Linked From
-1 Not found: The server name or address could not be resolved	http://biostat.mc.vanderbilt.edu/wiki/Main/ChrisFonnesbeck	Chris Fonnesbeck	https://docs.pymc.io/notebooks/GLM-hierarchical.html
-1 Not found: A connection with the server could not be established	https://sphinx-doc.org/	Sphinx	https://docs.pymc.io/notebooks/GLM-hierarchical.html
403 Forbidden	http://f.cl.ly/items/0R1W063h1h0W2M2C0S3M/Screen Shot 2013-10-10 at 8.22.21 AM.png	img/src	https://docs.pymc.io/notebooks/GLM-hierarchical.html
403 Forbidden	http://f.cl.ly/items/38020n2t2Y2b1p3t0B0e/Screen Shot 2013-10-10 at 8.23.36 AM.png	img/src	https://docs.pymc.io/notebooks/GLM-hierarchical.html
403 Forbidden	http://f.cl.ly/items/1B3U223i002y3V2W3r0W/Screen Shot 2013-10-10 at 8.25.05 AM.png	img/src	https://docs.pymc.io/notebooks/GLM-hierarchical.html
404 Not Found	https://docs.pymc.io/_static/semantic-sphinx.css	link/href	https://docs.pymc.io/notebooks/GLM-hierarchical.html
404 Not Found	https://docs.pymc.io/_static/default.css	link/href	https://docs.pymc.io/notebooks/GLM-hierarchical.html
-1 Not found: The host name in the certificate is invalid or does not match	https://www.stat.columbia.edu/~gelman/book/	Book website	https://docs.pymc.io/learn.html
403 Forbidden	https://lh5.googleusercontent.com/Ms2ssellxl7cM6OEL_kpiKRojcj2E4ZaUWDXOa8zEwi-v9orJGYuhjczbwFSDJNsEb_ruiwtCJONNjoo7T1c7qorZm3LsAnroMAm4S5WzNT_PVqWz9aE=w1280	img/src	https://docs.pymc.io/learn.html
530	https://quantopian.com/		https://docs.pymc.io/
999 Non-standard	https://www.linkedin.com/pub/danne-elbers/69/3a2/7ba	Danne Elbers [301 from http://www.linkedin.com/pub/danne-elbers/69/3a2/7ba]	https://docs.pymc.io/notebooks/GLM-hierarchical.html
-1 Timeout	http://deeplearning.net/software/theano/	Theano	https://docs.pymc.io/developer_guide.html
404 Not Found	https://cdasr.mclean.harvard.edu/about-us/current-lab-members/14-faculty/62-daniel-dillon	Dan Dillon [301 from http://cdasr.mclean.harvard.edu/index.php/about-us/current-lab-members/14-faculty/62-daniel-dillon] [301 from https://cdasr.mclean.harvard.edu/index.php/about-us/current-lab-members/14-faculty/62-daniel-dillon]	https://docs.pymc.io/notebooks/GLM-hierarchical.html
404 Not Found	https://github.com/pymc-devs/pymc3/blob/master/docs/source/notebooks/weibull_aft.ipynb	this example notebook	https://docs.pymc.io/api/bounds.html
403 Forbidden	http://bayesiandeeplearning.org/papers/BDL_21.pdf	http://bayesiandeeplearning.org/papers/BDL_21.pdf	https://docs.pymc.io/api/inference.html
404 Not Found	https://arviz-devs.github.io/arviz/notebooks/Introduction.html	https://arviz-devs.github.io/arviz/notebooks/Introduction.html	https://docs.pymc.io/api/data.html
404 Not Found	https://numpy.org/doc/stable/neps/npy-format.html	https://docs.scipy.org/doc/numpy/neps/npy-format.html [301 from https://docs.scipy.org/doc/numpy/neps/npy-format.html]	https://docs.pymc.io/api/backends.html
404 Not Found	https://docs.pymc.io/pymc-examples/examples/api/distributions.rst	pymc3.distributions	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
404 Not Found	https://docs.pymc.io/pymc-examples/examples/api/distributions/continuous.rst	continuous	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
404 Not Found	https://docs.pymc.io/pymc-examples/examples/api/distributions/discrete.rst	discrete	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
404 Not Found	https://docs.pymc.io/pymc-examples/examples/api/distributions/timeseries.rst	timeseries	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
404 Not Found	https://docs.pymc.io/pymc-examples/examples/api/distributions/mixture.rst	mixture	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
404 Not Found	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/sampler-stats.ipynb	here	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
404 Not Found	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/Diagnosing_biased_Inference_with_Divergences.ipynb	here	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
-1 Timeout	http://deeplearning.net/software/theano/library/tensor/index.html	the theano api docs	https://docs.pymc.io/PyMC3_and_Theano.html
404 Not Found	https://docs.pymc.io/prob_dists.html	custom distributions	https://docs.pymc.io/notebooks/blackbox_external_likelihood.html
404 Not Found	https://docs.pymc.io/advanced_theano.html	custom Theano Op	https://docs.pymc.io/notebooks/blackbox_external_likelihood.html
-1 Timeout	http://deeplearning.net/software/theano/extending/extending_theano.html	Theano Op	https://docs.pymc.io/notebooks/blackbox_external_likelihood.html
-1 Timeout	http://deeplearning.net/software/theano/extending/op.html	grad() method	https://docs.pymc.io/notebooks/blackbox_external_likelihood.html
-1 Timeout	http://deeplearning.net/software/theano/library/compile/function.html	Theano function	https://docs.pymc.io/notebooks/blackbox_external_likelihood.html
-1 Timeout	http://deeplearning.net/software/theano/library/gradient.html	Theano tensor gradient	https://docs.pymc.io/notebooks/blackbox_external_likelihood.html
404 Not Found	http://docs.pymc.io/examples.html	these examples [301 from http://pymc-devs.github.io/pymc3/examples.html]	https://docs.pymc.io/pymc-examples/examples/pymc3_howto/api_quickstart.html
-1 Not found: The server name or address could not be resolved	http://5047-presscdn.pagely.netdna-cdn.com/wp-content/uploads/2015/04/iris_petal_sepal.png	img/src	https://docs.pymc.io/pymc-examples/examples/variational_inference/variational_api_quickstart.html
-1 Timeout	http://deeplearning.net/software/theano/library/tensor/basic.html	an overview of the available types	https://docs.pymc.io/notebooks/getting_started.html
404 Not Found	https://github.com/pymc-devs/pymc3/blob/master/pymc3/examples/disaster_model_theano_op.py	a more elaborate example of the usage of as_op	https://docs.pymc.io/notebooks/getting_started.html
-1 Timeout	http://deeplearning.net/software/theano/extending/index.html	documentation,	https://docs.pymc.io/Advanced_usage_of_Theano_in_PyMC3.html

