Minor unit test fails on Windows 11 [Version 10.0.26220.7523]

[rwbaer]

I don't really understand the error, but it looks it might be related to .Machine epsilon values. I don't know if this is an OS thing of no concern or something more concerning, but I thought I'd share back.

(c) Microsoft Corporation. All rights reserved.

D:\VSCode_Projects\FlowIO>conda activate flowkit

(flowkit) D:\VSCode_Projects\FlowIO>python -V
Python 3.13.11
numpy 2.3.5
FlowIO 1.4.0

(flowkit) D:\VSCode_Projects\FlowIO>python run_tests.py
.................F.................E..
======================================================================
ERROR: test_write_fcs_preserves_channels (tests.test_flowdata.FlowDataTestCase.test_write_fcs_preserves_channels)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "D:\VSCode_Projects\FlowIO\tests\test_flowdata.py", line 206, in test_write_fcs_preserves_channels
    orig_fd.write_fcs(tmp_file.name)
    ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^
  File "C:\Users\rbaer\anaconda3\envs\flowkit\Lib\site-packages\flowio\flowdata.py", line 814, in write_fcs
    fh = open(filename, 'wb')
PermissionError: [Errno 13] Permission denied: 'C:\\Users\\rbaer\\AppData\\Local\\Temp\\tmpz7finsf_'

======================================================================
FAIL: test_as_array_with_preprocessing (tests.test_flowdata.FlowDataTestCase.test_as_array_with_preprocessing)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "D:\VSCode_Projects\FlowIO\tests\test_flowdata.py", line 48, in test_as_array_with_preprocessing
    np.testing.assert_array_equal(flow_data_npy, truth_npy)
    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\rbaer\anaconda3\envs\flowkit\Lib\site-packages\numpy\testing\_private\utils.py", line 1054, in assert_array_equal
    assert_array_compare(operator.__eq__, actual, desired, err_msg=err_msg,
    ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                         verbose=verbose, header='Arrays are not equal',
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                         strict=strict)
                         ^^^^^^^^^^^^^^
  File "C:\Users\rbaer\anaconda3\envs\flowkit\Lib\site-packages\numpy\testing\_private\utils.py", line 919, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not equal

Mismatched elements: 5 / 106936 (0.00468%)
Max absolute difference among violations: 2.84217094e-14
Max relative difference among violations: 1.42189964e-16
 ACTUAL: array([[ 88.010899,  27.25    ,   7.233942, ...,   5.      ,   5.186134,
          0.      ],
       [ 19.073569,   5.375   ,  36.517413, ...,   0.      ,   4.29351 ,...
 DESIRED: array([[ 88.010899,  27.25    ,   7.233942, ...,   5.      ,   5.186134,
          0.      ],
       [ 19.073569,   5.375   ,  36.517413, ...,   0.      ,   4.29351 ,...

----------------------------------------------------------------------
Ran 38 tests in 4.643s

FAILED (failures=1, errors=1)

(flowkit) D:\VSCode_Projects\FlowIO>pip show FlowIO
Name: FlowIO
Version: 1.4.0
Summary: FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS) files
Home-page: https://github.com/whitews/flowio
Author:
Author-email: Scott White <whitews@gmail.com>
License: BSD 3-Clause License

Copyright (c) 2019, Scott White
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
  list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,
  this list of conditions and the following disclaimer in the documentation
  and/or other materials provided with the distribution.

* Neither the name of the copyright holder nor the names of its
  contributors may be used to endorse or promote products derived from
  this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Location: C:\Users\rbaer\anaconda3\envs\flowkit\Lib\site-packages
Requires: numpy
Required-by: FlowKit

[whitews]

Hi Rob,

This looks like floating point differences in different compiler/architectures. With 5 out of 100,000 values being off by a max of 1e-15 I'm not too concerned. The latest FlowKit release was held up by similar floating point differences, except they crept into the 1e-8 range and occurred only in recent MacOS versions. That ended up being a compiler flag issue in FlowUtils that I addressed in the latest FlowUtils version.

FlowIO doesn't have as comprehensive a test suite as FlowKit (~350 tests), but is covered extensively by those FlowKit tests since it is a major dependency. And, the FlowKit test runners cover Windows, Mac, and Linux for all the supported Python versions. I can't say what the difference is for your setup, but at differences of ~1e-15 I'm less concerned unless I start seeing larger discrepancies.

Still, thanks for submitting this issue. I'd rather hear about these than not, you never know when and where a new issue may crop up and having a history of such reports is very useful.

All the best,
Scott