Failure to Start GUI

[Nike-Nay]

Bug description

I have installed sleap using mambaforge and installed it via the 'conda package' instructions at https://sleap.ai/installation.html
I believe everything is installed correctly as I can activate sleap in the terminal.
However, when I attempt to load up the GUI using 'sleap-label' it returns the following:
FileNotFoundError: [Errno 2] No such file or directory: 'c:\users\asus\mambaforge\envs\sleap\lib\site-packages\tensorflow_estimator-2.6.0.dist-info\METADATA'

I am not sure why there is no METADATA file. Is this an issue with the downloaded package or an issue on my system?

Expected behaviour

Actual behaviour

Your personal set up

• OS: Microsoft Windows 10 Home

• Version(s): SLEAP v1.3.1, python 3.7.12

• SLEAP installation method (listed here):
  • Conda from package
  • Conda from source
  • pip package
  • Apple Silicon Macs

Environment packages

# paste output of `pip freeze` or `conda list` here
(sleap) C:\Users\asus>sleap-label
Traceback (most recent call last):
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 573, in _build_master
    ws.require(__requires__)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 891, in require
    needed = self.resolve(parse_requirements(requirements))
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 782, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (importlib-metadata 4.13.0 (c:\users\asus\mambaforge\envs\sleap\lib\site-packages), Requirement.parse('importlib-metadata<4.3; python_version < "3.8"'), {'hdmf'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3031, in _dep_map
    return self.__dep_map
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 2828, in __getattr__
    raise AttributeError(attr)
AttributeError: _DistInfoDistribution__dep_map

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3022, in _parsed_pkg_info
    return self._pkg_info
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 2828, in __getattr__
    raise AttributeError(attr)
AttributeError: _pkg_info

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-label-script.py", line 33, in <module>
    sys.exit(load_entry_point('sleap==1.3.1', 'console_scripts', 'sleap-label')())
  File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-label-script.py", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\importlib_metadata\__init__.py", line 207, in load
    module = import_module(match.group('module'))
  File "C:\Users\asus\mambaforge\envs\sleap\lib\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 953, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
  File "<frozen importlib._bootstrap>", line 983, in _find_and_load
  File "<frozen importlib._bootstrap>", line 953, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  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 "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\__init__.py", line 10, in <module>
    from sleap.io.dataset import Labels, load_file
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\dataset.py", line 71, in <module>
    from sleap.instance import (
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\instance.py", line 32, in <module>
    from sleap.io.video import Video
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\video.py", line 17, in <module>
    from sleap.util import json_loads, json_dumps
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\util.py", line 22, in <module>
    from pkg_resources import Requirement, resource_filename
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3266, in <module>
    @_call_aside
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3241, in _call_aside
    f(*args, **kwargs)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3279, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 575, in _build_master
    return cls._build_from_requirements(__requires__)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 588, in _build_from_requirements
    dists = ws.resolve(reqs, Environment())
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 785, in resolve
    new_requirements = dist.requires(req.extras)[::-1]
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 2749, in requires
    dm = self._dep_map
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3033, in _dep_map
    self.__dep_map = self._compute_dependencies()
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3042, in _compute_dependencies
    for req in self._parsed_pkg_info.get_all('Requires-Dist') or []:
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3024, in _parsed_pkg_info
    metadata = self.get_metadata(self.PKG_INFO)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 1412, in get_metadata
    value = self._get(path)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 1616, in _get
    with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: 'c:\\users\\asus\\mambaforge\\envs\\sleap\\lib\\site-packages\\tensorflow_estimator-2.6.0.dist-info\\METADATA'

Logs

(sleap) C:\Users\asus>sleap-diagnostic
Traceback (most recent call last):
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 573, in _build_master
    ws.require(__requires__)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 891, in require
    needed = self.resolve(parse_requirements(requirements))
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 782, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (importlib-metadata 4.13.0 (c:\users\asus\mambaforge\envs\sleap\lib\site-packages), Requirement.parse('importlib-metadata<4.3; python_version < "3.8"'), {'hdmf'})

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-diagnostic-script.py", line 33, in <module>
    sys.exit(load_entry_point('sleap==1.3.1', 'console_scripts', 'sleap-diagnostic')())
  File "C:\Users\asus\mambaforge\envs\sleap\Scripts\sleap-diagnostic-script.py", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\importlib_metadata\__init__.py", line 207, in load
    module = import_module(match.group('module'))
  File "C:\Users\asus\mambaforge\envs\sleap\lib\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 953, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  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 "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\__init__.py", line 10, in <module>
    from sleap.io.dataset import Labels, load_file
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\dataset.py", line 71, in <module>
    from sleap.instance import (
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\instance.py", line 32, in <module>
    from sleap.io.video import Video
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\io\video.py", line 17, in <module>
    from sleap.util import json_loads, json_dumps
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\sleap\util.py", line 22, in <module>
    from pkg_resources import Requirement, resource_filename
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3266, in <module>
    @_call_aside
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3241, in _call_aside
    f(*args, **kwargs)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 3279, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 575, in _build_master
    return cls._build_from_requirements(__requires__)
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 588, in _build_from_requirements
    dists = ws.resolve(reqs, Environment())
  File "C:\Users\asus\mambaforge\envs\sleap\lib\site-packages\pkg_resources\__init__.py", line 782, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.21.6 (c:\users\asus\mambaforge\envs\sleap\lib\site-packages), Requirement.parse('numpy~=1.19.2'), {'six'})

Screenshots

How to reproduce

1. conda activate sleap
2. sleap-label

[roomrys]

Hi @Nike-Nay,

From reading through some of the linked issues below, it seems this is an error with a failed pip install during the SLEAP installation process. Thanks for sending the output of sleap-label and sleap-diagnostic. Are you able to also send the packages that were installed (pip freeze and mamba list while in your SLEAP environment).

