Switch to src/ layout

[flying-sheep]

See here for places recommending it:

• PyPA discussion, protocol

  (Note that “single module” uses official terminology in which “module” means x.is_file() and x.suffix == '.py' and “package” means x.is_dir() and x.join('__init__.py').is_file().)

• Ionel’s blog

• Hypermodern Python defers to Hynek’s blog

Furthermore I think:

• The symmetry makes sense: ls *(/) will yield src tests docs, package specific names start appearing inside of those
• adding {project}/src to PYTHONPATH or doing pip install -e . is safer than adding {project}

(Resolution: Try it out after all PRs touching the code got merged)

[flying-sheep]

Since finding the discussion, I also found that both the Hypermodern Python package guide and Ionel’s blog (i.e. all places that I found that gives reasons for choosing a layout) picked this one.

[ivirshup]

It may not have been clear due to the hybrid meeting (which we definitely didn't prepare well for), but I think everyone else was against this. I think I'm going to revert this, though we can always add it if it gets some support.

[flying-sheep]

You said “let’s try it”.

Also the only argument against it was “familiarity”. When weighing that against the arguments above, I don’t see how it can possibly win out.

[ivirshup]

Ah yeah, so what I had meant there (and I think was in response to others) was: "lets try it out for a project before making it a part of the template".

[flying-sheep]

Aah, I see! How far did you get with the stats package yesterday?

[flying-sheep]

The more I read about it the more convinced I become: Python adds an option to turn off adding the current directory to sys.path

[grst]

It seems unnecessary and reminded me of Java

That was exactly my feeling, but Hynek makes a few good points.

I think I'm slightly in favor of src now, but the question remains whether it's worth the effort changing something.

[flying-sheep]

Glad you see it that way! I organized scanpy and anndata without it originally because I also had that initial thought and didn’t think further, but all substantial arguments point towards the src layout.

• it being one level deeper doesn’t matter because we usually interact with code repos using editors, and those will collapse it just like GitHub:
  
• “looks like Java and I don’t like Java” isn’t even a real aesthetic argument, it’s guilt by association. And aesthetically, src, docs, tests is more symmetric than {{package_name}}, docs, test!

whether it's worth the effort changing something

I don’t think I understand what kind of change you’re referring to.

For the code changes it’s mkdir src; git mv '{{cookiecutter.package_name}}' src/

And what other kind of change is there?

[grst]

I guess it would imply that at some point would want to update all scverse core packages

…

On Fri, May 20, 2022, 10:59 Philipp A. ***@***.***> wrote: whether it's worth the effort changing something I don’t think I understand what kind of change you’re referring to. For the code changes it’s mkdir src; git mv '{{cookiecutter.package_name}}' src/ And what other kind of change is there? — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABVZRV5YTFUST7V5MMBBRUDVK5H55ANCNFSM5U6H45EA> . You are receiving this because you commented.Message ID: ***@***.***>

[flying-sheep]

idk, the disruption of breaking all PRs is high. We could just do all new ones that way and upgrade smaller ones

[grst]

Done in #79