[BUG] building docs fails on python 3.14 due to issue with rapidyaml

[PolarBean]

As titled. make html fails. pip install -e "downloads/brainglobe-atlasapi[atlasgen]" solves this, I'll open a pull request addressing this.

[PolarBean]

I think
https://github.com/brainglobe/brainglobe.github.io/blob/main/docs/fetch_repos.py#L42C1-L42C83
should be
subprocess.run(["pip", "install", "-e", f"'{path}{optional_deps}'"], check=True)

[PolarBean]

This seems to fail in Python=3.14 and work in Python 3.12

[PolarBean]

In 3.14

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for rapidyaml
Successfully built brainglobe-atlasapi
Failed to build rapidyaml
error: failed-wheel-build-for-install

× Failed to build installable wheels for some pyproject.toml based projects
╰─> rapidyaml
Traceback (most recent call last):
  File "/home/harryc/github/brainglobe.github.io/docs/fetch_repos.py", line 42, in <module>
    subprocess.run(["pip", "install", "-e", f"{path}{optional_deps}"], check=True)
    ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/harryc/anaconda3/envs/bgdocs/lib/python3.14/subprocess.py", line 577, in run
    raise CalledProcessError(retcode, process.args,
                             output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['pip', 'install', '-e', 'downloads/brainglobe-atlasapi[atlasgen]']' returned non-zero exit status 1.
make: *** [Makefile:45: fetch_repos] Error 1

[PolarBean]

This actually seems to be an issue with rapidyaml on python 3.14. Not sure of a fix other than to use earlier python versions.

[alessandrofelder]

I confirm I can reproduce this locally.
Have opened an issue on the rapidyaml side

@PolarBean ,

• do you know off the top of your head why the docs need rapidyaml? Must be in one of our external dependencies, I think?
• is the quotation mark part still an issue? Is it related what shell you are building the docs from (e.g. zsh v bash handle [] differently, so you need quotes in zsh)?
  

[IgorTatarnikov]

The docs need rapidyaml because the build step needs to install brainglobe-atlasapi to build the API docs. rapidyaml is fetched as a dependency for brainglobe-utils.

[PolarBean]

yes I think it is still an issue in zsh. I'll add the quotes and the rapidyaml issue can wait until they patch it

[alessandrofelder]

as a dependency for brainglobe-utils.

Thanks @IgorTatarnikov - that now makes sense (I thought it was just cellfinder that uses rapidyaml but actually it's brainglobe-utils!)

The rapidyaml devs have kindly addressed the rapidyaml issue 🎉 - we can close this when they cut the next rapidyaml release.

[adamltyson]

Is this an issue we need to fix on the website side? BrainGlobe doesn't (yet) support 3.14, and when it does, the website build will also

[adamltyson]

It was decided in the dev meeting today that this issue isn't something we need to fix, as it will be addressed once BrainGlobe supports Python 3.14