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talmolab / sleap

A deep learning framework for multi-animal pose tracking.
https://sleap.ai
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M1 installation instructions not working #1078

Closed shwan19 closed 1 year ago

shwan19 commented 1 year ago

We were trying to install sleap on an Apple M1 laptop.

We followed the given instructions with the exception of using anaconda for M1 (already installed) instead of miniconda for M1, but after the installation steps complete and we attempt to launch sleap-label, we run into an error relating to PySide6 not being available.

Guidance would be appreciated!

roomrys commented 1 year ago

Hi @shwan19,

Do you mind posting the full error message that you are running into? And also the output after running the sleap-diagnostic command?

Nitty Gritty

We do not have PySide6 listed as a dependency anywhere and we changed all our Qt references to use qtpy as an abstraction layer for either PyQt5/PySide2/PyQt6/PySide6.

We instead list PySide2 as a dependency: https://github.com/talmolab/sleap/blob/ebd2e1ec8f062efaf2588884bb46e92a8030ddcd/requirements.txt#L15-L17

So I would expect qtpy to call PySide2 IF it is installed. We can figure out what is installed by looking at the output of the sleap-diagnostic command.

Possible Workaround

After running sleap-diagnostic (just to give me some info to trouble shoot please), a workaround you could try would be to pip install PySide2 in your SLEAP conda environment.

Thanks, Liezl

kdquine commented 1 year ago

Hi roomrys!

(I work with the first poster)

We recreated the environment and have a pristine copy of the repository, and are still having the issue.

I am pasting a traceback and the sleap-diagnostic output. I'm really pretty unclear at whether there are additional steps we haven't done outside the instructions? I notice there's a homebrew recommendation in the instructions, but am not sure how that's connected to the other installation instructions.

Thank you!

Traceback (most recent call last):
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 551, in find_python_name
    __import__(module_name)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 139, in _import
    return original_import(name, *args, **kwargs)
ModuleNotFoundError: No module named 'PySide6'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/bin/sleap-label", line 33, in <module>
    sys.exit(load_entry_point('sleap', 'console_scripts', 'sleap-label')())
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/bin/sleap-label", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/importlib/metadata.py", line 86, in load
    module = import_module(match.group('module'))
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 850, in exec_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
  File "/Users/sleapuser/Desktop/sleap/sleap/gui/app.py", line 67, in <module>
    from sleap.gui.dialogs.metrics import MetricsTableDialog
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 139, in _import
    return original_import(name, *args, **kwargs)
  File "/Users/sleapuser/Desktop/sleap/sleap/gui/dialogs/metrics.py", line 11, in <module>
    from sleap.gui.dataviews import GenericTableModel, GenericTableView
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 139, in _import
    return original_import(name, *args, **kwargs)
  File "/Users/sleapuser/Desktop/sleap/sleap/gui/dataviews.py", line 28, in <module>
    from sleap.gui.commands import CommandContext
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 139, in _import
    return original_import(name, *args, **kwargs)
  File "/Users/sleapuser/Desktop/sleap/sleap/gui/commands.py", line 56, in <module>
    from sleap.gui.dialogs.importvideos import ImportVideos
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 139, in _import
    return original_import(name, *args, **kwargs)
  File "/Users/sleapuser/Desktop/sleap/sleap/gui/dialogs/importvideos.py", line 34, in <module>
    from sleap.gui.widgets.video import GraphicsView
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 139, in _import
    return original_import(name, *args, **kwargs)
  File "/Users/sleapuser/Desktop/sleap/sleap/gui/widgets/video.py", line 69, in <module>
    from sleap.prefs import prefs
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/shiboken2/files.dir/shibokensupport/feature.py", line 139, in _import
    return original_import(name, *args, **kwargs)
  File "/Users/sleapuser/Desktop/sleap/sleap/prefs.py", line 77, in <module>
    prefs = Preferences()
  File "/Users/sleapuser/Desktop/sleap/sleap/prefs.py", line 34, in __init__
    self.load()
  File "/Users/sleapuser/Desktop/sleap/sleap/prefs.py", line 39, in load
    self.load_()
  File "/Users/sleapuser/Desktop/sleap/sleap/prefs.py", line 44, in load_
    self._prefs = util.get_config_yaml(self._filename)
  File "/Users/sleapuser/Desktop/sleap/sleap/util.py", line 317, in get_config_yaml
    return yaml.load(f, Loader=yaml.Loader)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/__init__.py", line 81, in load
    return loader.get_single_data()
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 51, in get_single_data
    return self.construct_document(node)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 60, in construct_document
    for dummy in generator:
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 413, in construct_yaml_map
    value = self.construct_mapping(node)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 218, in construct_mapping
    return super().construct_mapping(node, deep=deep)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 143, in construct_mapping
    value = self.construct_object(value_node, deep=deep)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 102, in construct_object
    data = constructor(self, tag_suffix, node)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 648, in construct_python_object_apply
    instance = self.make_python_instance(suffix, node, args, kwds, newobj)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 722, in make_python_instance
    return super(UnsafeConstructor, self).make_python_instance(
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 585, in make_python_instance
    cls = self.find_python_name(suffix, node.start_mark)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 719, in find_python_name
    return super(UnsafeConstructor, self).find_python_name(name, mark, unsafe=True)
  File "/Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/yaml/constructor.py", line 553, in find_python_name
    raise ConstructorError("while constructing a Python object", mark,
yaml.constructor.ConstructorError: while constructing a Python object
cannot find module 'PySide6.QtCore' (No module named 'PySide6')
  in "/Users/sleapuser/.sleap/1.2.9/preferences.yaml", line 15, column 15

