Remove imageio pin
#1501
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Remove imageio pin
#1501
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I've manually tested the wheel by creating the following environment on Windows/Linux: mamba create -c conda-forge pip python=3.7.12 cudatoolkit=11.3 cudnn=8.2 -n <env_name>and then The GPUs are automatically detected on Windows, but on Linux, we need to set the mkdir -p $CONDA_PREFIX/etc/conda/activate.d
echo '#!/bin/sh' >> $CONDA_PREFIX/etc/conda/activate.d/sleap_activate.sh
echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH' >> $CONDA_PREFIX/etc/conda/activate.d/sleap_activate.sh
source $CONDA_PREFIX/etc/conda/activate.d/sleap_activate.shTraining and inference have both run successfully on both Windows and Linux. The wheel is successfully running training/inference on Colab: Linux environmentpip freezeabsl-py==1.4.0
astunparse==1.6.3
attrs==21.4.0
backports.zoneinfo==0.2.1
cachetools==5.3.1
cattrs==1.1.1
certifi==2023.7.22
charset-normalizer==3.2.0
colorama==0.4.6
commonmark==0.9.1
cycler==0.11.0
efficientnet==1.0.0
flatbuffers==23.5.26
fonttools==4.38.0
gast==0.5.4
google-auth==2.23.0
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
grpcio==1.58.0
h5py==3.8.0
hdmf==3.6.1
idna==3.4
image-classifiers==1.0.0
imageio==2.31.2
imgaug==0.4.0
imgstore==0.2.9
importlib-metadata==4.2.0
importlib-resources==5.12.0
joblib==1.3.2
jsmin==3.0.1
jsonpickle==1.2
jsonschema==4.17.3
keras==2.8.0
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.2
kiwisolver==1.4.5
libclang==16.0.6
Markdown==3.3.4
MarkupSafe==2.1.3
matplotlib==3.5.3
ndx-pose==0.1.1
networkx==2.6.3
nixio==1.5.3
numpy==1.21.6
oauthlib==3.2.2
opencv-python==4.5.5.64
opt-einsum==3.3.0
packaging==23.1
pandas==1.3.5
Pillow==8.4.0
pkgutil_resolve_name==1.3.10
protobuf==3.19.6
psutil==5.9.5
pyasn1==0.5.0
pyasn1-modules==0.3.0
Pygments==2.16.1
pykalman==0.9.5
pynwb==2.3.3
pyparsing==3.1.1
pyrsistent==0.19.3
PySide2==5.14.1
python-dateutil==2.8.2
python-rapidjson==1.11
pytz==2023.3.post1
PyWavelets==1.3.0
PyYAML==6.0.1
pyzmq==25.1.1
qimage2ndarray==1.10.0
QtPy==2.4.0
requests==2.31.0
requests-oauthlib==1.3.1
rich==10.16.1
rsa==4.9
ruamel.yaml==0.17.32
ruamel.yaml.clib==0.2.7
scikit-image==0.19.3
scikit-learn==1.0.2
scikit-video==1.1.11
scipy==1.7.3
seaborn==0.12.2
segmentation-models==1.0.1
shapely==2.0.1
shiboken2==5.14.1
six==1.16.0
sleap @ file:///home/talmolab/sleap-estimates-animal-poses/pull-requests/sleap
tensorboard==2.8.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorflow==2.8.4
tensorflow-estimator==2.8.0
tensorflow-hub==0.14.0
tensorflow-io-gcs-filesystem==0.34.0
termcolor==2.3.0
threadpoolctl==3.1.0
tifffile==2021.11.2
typing_extensions==4.7.1
tzlocal==5.0.1
urllib3==1.26.16
Werkzeug==2.2.3
wrapt==1.15.0
zipp==3.15.0micromamba list Name Version Build Channel
──────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
ca-certificates 2023.7.22 hbcca054_0 conda-forge
cudatoolkit 11.3.1 hb98b00a_12 conda-forge
cudnn 8.2.1.32 h86fa8c9_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_0 conda-forge
libgomp 13.2.0 h807b86a_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsqlite 3.43.0 h2797004_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
ncurses 6.4 hcb278e6_0 conda-forge
openssl 3.1.2 hd590300_0 conda-forge
pip 23.2.1 pyhd8ed1ab_0 conda-forge
python 3.7.12 hf930737_100_cpython conda-forge
readline 8.2 h8228510_1 conda-forge
setuptools 68.2.2 pyhd8ed1ab_0 conda-forge
sqlite 3.43.0 h2c6b66d_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
wheel 0.41.2 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forgeWindows environmentmamba list |
WalkthroughThis change primarily involves package updates in the Changes
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talmo
approved these changes
Sep 14, 2023
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Description
In an effort to get
sleap-ioandsleapin the same environment, we would like the dependencies to line up. This PR remove the pin fromimagio.In fact, this PR removes listing
imageioas a dependency at all - although it is still pulled in as a dependency of a dependency.Types of changes
Does this address any currently open issues?
[list open issues here]
Outside contributors checklist
Thank you for contributing to SLEAP!
❤️
Summary by CodeRabbit
pypi_requirements.txt. Removed theimageiopackageand added theThese changes are part of ongoing efforts to keep our software up-to-date and secure. Please update your environment accordingly.imgaugpackage with a specific version constraint. Also, updated the version constraint for thescipypackage.