I'm linking some related issues here:

• While installing tensorflow-gpu, got error message that told me to open an issue ticket. pypa/pip#8729
• 'METADATA' crash during 'pip install' pypa/pip#8676
• conda doesn't correctly uninstalls packages installed by pip conda/conda#10357

Thanks,
Liezl

[Nike-Nay]

Hi Liezl, thanks for the quick response. I have added the output for both pip freeze and mamba list here:

pip freeze

(sleap) C:\Users\asus>pip freeze
WARNING: No metadata found in c:\users\asus\mambaforge\envs\sleap\lib\site-packages
absl-py==0.15.0
astunparse==1.6.3
attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1640799537051/work
backports.zoneinfo==0.2.1
cached-property==1.5.2
cachetools==4.2.4
cattrs @ file:///home/conda/feedstock_root/build_artifacts/cattrs_1604136207372/work
certifi==2023.7.22
charset-normalizer==2.0.9
clang==5.0
cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1674202310934/work
cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work
cytoolz @ file:///D:/bld/cytoolz_1657553564801/work
dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1644602974678/work
efficientnet==1.0.0
flatbuffers==1.12
fonttools @ file:///D:/bld/fonttools_1666390069478/work
fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1674184942191/work
gast==0.4.0
google-auth==1.35.0
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
grpcio==1.43.0
h5py==3.1.0
hdmf==3.6.1
idna==3.3
image-classifiers==1.0.0
imagecodecs @ file:///D:/bld/imagecodecs_1644819718476/work
imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1686552404404/work
imgaug @ file:///home/conda/feedstock_root/build_artifacts/imgaug_1640909786103/work
imgstore==0.2.9
importlib-metadata==4.13.0
importlib-resources==5.12.0
joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1691577114857/work
jsmin @ file:///home/conda/feedstock_root/build_artifacts/jsmin_1642532731678/work
jsonpickle==1.2
jsonschema==4.17.3
keras==2.6.0
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.2
kiwisolver @ file:///D:/bld/kiwisolver_1657953189205/work
libclang==12.0.0
locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work
Markdown==3.3.6
markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1677100944732/work
matplotlib @ file:///D:/bld/matplotlib-suite_1661439973878/work
mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1639515908913/work
munkres==1.1.4
ndx-pose==0.1.1
networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1635253012265/work
nixio==1.5.3
numpy==1.19.2
oauthlib==3.1.1
opencv-python-headless==4.2.0.34
opt-einsum==3.3.0
packaging==21.3
pandas @ file:///D:/bld/pandas_1639398349358/work
partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1681246756246/work
patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1665356157073/work
Pillow @ file:///D:/bld/pillow_1660386017560/work
pkgutil_resolve_name==1.3.10
protobuf==3.19.1
psutil @ file:///D:/bld/psutil_1666155596250/work
pyasn1==0.4.8
pyasn1-modules==0.2.8
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1691408637400/work
pykalman==0.9.5
pynwb==2.3.3
pyparsing==3.0.6
pyrsistent==0.19.3
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work
python-rapidjson @ file:///D:/bld/python-rapidjson_1666000124084/work
pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1680088766131/work
PyWavelets @ file:///D:/bld/pywavelets_1649616556601/work
PyYAML @ file:///D:/bld/pyyaml_1648757357341/work
pyzmq @ file:///D:/bld/pyzmq_1663830622471/work
qimage2ndarray==1.10.0
QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1693347765905/work
requests==2.26.0
requests-oauthlib==1.3.0
rich @ file:///home/conda/feedstock_root/build_artifacts/rich-split_1690807641695/work/dist
rsa==4.8
ruamel.yaml==0.17.32
ruamel.yaml.clib==0.2.7
scikit-image @ file:///D:/bld/scikit-image_1660146603458/work
scikit-learn @ file:///D:/bld/scikit-learn_1632611530541/work
scikit-video==1.1.11
scipy @ file:///C:/bld/scipy_1637806996411/work
seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1672497695270/work
segmentation-models==1.0.1
setuptools-scm==6.3.2
Shapely==1.8.5
six==1.15.0
sleap==1.3.1
statsmodels @ file:///D:/bld/statsmodels_1654787262041/work
tensorboard==2.6.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
tensorflow==2.6.3
tensorflow-estimator==2.6.0
tensorflow-hub @ file:///home/conda/feedstock_root/build_artifacts/tensorflow-hub_1618768305670/work/wheel_dir/tensorflow_hub-0.12.0-py2.py3-none-any.whl
tensorflow-io-gcs-filesystem==0.23.1
termcolor==1.1.0
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1643647933166/work
tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1635944860688/work
tomli==2.0.0
toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work
typing-extensions==3.10.0.2
tzdata==2023.3
tzlocal==5.0.1
unicodedata2 @ file:///D:/bld/unicodedata2_1649112131705/work
urllib3==1.26.7
Werkzeug==2.0.2
wrapt==1.12.1
zipp==3.15.0