And then sleap-diagnostic:

==========SYSTEM==========

utc:            2022-12-13 19:55:28.073193
python:         3.9.15
system:         Darwin, arm64, 22.1.0, Darwin Kernel Version 22.1.0: Sun Oct  9 20:14:30 PDT 2022; root:xnu-8792.41.9~2/RELEASE_ARM64_T8103
path:           /Users/sleapuser/opt/anaconda3/envs/sleap/bin:/Users/sleapuser/opt/anaconda3/condabin:/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin

==========IMPORTS==========

sleap import:           True
sleap path:         /Users/sleapuser/Desktop/sleap/sleap/__init__.py
sleap version:          1.2.9
pyside2 import:         True
pyside path:            /Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/PySide2/__init__.py
successfully created PySide2.QtWidgets.QApplication instance

pyside6 import:         False
cv2 import:         True

==========GIT==========

846ce932479085cbec128b235a1172f12404abc8

develop

==========TENSORFLOW==========

tensorflow import:          True
tensorflow version:         2.9.2
tensorflow path:            /Users/sleapuser/opt/anaconda3/envs/sleap/lib/python3.9/site-packages/tensorflow/__init__.py
gpus:           [PhysicalDevice(name='/physical_device:GPU:0', device_type='GPU')]

==========CONDA==========

# packages in environment at /Users/sleapuser/opt/anaconda3/envs/sleap:
#
# Name                    Version                   Build  Channel
absl-py                   1.3.0                    pypi_0    pypi
alabaster                 0.7.12                   pypi_0    pypi
anyio                     3.6.2                    pypi_0    pypi
aom                       3.5.0                h7ea286d_0    conda-forge
appdirs                   1.4.4                    pypi_0    pypi
appnope                   0.1.3                    pypi_0    pypi
argon2-cffi               21.3.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
asttokens                 2.2.1                    pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
attrs                     21.4.0                   pypi_0    pypi
babel                     2.11.0                   pypi_0    pypi
backcall                  0.2.0                    pypi_0    pypi
beautifulsoup4            4.11.1                   pypi_0    pypi
black                     21.6b0                   pypi_0    pypi
bleach                    5.0.1                    pypi_0    pypi
bzip2                     1.0.8                h3422bc3_4    conda-forge
c-ares                    1.18.1               h3422bc3_0    conda-forge
ca-certificates           2022.12.7            h4653dfc_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cachetools                5.2.0                    pypi_0    pypi
cairo                     1.16.0            h73a0509_1014    conda-forge
cattrs                    1.1.1                    pypi_0    pypi
certifi                   2021.10.8                pypi_0    pypi
cffi                      1.15.1                   pypi_0    pypi
cfgv                      3.3.1                    pypi_0    pypi
charset-normalizer        2.1.1                    pypi_0    pypi
click                     8.0.4                    pypi_0    pypi
colorama                  0.4.6                    pypi_0    pypi
comm                      0.1.2                    pypi_0    pypi
commonmark                0.9.1                    pypi_0    pypi
contourpy                 1.0.6                    pypi_0    pypi
coverage                  6.5.0                    pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
debugpy                   1.6.4                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
deprecated                1.2.13                   pypi_0    pypi
distlib                   0.3.6                    pypi_0    pypi
docutils                  0.17.1                   pypi_0    pypi
efficientnet              1.0.0                    pypi_0    pypi
entrypoints               0.4                      pypi_0    pypi
exceptiongroup            1.0.4                    pypi_0    pypi
executing                 1.2.0                    pypi_0    pypi
expat                     2.5.0                hb7217d7_0    conda-forge
ffmpeg                    4.4.2           gpl_h4ccb4f7_111    conda-forge
filelock                  3.8.2                    pypi_0    pypi
flatbuffers               1.12                     pypi_0    pypi
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.14.1               h82840c6_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.38.0                   pypi_0    pypi
freetype                  2.12.1               hd633e50_1    conda-forge
gast                      0.4.0                    pypi_0    pypi
geos                      3.9.1                h9f76cd9_2    conda-forge
gettext                   0.21.1               h0186832_0    conda-forge
giflib                    5.2.1                h27ca646_2    conda-forge
gitdb                     4.0.10                   pypi_0    pypi
gitpython                 3.1.29                   pypi_0    pypi
glib                      2.74.1               hb5ab8b9_1    conda-forge
glib-tools                2.74.1               hb5ab8b9_1    conda-forge
gmp                       6.2.1                h9f76cd9_0    conda-forge
gnutls                    3.7.8                h9f1a10d_0    conda-forge
google-auth               2.15.0                   pypi_0    pypi
google-auth-oauthlib      0.4.6                    pypi_0    pypi
google-pasta              0.2.0                    pypi_0    pypi
graphite2                 1.3.13            h9f76cd9_1001    conda-forge
grpc-cpp                  1.48.1               haeec53e_1    conda-forge
