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Implement FlowSample on top of AxisArrays #15

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merged 25 commits into from
Nov 2, 2022
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Commits on Sep 29, 2022

  1. Rewriting of tests and addition of indexing interface tests

    The existing tests have been rewritten to take their test data from
    local files instead of attempting to download them --- the urls were
    broken.
    
    The large file test has been deleted.
    
    New tests have been added for:
      - the key-based indexing of channels, which is existing
      functionality
      - the key-based indexing of multiple channels, which is to be
      implemented
      - the integer indexing of individual samples, which is to be
      implemented
      - the collection of integer indexing of multiple samples, which is
      to be implemented
    lgrozinger committed Sep 29, 2022
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  2. Implements different kinds of indexing for FlowSample

    Multiple channels can be indexed using a Vector of Strings
    Individual samples can be indexed using an Integer
    Multiple samples can be indexed using a Vector of Integers
    lgrozinger committed Sep 29, 2022
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Commits on Sep 30, 2022

  1. Changing course to wrap AxisArray with FlowSample

    I realised I was just rewriting the implementation of AxisArray. This
    commit introduces the tests for a new FlowSample struct which is a
    simple wrapper for AxisArray with some params attached.
    
    AxisArray performance is supposed to be good, the interface doesn't
    have to change, and they can easily be converted to matrices as needed
    by GigaSOM.
    lgrozinger committed Sep 30, 2022
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  2. Wrapped the AxisArray in FlowSample

    These changes add lots of indexing options for FlowSamples.
    
    I have tried to keep backwards compatibility with the old FlowSample,
    I think we have it, but cannot be absolutely certain.
    lgrozinger committed Sep 30, 2022
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Commits on Oct 1, 2022

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Commits on Oct 2, 2022

  1. Merge pull request #1 from lgrozinger/compathelper/new_version/2022-1…

    …0-01-00-09-49-374-1964714061
    
    CompatHelper: add new compat entry for "AxisArrays" at version "0.4"
    lgrozinger authored Oct 2, 2022
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  4. Requested changes

    The axes of the FlowSample data are now called :param and :event
    
    size calls refactored to include dimension
    
    version bumped
    
    Base.axes redefined to call out to AxisArrays versions
    
    Tests for large file added back in
    lgrozinger committed Oct 2, 2022
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  6. Tests for iteration

    Iterate just forwards the method to AxisArrays
    lgrozinger committed Oct 2, 2022
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Commits on Oct 5, 2022

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  3. Deprecates params and data

    A warning is emitted when the user tries to access params or data
    directly.
    
    Tests for these warnings are also added.
    lgrozinger committed Oct 5, 2022
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  4. Adds dot syntax access to FCS keywords in params

    FCS TEXT segment keywords can now be accessed using the dot
    syntax. E.g. `flowrun.par` retrieves the "\$PAR" keyword value.
    
    Dot syntax access to `data` and `params` throws deprecation warnings.
    
    `Base.propertynames` produces a list of the keywords for the
    `FlowSample`.
    
    This commit adds tests for these features also.
    lgrozinger committed Oct 5, 2022
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Commits on Oct 22, 2022

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  2. Increment major version

    lgrozinger committed Oct 22, 2022
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  3. Code formatting README

    lgrozinger authored Oct 22, 2022
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Commits on Nov 2, 2022

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