ContextualVersionConflict in Google Colab

[fepegar]

Hi,

I'm having a lot of trouble with this package on Google Colab:

!pip install --quiet niwidgets
from niwidgets import NiftiWidget

---------------------------------------------------------------------------
ContextualVersionConflict                 Traceback (most recent call last)
<ipython-input-2-80347fcf605d> in <module>()
      1 get_ipython().system('pip install --quiet niwidgets')
----> 2 from niwidgets import NiftiWidget

5 frames
/usr/local/lib/python3.6/dist-packages/pkg_resources/__init__.py in resolve(self, requirements, env, installer, replace_conflicting, extras)
    789                 # Oops, the "best" so far conflicts with a dependency
    790                 dependent_req = required_by[req]
--> 791                 raise VersionConflict(dist, req).with_context(dependent_req)
    792 
    793             # push the new requirements onto the stack

ContextualVersionConflict: (nibabel 2.3.3 (/usr/local/lib/python3.6/dist-packages), Requirement.parse('nibabel<3.0,>=2.4'), {'niwidgets'})

Can the requirements be made a bit more flexible or updated?

Here's the notebook: https://colab.research.google.com/drive/1k6QK75t0Ab1Zo-_j2YG3x85EvRSVjGLT

Thanks

[fepegar]

If I restart the runtime and run again, it doesn't complain. But this is just a hack.

[janfreyberg]

I'm not familiar with how Google Colab handles dependencies (e.g., where does 2.3.3 come from? is it installed by default on collab? Or is this actually a conflict within niwidget's dependencies?)

I doubt the version constraints need to be this strict, though, so I will look into this.

[fepegar]

Thanks for looking into this. I'm not familiar either. I think they preinstall a bunch of libraries by default:

