Opened 14 years ago

Closed 14 years ago

#27919 closed enhancement (fixed)

py*-biopython: Add flex variant

Reported by: michelle.lynn.gill@… Owned by: mamoll (Mark Moll)
Priority: Normal Milestone:
Component: ports Version: 1.9.2
Keywords: python science Cc: mww@…, ryandesign (Ryan Carsten Schmidt)
Port: py-biopython, py25-biopython, py26-biopython, py27-biopython

Description

Biopython does not install a portion of the mmCIF parser by default. Enabling the installation of this feature requires uncommenting a portion of the setup.py file. I have created a variant and patchfile that uncomments the appropriate section of setup.py and installs the required flex port.

Attachments (4)

PortIndex (1.7 KB) - added by michelle.lynn.gill@… 14 years ago.
Portfile (1.6 KB) - added by michelle.lynn.gill@… 14 years ago.
patch-setup (874 bytes) - added by michelle.lynn.gill@… 14 years ago.
Portfile.diff (443 bytes) - added by michelle.lynn.gill@… 14 years ago.

Download all attachments as: .zip

Change History (13)

Changed 14 years ago by michelle.lynn.gill@…

Attachment: PortIndex added

Changed 14 years ago by michelle.lynn.gill@…

Attachment: Portfile added

Changed 14 years ago by michelle.lynn.gill@…

Attachment: patch-setup added

comment:1 Changed 14 years ago by michelle.lynn.gill@…

Please ignore the accidental uploading of my local PortIndex file. I don't seem to be able to figure out how to remove it. Apologies.

comment:2 Changed 14 years ago by jmroot (Joshua Root)

It's much preferred for changes to existing files to be submitted in the form of a unified diff.

comment:3 Changed 14 years ago by michelle.lynn.gill@…

Sorry. I had a diff file and in my distraction over the PortIndex snafu, I uploaded the main file. I have added the diff.

Changed 14 years ago by michelle.lynn.gill@…

Attachment: Portfile.diff added

comment:4 Changed 14 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: mww@… added; mmoll@… removed
Owner: changed from macports-tickets@… to mmoll@…
Port: py-biopython py25-biopython py27-biopython added
Summary: Add flex variant to py26-biopythonpy*-biopython: Add flex variant

Presumably the same change should be made to py-biopython, py25-biopython, and py27-biopython.

comment:5 Changed 14 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: ryandesign@… added

The comments in the setup file say it is a build dependency on flex, but you have indicated in the portfile a library dependency on flex.

Flex is not so large a dependency. Perhaps we should just dispense with the variant and enable this all the time? Having fewer variants is better, as is providing a fully-functional port by default.

comment:6 in reply to:  4 Changed 14 years ago by michelle.lynn.gill@…

Replying to ryandesign@…:

Presumably the same change should be made to py-biopython, py25-biopython, and py27-biopython.

Yes, I presume so. Unfortunately, I do not have other python versions to test. Be ware that py-biopython (the python 2.4 version) is actually for an older version of biopython, so the patchfile for setup.py might be different. There could also be other issues of which I am not aware. Again, I don't have python 2.4 and can't test.

comment:7 in reply to:  5 Changed 14 years ago by michelle.lynn.gill@…

Replying to ryandesign@…:

The comments in the setup file say it is a build dependency on flex, but you have indicated in the portfile a library dependency on flex.

Flex is not so large a dependency. Perhaps we should just dispense with the variant and enable this all the time? Having fewer variants is better, as is providing a fully-functional port by default.

Yes, I think this is fine too. In fact, I originally setup the Portfile this way. I ended up creating a variant since I'm not the maintainer and wasn't sure if there was a reason for not including it to begin with.

comment:8 in reply to:  5 Changed 14 years ago by mamoll (Mark Moll)

Replying to ryandesign@…:

Flex is not so large a dependency. Perhaps we should just dispense with the variant and enable this all the time? Having fewer variants is better, as is providing a fully-functional port by default.

I agree. I don't really feel like updating py-biopython, since python2.4 is so old. Even updating py25-* ports is IMHO a low priority. I'll give mww (maintainer for these older Ports) a a chance to indicate whether he's interested in making the changes suggested above to his ports.

comment:9 Changed 14 years ago by mamoll (Mark Moll)

Resolution: fixed
Status: newclosed

Changes to py2[567] committed in r75633.

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