mamba list

(sleap) C:\Users\asus>mamba list
# packages in environment at C:\Users\asus\mambaforge\envs\sleap:
#
# Name                    Version                   Build  Channel
absl-py                   0.15.0                   pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
backports-zoneinfo        0.2.1                    pypi_0    pypi
blosc                     1.21.5               hdccc3a2_0    conda-forge
brotli                    1.0.9                hcfcfb64_9    conda-forge
brotli-bin                1.0.9                hcfcfb64_9    conda-forge
bzip2                     1.0.8                h8ffe710_4    conda-forge
c-blosc2                  2.10.2               h183a6f4_0    conda-forge
ca-certificates           2023.7.22            h56e8100_0    conda-forge
cached-property           1.5.2                    pypi_0    pypi
cachetools                4.2.4                    pypi_0    pypi
cattrs                    1.1.1              pyhd8ed1ab_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cfitsio                   4.0.0                hd67004f_0    conda-forge
charls                    2.3.4                h39d44d4_0    conda-forge
charset-normalizer        2.0.9                    pypi_0    pypi
clang                     5.0                      pypi_0    pypi
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
cuda-nvcc                 11.3.58              hb8d16a4_0    nvidia
cudatoolkit               11.3.1              hf2f0253_12    conda-forge
cudnn                     8.2.1.32             h754d62a_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py37hcc03f2d_0    conda-forge
dask-core                 2022.2.0           pyhd8ed1ab_0    conda-forge
efficientnet              1.0.0                    pypi_0    pypi
flatbuffers               1.12                     pypi_0    pypi
fonttools                 4.38.0           py37h51bd9d9_0    conda-forge
freeglut                  3.2.2                h63175ca_2    conda-forge
freetype                  2.12.1               h546665d_1    conda-forge
fsspec                    2023.1.0           pyhd8ed1ab_0    conda-forge
gast                      0.4.0                    pypi_0    pypi
geos                      3.11.0               h39d44d4_0    conda-forge
giflib                    5.2.1                h64bf75a_3    conda-forge
google-auth               1.35.0                   pypi_0    pypi
google-auth-oauthlib      0.4.6                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
grpcio                    1.43.0                   pypi_0    pypi
h5py                      3.1.0                    pypi_0    pypi
hdmf                      3.6.1                    pypi_0    pypi
icu                       69.1                 h0e60522_0    conda-forge
idna                      3.3                      pypi_0    pypi
image-classifiers         1.0.0                    pypi_0    pypi
imagecodecs               2021.11.20       py37hfea8715_2    conda-forge
imageio                   2.31.1             pyh24c5eb1_0    conda-forge
imgaug                    0.4.0              pyhd8ed1ab_1    conda-forge
imgstore                  0.2.9                    pypi_0    pypi
importlib-metadata        4.13.0                   pypi_0    pypi
importlib-resources       5.12.0                   pypi_0    pypi
intel-openmp              2023.2.0         h57928b3_49496    conda-forge
jasper                    2.0.33               hc2e4405_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hcfcfb64_3    conda-forge
jsmin                     3.0.1              pyhd8ed1ab_0    conda-forge
jsonpickle                1.2                        py_0    conda-forge
jsonschema                4.17.3                   pypi_0    pypi
jxrlib                    1.1                  h8ffe710_2    conda-forge
keras                     2.6.0                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
kiwisolver                1.4.4            py37h8c56517_0    conda-forge
krb5                      1.20.1               h6609f42_0    conda-forge
lcms2                     2.14                 h90d422f_0    conda-forge
lerc                      3.0                  h0e60522_0    conda-forge
libaec                    1.0.6                h63175ca_1    conda-forge
libblas                   3.9.0              17_win64_mkl    conda-forge
libbrotlicommon           1.0.9                hcfcfb64_9    conda-forge
libbrotlidec              1.0.9                hcfcfb64_9    conda-forge
libbrotlienc              1.0.9                hcfcfb64_9    conda-forge
libcblas                  3.9.0              17_win64_mkl    conda-forge
libclang                  12.0.0                   pypi_0    pypi
libcurl                   8.1.2                h68f0423_0    conda-forge
libdeflate                1.10                 h8ffe710_0    conda-forge
libhwloc                  2.9.1                h51c2c0f_0    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
liblapack                 3.9.0              17_win64_mkl    conda-forge
liblapacke                3.9.0              17_win64_mkl    conda-forge
libopencv                 4.5.1            py37ha0199f4_0    conda-forge
libpng                    1.6.39               h19919ed_0    conda-forge
libprotobuf               3.21.8               h12be248_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.43.0               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h680486a_3    conda-forge
libtiff                   4.4.0                hc4061b1_0    conda-forge
libwebp-base              1.3.1                hcfcfb64_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.10.4               hc3477c8_0    conda-forge
libxslt                   1.1.37               h0192164_0    conda-forge
libzlib                   1.2.13               hcfcfb64_5    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lz4-c                     1.9.3                h8ffe710_1    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
markdown                  3.3.6                    pypi_0    pypi
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
matplotlib-base           3.5.3            py37hbaab90a_2    conda-forge
mdurl                     0.1.0              pyhd8ed1ab_0    conda-forge
mkl                       2022.1.0           h6a75c08_874    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ndx-pose                  0.1.1                    pypi_0    pypi
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
nixio                     1.5.3                    pypi_0    pypi
numpy                     1.19.2                   pypi_0    pypi
oauthlib                  3.1.1                    pypi_0    pypi
opencv                    4.5.1            py37h03978a9_0    conda-forge
opencv-python-headless    4.2.0.34                 pypi_0    pypi
openjpeg                  2.5.0                hc9384bd_1    conda-forge
openssl                   1.1.1v               hcfcfb64_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 21.3                     pypi_0    pypi
pandas                    1.3.5            py37h9386db6_0    conda-forge
partd                     1.4.0              pyhd8ed1ab_0    conda-forge
patsy                     0.5.3              pyhd8ed1ab_0    conda-forge
pillow                    9.2.0            py37h42a8222_2    conda-forge
pip                       23.2.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10                   pypi_0    pypi
protobuf                  3.19.1                   pypi_0    pypi
psutil                    5.9.3            py37h51bd9d9_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
py-opencv                 4.5.1            py37heaed05f_0    conda-forge
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.8                    pypi_0    pypi
pygments                  2.16.1             pyhd8ed1ab_0    conda-forge
pykalman                  0.9.5                      py_1    conda-forge
pynwb                     2.3.3                    pypi_0    pypi
pyparsing                 3.0.6                    pypi_0    pypi
pyrsistent                0.19.3                   pypi_0    pypi
pyside2                   5.13.2           py37h760f651_8    conda-forge
python                    3.7.12          h7840368_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-rapidjson          1.9              py37h7f67f24_0    conda-forge
python_abi                3.7                     3_cp37m    conda-forge
pytz                      2023.3             pyhd8ed1ab_0    conda-forge
pywavelets                1.3.0            py37h3a130e4_1    conda-forge
pyyaml                    6.0              py37hcc03f2d_4    conda-forge
pyzmq                     24.0.1           py37h7347f05_0    conda-forge
qimage2ndarray            1.10.0                   pypi_0    pypi
qt                        5.12.9               h556501e_6    conda-forge
qtpy                      2.4.0              pyhd8ed1ab_0    conda-forge
requests                  2.26.0                   pypi_0    pypi
requests-oauthlib         1.3.0                    pypi_0    pypi
rich                      13.5.1             pyhd8ed1ab_0    conda-forge
ruamel-yaml               0.17.32                  pypi_0    pypi
ruamel-yaml-clib          0.2.7                    pypi_0    pypi
scikit-image              0.19.3           py37h3182a2c_1    conda-forge
scikit-learn              1.0              py37ha78be43_1    conda-forge
scikit-video              1.1.11             pyh24bf2e0_0    conda-forge
scipy                     1.7.3            py37hb6553fb_0    conda-forge
seaborn                   0.12.2               hd8ed1ab_0    conda-forge
seaborn-base              0.12.2             pyhd8ed1ab_0    conda-forge
segmentation-models       1.0.1                    pypi_0    pypi
setuptools                59.8.0           py37h03978a9_1    conda-forge
setuptools-scm            6.3.2                    pypi_0    pypi
shapely                   1.8.5            py37h475e9a0_0    conda-forge
six                       1.15.0                   pypi_0    pypi
sleap                     1.3.1                    pypi_0    pypi
snappy                    1.1.10               hfb803bf_0    conda-forge
sqlite                    3.43.0               hcfcfb64_0    conda-forge
statsmodels               0.13.2           py37h3a130e4_0    conda-forge
tbb                       2021.9.0             h91493d7_0    conda-forge
tensorboard               2.6.0                    pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-wit    1.8.0                    pypi_0    pypi
tensorflow                2.6.3                    pypi_0    pypi
tensorflow-hub            0.12.0             pyhca92ed8_0    conda-forge
tensorflow-io-gcs-filesystem 0.23.1                   pypi_0    pypi
termcolor                 1.1.0                    pypi_0    pypi
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tifffile                  2021.11.2          pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h8ffe710_0    conda-forge
tomli                     2.0.0                    pypi_0    pypi
toolz                     0.12.0             pyhd8ed1ab_0    conda-forge
typing-extensions         3.10.0.2                 pypi_0    pypi
typing_extensions         4.7.1              pyha770c72_0    conda-forge
tzdata                    2023.3                   pypi_0    pypi
tzlocal                   5.0.1                    pypi_0    pypi
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
unicodedata2              14.0.0           py37hcc03f2d_1    conda-forge
urllib3                   1.26.7                   pypi_0    pypi
vc                        14.3                h64f974e_17    conda-forge
vc14_runtime              14.36.32532         hfdfe4a8_17    conda-forge
vs2015_runtime            14.36.32532         h05e6639_17    conda-forge
werkzeug                  2.0.2                    pypi_0    pypi
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
wrapt                     1.12.1                   pypi_0    pypi
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zfp                       0.5.5                h0e60522_8    conda-forge
zipp                      3.15.0                   pypi_0    pypi
zlib                      1.2.13               hcfcfb64_5    conda-forge
zlib-ng                   2.0.7                hcfcfb64_0    conda-forge
zstd                      1.5.5                h12be248_0    conda-forge

