DOC: Some links still point to old (no longer existing) Github URLs

[corneliusroemer]

Matthijs Welkers kindly reported that our docs still contain links to Github release assets based on v1 binary names.

It would be great if we could sift through docs and replace things

Example:

[j23414]

In case it helps, there may be a way to programmatically find the broken links:

• Jekyll Page using bundle exec htmlproofer - link to more info
• Sphinx Page using sphinx-build -b linkcheck - link to more info

It's been a couple years since I looked at automagically link-checking Jekyll pages, and I think we've since moved to Sphinx.

[ivan-aksamentov]

Fixed in https://github.com/nextstrain/nextclade/pull/964

[ivan-aksamentov]

@j23414 Can you please advice on how to integrate the linkcheck to the current build system? https://github.com/nextstrain/nextclade/blob/18aa4e308c4dc566b71c85097f4ee0cada28f8b2/docs/Makefile#L6

[j23414]

Sure, I'm willing to explore! I'll try building docs locally using that makefile. Hopefully it's only SPHINXOPT='-b linkcheck' and somehow capture the list of broken links.

Hmm, I wouldn't put it as a github action as I wouldn't want the build to "fail" just because of a broken link. Just flag the broken link so someone can fix it later.

[ivan-aksamentov]

Hopefully it's only SPHINXOPT='-b linkcheck' and somehow capture the list of broken links.

I tried, but nothing happened. I just don't fully understand how it works.

wouldn't want the build to "fail" just because of a broken link.

Definitely not need to fail the build. Some warning in the terminal would be alright.

[j23414]

Ah, here's the local build:

git clone https://github.com/nextstrain/nextclade.git
cd nextclade/docs
conda env create
conda activate docs.clades.nextstrain.org

# Add the link check
make -b linkcheck html &> msgs.txt

# Pull broken links, ignore any changelog messages since they should be out of date
cat msgs.txt \
  | grep "broken" \
  | grep -v "CHANGELOG" \
  | sort 
  | less

which gave me:

(   user/datasets: line  158) broken    https://github.com/nextstrain/nextclade_data_workflows - 404 Client Error: Not Found for url: https://github.com/nextstrain/nextclade_data_workflows
(user/algorithm/01-sequence-alignment: line    5) broken    nextclade-cli - 
(user/algorithm/02-translation: line    5) broken    ../terminology.html#gene-map - 
(user/algorithm/02-translation: line    5) broken    nextalign-cli - 
(user/algorithm/02-translation: line    5) broken    nextclade-web - 
(user/algorithm/02-translation: line   13) broken    ../terminology.html#peptide - 
(user/algorithm/06-clade-assignment: line    3) broken    ../terminology.html#clade - 
(user/algorithm/06-clade-assignment: line    5) broken    05-phylogenetic-placement.html#known-limitations - 
(user/algorithm/nextclade-pango: line   12) broken    https://academic.oup.com/ve/article/7/2/veab064/6315289 - 403 Client Error: Forbidden for url: https://academic.oup.com/ve/article/7/2/veab064/6315289
(user/algorithm/nextclade-pango: line   40) broken    https://academic.oup.com/mbe/article/37/5/1530/5721363 - 403 Client Error: Forbidden for url: https://academic.oup.com/mbe/article/37/5/1530/5721363
(user/algorithm/nextclade-pango: line   46) broken    https://academic.oup.com/ve/article/4/1/vex042/4794731 - 403 Client Error: Forbidden for url: https://academic.oup.com/ve/article/4/1/vex042/4794731
(user/input-files: line    7) broken    terminology.html#query-sequence - 
(user/nextclade-cli: line  157) broken    (https://anaconda.org/bioconda/nextclade) - 
(user/output-files: line    7) broken    ../_images/web_download-options.png - 
(user/output-files: line  368) broken    terminology.html#reference-tree-concept - 
(user/terminology: line  125) broken    algorithm#alignment - 
(user/terminology: line  145) broken    algorithm#phylogenetic-placement - 

Summarized fixes here: 👈

• [x] On user/datasets, fix the "nextstrain/nextclade_data_workflows" link
• [x] On user/algorithm/01-sequence-alignment, fix "nextclade-cli" link
• [x] On user/algorithm/02-translation, fix all links "Nextclade Web" and "Nextalign CLI".
• [x] On user/nextclade-cli, fix link "Nextclade conda package"... there's an extra parenthesis around the link.

The rest of the flagged links worked fine, and may be some issues with linkcheck failing to follow an anchor link or some kinda of user agent problem.