Fixed empty timestep value issue

[ikonsta]

Added try-except for timestep reading, because in some cases timestep key was in dictionary, but the value was equal to - " " e.g. string with one space

[codecov]

Codecov Report

Attention: Patch coverage is 33.33333% with 4 lines in your changes missing coverage. Please review.

Project coverage is 93.00%. Comparing base (3e9b06f) to head (05232ba).
Report is 2 commits behind head on develop.

Files with missing lines	Patch %	Lines
src/flowio/flowdata.py	33.33%	4 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #33      +/-   ##
===========================================
- Coverage    93.76%   93.00%   -0.76%     
===========================================
  Files            7        7              
  Lines          481      486       +5     
===========================================
+ Hits           451      452       +1     
- Misses          30       34       +4     

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[whitews]

Thanks Konstantin!

For future reference, see related discussion here: whitews/FlowKit#247

[whitews]

Hi Konstantin,

I'm looking through the files in the Zenodo archive link you provided in the previous PR and having trouble finding an example with the empty string timestep value. Could you to let me know which ones have these values? Just want to add it to the tests.

Thanks,
Scott

[ikonsta]

Hi Scott,

Sure! It was Ki67-117 tube 1.LMD sample. By the way, the next sample e.g. Ki67-117 tube 2.LMD has two samples within it, so if I understood correctly there is no way currently to read those samples using fk.Sample (only with flowio.read_multiple_data_sets), but this I should probably raise in a separate issue.

Sincerely,
Konstantin

[whitews]

Thanks! I'll include that one in the tests.

For the multi-set samples, the read_multiple_data_sets function is the way to read those and it returns a list of FlowData instances corresponding to each sample in the file. For reading a set of FCS files where you do not know which are multi-set, I created the custom error MultipleDataSetsError to catch these files (e.g. in a loop):

for fp in fcs_file_paths:
    try:
        fd = flowio.FlowData(fp)
    except MultipleDataSetsError:
        fd_list = flowio.read_multiple_data_sets(fp)

[whitews]

Sorry, I didn't realize you were referencing FlowKit. In FlowKit there is a similar function read_multi_dataset_fcs (docs here)