[rgough5]

I see you have tensorflow version 2.6.3. After the conda install, did you downgrade tensorflow via pip? I believe the issue is due to issues with dependency management between conda and pip. My solution was to install SLEAP via pip and then downgrade tf. This resulted in both the GPU being detected by tf and the gui loading.

[roomrys]

Hi @rgough5,

Did you have a similar problem with the conda package? On Windows as well?

@Nike-Nay we released a new package and I am wondering if this would bypass your problem?

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2

If it does end up in a failure, would you mind posting the output of the installation command and the sleap-label command.

Thanks,
Liezl

[rgough5]

@roomrys I had a similar issue on SLEAP v1.3.2 although on Fedora Linux. I tried installing with conda from both the package and source, but in both cases tensorflow could not detect our GPU (NVIDIA GeForce RTX 4090). Downgrading tensorflow via pip did allow for the GPU to be detected, but the GUI would not open with sleap-label. I tried downgrading with conda to tensorflow 2.6.2, but it was unable resolve the environment.

[talmo]

Hi @rgough5,

Could you try:

0. Start fresh: mamba env remove -n sleap
1. Create a SLEAP conda environment: mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2
2. Reinstall tensorflow via pip: pip install --upgrade --no-deps tensorflow==2.6.2

You could also try the same method but with tensorflow==2.7.0 in the last step.

Let us know what you get!