!pip freeze

absl-py==0.9.0
alabaster==0.7.12
albumentations==0.1.12
altair==4.0.0
asgiref==3.2.3
astor==0.8.1
astropy==4.0
atari-py==0.2.6
atomicwrites==1.3.0
attrs==19.3.0
audioread==2.1.8
autograd==1.3
Babel==2.8.0
backcall==0.1.0
backports.tempfile==1.0
backports.weakref==1.0.post1
beautifulsoup4==4.6.3
bleach==3.1.0
blis==0.2.4
bokeh==1.4.0
boto==2.49.0
boto3==1.10.47
botocore==1.13.47
Bottleneck==1.3.1
branca==0.3.1
bs4==0.0.1
bz2file==0.98
cachetools==4.0.0
certifi==2019.11.28
cffi==1.13.2
chainer==6.5.0
chardet==3.0.4
chart-studio==1.0.0
Click==7.0
cloudpickle==1.2.2
cmake==3.12.0
colorlover==0.3.0
community==1.0.0b1
contextlib2==0.5.5
convertdate==2.2.0
coverage==3.7.1
coveralls==0.5
crcmod==1.7
cufflinks==0.17.0
cupy-cuda101==6.5.0
cvxopt==1.2.3
cvxpy==1.0.25
cycler==0.10.0
cymem==2.0.3
Cython==0.29.14
daft==0.0.4
dask==2.9.1
dataclasses==0.7
datascience==0.10.6
decorator==4.4.1
defusedxml==0.6.0
descartes==1.1.0
dill==0.3.1.1
distributed==1.25.3
Django==3.0.2
dlib==19.18.0
dm-sonnet==1.35
docopt==0.6.2
docutils==0.15.2
dopamine-rl==1.0.5
earthengine-api==0.1.209
easydict==1.9
ecos==2.0.7.post1
editdistance==0.5.3
en-core-web-sm==2.1.0
entrypoints==0.3
et-xmlfile==1.0.1
fa2==0.3.5
fancyimpute==0.4.3
fastai==1.0.60
fastcache==1.1.0
fastdtw==0.3.4
fastprogress==0.2.2
fastrlock==0.4
fbprophet==0.5
feather-format==0.4.0
featuretools==0.4.1
filelock==3.0.12
fix-yahoo-finance==0.0.22
Flask==1.1.1
folium==0.8.3
fsspec==0.6.2
future==0.16.0
gast==0.2.2
GDAL==2.2.2
gdown==3.6.4
gensim==3.6.0
geographiclib==1.50
geopy==1.17.0
gevent==1.4.0
gin-config==0.3.0
glob2==0.7
google==2.0.3
google-api-core==1.15.0
google-api-python-client==1.7.11
google-auth==1.4.2
google-auth-httplib2==0.0.3
google-auth-oauthlib==0.4.1
google-cloud-bigquery==1.21.0
google-cloud-core==1.0.3
google-cloud-datastore==1.8.0
google-cloud-language==1.2.0
google-cloud-storage==1.16.2
google-cloud-translate==1.5.0
google-colab==1.0.0
google-pasta==0.1.8
google-resumable-media==0.4.1
googleapis-common-protos==1.6.0
googledrivedownloader==0.4
graph-nets==1.0.5
graphviz==0.10.1
greenlet==0.4.15
grpcio==1.15.0
gspread==3.0.1
gspread-dataframe==3.0.3
gunicorn==20.0.4
gym==0.15.4
h5py==2.8.0
HeapDict==1.0.1
holidays==0.9.12
html5lib==1.0.1
httpimport==0.5.18
httplib2==0.11.3
humanize==0.5.1
hyperopt==0.1.2
ideep4py==2.0.0.post3
idna==2.8
image==1.5.27
imageio==2.4.1
imagesize==1.2.0
imbalanced-learn==0.4.3
imblearn==0.0
imgaug==0.2.9
importlib-metadata==1.4.0
imutils==0.5.3
inflect==2.1.0
intel-openmp==2020.0.133
intervaltree==2.1.0
ipykernel==4.6.1
ipython==5.5.0
ipython-genutils==0.2.0
ipython-sql==0.3.9
ipywidgets==7.5.1
itsdangerous==1.1.0
jax==0.1.52
jaxlib==0.1.36
jdcal==1.4.1
jedi==0.15.2
jieba==0.40
Jinja2==2.10.3
jmespath==0.9.4
joblib==0.14.1
jpeg4py==0.1.4
jsonschema==2.6.0
jupyter==1.0.0
jupyter-client==5.3.4
jupyter-console==5.2.0
jupyter-core==4.6.1
kaggle==1.5.6
kapre==0.1.3.1
Keras==2.2.5
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.0
keras-vis==0.4.1
kfac==0.2.0
kiwisolver==1.1.0
knnimpute==0.1.0
librosa==0.6.3
lightgbm==2.2.3
llvmlite==0.31.0
lmdb==0.98
lucid==0.3.8
lunardate==0.2.0
lxml==4.2.6
magenta==0.3.19
Markdown==3.1.1
MarkupSafe==1.1.1
matplotlib==3.1.2
matplotlib-venn==0.11.5
mesh-tensorflow==0.1.8
mido==1.2.6
mir-eval==0.5
missingno==0.4.2
mistune==0.8.4
mizani==0.6.0
mkl==2019.0
mlxtend==0.14.0
more-itertools==8.0.2
moviepy==0.2.3.5
mpi4py==3.0.3
mpmath==1.1.0
msgpack==0.5.6
multiprocess==0.70.9
multitasking==0.0.9
murmurhash==1.0.2
music21==5.5.0
natsort==5.5.0
nbconvert==5.6.1
nbformat==5.0.3
networkx==2.4
nibabel==2.3.3
nltk==3.2.5
notebook==5.2.2
