Ignore NaN reagents in create_fcs

[zbjornson]

"None" and "" in Pandas indices become NaNs, which causes problems here when writing FCS files.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.47%. Comparing base (d9f419c) to head (37163c6).
Report is 1 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #29      +/-   ##
===========================================
+ Coverage    91.45%   91.47%   +0.01%     
===========================================
  Files            7        7              
  Lines          433      434       +1     
===========================================
+ Hits           396      397       +1     
  Misses          37       37              

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[whitews]

Hi Zach,

Appreciate the PR. Can you expound more on the use case that this addresses?

Thanks,
Scott

[zbjornson]

Sorry for the slow reply, I went on vacation just after opening this. Here's an example:

import flowio
import pandas
import numpy as np

df = pandas.DataFrame(
    np.random.randn(6,3),
    columns=[["Ax488-A", "PE-A", "Cluster ID"],
             ["CD3", "CD4", None]],
    dtype="float32"
)

fh = open('data_set1.fcs', 'wb')
flowio.create_fcs(
    file_handle=fh,
    event_data=df.to_numpy().flatten(),
    channel_names=df.columns.get_level_values(0).tolist(),
    opt_channel_names=df.columns.get_level_values(1).tolist()  # This is the problem line
)
fh.close()

The indicated line becomes ['CD3', 'CD4', nan] and causes this error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\zachb\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\site-packages\flowio\create_fcs.py", line 254, in create_fcs
    text_string = _build_text(
  File "C:\Users\zachb\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.10_qbz5n2kfra8p0\LocalCache\local-packages\Python310\site-packages\flowio\create_fcs.py", line 47, in _build_text
    required_dict[key].replace(text_delimiter, text_delimiter * 2),
AttributeError: 'float' object has no attribute 'replace'

But I should probably just handle this upstream since it makes no sense to pass nan here. Sorry for the noise!

[whitews]

No worries, thanks for the update. I agree that NaN values would best be handled upstream.