Move OpenIJTIFF python to module/conda-package

[k-dominik]

This will enable installing OpenIJTIFF as a module. I didn't change the name of the module (although it's not canonical, and the name doesn't work for a conda package). So no code changes needed in the notebooks.

Summary:

• I ran black over it for some objective code style
• Improved/fixed typing and docstrings (google python docstring style)
• consistent behavior for downloading files among osses:
  • previously windows would sneakily hide OSErrors which happened when cleaning up the temporary directory while having the file open in tifffile. Disabled cleaning up on all osses now - linux and osx will likely clean up on reboot, and on windows (which wouldn't cleanup before anyways) users can trigger temp cleanup themselves.
• Made it a python package
• Added conda recipe
• removed all sys.path modifications as those are not necessary anymore to use the functionality

I also felt an itch to remove the fetching of extra metadata (as it doesn't seem to be used in the tutorial and complicates typing. Also variable number of return values is not a good pattern. But left it for now.

CC: @bugraoezdemir @tischi

[tischi]

@k-dominik thanks a lot for working on this!

Sorry, this may be a dump question, becuase I don't know enough about python: How would the students install the OpenIJTIFF python module?

[k-dominik]

Hi @tischi,

before being able to install the package has to be built first - there are several options.

• For "development" installation (say you want to change/improve OpenIJTIFF, you could pip install --editable functions/python_modules/OpenIJTIFF from the repository root
• for users of this tutorial, it would be good to (after merging) build and upload this package to some conda channel. (conda build functions/python_modules/OpenIJTIFF/conda-recipe and (with anaconda client installed) upload with something like (you can also configure conda build to do this automatically, we could have CI here to do it, many options) anaconda upload /Users/kutra/mambaforge/conda-bld/noarch/openijtiff-2024.4.0-py_0.tar.bz2
• Then users can create the env as per our instructions, add the channel with -c and also add the openijtiff package as dependency.

[tischi]

OK, thanks, then I will just merge such that we can go ahead.

[bugraoezdemir]

I have built the package and uploaded it to our conda channel (euro-bioimaging). When I installed it to a fresh conda environment and briefly tested the open_ij_tiff function, it worked as expected. It would be good to test it also in the course environment to see if there is any conflict with the other packages. Here is the installation command:
conda install euro-bioimaging::openijtiff.

[bugraoezdemir]

If there is an environment.yml for the course environment, we could include the package in it.