grpcio                    1.48.1           py39h8e34ec7_1    conda-forge
gst-plugins-base          1.20.3               h8b7775e_2    conda-forge
gstreamer                 1.20.3               hcb7b3dd_2    conda-forge
h5py                      3.6.0           nompi_py39hd982b79_100    conda-forge
harfbuzz                  5.3.0                hddbc195_0    conda-forge
hdf5                      1.12.1          nompi_hf9525e8_104    conda-forge
hdmf                      3.4.7                    pypi_0    pypi
icu                       70.1                 h6b3803e_0    conda-forge
identify                  2.5.9                    pypi_0    pypi
idna                      3.4                      pypi_0    pypi
image-classifiers         1.0.0                    pypi_0    pypi
imageio                   2.15.0                   pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
imgaug                    0.4.0                    pypi_0    pypi
imgstore                  0.2.9                    pypi_0    pypi
importlib-metadata        5.1.0                    pypi_0    pypi
iniconfig                 1.1.1                    pypi_0    pypi
ipykernel                 6.19.2                   pypi_0    pypi
ipython                   8.7.0                    pypi_0    pypi
ipython-genutils          0.2.0                    pypi_0    pypi
ipywidgets                7.7.2                    pypi_0    pypi
jaraco-classes            3.2.3                    pypi_0    pypi
jasper                    2.0.33               hba35424_0    conda-forge
jedi                      0.17.2                   pypi_0    pypi
jinja2                    3.1.2                    pypi_0    pypi
joblib                    1.2.0                    pypi_0    pypi
jpeg                      9e                   he4db4b2_2    conda-forge
jsmin                     3.0.1                    pypi_0    pypi
json5                     0.9.10                   pypi_0    pypi
jsonpickle                1.2                      pypi_0    pypi
jsonschema                4.17.3                   pypi_0    pypi
jupyter-cache             0.4.3                    pypi_0    pypi
jupyter-client            7.4.8                    pypi_0    pypi
jupyter-core              5.1.0                    pypi_0    pypi
jupyter-server            1.13.5                   pypi_0    pypi
jupyter-server-mathjax    0.2.6                    pypi_0    pypi
jupyter-sphinx            0.3.2                    pypi_0    pypi
jupyterlab                3.3.4                    pypi_0    pypi
jupyterlab-pygments       0.2.2                    pypi_0    pypi
jupyterlab-server         2.16.3                   pypi_0    pypi
jupyterlab-widgets        1.1.1                    pypi_0    pypi
keras                     2.9.0                    pypi_0    pypi
keras-applications        1.0.8                    pypi_0    pypi
keras-preprocessing       1.1.2                    pypi_0    pypi
keyring                   23.11.0                  pypi_0    pypi
kiwisolver                1.4.4                    pypi_0    pypi
krb5                      1.19.3               hf9b2bbe_0    conda-forge
lame                      3.100             h1a8c8d9_1003    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
libabseil                 20220623.0      cxx17_h28b99d4_6    conda-forge
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libclang                  14.0.6                   pypi_0    pypi
libclang13                14.0.6          default_he70ec0d_0    conda-forge
libcurl                   7.86.0               hd538317_1    conda-forge
libcxx                    14.0.6               h2692d47_0    conda-forge
libdeflate                1.14                 h1a8c8d9_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h642e427_1    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           11_3_0_hd922786_26    conda-forge
libgfortran5              11.3.0              hdaf2cc0_26    conda-forge
libglib                   2.74.1               h4646484_1    conda-forge
libiconv                  1.17                 he4db4b2_0    conda-forge
libidn2                   2.3.4                h1a8c8d9_0    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
liblapacke                3.9.0           16_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hf6e71e7_1    conda-forge
libnghttp2                1.47.0               h232270b_1    conda-forge
libogg                    1.3.4                h27ca646_1    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libopencv                 4.6.0            py39hb16ced2_2    conda-forge
libopus                   1.3.1                h27ca646_1    conda-forge
libpng                    1.6.39               h76d750c_0    conda-forge
libpq                     14.5                 hb650857_3    conda-forge
libprotobuf               3.20.2               hb5ab8b9_0    conda-forge
libsqlite                 3.40.0               h76d750c_0    conda-forge
libssh2                   1.10.0               hb80f160_3    conda-forge
libtasn1                  4.19.0               h1a8c8d9_0    conda-forge
libtiff                   4.4.0                hfa0b094_4    conda-forge
libunistring              0.9.10               h3422bc3_0    conda-forge
libvorbis                 1.3.7                h9f76cd9_0    conda-forge
libvpx                    1.11.0               hc470f4d_3    conda-forge
libwebp                   1.2.4                h328b37c_0    conda-forge
libwebp-base              1.2.4                h57fd34a_0    conda-forge
libxml2                   2.10.3               h87b0503_0    conda-forge