Cheers,

Talmo

[rgough5]

@talmo

Unforunately, it did not work. I did get a different error

File "/home/redacted/Miniconda3/envs/sleap/lib/python3.7/site-packages/tensorflow/python/eager/monitoring.py", line 135, in __init__
    self._metric = self._metric_methods[self._label_length].create(*args)
tensorflow.python.framework.errors_impl.AlreadyExistsError: Another metric with the same name already exists.

as opposed to the previous error when I just used pip install tensorflow==2.6.3

  File "/home/redacted/Miniconda3/envs/sleap1/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1616, in _get
    with open(path, 'rb') as stream:
FileNotFoundError: [Errno 2] No such file or directory: '/home/redacted/Miniconda3/envs/sleap1/lib/python3.7/site-packages/six-1.16.0.dist-info/METADATA'

If it helps, when I downgrade using the second method I get the warning

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.
rich 13.5.1 requires typing-extensions<5.0,>=4.0.0; python_version < "3.9", but you have typing-extensions 3.10.0.2 which is incompatible.
tensorflow-hub 0.13.0 requires protobuf>=3.19.6, but you have protobuf 3.16.0 which is incompatible.

Which is why I switched to installing everything via pip. Installing with pip came with it's own set of issues, but it didn't take too much effort to get it working from there.

[roomrys]

Linux-5.15.0-78-generic-x86_64-with-debian-bookworm-sid

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.2

sleap-label GUI launches, but does not auto-detect anaconda

(sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ sleap-label
2023-09-12 10:09:46.962824: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2023-09-12 10:09:46.962865: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml
Restoring GUI state...
2023-09-12 10:09:50.526712: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2023-09-12 10:09:50.527690: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527752: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcublas.so.11'; dlerror: libcublas.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527793: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcublasLt.so.11'; dlerror: libcublasLt.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527830: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcufft.so.10'; dlerror: libcufft.so.10: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527867: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcurand.so.10'; dlerror: libcurand.so.10: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527904: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcusolver.so.11'; dlerror: libcusolver.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527941: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcusparse.so.11'; dlerror: libcusparse.so.11: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527978: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory
2023-09-12 10:09:50.527984: W tensorflow/core/common_runtime/gpu/gpu_device.cc:1850] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.
Skipping registering GPU devices...

Software versions:
SLEAP: 1.3.2
TensorFlow: 2.7.0
Numpy: 1.19.5
Python: 3.7.12
OS: Linux-5.15.0-78-generic-x86_64-with-debian-bookworm-sid

Happy SLEAPing! :)
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml

Setting LD_LIBRARY_PATH and then running sleap-label detects GPU

We can run the following commands to set the LD_LIBRARY_PATH environment variable upon activating our environment. These commands will be run each time we activate our environment, so no need to always run them - just once is fine! Make sure you are in the environment you want GPUs to be found (i.e. sleap for our use case)! We can build an activate script into our recipe for #1484 so users don't need to do this manually. This is related to #1390.

mkdir -p $CONDA_PREFIX/etc/conda/activate.d
echo '#!/bin/sh' >> $CONDA_PREFIX/etc/conda/activate.d/libcudart_activate.sh
echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH' >> $CONDA_PREFIX/etc/conda/activate.d/libcudart_activate.sh
source $CONDA_PREFIX/etc/conda/activate.d/libcudart_activate.sh

(sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ sleap-label
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml
Restoring GUI state...
2023-09-12 10:19:31.051975: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2023-09-12 10:19:31.081791: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2023-09-12 10:19:31.082752: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:939] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero

Software versions:
SLEAP: 1.3.2
TensorFlow: 2.7.0
Numpy: 1.19.5
Python: 3.7.12
OS: Linux-5.15.0-78-generic-x86_64-with-debian-bookworm-sid

Happy SLEAPing! :)
Saving config: /home/talmolab/.sleap/1.3.2/preferences.yaml

conda dependencies

(sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ mm list
List of packages in environment: "/home/talmolab/micromamba/envs/sleap"

