py*-biopython: Add flex variant

[michelle.lynn.gill@…]

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.

[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.

[jmroot (Joshua Root)]

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

[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.

[ryandesign (Ryan Carsten Schmidt)]

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

[ryandesign (Ryan Carsten Schmidt)]

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.

[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.

[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.

[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.

[mamoll (Mark Moll)]

Changes to py2[567] committed in r75633.