libxslt                   1.1.37               h1bd8bc4_0    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
linkify-it-py             2.0.0                    pypi_0    pypi
livereload                2.6.3                    pypi_0    pypi
llvm-openmp               15.0.6               h7cfbb63_0    conda-forge
lxml                      4.9.1                    pypi_0    pypi
markdown                  3.4.1                    pypi_0    pypi
markdown-it-py            1.1.0                    pypi_0    pypi
markupsafe                2.1.1                    pypi_0    pypi
matplotlib                3.6.2                    pypi_0    pypi
matplotlib-inline         0.1.6                    pypi_0    pypi
mdit-py-plugins           0.2.8                    pypi_0    pypi
mistune                   0.8.4                    pypi_0    pypi
more-itertools            9.0.0                    pypi_0    pypi
mypy-extensions           0.4.3                    pypi_0    pypi
mysql-common              8.0.31               hab468bb_0    conda-forge
mysql-libs                8.0.31               hea58576_0    conda-forge
myst-nb                   0.13.2                   pypi_0    pypi
myst-parser               0.15.2                   pypi_0    pypi
nbclassic                 0.4.8                    pypi_0    pypi
nbclient                  0.5.13                   pypi_0    pypi
nbconvert                 6.5.4                    pypi_0    pypi
nbdime                    3.1.1                    pypi_0    pypi
nbformat                  5.1.3                    pypi_0    pypi
ncurses                   6.3                  h07bb92c_1    conda-forge
ndx-pose                  0.1.1                    pypi_0    pypi
nest-asyncio              1.5.6                    pypi_0    pypi
nettle                    3.8.1                h63371fa_1    conda-forge
networkx                  2.8.8                    pypi_0    pypi
nodeenv                   1.7.0                    pypi_0    pypi
notebook                  6.5.2                    pypi_0    pypi
notebook-shim             0.2.2                    pypi_0    pypi
nspr                      4.35                 hb7217d7_0    conda-forge
nss                       3.78                 h1483a63_0    conda-forge
numpy                     1.22.3           py39h64940a9_2    conda-forge
oauthlib                  3.2.2                    pypi_0    pypi
opencv                    4.6.0            py39hdf13c20_2    conda-forge
openh264                  2.3.1                hb7217d7_1    conda-forge
openssl                   1.1.1s               h03a7124_1    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
p11-kit                   0.24.1               h29577a5_0    conda-forge
packaging                 22.0               pyhd8ed1ab_0    conda-forge
pandas                    1.5.2                    pypi_0    pypi
pandocfilters             1.5.0                    pypi_0    pypi
parso                     0.7.1                    pypi_0    pypi
pathspec                  0.10.3                   pypi_0    pypi
pcre2                     10.40                hb34f9b4_0    conda-forge
pexpect                   4.8.0                    pypi_0    pypi
pickleshare               0.7.5                    pypi_0    pypi
pillow                    8.4.0                    pypi_0    pypi
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h27ca646_0    conda-forge
pkginfo                   1.9.2                    pypi_0    pypi
platformdirs              2.6.0                    pypi_0    pypi
pluggy                    1.0.0                    pypi_0    pypi
pre-commit                2.20.0                   pypi_0    pypi
prometheus-client         0.15.0                   pypi_0    pypi
prompt-toolkit            3.0.36                   pypi_0    pypi
protobuf                  3.19.6                   pypi_0    pypi
psutil                    5.9.4                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.2                    pypi_0    pypi
py-opencv                 4.6.0            py39hfa6204d_2    conda-forge
pyasn1                    0.4.8                    pypi_0    pypi
pyasn1-modules            0.2.8                    pypi_0    pypi
pycparser                 2.21                     pypi_0    pypi
pydata-sphinx-theme       0.8.1                    pypi_0    pypi
pygithub                  1.57                     pypi_0    pypi
pygments                  2.13.0                   pypi_0    pypi
pyjwt                     2.6.0                    pypi_0    pypi
pykalman                  0.9.5                    pypi_0    pypi
pynacl                    1.5.0                    pypi_0    pypi
pynwb                     2.2.0                    pypi_0    pypi
pyparsing                 3.0.9                    pypi_0    pypi
pyrsistent                0.19.2                   pypi_0    pypi
pyside2                   5.15.5           py39h46bc059_1    conda-forge
pytest                    7.2.0                    pypi_0    pypi
pytest-cov                3.0.0                    pypi_0    pypi
pytest-qt                 4.2.0                    pypi_0    pypi
pytest-xvfb               2.0.0                    pypi_0    pypi
python                    3.9.15          h2d96c93_0_cpython    conda-forge
python-dateutil           2.8.2                    pypi_0    pypi
python-rapidjson          1.9                      pypi_0    pypi
python_abi                3.9                      3_cp39    conda-forge
pytz                      2022.6                   pypi_0    pypi
pytz-deprecation-shim     0.1.0.post0              pypi_0    pypi
pyvirtualdisplay          3.0                      pypi_0    pypi
