Many of the files copy, incorporate, translate, or derive from other code packages.
So while the GPL>=3 license applies to the repository as a whole -- code that is 
directly copied (unmodified) from other packages remains additionally under their original
license terms and copyright holders.

Note that I cast a wide net for what packages I included in this list -- not all actually contributed substantial code 
or would add aalternate licensing options on top of GPL-3. 
Packages with a parenthetical note on their use (like "by translation") often fall in this cateogry where no code in palmettobug 
is directly copied and could fall fully under the original license, but instead some amount of derivation / modification occurred.

Note that many R packages do not have copies of their licenses in their github repositories, and essentially never a direct copyright note (copyright author / date). 
This seems to be standard practice for many R packages.
However, they do list the name of the license (like "GPL>=2") in a DESCRIPTION files, as well as authors, and sometimes a date. 
I provide here what information is available on these packages, but note that the copyright holder may be the institution, 
not the authors. And the exact date is similarly uncertain.
I have asked (by github issue) a number of packages lacking copyright statements what copyright statement to include here.

Files (see file headers for more specifics / modifications of the packages):
    -- palmettobug/Assets:
        -- all files in palmettobug/Assets/ctkThemeBuilderThemes were copied from the package ctk_theme_builder:
             https://github.com/avalon60/ctk_theme_builder MIT license, Copyright (c) 2023 avalon60 (Clive Bostock)

        -- All mascot files (Capture****.png --- except Capture_blank.png) were created using an OpenAI model, and 
        therefore are automatically in the public domain

    -- palmettobug/_vendor   (individual files in this folder also contain the source license):
        -- All files in this folder are copied (and modified) from existing software packages:
            -- fcsparser       MIT license, Copyright (c) 2018 Eugene Yurtsev    https://github.com/eyurtsev/fcsparser 
            -- fcsy            MIT, Copyright (c) 2018, yc                       https://github.com/nehcgnay/fcsy
            -- pyometiff       GPL-3, Copyright (c) 2021, Filippo Maria Castelli https://github.com/filippocastelli/pyometiff 
                  - pyometiff also includes BSD-3 licensed code from:  https://github.com/CellProfiler/python-bioformats/blob/master/bioformats/omexml.py Copyright (c) 2009-2013 Broad Institute
            -- qnorm,          MIT, Copyright (c) 2020, Maarten van der Sande    https://github.com/Maarten-vd-Sande/qnorm
            -- readimc         MIT, Copyright (c) 2021 University of Zurich      https://github.com/BodenmillerGroup/readimc
            -- sigfig          MIT, Copyright (c) 2022 drakegroup                https://github.com/drakegroup/sigfig
            -- steinbock       MIT, Copyright (c) 2021 University of Zurich      https://github.com/BodenmillerGroup/steinbock

    -- Packages used in parts of other files:
        -- palmettobug/Utils/sharedClasses.py
            -- Singleton,     MIT, Copyright (c) 2019, James Roeder              https://github.com/jmaroeder/python-singletons 

        -- palmettobug/Pixel_Classification/Classifiers.py
            Code was translated or heavily based on packages:
                -- QuPath (by translation) GPL-3, 
                        -- File translated: Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh  
                        -- QuPath (0.5.1) as a whole: Copyright (C) 2018 - 2023 QuPath developers, The University of Edinburgh, Copyright 2014-2016 The Queen's University of Belfast, Northern Ireland 
                -- scikit-image (code heavily based on their documentation)    BSD-3, Copyright: 2009-2022 the scikit-image team,  https://github.com/scikit-image/scikit-image, 
                -- ark-analysis (only inspiration / mathematical order & details for unsupervised classifiers -- 
                                likely not copyrightable as more conceptual borrowing than copying of actual code/expression) MIT, Copyright © 2023 Angelo Lab https://github.com/angelolab/ark-analysis
                -- structure of classifier.json files based on / derived from the structure of opencv's ANN_MLP .json files (Apache-2.0 license )
                        Under Apache 2.0 License, a work like PalmettoBUG that merely links to opencv (or is separatable) is not derivative, therefore I will not include the license here
                        nor the copyright statement. See https://github.com/opencv/opencv for more information about this package

