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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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Feature request: support Python >3.3 #644

Closed daveuu closed 8 years ago

daveuu commented 9 years ago

3.5 is now out. I'm wondering whether there are known incompatibilities with >3.3 or if those versions haven't been tested yet ("unknown unknowns")?

wasade commented 9 years ago

There is: the pyqi dependency. We've been meaning to move to click but are short on developer effort right now. We'd greatly welcome a PR though as we're really excited about Python 3

On Wed, Oct 7, 2015 at 10:14 AM, daveuu notifications@github.com wrote:

3.5 is now out. I'm wondering whether there are known incompatibilities with >3.3 or if those versions haven't been tested yet ("unknown unknowns")?

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/644.

gregcaporaso commented 8 years ago

Note that biom doesn't work with Python 3.3 either, so this issue really is about Py3 compatibility (not >3.3 compatibility). Here's the error I get: 

$ python
Python 3.3.5 |Continuum Analytics, Inc.| (default, Jun  4 2015, 15:22:11)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import biom
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/gregcaporaso/.conda/envs/uc2biom/lib/python3.3/site-packages/biom/__init__.py", line 51, in <module>
    from .table import Table
  File "/home/gregcaporaso/.conda/envs/uc2biom/lib/python3.3/site-packages/biom/table.py", line 182, in <module>
    from itertools import izip
ImportError: cannot import name izip
wasade commented 8 years ago

Likely some other py3 incompatibilities have slipped through as a result of not formally checking

gregcaporaso commented 8 years ago

@wasade, @jairideout and @ebolyen are going to try to sprint on this on Monday. The plan would be to keep the CLI backward compatible, but under the hood drop pyqi in favor of click. At that point, biom-format >= 2.1.5 < 2.2.0 would support Python 2.7 and Python 3.5(?). Does that sound right?

wasade commented 8 years ago

:+1: On Oct 14, 2015 15:26, "Greg Caporaso" notifications@github.com wrote:

@wasade https://github.com/wasade, @jairideout https://github.com/jairideout and @ebolyen https://github.com/ebolyen are going to try to sprint on this on Monday. The plan would be to keep the CLI backward compatible, but under the hood drop pyqi in favor of click. At that point, biom-format >= 2.1.5 < 2.2.0 would support Python 2.7 and Python 3.5(?). Does that sound right?

— Reply to this email directly or view it on GitHub https://github.com/biocore/biom-format/issues/644#issuecomment-148207449 .

gregcaporaso commented 8 years ago

This is basically the milestone, and a duplicate of #647. Closing.