[OriolAbril]

Thanks! I have added a note on this at https://github.com/pymc-devs/pymc-examples/wiki/Notebook-updates-overview. You mention a dead link checker, do you know if it could be added as a step to our CI?

It currently checks format, execution order and a couple other things and it would be great to also check that. Especially given that sometimes reviewnb doesn't render the links correctly. i.e. the link may not work for me when reviewing even when the link does work locally and once rendered on the website.

[hectormz]

@OriolAbril I had just used https://www.deadlinkchecker.com, which seems a little stochastic and not practically useful here. Would you want to use something in pre-commit and/or a github action?

[hectormz]

I found pytest-check-links which works on:

• .html
• .rst
• .md
• .ipynb (requires nbconvert)

One consideration is if you want to check the source files for broken links, or check resulting files/website itself

[OriolAbril]

I think checking the source files is fine, maybe even better. There will be links that are sphinx generated and therefore won't be checked in this approach, but these rely on intersphinx which should be quite robust and error out when building the docs if there is an issue.

[hectormz]

Maybe pytest-check-links is worth checking out then. Depending on how long it takes, it can be done by CI for PR, etc

[chkunkel]

I don't know if this deserves a (separate) issue, since its very minor. Yet, I want to mention it at least.
In https://www.pymc.io/projects/examples/en/latest/gallery.html the card for "GLM: Linear regression" does not include a hyperlink. Since the link is set as "pymc:GLM_linear" in gallery.rst, it could just be related to this capitalization issue in sphinx: https://github.com/sphinx-doc/sphinx/issues/8982

[OriolAbril]

Thanks, it looks like we should update the target and reference to be both lowercase only as the issue is a bit old already and doesn't look active. Do you want to send the PRs for this?

The target is defined in https://github.com/pymc-devs/pymc/blob/main/docs/source/learn/core_notebooks/GLM_linear.ipynb (top of the file)