Packages not on conda-forge are now optional dependencies

[willGraham01]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?
Some BrainGlobe packages are not yet available on conda-forge, and thus we cannot put this meta-package on conda-forge yet.

Pending an upload of the missing dependencies, we can turn them into optional dependencies for the time being which will allow us to get the "base" package onto conda-forge.

What does this PR do?
cellfinder and morphapi are now optional dependencies, and can be specified when pip-installing.

• cellfinder is nominated for removal anyway, so this package may simply be removed in a future update (see Simplifying the BrainGlobe (meta-)package structure for users and developers BrainGlobe#20)
• morphapi is being worked on as per morphapi external dependency is not available on conda-forge #9.

References

• Concerns morphapi external dependency is not available on conda-forge #9 | Comment

How has this PR been tested?

Testing via upload to testpypi and clean install into a conda environment.

Is this a breaking change?

Kind of - installation now requires optional dependencies to reach the same state as v.0.0.0. But otherwise all existing scripts/workflows will be backwards compatible.

Does this PR require an update to the documentation?

README.md has been updated to reflect these changes. Overall documentation doesn't need to change.

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[codecov-commenter]

Codecov Report

Patch coverage: 100.00% and project coverage change: +8.18 🎉

Comparison is base (c02e162) 81.81% compared to head (2b6a2eb) 90.00%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #11      +/-   ##
==========================================
+ Coverage   81.81%   90.00%   +8.18%     
==========================================
  Files           1        1              
  Lines          11       20       +9     
==========================================
+ Hits            9       18       +9     
  Misses          2        2              

Impacted Files	Coverage Δ
brainglobe/__init__.py	90.00% <100.00%> (+8.18%)	⬆️

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[adamltyson]

@willGraham01 it's definately worth getting cellfinder on coda-forge. It will be a while before we fully get rid of it. It's pure Python, and I think all of it's dependencies are on conda-forge so it shouldn't be too tricky.

[willGraham01]

@willGraham01 it's definately worth getting cellfinder on coda-forge. It will be a while before we fully get rid of it. It's pure Python, and I think all of it's dependencies are on conda-forge so it shouldn't be too tricky.

I have a staged recipe ready to go: conda-forge/staged-recipes#23116.

We just need multiprocessing-logging to bump their version on conda-forge up to v0.3.4 - they have an open PR on their feedstock but it's not merged yet.

Once that's done, I'll open another PR which'll make cellfinder part of the base package again.