Trouble installing dependencies for multiparametricslide

[jacob-rosenthal]

I just tried installing PathML and running the tests on a new VM and ran into problems with multiparametricslide.

(pathml) jupyter@shared-dxvm-gpu:~/pathml$ python -m pytest
============================================= test session starts =============================================
platform linux -- Python 3.8.6, pytest-6.2.1, py-1.10.0, pluggy-0.13.1
rootdir: /home/jupyter/pathml
collected 74 items / 1 error / 73 selected                                                                    

=================================================== ERRORS ====================================================
___________________ ERROR collecting tests/preprocessing_tests/test_multiparametricslide.py ___________________
ImportError while importing test module '/home/jupyter/pathml/tests/preprocessing_tests/test_multiparametricslide.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pathml/preprocessing/multiparametricslide.py:10: in <module>
    import bioformats
E   ModuleNotFoundError: No module named 'bioformats'

During handling of the above exception, another exception occurred:
/opt/conda/envs/pathml/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/preprocessing_tests/test_multiparametricslide.py:5: in <module>
    from pathml.preprocessing.multiparametricslide import MultiparametricSlide2d
pathml/preprocessing/multiparametricslide.py:25: in <module>
    raise ImportError("MultiparametricSlide2d requires javabridge and bioformats")
E   ImportError: MultiparametricSlide2d requires javabridge and bioformats
============================================== warnings summary ===============================================
pathml/preprocessing/multiparametricslide.py:16
  /home/jupyter/pathml/pathml/preprocessing/multiparametricslide.py:16: UserWarning: MultiparametricSlide2d requires a jvm to interface with java bioformats library.
              See: https://pythonhosted.org/javabridge/installation.html. You can install using:
                  
                  sudo apt-get install openjdk-8-jdk
                  pip install javabridge
                  pip install python-bioformats
          
    warn(

-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================================== short test summary info ===========================================
ERROR tests/preprocessing_tests/test_multiparametricslide.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
========================================= 1 warning, 1 error in 0.62s =========================================

So then I tried to install openjdk using the instructions, but that didn't work:

(pathml) jupyter@shared-dxvm-gpu:~/pathml$ sudo apt-get install openjdk-8-jdk
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package openjdk-8-jdk is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

E: Package 'openjdk-8-jdk' has no installation candidate

OS info:

(pathml) jupyter@shared-dxvm-gpu:~/pathml$ cat /etc/os-release
PRETTY_NAME="Debian GNU/Linux 10 (buster)"
NAME="Debian GNU/Linux"
VERSION_ID="10"
VERSION="10 (buster)"
VERSION_CODENAME=buster
ID=debian
HOME_URL="https://www.debian.org/"
SUPPORT_URL="https://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/"
(pathml) jupyter@shared-dxvm-gpu:~/pathml$ uname -a
Linux shared-dxvm-gpu 4.19.0-12-cloud-amd64 #1 SMP Debian 4.19.152-1 (2020-10-18) x86_64 GNU/Linux

After some searching online, it seems like openjdk-8-jdk is not supported anymore (see here for example). I think the issue is that python-javabridge is not really being actively developed (see here). We need to find a better solution - either give users very detailed instructions for how to install openjdk-8 (which doesn't seem like a great solution since it isn't officially supported anymore) or drop bioformats/javabridge dependency and use a different tool to support multiparametric slides.

I am also confused why the tests pass successfully, which also use sudo apt-get install openjdk-8-jdk