Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

links to tutorial notebooks are not working!? #2604

Closed
ctb opened this issue May 2, 2023 · 0 comments · Fixed by #2633
Closed

links to tutorial notebooks are not working!? #2604

ctb opened this issue May 2, 2023 · 0 comments · Fixed by #2633

Comments

@ctb
Copy link
Contributor

ctb commented May 2, 2023

on https://sourmash.readthedocs.io/en/latest/tutorials.html#background-and-details, we have four tutorials:

Screenshot 2023-05-02 at 6 09 09 PM

The links to the first three are not working right: they are

https://sourmash.readthedocs.io/en/latest/tutorials.html#kmers-and-minhash.md
https://sourmash.readthedocs.io/en/latest/tutorials.html#sourmash-examples.md
https://sourmash.readthedocs.io/en/latest/tutorials.html#sourmash-collections.md

the fourth one is correct, but ...it's not a notebook?

https://sourmash.readthedocs.io/en/latest/tutorial-lin-taxonomy.html

So to me it looks like the notebook plugin isn't working right.

@ctb ctb closed this as completed in #2633 Jun 22, 2023
ctb added a commit that referenced this issue Jun 22, 2023
Fixes #2604

This PR fixes links to binder tutorials that apparently have been broken
since 2020 😱 , when the docs were switched over to myst-parser in
#1021.

To be fair, it's the kind of subtle bug that would leave users
scratching their head going "maybe it's me?" - the links simply went
back to the tutorial page... not sure why they weren't flagged by sphinx
or myst-parser as being bad!?

This PR also updates environment.yml to properly build:
* includes pip
* specifies minimum python version
* specifies minimum sourmash version

ref #2503 for why
specifying the minimum sourmash and/or python versions can be important!

And, finally, I ran and fixed all the notebooks...

Note: I confirmed that this branch launches properly in binder. The URL
is: https://mybinder.org/v2/gh/sourmash-bio/sourmash/fix/tutorial-nb

---------

Co-authored-by: ccbaumler <63077899+ccbaumler@users.noreply.github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant