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Python CLI changes for Windows image piping #2969

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Python CLI changes for Windows image piping #2969

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Commits on Sep 5, 2024

  1. Python CLI changes for Windows image piping 

    - More extensive use of pathlib.Path throughout API modules.
- When running in a Windows environment, explicitly invoke cygwin.exe to translate piped image filesystem paths between Posix and Windows formats. While this is not necessary if piping an image from one Python command to another, it is necessary for compatibility in piping between Python and C++ commands.
- Move helper function responsible for creating modified pathlib.Path class that quote-escapes when used in an f-string out of app.Parser and into app, since it may be useful outside of the context of command-line parsing.
- Add intermediate classes for CLI input filesystem paths for centralising the checking of user-specified input paths, similarly to what had already been done for output user-specified paths.
- dwinormalise group: Dynamically delete more images from the scratch directory as they are used.
- fsl.eddy_binary(): Make full use of pathlib.Path functionalities.
- mrtrix3.path.wait_for(): In addition to pathlib.Path adoption, includes duplication of fixes in 9ad39a8 and e866aa4 for simplicity of testing.
- mrtrix3.utils.load_keyval(): Yield a dictionary of strings / lists of strings for multi-line keys. Do not split lines; that interpretation is deferred to downstream code (only current usage is population_template calling transformcalc decomp).
- utils.name_temporary(): Fix creation of filesystem paths for temporary directories.
    @Lestropie
    Lestropie committed Sep 5, 2024
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  2. Python: Initial fixes to piped image support on Windows

    @Lestropie
    Lestropie committed Sep 5, 2024
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  3. mrtrix3.app: Changes to filesystem path handling 

    - Remove function app.make_quote_escaped_path_object() and replace with class FSQEPath (F-string quote-escaped path). This exploits runtime inheritance to discover the type of pathlib.Path and inherit from it, rather than using clumsy multiple inheritance.
- Fix cygpath invocation for input image pipes.
- Improve run.command() printed terminal strings with use of this new class.
    @Lestropie
    Lestropie committed Sep 5, 2024
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