Test issue with pandas1.0

[tillea]

Hi,
the Debian packaged biom-format received a bug report in connection with pandas 1.0:

======================================================================
ERROR: test_to_dataframe (biom.tests.test_table.TableTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/build/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py",
line 1476, in test_to_dataframe
    exp = pd.SparseDataFrame(np.array([[0.0, 1.0, 2.0], [3.0, 4.0, 5.0]]),
TypeError: SparseDataFrame() takes no arguments

======================================================================
ERROR: test_to_dataframe_is_sparse (biom.tests.test_table.TableTests)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/build/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/tests/test_table.py",
line 1484, in test_to_dataframe_is_sparse
    df = example_table.to_dataframe()
  File
"/build/python-biom-format-2.1.8+dfsg/.pybuild/cpython3_3.8_biom-format/build/biom/table.py",
line 4053, in to_dataframe
    return constructor(mat, index=index, columns=columns)
TypeError: SparseDataFrame() takes no arguments

----------------------------------------------------------------------
Ran 343 tests in 5.493s

Could you please have a look into this?
Kind regards, Andreas.

[mortonjt]

@wasade fyi - I'm also able to reproduce this issue in the mmvec tutorials.

[mr-c]

Hello. This bug has resulted in biom-format being removed from Debian's testing distribution, and it is likely to result in complete removal from Debian if not fixed. Any progress on this?

Many thanks,

[wasade]

Hi @mr-c, this has been fixed (see this comment, and commits cf1901c and 87dbdec). I didn't see the cross reference to this issue when working on the other PR, and am closing it now. If I cut a release today, could it be restored in Debian's testing distribution?

[mr-c]

@wasade Yes, a new release would be very appreciated! We tried cherry-picking some of those commits, but without everything all together it was too much for us.

[wasade]

Okay, great! Sorry for such a delay on this. It's been, you know, a weird few months :)

[wasade]

@mr-c, there is at least one more issue I'd like to knock out for this release. I'll ask for expedited review when I get the PR in. I'll send a ping once up on pypi.

[mr-c]

No worries @wasade , I understand and I appreciate it!

[wasade]

@mr-c, I just pushed 2.1.9 to pypi. Am going to update bioconda shortly.

[mr-c]

Huzzah, thank you!