pywavelets                1.4.1                    pypi_0    pypi
pyyaml                    6.0                      pypi_0    pypi
pyzmq                     24.0.1                   pypi_0    pypi
qimage2ndarray            1.9.0                    pypi_0    pypi
qt-main                   5.15.6               h96bf0dc_0    conda-forge
qt-webengine              5.15.4               h43c6231_3    conda-forge
qtpy                      2.3.0              pyhd8ed1ab_0    conda-forge
re2                       2022.06.01           h9a09cb3_1    conda-forge
readline                  8.1.2                h46ed386_0    conda-forge
readme-renderer           37.3                     pypi_0    pypi
regex                     2022.10.31               pypi_0    pypi
requests                  2.28.1                   pypi_0    pypi
requests-oauthlib         1.3.1                    pypi_0    pypi
requests-toolbelt         0.10.1                   pypi_0    pypi
rfc3986                   2.0.0                    pypi_0    pypi
rich                      10.16.1                  pypi_0    pypi
rsa                       4.9                      pypi_0    pypi
ruamel-yaml               0.17.21                  pypi_0    pypi
ruamel-yaml-clib          0.2.7                    pypi_0    pypi
scikit-image              0.19.3                   pypi_0    pypi
scikit-learn              1.0.2                    pypi_0    pypi
scikit-video              1.1.11                   pypi_0    pypi
scipy                     1.7.3            py39h18313fe_1    conda-forge
seaborn                   0.12.1                   pypi_0    pypi
segmentation-models       1.0.1                    pypi_0    pypi
send2trash                1.8.0                    pypi_0    pypi
setuptools                65.5.1             pyhd8ed1ab_0    conda-forge
shapely                   1.7.1            py39he81bf5d_5    conda-forge
six                       1.15.0                   pypi_0    pypi
sleap                     1.2.9                     dev_0    <develop>
smmap                     5.0.0                    pypi_0    pypi
sniffio                   1.3.0                    pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
soupsieve                 2.3.2.post1              pypi_0    pypi
sphinx                    4.5.0                    pypi_0    pypi
sphinx-autobuild          2021.3.14                pypi_0    pypi
sphinx-book-theme         0.3.3                    pypi_0    pypi
sphinx-copybutton         0.5.1                    pypi_0    pypi
sphinx-togglebutton       0.3.2                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.2                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.2                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.0.0                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.3                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.5                    pypi_0    pypi
sqlalchemy                1.4.45                   pypi_0    pypi
sqlite                    3.40.0               h2229b38_0    conda-forge
stack-data                0.6.2                    pypi_0    pypi
svt-av1                   1.4.0                h7ea286d_0    conda-forge
tensorboard               2.9.1                    pypi_0    pypi
tensorboard-data-server   0.6.1                    pypi_0    pypi
tensorboard-plugin-wit    1.8.1                    pypi_0    pypi
tensorflow-deps           2.9.0                         0    apple
tensorflow-estimator      2.9.0                    pypi_0    pypi
tensorflow-macos          2.9.2                    pypi_0    pypi
tensorflow-metal          0.5.0                    pypi_0    pypi
termcolor                 2.1.1                    pypi_0    pypi
terminado                 0.17.1                   pypi_0    pypi
threadpoolctl             3.1.0                    pypi_0    pypi
tifffile                  2022.10.10               pypi_0    pypi
tinycss2                  1.2.1                    pypi_0    pypi
tk                        8.6.12               he1e0b03_0    conda-forge
toml                      0.10.2                   pypi_0    pypi
tomli                     2.0.1                    pypi_0    pypi
tornado                   6.2                      pypi_0    pypi
tqdm                      4.64.1                   pypi_0    pypi
traitlets                 5.7.1                    pypi_0    pypi
twine                     3.3.0                    pypi_0    pypi
typing-extensions         4.4.0                    pypi_0    pypi
tzdata                    2022.7                   pypi_0    pypi
tzlocal                   4.2                      pypi_0    pypi
uc-micro-py               1.0.1                    pypi_0    pypi
urllib3                   1.26.13                  pypi_0    pypi
virtualenv                20.17.1                  pypi_0    pypi
wcwidth                   0.2.5                    pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.4.2                    pypi_0    pypi
werkzeug                  2.2.2                    pypi_0    pypi
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.1                    pypi_0    pypi
wrapt                     1.14.1                   pypi_0    pypi
x264                      1!164.3095           h57fd34a_2    conda-forge
x265                      3.5                  hbc6ce65_3    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
zipp                      3.11.0                   pypi_0    pypi
zlib                      1.2.13               h03a7124_4    conda-forge
zstd                      1.5.2                h8128057_4    conda-forge

