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Update to work with nixpkgs unstable #1

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Mar 22, 2023
Merged

Update to work with nixpkgs unstable #1

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eb71b70
replace keyrings-alt with keyrings-cryptfile
bcdarwin Mar 9, 2023
a05bf1a
update to work with nixpkgs unstable
bcdarwin Feb 22, 2023
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34 changes: 25 additions & 9 deletions container/dependencies.nix
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ let patched_rPackages =
which
curl wget
zip unzip
pandoc
pandoc quarto
dcm2niix dcmtk gdcm simpleitk ants
cudaPackages.cudatoolkit
snakemake
Expand Down Expand Up @@ -65,6 +65,7 @@ let patched_rPackages =
avro
backcall
bleach
bokeh
catboost
certifi
cffi
Expand All @@ -73,20 +74,24 @@ let patched_rPackages =
cryptography
cycler
cython
dask
datasets
debugpy
decorator
defusedxml
deid
#efficientnet-pytorch
entrypoints
evaluate
einops
grad-cam
#grad-cam # waiting for https://github.com/NixOS/nixpkgs/issues/220341
fastai
greenlet
h5py
httplib2
hupper
idna
ignite
imageio
importlib-metadata
ipykernel
Expand All @@ -98,6 +103,8 @@ let patched_rPackages =
#nipype
antspyx
iso8601
jax
jaxlibWithCuda
jedi
jinja2
joblib
Expand All @@ -112,7 +119,7 @@ let patched_rPackages =
kaggle
keras
keyring
keyrings-alt
keyrings-cryptfile
kiwisolver
lightgbm
llvmlite
Expand All @@ -127,6 +134,7 @@ let patched_rPackages =
mdai
nbclient
nbconvert
nbdev
nbformat
nest-asyncio
networkx
Expand Down Expand Up @@ -155,6 +163,7 @@ let patched_rPackages =
protobuf
ptyprocess
pudb
#pycm
pycparser
pycrypto
pydicom
Expand All @@ -178,6 +187,7 @@ let patched_rPackages =
pyzmq
qtconsole
qtpy
qudida
requests
requests-cache
requests_oauthlib
Expand All @@ -187,24 +197,30 @@ let patched_rPackages =
scipy
secretstorage
send2trash
six
slicer
sqlalchemy
tables
terminado
terminaltables
testpath
text-unidecode
plotnine
polars
pymc3
pytorchWithCuda
pytorch-lightning
tensorflow
tensorboardx
torchvision
torchmetrics
rising
simpleitk
seaborn
sentencepiece # for transformers tokenizing
sentencepiece
siuba
skorch
statsmodels
tensorflow
tensorboardx
torchvision
torchmetrics
timm
torchio
tornado
tqdm
Expand Down
2 changes: 0 additions & 2 deletions container/nix-requirements.txt
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Expand Up @@ -195,8 +195,6 @@ networkx
nibabel
nilearn
nipype
niwidgets
nose
notebook
numba
numpy
Expand Down
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