Summary: | pydoc keyword searching is broken with <sci-biology/biopython-1.56[-mysql] and dev-python/pyopengl | ||
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Product: | Gentoo Linux | Reporter: | David Suarez <darw_dobz> |
Component: | New packages | Assignee: | Python Gentoo Team <python> |
Status: | RESOLVED FIXED | ||
Severity: | normal | CC: | gentoo, jlec, sci-biology, tomka |
Priority: | High | ||
Version: | unspecified | ||
Hardware: | AMD64 | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
Error messages when pydoc tries to search keywords through biopython module
Error messages obtained when pydoc tries to search keywords through pyopengl module |
Description
David Suarez
2010-04-04 19:41:19 UTC
Created attachment 226587 [details]
Error messages when pydoc tries to search keywords through biopython module
Created attachment 226589 [details]
Error messages obtained when pydoc tries to search keywords through pyopengl module
Bug report QA messages: * Please use full package qualifiers (e.g. "sys-apps/portage", not just "portage") in bug report titles, at the beginning ideally, in the future. Thank you! (In reply to comment #3) > Bug report QA messages: > > * Please use full package qualifiers > (e.g. "sys-apps/portage", not just "portage") > in bug report titles, at the beginning ideally, > in the future. Thank you! > Yep, sorry. I'll remember that. Thank you! I wonder if Biopython were to use a subclass of ImportError, rather than its own Bio.MissingExternalDependencyError this would help? e.g. http://github.com/peterjc/biopython/tree/import-exception Still present in current versions. @python-team. Can you comment on that? e.g. for biopython forcing USE="mysql" should not be an option. On the other hand, breaking pydoc by installing biopython is not an option either. (In reply to comment #5) > I wonder if Biopython were to use a subclass of ImportError, rather than > its own Bio.MissingExternalDependencyError this would help? e.g. > > http://github.com/peterjc/biopython/tree/import-exception > Looking at the code for pkgutil.py and function walk_packages in particular, it will cope with exceptions which are of class ImportError (or a subclass). In this case, both Biopython and pyopengl are (currently) not raising an ImportError, and this could be changed if appropriate. I've fixed this particular case (Bio.GFF) on the Biopython trunk and the change will be included as part of Biopython 1.56 due later this year: http://github.com/biopython/biopython/commit/cb1f54499c0273e1bd45a163781f8a0680e3fc6e However, I think this is a really bug in pydoc for not copying with an import failure where a non-ImportError is raised. I agree with Peter, this seems to be a Pydoc upstream problem - even though all such errors should be ImportErrors, you can't rely on all packages conforming to this rule. (In reply to comment #7) > (In reply to comment #5) > > I wonder if Biopython were to use a subclass of ImportError, rather than > > its own Bio.MissingExternalDependencyError this would help? e.g. > > > > http://github.com/peterjc/biopython/tree/import-exception > > > > Looking at the code for pkgutil.py and function walk_packages in particular, > it will cope with exceptions which are of class ImportError (or a subclass). > > In this case, both Biopython and pyopengl are (currently) not raising an > ImportError, and this could be changed if appropriate. I've fixed this > particular case (Bio.GFF) on the Biopython trunk and the change will be > included as part of Biopython 1.56 due later this year: > > http://github.com/biopython/biopython/commit/cb1f54499c0273e1bd45a163781f8a0680e3fc6e > > However, I think this is a really bug in pydoc for not copying with an > import failure where a non-ImportError is raised. > Fixed by this commit 23 Jun 2011; Markos Chandras <hwoarang@gentoo.org> -biopython-1.56.ebuild: Remove old ebuilds. Requested by Arfrever |