Miscellaneous fixes/improvements to various formulas

[alexreg]

• Use formula-based rather than hard-coded paths.
• Replace #{bin} with #{opt_bin} in tests, which doesn't rely on linkage of formual.
• Remove obsolete formula apbspdb2pqr (which also depends on obsolete Python v2).
• Stylistic conventions

• [x] Have you followed the guidelines for contributing?
• [x] Have you checked that there aren't other open pull requests for the same formula update/change?
• [x] Have you built your formula locally with brew install --build-from-source FORMULA, where FORMULA is the name of the formula you're submitting?
• [ ] Does your build pass brew audit --strict FORMULA (after doing brew install FORMULA)?

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[alexreg]

@jonchang I think this is all in order now. The only formula I couldn't upgrade to [email protected] is apbs, which seems to have problems with undefined symbols.

[alexreg]

Ah, it seems there are some pre-existing issues with velvet and gmap-gsnap. I managed to resolve the former already, and am working on the latter.

[jonchang]

Replace #{bin} with #{opt_bin} in tests, which doesn't rely on linkage of formual.

We don't need to make this change.

All changes from python -> python3.10 need revision bumps. In addition, I suggest updating all python3 dependencies to rely on a function that can easily be changed. See brew cat bde from homebrew/core for an example.

[alexreg]

@jonchang Ah yes, I should have remembered about the revision bumps!

Re opt_bin, it's indeed not necessary, though it's considered "good practice" (at least by the maintainers of homebrew-core). So I'll leave that in, unless you prefer I take it out.

Cheers.

[jonchang]

Re opt_bin, it's indeed not necessary, though it's considered "good practice" (at least by the maintainers of homebrew-core). So I'll leave that in, unless you prefer I take it out.

opt_bin is not necessary in test do blocks because you can't brew test unlinked formulae.

% brew install hello && brew unlink hello && brew test hello
==> Downloading https://ghcr.io/v2/homebrew/core/hello/manifests/2.12.1
==> Downloading https://ghcr.io/v2/homebrew/core/hello/blobs/sha256:a0103553329c
==> Pouring hello--2.12.1.arm64_monterey.bottle.tar.gz
/opt/homebrew/Cellar/hello/2.12.1: 11 files, 177KB
==> Running `brew cleanup hello`...
Unlinking /opt/homebrew/Cellar/hello/2.12.1... 3 symlinks removed.
Error: hello is not linked

[alexreg]

opt_bin is not necessary in test do blocks because you can't brew test unlinked formulae.

Okay, I've now undone this change, fixed gmap-gsnap, and another style issue. Hopefully tests will past now (or almost).

[alexreg]

@jonchang Looks like the CI checks were passing but timed out... what should we do about this?

[alexreg]

@jonchang @YoshitakaMo Hello, did this get (partially) merged in the end? If not, may I ask why it was closed?