CLI fails after FSLeyes install

When installing ADS alone, everything is working fine. When installing both ADS and FSLeyes, CLI and axondeepseg_test are no longer working (Ubuntu 20.04 in WSL1).

Error message

Traceback (most recent call last):
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 567, in _build_master
    ws.require(__requires__)
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 884, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 775, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (Pillow 8.0.1 (/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages), Requirement.parse('pillow==6.2.0'), {'AxonDeepSeg'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/bin/axondeepseg_test", line 33, in <module>
    sys.exit(load_entry_point('AxonDeepSeg', 'console_scripts', 'axondeepseg_test')())
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/bin/axondeepseg_test", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/importlib_metadata/__init__.py", line 93, in load
    module = import_module(match.group('module'))
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 728, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/mhbourget/axondeepseg/AxonDeepSeg/integrity_test.py", line 9, in <module>
    from AxonDeepSeg.testing.segmentation_scoring import *
  File "/home/mhbourget/axondeepseg/AxonDeepSeg/testing/segmentation_scoring.py", line 18, in <module>
    import AxonDeepSeg.ads_utils
  File "/home/mhbourget/axondeepseg/AxonDeepSeg/ads_utils.py", line 18, in <module>
    import imageio
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/imageio/__init__.py", line 22, in <module>
    from .core import FormatManager, RETURN_BYTES
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/imageio/core/__init__.py", line 10, in <module>
    from .util import Image, Dict, asarray, image_as_uint, urlopen
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/imageio/core/util.py", line 20, in <module>
    import pkg_resources
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3238, in <module>
    @_call_aside
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3222, in _call_aside
    f(*args, **kwargs)
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3251, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 569, in _build_master
    return cls._build_from_requirements(__requires__)
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 582, in _build_from_requirements
    dists = ws.resolve(reqs, Environment())
  File "/home/mhbourget/miniconda/envs/ads_venv_test_fsl/lib/python3.7/site-packages/pkg_resources/__init__.py", line 770, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'wheel>=0.26' distribution was not found and is required by tensorflow

This seems related to #393 and #395, with a discrepancy of the Pillow package.

I tried re-installing ADS after FSLeyes, it fixes the problem for CLI and axondeepseg_test, also FSLeyes is working as expected. Here is the packages that were re-insatlled:

Re-installed packages

Installing collected packages: numpy, scipy, pillow, matplotlib, urllib3, idna, requests, AxonDeepSeg
  Attempting uninstall: numpy
    Found existing installation: numpy 1.19.4
    Uninstalling numpy-1.19.4:
      Successfully uninstalled numpy-1.19.4
  Attempting uninstall: scipy
    Found existing installation: scipy 1.5.3
    Uninstalling scipy-1.5.3:
      Successfully uninstalled scipy-1.5.3
  Attempting uninstall: pillow
    Found existing installation: Pillow 8.0.1
    Uninstalling Pillow-8.0.1:
      Successfully uninstalled Pillow-8.0.1
  Attempting uninstall: matplotlib
    Found existing installation: matplotlib 3.3.3
    Uninstalling matplotlib-3.3.3:
      Successfully uninstalled matplotlib-3.3.3
  Attempting uninstall: urllib3
    Found existing installation: urllib3 1.25.11
    Uninstalling urllib3-1.25.11:
      Successfully uninstalled urllib3-1.25.11
  Attempting uninstall: idna
    Found existing installation: idna 2.10
    Uninstalling idna-2.10:
      Successfully uninstalled idna-2.10
  Attempting uninstall: requests
    Found existing installation: requests 2.25.0
    Uninstalling requests-2.25.0:
      Successfully uninstalled requests-2.25.0
  Attempting uninstall: AxonDeepSeg
    Found existing installation: AxonDeepSeg 3.2.0
    Uninstalling AxonDeepSeg-3.2.0:
      Successfully uninstalled AxonDeepSeg-3.2.0
  Running setup.py develop for AxonDeepSeg
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
fslpy 3.4.0 requires dataclasses, which is not installed.
Successfully installed AxonDeepSeg idna-2.7 matplotlib-3.1.0 numpy-1.16.4 pillow-6.2.0 requests-2.20.1 scipy-1.3.0 urllib3-1.24.3

We were planning in #395 to update the documentation to mention to re-install FSLeyes after ADS. I think it would be better to always re-install ADS after FSLeyes. That way, we would have the same versions installed whether FSLeyes is installed or not (which is not the case right now).

[ahill187]

Thank you for your detailed issue report @ahill187 !

When MacOSX Big Sur got released, we found out that the default FSLeyes installation is incompatible by default with this OS, and the FSLeyes developers have not expressed a desire to fix it anytime soon. However someone in the community has found a quick fix that you can do yourself by editing a specific file, which I tried and worked for me! https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;8ee55ea9.2011

I’d say give that a shot! If you have questions, let us know.

@mariehbourget maybe we should add a warning and the link above in the installation doc re: Big Sur & FSLeyes?

@mathieuboudreau that makes sense, thank you! Yah I think a warning note in the documentation and maybe a link to the fix could be a good idea?

[mathieuboudreau]

Closing because this was resolved when we moved to a conda env install with FSLeyes installed automatically.