np-utils==0.5.12.1
numba==0.47.0
numexpr==2.7.1
numpy==1.17.5
nvidia-ml-py3==7.352.0
oauth2client==4.1.3
oauthlib==3.1.0
okgrade==0.4.3
opencv-contrib-python==4.1.2.30
opencv-python==4.1.2.30
openpyxl==2.5.9
opt-einsum==3.1.0
osqp==0.6.1
packaging==20.0
palettable==3.3.0
pandas==0.25.3
pandas-datareader==0.7.4
pandas-gbq==0.11.0
pandas-profiling==1.4.1
pandocfilters==1.4.2
parso==0.5.2
pathlib==1.0.1
patsy==0.5.1
pexpect==4.7.0
pickleshare==0.7.5
Pillow==6.2.2
pip-tools==4.2.0
plac==0.9.6
plotly==4.4.1
plotnine==0.6.0
pluggy==0.7.1
portpicker==1.2.0
prefetch-generator==1.0.1
preshed==2.0.1
pretty-midi==0.2.8
prettytable==0.7.2
progressbar2==3.38.0
prometheus-client==0.7.1
promise==2.3
prompt-toolkit==1.0.18
protobuf==3.10.0
psutil==5.4.8
psycopg2==2.7.6.1
ptyprocess==0.6.0
py==1.8.1
pyarrow==0.14.1
pyasn1==0.4.8
pyasn1-modules==0.2.7
pycocotools==2.0.0
pycparser==2.19
pydata-google-auth==0.2.1
pydot==1.3.0
pydot-ng==2.0.0
pydotplus==2.0.2
PyDrive==1.3.1
pyemd==0.5.1
pyglet==1.3.2
Pygments==2.1.3
pygobject==3.26.1
pymc3==3.7
PyMeeus==0.3.6
pymongo==3.10.0
pymystem3==0.2.0
PyOpenGL==3.1.5
pyparsing==2.4.6
pypng==0.0.20
pyrsistent==0.15.7
pysndfile==1.3.8
PySocks==1.7.1
pystan==2.19.1.1
pytest==3.6.4
python-apt==1.6.4
python-chess==0.23.11
python-dateutil==2.6.1
python-louvain==0.13
python-rtmidi==1.3.1
python-slugify==4.0.0
python-utils==2.3.0
pytz==2018.9
PyWavelets==1.1.1
PyYAML==3.13
pyzmq==17.0.0
qtconsole==4.6.0
regex==2019.12.20
requests==2.21.0
requests-oauthlib==1.3.0
resampy==0.2.2
retrying==1.3.3
rpy2==2.9.5
rsa==4.0
s3fs==0.4.0
s3transfer==0.2.1
scikit-image==0.16.2
scikit-learn==0.22.1
scipy==1.4.1
screen-resolution-extra==0.0.0
scs==2.1.1.post2
seaborn==0.9.0
semantic-version==2.8.4
Send2Trash==1.5.0
setuptools-git==1.2
Shapely==1.6.4.post2
simplegeneric==0.8.1
six==1.12.0
sklearn==0.0
sklearn-pandas==1.8.0
smart-open==1.9.0
snowballstemmer==2.0.0
sortedcontainers==2.1.0
spacy==2.1.9
Sphinx==1.8.5
sphinxcontrib-websupport==1.1.2
SQLAlchemy==1.3.12
sqlparse==0.3.0
srsly==1.0.1
stable-baselines==2.2.1
statsmodels==0.10.2
sympy==1.1.1
tables==3.4.4
tabulate==0.8.6
tblib==1.6.0
tensor2tensor==1.14.1
tensorboard==1.15.0
tensorboardcolab==0.0.22
tensorflow==1.15.0
tensorflow-datasets==1.3.2
tensorflow-estimator==1.15.1
tensorflow-gan==2.0.0
tensorflow-hub==0.7.0
tensorflow-metadata==0.15.2
tensorflow-privacy==0.2.2
tensorflow-probability==0.7.0
termcolor==1.1.0
terminado==0.8.3
testpath==0.4.4
text-unidecode==1.3
textblob==0.15.3
textgenrnn==1.4.1
tflearn==0.3.2
Theano==1.0.4
thinc==7.0.8
toolz==0.10.0
torch==1.3.1
torchsummary==1.5.1
torchtext==0.3.1
torchvision==0.4.2
tornado==4.5.3
tqdm==4.28.1
traitlets==4.3.3
tweepy==3.6.0
typing==3.6.6
typing-extensions==3.6.6
tzlocal==1.5.1
umap-learn==0.3.10
uritemplate==3.0.1
urllib3==1.24.3
vega-datasets==0.8.0
wasabi==0.6.0
wcwidth==0.1.8
webencodings==0.5.1
Werkzeug==0.16.0
widgetsnbextension==3.5.1
wordcloud==1.5.0
wrapt==1.11.2
xarray==0.14.1
xgboost==0.90
xkit==0.0.0
xlrd==1.1.0
xlwt==1.3.0
yellowbrick==0.9.1
zict==1.0.0
zipp==0.6.0
zmq==0.0.0

For some packages, it says "0.0" or similar, I don't know why. I've had this Error with sklearn too, depending on the imports order, I suppose.

[janfreyberg]

Interesting! Surprising that they include a version of nibabel at all, seems an unusual choice. I'll have to test niwidgets with 2.3.3 and will drop to that version if it works.

[fepegar]

With sklearn I was having the opposite problem (requirement too old) in this notebook when importing niwidgets after all those imports in the second code cell.

[zaineb-abdelli]

hey, did you solve the problem? am facing the same!