  Name               Version       Build                   Channel    
────────────────────────────────────────────────────────────────────────
  _libgcc_mutex      0.1           conda_forge             conda-forge
  _openmp_mutex      4.5           2_gnu                   conda-forge
  alsa-lib           1.2.3.2       h166bdaf_0              conda-forge
  attrs              21.4.0        pyhd8ed1ab_0            conda-forge
  blosc              1.21.5        h0f2a231_0              conda-forge
  brotli             1.0.9         h166bdaf_9              conda-forge
  brotli-bin         1.0.9         h166bdaf_9              conda-forge
  brunsli            0.1           h9c3ff4c_0              conda-forge
  bzip2              1.0.8         h7f98852_4              conda-forge
  c-ares             1.19.1        hd590300_0              conda-forge
  c-blosc2           2.10.2        hb4ffafa_0              conda-forge
  ca-certificates    2023.7.22     hbcca054_0              conda-forge
  cached-property    1.5.2         hd8ed1ab_1              conda-forge
  cached_property    1.5.2         pyha770c72_1            conda-forge
  cairo              1.16.0        h6cf1ce9_1008           conda-forge
  cattrs             1.1.1         pyhd8ed1ab_0            conda-forge
  certifi            2023.7.22     pyhd8ed1ab_0            conda-forge
  cfitsio            4.0.0         h9a35b8e_0              conda-forge
  charls             2.3.4         h9c3ff4c_0              conda-forge
  cloudpickle        2.2.1         pyhd8ed1ab_0            conda-forge
  cuda-nvcc          11.3.58       h2467b9f_0              nvidia     
  cudatoolkit        11.3.1        hb98b00a_12             conda-forge
  cudnn              8.2.1.32      h86fa8c9_0              conda-forge
  cycler             0.11.0        pyhd8ed1ab_0            conda-forge
  cytoolz            0.12.0        py37h540881e_0          conda-forge
  dask-core          2022.2.0      pyhd8ed1ab_0            conda-forge
  dbus               1.13.6        h5008d03_3              conda-forge
  expat              2.5.0         hcb278e6_1              conda-forge
  ffmpeg             4.3.2         h37c90e5_3              conda-forge
  fontconfig         2.14.2        h14ed4e7_0              conda-forge
  fonttools          4.38.0        py37h540881e_0          conda-forge
  freetype           2.12.1        hca18f0e_1              conda-forge
  fsspec             2023.1.0      pyhd8ed1ab_0            conda-forge
  geos               3.11.0        h27087fc_0              conda-forge
  gettext            0.21.1        h27087fc_0              conda-forge
  giflib             5.2.1         h0b41bf4_3              conda-forge
  gmp                6.2.1         h58526e2_0              conda-forge
  gnutls             3.6.13        h85f3911_1              conda-forge
  graphite2          1.3.13        h58526e2_1001           conda-forge
  gst-plugins-base   1.18.5        hf529b03_3              conda-forge
  gstreamer          1.18.5        h9f60fe5_3              conda-forge
  h5py               3.1.0         nompi_py37h1e651dc_100  conda-forge
  harfbuzz           2.9.1         h83ec7ef_1              conda-forge
  hdf5               1.10.6        nompi_h6a2412b_1114     conda-forge
  icu                68.2          h9c3ff4c_0              conda-forge
  imagecodecs        2021.11.20    py37h119f88a_2          conda-forge
  imageio            2.31.1        pyh24c5eb1_0            conda-forge
  imgaug             0.4.0         pyhd8ed1ab_1            conda-forge
  jasper             1.900.1       h07fcdf6_1006           conda-forge
  joblib             1.3.2         pyhd8ed1ab_0            conda-forge
  jpeg               9e            h0b41bf4_3              conda-forge
  jsmin              3.0.1         pyhd8ed1ab_0            conda-forge
  jsonpickle         1.2           py_0                    conda-forge
  jxrlib             1.1           h7f98852_2              conda-forge
  keyutils           1.6.1         h166bdaf_0              conda-forge
  kiwisolver         1.4.4         py37h7cecad7_0          conda-forge
  krb5               1.19.3        h3790be6_0              conda-forge
  lame               3.100         h166bdaf_1003           conda-forge
  lcms2              2.14          h6ed2654_0              conda-forge
  ld_impl_linux-64   2.40          h41732ed_0              conda-forge
  lerc               3.0           h9c3ff4c_0              conda-forge
  libaec             1.0.6         hcb278e6_1              conda-forge
  libblas            3.9.0         18_linux64_openblas     conda-forge
  libbrotlicommon    1.0.9         h166bdaf_9              conda-forge
  libbrotlidec       1.0.9         h166bdaf_9              conda-forge
  libbrotlienc       1.0.9         h166bdaf_9              conda-forge
  libcblas           3.9.0         18_linux64_openblas     conda-forge
  libclang           11.1.0        default_ha53f305_1      conda-forge
  libcurl            7.86.0        h7bff187_1              conda-forge
  libdeflate         1.10          h7f98852_0              conda-forge
  libedit            3.1.20191231  he28a2e2_2              conda-forge
  libev              4.33          h516909a_1              conda-forge
  libevent           2.1.10        h9b69904_4              conda-forge
  libexpat           2.5.0         hcb278e6_1              conda-forge
  libffi             3.4.2         h7f98852_5              conda-forge
  libgcc-ng          13.2.0        h807b86a_0              conda-forge
  libgfortran-ng     13.2.0        h69a702a_0              conda-forge
  libgfortran5       13.2.0        ha4646dd_0              conda-forge
  libglib            2.78.0        hebfc3b9_0              conda-forge
  libgomp            13.2.0        h807b86a_0              conda-forge
  libiconv           1.17          h166bdaf_0              conda-forge
  liblapack          3.9.0         18_linux64_openblas     conda-forge
  liblapacke         3.9.0         18_linux64_openblas     conda-forge
  libllvm11          11.1.0        he0ac6c6_5              conda-forge
  libnghttp2         1.51.0        hdcd2b5c_0              conda-forge
  libnsl             2.0.0         h7f98852_0              conda-forge
  libogg             1.3.4         h7f98852_1              conda-forge
  libopenblas        0.3.24        pthreads_h413a1c8_0     conda-forge
  libopencv          4.5.3         py37h25009ff_1          conda-forge
  libopus            1.3.1         h7f98852_1              conda-forge
  libpng             1.6.39        h753d276_0              conda-forge
  libpq              13.8          hd77ab85_0              conda-forge
  libprotobuf        3.16.0        h780b84a_0              conda-forge
  libsodium          1.0.18        h36c2ea0_1              conda-forge
  libsqlite          3.43.0        h2797004_0              conda-forge
  libssh2            1.10.0        haa6b8db_3              conda-forge
