sci-biology/GFF3toolkit: hint for a new package

[mmokrejs]

Something is still broken, please fix it on your own
and cherrypick

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs [email protected]

[thesamesam]

What's broken? Can you share some information to help you fix it...?

[mmokrejs]

It installs only README file. And also the downloads in setup.py's CustomBuildCommand() look we want to disable them. But maybe they don't get triggered ... I just thought somebody may be faster getting this into shape. Thank you.

[thesamesam]

This should be a good place to start

[Nowa-Ammerlaan]

This package tries to fetch ncbi-blast+, extract it, and place it in gff3tool/lib/ncbi-blast+. To make this work we have to sed out CustomBuildCommand and manually place a symlink in the install phase from the ncbi-tools+ files to the location where gff3toolkit expects them to be.

Then there is the next issue, namely that many files in this package have #! /usr/local/bin/python3 in the header, which is obviously not going to work .... :/

Overall, I'm not sure if this is worth the effort, the whole thing should just be fixed upstream to not hardcode all the things IMO.

[leycec]

Something is still broken, please fix it on your own
and cherrypick

...well, alrighty then. 🙉

This should probably be closed with apologies – which is awful but the lesser of multiple evils here.

[mmokrejs]

Well it was a proposal for a new package but I agree it has issues like many biology-oriented tools. Thanks you for your efforts, I understand we are all short on time.

[leycec]

I'd happily lend a hand even though biology is outside my wheelhouse. Sadly, there are just a few too many unresolved issues here.

On the one hand, disabling downloads in setup.py usually just requires a sed one-liner to patch out the function call performing the downloads. Here's one I previously hacked together for dev-python/panel in this repository:

	sed -i -e '/^\s*_build_paneljs()$/d' setup.py || die

On the other hand, manually fetching, extracting, and symlink ncbi-blast+ in is quite a bit more work – as is recursively patching bogus #! /usr/local/bin/python3 headers. The latter is also a code smell that suggests upstream may be out of its depth; the standard POSIX-compliant shebang line for Python 3 is #!/usr/bin/env python3. #! /usr/local/bin/python3 is basically never right, so that's dark and suspicious.

But the worst offence is setup.py only installing a single README. Like, how does something like that even happen? O_o

[Nowa-Ammerlaan]

On the one hand, disabling downloads in setup.py usually just requires a sed one-liner to patch out the function call performing the downloads.

When I tried this earlier a simple sed -i -e "/'build': CustomBuildCommand,/d" setup.py did the trick.

However, then I tried to enable the test phase with:

python_test() {
      sh test.py || die
}

(Yes, you need to run the .py file with (ba)sh, because the file name extension is wrong for some reason)
And then I ran into the Interpreter Not Found error, and lost all faith in that this can be made to work.

The latter is also a code smell that suggests upstream may be out of its depth; the standard POSIX-compliant shebang line for Python 3 is #!/usr/bin/env python3. #! /usr/local/bin/python3 is basically never right, so that's dark and suspicious.

I have a very strong suspicion that upstream is using MacOS, since non-system versions of python are often (always?) installed in /usr/local/ on that operating system. Of course that is no excuse for using a hardcoded shebang.

In theory the eclasses should automatically fix this, since somewhere in the install phase python_fix_shebang is called (I think). But for some reason it is not working in this package.