        -- palmettobug/ImageProcessing/ImageAnalysisClass.py
            -- steinbock       MIT, Copyright (c) 2021 University of Zurich      https://github.com/BodenmillerGroup/steinbock
        
        -- palmettobug/Analysis_functions/Analysis.py    (and perhaps WholeClassAnalysis.py, which was derived from it)
            -- CATALYST (intentionally mimics or translated from CATALYST),     GPL>=2, https://github.com/HelenaLC/CATALYST/ (no direct copyright statement found. Following information copied & edited 
                                                                                                      from DESCRIPTION file:
                                                                                                          Authors = 
                                                                                                               Helena L. Crowell, Vito R.T. Zanotelli,
                                                                                                               Stéphane Chevrier, Mark D. Robinson,
                                                                                                               Bernd Bodenmiller
                                                                                                          All Authors affiliated with the University of Zurich at time of first publication
                                                                                                      Date -- no date provided in DESCRIPTION, scientific puclications in 2017-2018. Accessed for translation in 2024
                                                                                                      )
            -- diffcyt (only mimics stats options, which is not copyrightable. Attribution included here for completeness, NO CODE in PalmettoBUG should fall under the diffcyt
                       license): MIT, Copyright (c) 2018 Lukas M. Weber https://github.com/lmweber/diffcyt 

        -- palmettobug/Analysis_functions/SpatialANOVA.py
            (By translation from R, especially spatstat which was a more direct translation)
            -- spatstat,      GPL >=2 license                             https://github.com/spatstat (Copyright (c) 2001-2022 Adrian Baddeley, Ege Rubak and Rolf Turner [Files used did not mention any additional contributors])
            -- SpaceANOVA,    GPL-2 (but palmettobug explicitly allowed as GPL-3 by author)   https://github.com/sealx017/SpaceANOVA (no direct copyright statement. Author = Souvik Seal, 
                                                                                                                                        affiliated with Medical University of South Carolina.
                                                                                                                                        Published [and accessed for translation] in 2024)

        -- palmettobug/Entrypoint/bead_norm.py
            --  Premessa (re-implementation / translation from R)     GPL-3, https://github.com/ParkerICI/premessa Copyright 2016 Parker Institute for Cancer Immunotherapy.   
                    (which was in turn a re-implementation of: https://github.com/nolanlab/bead-normalization, GPL-3, no direct copyright statement [author / date], nor a description file. 
                    However, only Premessa was translated into PalmettoBUG, not the bead-normalization MatLab scripts. FCS files in the bead-normalization repository were used to generate
                    jupyter-notebook tutorial documentation.)

        -- The GitLab / GitHub actions .yml files were modified from MIT-licensed templates
              link: https://github.com/actions/starter-workflows
              Copyright (c) 2020 GitHub

Additionally, much of the structure of PalmettoBUG folder directories is inspired / derived from CATALYST, steinbock.

LICENSE TEXTS (except GPL-3, which is in the main license file):
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

~~~~~~~~~~~~~~~~~
MIT License text:
~~~~~~~~~~~~~~~~~

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in 
the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the 
Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, 
WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BSD-3 license text (specifically from scikit-image):
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

License: BSD-3-Clause

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
   notice, this list of conditions and the following disclaimer.
2. 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.
3. Neither the name of the University 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 HOLDERS 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.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GPL-2 license text is not included here, because GPL-2 I DO NOT APPLY TO ANY OF THE CODE released in PalmettoBUG! 
Even though some of the packages listed above are GPL>=2, GPL-2 cannot apply HERE, because some of the packages 
from which PalmettoBUG was derived or those that it links to are under GPL-3 (not allowing earlier versions of
GPL).

HOWEVER! If you go to the original sources of the GPL>=2 packages listed above, then the associated code in those repositories
will stil be under GPL-2 (and >=2). To see information about GPL licenses you can go to: https://www.gnu.org/licenses/ (as also 
indicated by the GPL-3 license)

For GPL-3 license text, see the main LICENSE.txt file.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~