  libstdcxx-ng       13.2.0        h7e041cc_0              conda-forge
  libtiff            4.4.0         h0fcbabc_0              conda-forge
  libuuid            2.38.1        h0b41bf4_0              conda-forge
  libvorbis          1.3.7         h9c3ff4c_0              conda-forge
  libwebp-base       1.3.1         hd590300_0              conda-forge
  libxcb             1.13          h7f98852_1004           conda-forge
  libxkbcommon       1.0.3         he3ba5ed_0              conda-forge
  libxml2            2.9.12        h72842e0_0              conda-forge
  libxslt            1.1.33        h15afd5d_2              conda-forge
  libzlib            1.2.13        hd590300_5              conda-forge
  libzopfli          1.0.3         h9c3ff4c_0              conda-forge
  locket             1.0.0         pyhd8ed1ab_0            conda-forge
  lz4-c              1.9.3         h9c3ff4c_1              conda-forge
  markdown-it-py     2.2.0         pyhd8ed1ab_0            conda-forge
  matplotlib-base    3.5.3         py37hf395dca_2          conda-forge
  mdurl              0.1.0         pyhd8ed1ab_0            conda-forge
  munkres            1.1.4         pyh9f0ad1d_0            conda-forge
  mysql-common       8.0.32        h14678bc_0              conda-forge
  mysql-libs         8.0.32        h54cf53e_0              conda-forge
  ncurses            6.4           hcb278e6_0              conda-forge
  nettle             3.6           he412f7d_0              conda-forge
  networkx           2.7           pyhd8ed1ab_0            conda-forge
  nspr               4.35          h27087fc_0              conda-forge
  nss                3.92          h1d7d5a4_0              conda-forge
  numpy              1.21.6        py37h976b520_0          conda-forge
  opencv             4.5.3         py37h89c1867_1          conda-forge
  openh264           2.1.1         h780b84a_0              conda-forge
  openjpeg           2.5.0         h7d73246_1              conda-forge
  openssl            1.1.1w        hd590300_0              conda-forge
  packaging          23.1          pyhd8ed1ab_0            conda-forge
  pandas             1.3.5         py37he8f5f7f_0          conda-forge
  partd              1.4.0         pyhd8ed1ab_0            conda-forge
  patsy              0.5.3         pyhd8ed1ab_0            conda-forge
  pcre2              10.40         hc3806b6_0              conda-forge
  pillow             9.2.0         py37h850a105_2          conda-forge
  pip                23.2.1        pyhd8ed1ab_0            conda-forge
  pixman             0.40.0        h36c2ea0_0              conda-forge
  protobuf           3.16.0        py37hcd2ae1e_0          conda-forge
  psutil             5.9.3         py37h540881e_0          conda-forge
  pthread-stubs      0.4           h36c2ea0_1001           conda-forge
  py-opencv          4.5.3         py37h6531663_1          conda-forge
  pygments           2.16.1        pyhd8ed1ab_0            conda-forge
  pykalman           0.9.5         py_1                    conda-forge
  pyparsing          3.1.1         pyhd8ed1ab_0            conda-forge
  pyside2            5.13.2        py37hfa98aef_7          conda-forge
  python             3.7.12        hb7a2778_100_cpython    conda-forge
  python-dateutil    2.8.2         pyhd8ed1ab_0            conda-forge
  python-rapidjson   1.9           py37hd23a5d3_0          conda-forge
  python_abi         3.7           3_cp37m                 conda-forge
  pytz               2023.3.post1  pyhd8ed1ab_0            conda-forge
  pywavelets         1.3.0         py37hda87dfa_1          conda-forge
  pyyaml             6.0           py37h540881e_4          conda-forge
  pyzmq              24.0.1        py37h0c0c2a8_0          conda-forge
  qt                 5.12.9        hda022c4_4              conda-forge
  qtpy               2.4.0         pyhd8ed1ab_0            conda-forge
  readline           8.2           h8228510_1              conda-forge
  rich               13.5.1        pyhd8ed1ab_0            conda-forge
  scikit-image       0.19.2        py37he8f5f7f_0          conda-forge
  scikit-learn       1.0           py37hf0f1638_1          conda-forge
  scikit-video       1.1.11        pyh24bf2e0_0            conda-forge
  scipy              1.7.3         py37hf2a6cf1_0          conda-forge
  seaborn            0.12.2        hd8ed1ab_0              conda-forge
  seaborn-base       0.12.2        pyhd8ed1ab_0            conda-forge
  setuptools         59.8.0        py37h89c1867_1          conda-forge
  shapely            1.8.5         py37ha4e3bd1_0          conda-forge
  six                1.16.0        pyh6c4a22f_0            conda-forge
  sleap              1.3.2         py37_1                  sleap      
  snappy             1.1.10        h9fff704_0              conda-forge
  sqlite             3.43.0        h2c6b66d_0              conda-forge
  statsmodels        0.13.2        py37hda87dfa_0          conda-forge
  tensorflow         2.7.0         py37hb93dfd8_3          sleap      
  tensorflow-hub     0.13.0        pyh56297ac_0            conda-forge
  threadpoolctl      3.1.0         pyh8a188c0_0            conda-forge
  tifffile           2021.11.2     pyhd8ed1ab_0            conda-forge
  tk                 8.6.12        h27826a3_0              conda-forge
  toolz              0.12.0        pyhd8ed1ab_0            conda-forge
  typing-extensions  4.7.1         hd8ed1ab_0              conda-forge
  typing_extensions  4.7.1         pyha770c72_0            conda-forge
  unicodedata2       14.0.0        py37h540881e_1          conda-forge
  wheel              0.41.2        pyhd8ed1ab_0            conda-forge
  x264               1!161.3030    h7f98852_1              conda-forge
  xorg-kbproto       1.0.7         h7f98852_1002           conda-forge
  xorg-libice        1.1.1         hd590300_0              conda-forge
  xorg-libsm         1.2.4         h7391055_0              conda-forge
  xorg-libx11        1.8.4         h0b41bf4_0              conda-forge
  xorg-libxau        1.0.11        hd590300_0              conda-forge
  xorg-libxdmcp      1.1.3         h7f98852_0              conda-forge
  xorg-libxext       1.3.4         h0b41bf4_2              conda-forge
  xorg-libxrender    0.9.10        h7f98852_1003           conda-forge
  xorg-renderproto   0.11.1        h7f98852_1002           conda-forge
  xorg-xextproto     7.3.0         h0b41bf4_1003           conda-forge
  xorg-xproto        7.0.31        h7f98852_1007           conda-forge
  xz                 5.2.6         h166bdaf_0              conda-forge
  yaml               0.2.5         h7f98852_2              conda-forge
  zeromq             4.3.4         h9c3ff4c_1              conda-forge
  zfp                0.5.5         h9c3ff4c_8              conda-forge
  zlib               1.2.13        hd590300_5              conda-forge
  zlib-ng            2.0.7         h0b41bf4_0              conda-forge
  zstd               1.5.5         hfc55251_0              conda-forge

