Too many dependencies -> error in pyimagej initialisation in windows 10 - filename too long

[NicoKiaru]

Hi everybody and thanks for the awesome work!

I've been very confused about an initialisation problem in PyImageJ, but I may have found the reason of the issue.
I'm trying to start pyimagej with a rather large number of packages version specified:

imagej_core_dep = 'net.imagej:imagej:2.1.0'  #'sc.fiji:fiji:2.1.1'
imagej_legacy_dep = 'net.imagej:imagej-legacy:0.37.4'
bdv_core_dep = 'sc.fiji:bigdataviewer-core:10.2.0'
imglib2_ui_dep = 'net.imglib2:imglib2-ui:2.0.1'
bdv_vistools_dep = 'sc.fiji:bigdataviewer-vistools:1.0.0-beta-28'
imglib2_cache_dep = 'net.imglib2:imglib2-cache:1.0.0-beta-16'
abba_dep = 'ch.epfl.biop:ImageToAtlasRegister:0.1.50'
#bigwarp_dep = 'sc.fiji:bigwarp_fiji:7.0.1'

deps_pack = \
    [ \
     imagej_core_dep, \
     imagej_legacy_dep, \
     bdv_core_dep, \
     imglib2_ui_dep, \
     bdv_vistools_dep, \
     imglib2_cache_dep \
     abba_dep \
    ];

ij = imagej.init(deps_pack, headless=False)

All dependencies are needed, but I get an error when I try to keep them all. If I remove some dependencies, then the initialisation takes place normally.

When all dependencies are added, the relevant part of the error message is this one I think:

FileNotFoundError: [WinError 206] The filename or extension is too long: 'C:\\Users\\nico\\.jgo\\net.imglib2\\imglib2-imglyb\\1.0.0+net.imagej-imagej-legacy-0.37.4+net.imagej-imagej-2.1.0+net.imglib2-imglib2-cache-1.0.0-beta-16+net.imglib2-imglib2-ui-2.0.1+sc.fiji-bigdataviewer-core-10.2.0+sc.fiji-bigdataviewer-vistools-1.0.0-beta-28'

Full error message:

---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
<ipython-input-2-e2cde9326343> in <module>
     21     ];
     22 
---> 23 ij = imagej.init(deps_pack, headless=False)

~\.conda\envs\i2k-2020-pyimagej\lib\site-packages\imagej\__init__.py in init(ij_dir_or_version_or_endpoint, headless)
    160             sj.config.add_endpoints('net.imagej:imagej:' + version)
    161 
--> 162     sj.start_jvm()
    163 
    164     JObjectArray = JArray(JObject)

~\.conda\envs\i2k-2020-pyimagej\lib\site-packages\scyjava\__init__.py in start_jvm(options)
     43         endpoints = endpoints[:1] + sorted(endpoints[1:])
     44         _logger.debug('Using endpoints %s', endpoints)
---> 45         _, workspace = jgo.resolve_dependencies(
     46             '+'.join(endpoints),
     47             m2_repo=scyjava.config.get_m2_repo(),

~\.conda\envs\i2k-2020-pyimagej\lib\site-packages\jgo\jgo.py in resolve_dependencies(endpoint_string, cache_dir, m2_repo, link_type, update_cache, force_update, manage_dependencies, repositories, shortcuts, verbose)
    424         shutil.rmtree(workspace, True)
    425 
--> 426     os.makedirs(workspace, exist_ok=True)
    427 
    428     # TODO should this be for all endpoints or only the primary endpoint?

~\.conda\envs\i2k-2020-pyimagej\lib\os.py in makedirs(name, mode, exist_ok)
    221             return
    222     try:
--> 223         mkdir(name, mode)
    224     except OSError:
    225         # Cannot rely on checking for EEXIST, since the operating system

FileNotFoundError: [WinError 206] The filename or extension is too long: 'C:\\Users\\nico\\.jgo\\net.imglib2\\imglib2-imglyb\\1.0.0+net.imagej-imagej-legacy-0.37.4+net.imagej-imagej-2.1.0+net.imglib2-imglib2-cache-1.0.0-beta-16+net.imglib2-imglib2-ui-2.0.1+sc.fiji-bigdataviewer-core-10.2.0+sc.fiji-bigdataviewer-vistools-1.0.0-beta-28'

Is there a way to put an alias and make this folder name shorter ?

[ctrueden]

@NicoKiaru This bug was fixed by @kephale in scijava/jgo#62. Try upgrading to jgo 1.0.2?

[NicoKiaru]

Works, thanks!