Installation fails - versioning of libraries needed

[gusqgm]

Currently the main branch has no specifications for many libraries, and this is now leading to library version conflicts, as this has not been updated for a while. This issue was first reported by Jan-Daniel.

[gusqgm]

As a way to overcome this issue and have a more systematic look at refactoring LSTree to be able to work with newer libraries around, I have created the refactor_2023 branch. The setup.py is already updated and should contain fixed version of all libraries that allow LSTree to run.

One last issue is still remaining which concerns tensorflow, currently installed via the installation of dl-utils. One easy way to overcome this for now is to clone the repository of dl-utils, and manually change the setup.py file there so that:

tensorflow<2.4 so install_requires list inside the setup.py from dl-utils looks like:

install_requires=[
    'numpy<=1.19.5',  # numpy 1.2 incomptabile with tensorflow 2.3, see https://stackoverflow.com/questions/66207609/notimplementederror-cannot-convert-a-symbolic-tensor-lstm-2-strided-slice0-t
    'scipy',
    'tensorflow<2.4',
    'scikit-image>=0.13',
    'scikit-learn',
    'future',
    'tqdm',
    'pytest',
    'pyyaml',
    'h5py',
    'tensorflow-addons'
]

[gusqgm]

There is also an issue with pyvista. Setting pyvista==0.34.0 is not a solution because of some reshuffling in their libraries, see here for details.

One way to overcome this is to have the latest version of pyvista. I have made the corresponding changes in the setup.py from the 2023_refactor branch.

[jd-deleede]

Thanks Gustavo for fixing the issue above!

I found another issue while installing the refactor_2023 branch: dl-utils installs tensorflow-addons without specifying a version. This leads to the installation of tensorflow-addons version 0.19.0, which is incompatible with tensorflow 2.3. Downgrading tensorflow-addons to version 0.13.0 fixed this issue.

[gusqgm]

Thank you @jd-deleede for spotting this and providing a solution! Currently the installations instructions are still the old ones in the main, but I will try to merge the 2023 refactor to main soon so to have package versions updated there as well.