pypi dependencies

(sleap) talmolab@talmolab-01-ubuntu:~/sleap-estimates-animal-poses/pull-requests/sleap$ pip freeze
absl-py==1.0.0
astunparse==1.6.3
attrs @ file:///home/conda/feedstock_root/build_artifacts/attrs_1640799537051/work
backports.zoneinfo==0.2.1
cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work
cachetools==4.2.4
cattrs @ file:///home/conda/feedstock_root/build_artifacts/cattrs_1604136207372/work
certifi==2023.7.22
charset-normalizer==2.0.9
cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1674202310934/work
cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1635519461629/work
cytoolz @ file:///home/conda/feedstock_root/build_artifacts/cytoolz_1657553457169/work
dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1644602974678/work
efficientnet==1.0.0
flatbuffers==2.0
fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1666389892786/work
fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1674184942191/work
gast==0.4.0
google-auth==2.3.3
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
grpcio==1.43.0
h5py @ file:///home/conda/feedstock_root/build_artifacts/h5py_1604753641401/work
hdmf==3.6.1
idna==3.3
image-classifiers==1.0.0
imagecodecs @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs_1644819473370/work
imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1686552404404/work
imgaug @ file:///home/conda/feedstock_root/build_artifacts/imgaug_1640909786103/work
imgstore==0.2.9
importlib-metadata==4.10.0
importlib-resources==5.12.0
joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1691577114857/work
jsmin @ file:///home/conda/feedstock_root/build_artifacts/jsmin_1642532731678/work
jsonpickle==1.2
jsonschema==4.17.3
keras==2.7.0
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.2
kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1657953088445/work
libclang==12.0.0
locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work
Markdown==3.3.6
markdown-it-py @ file:///home/conda/feedstock_root/build_artifacts/markdown-it-py_1677100944732/work
matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1661439848456/work
mdurl @ file:///home/conda/feedstock_root/build_artifacts/mdurl_1639515908913/work
munkres==1.1.4
ndx-pose==0.1.1
networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1646092782768/work
nixio==1.5.3
numpy==1.19.5
oauthlib==3.1.1
opencv-python-headless==4.2.0.34
opt-einsum==3.3.0
packaging==21.3
pandas==1.3.5
partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1681246756246/work
patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1665356157073/work
Pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1660385854171/work
pkgutil_resolve_name==1.3.10
protobuf==3.16.0
psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1666155398032/work
pyasn1==0.4.8
pyasn1-modules==0.2.8
Pygments @ file:///home/conda/feedstock_root/build_artifacts/pygments_1691408637400/work
pykalman==0.9.5
pynwb==2.3.3
pyparsing==3.0.6
pyrsistent==0.19.3
PySide2==5.13.2
python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/python-dateutil_1626286286081/work
python-rapidjson @ file:///home/conda/feedstock_root/build_artifacts/python-rapidjson_1665999896718/work
pytz @ file:///home/conda/feedstock_root/build_artifacts/pytz_1693930252784/work
PyWavelets @ file:///home/conda/feedstock_root/build_artifacts/pywavelets_1649616401885/work
PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1648757092905/work
pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1663830492333/work
qimage2ndarray==1.10.0
QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1693347765905/work
requests==2.26.0
requests-oauthlib==1.3.0
rich @ file:///home/conda/feedstock_root/build_artifacts/rich-split_1690807641695/work/dist
rsa==4.8
ruamel.yaml==0.17.32
ruamel.yaml.clib==0.2.7
scikit-image @ file:///home/conda/feedstock_root/build_artifacts/scikit-image_1645196656256/work
scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1632611341839/work
scikit-video==1.1.11
scipy @ file:///home/conda/feedstock_root/build_artifacts/scipy_1637806658031/work
seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1672497695270/work
segmentation-models==1.0.1
setuptools-scm==6.3.2
Shapely @ file:///home/conda/feedstock_root/build_artifacts/shapely_1665624546039/work
shiboken2==5.13.2
six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work
sleap==1.3.2
statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1654787101575/work
tensorboard==2.7.0
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.0
tensorflow==2.7.0
tensorflow-estimator==2.7.0
tensorflow-hub @ file:///home/conda/feedstock_root/build_artifacts/tensorflow-hub_1678880940235/work/wheel_dir/tensorflow_hub-0.13.0-py2.py3-none-any.whl
tensorflow-io-gcs-filesystem==0.23.1
termcolor==1.1.0
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1643647933166/work
tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1635944860688/work
tomli==2.0.0
toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1657485559105/work
typing_extensions==4.0.1
tzlocal==5.0.1
unicodedata2 @ file:///home/conda/feedstock_root/build_artifacts/unicodedata2_1649111917568/work
urllib3==1.26.7
Werkzeug==2.0.2
wrapt==1.13.3
zipp==3.15.0

[roomrys]

Hi @Nike-Nay, @rgough5,

We released a new version at the end of last week which aimed to address the problems @rgough5 brought up and put restrictions on protobuf which seems to be used everywhere, so that could have also affected @Nike-Nay's problem as well. I am going to pre-emptively close this issue, but would feel more confident with some feedback on whether

mamba create -y -n sleap -c conda-forge -c nvidia -c sleap -c anaconda sleap=1.3.3

is working for both of you?

The pip package has also been updated @rgough5.

Thanks!
Liezl

[rgough5]

@roomrys No issues here: one line install and SLEAP work with our GPUs! Thank you so much.