Ticket #27919 (closed enhancement: fixed)
py*-biopython: Add flex variant
| Reported by: | michelle.lynn.gill@… | Owned by: | mmoll@… |
|---|---|---|---|
| Priority: | Normal | Milestone: | |
| Component: | ports | Version: | 1.9.2 |
| Keywords: | python science | Cc: | mww@…, ryandesign@… |
| 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
Change History
comment:1 Changed 2 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 2 years ago by jmr@…
It's much preferred for changes to existing files to be submitted in the form of a unified diff.
comment:3 Changed 2 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.
comment:4 follow-up: ↓ 6 Changed 2 years ago by ryandesign@…
- Owner changed from macports-tickets@… to mmoll@…
- Cc mww@… added; mmoll@… removed
- Port changed from py26-biopython to py-biopython, py25-biopython, py26-biopython, py27-biopython
- Summary changed from Add flex variant to py26-biopython to py*-biopython: Add flex variant
Presumably the same change should be made to py-biopython, py25-biopython, and py27-biopython.
comment:5 follow-ups: ↓ 7 ↓ 8 Changed 2 years ago by ryandesign@…
- 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 2 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 2 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 2 years ago by mmoll@…
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.