==========PIP==========

absl-py==1.3.0
alabaster==0.7.12
anyio==3.6.2
appdirs==1.4.4
appnope==0.1.3
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
asttokens==2.2.1
astunparse==1.6.3
attrs==21.4.0
Babel==2.11.0
backcall==0.2.0
beautifulsoup4==4.11.1
black==21.6b0
bleach==5.0.1
cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work
cachetools==5.2.0
cattrs==1.1.1
certifi==2021.10.8
cffi==1.15.1
cfgv==3.3.1
charset-normalizer==2.1.1
click==8.0.4
colorama==0.4.6
comm==0.1.2
commonmark==0.9.1
contourpy==1.0.6
coverage==6.5.0
cycler==0.11.0
debugpy==1.6.4
decorator==5.1.1
defusedxml==0.7.1
Deprecated==1.2.13
distlib==0.3.6
docutils==0.17.1
efficientnet==1.0.0
entrypoints==0.4
exceptiongroup==1.0.4
executing==1.2.0
filelock==3.8.2
flatbuffers==1.12
fonttools==4.38.0
gast==0.4.0
gitdb==4.0.10
GitPython==3.1.29
google-auth==2.15.0
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
grpcio @ file:///Users/runner/miniforge3/conda-bld/grpc-split_1662408190496/work
h5py @ file:///Users/runner/miniforge3/conda-bld/h5py_1637964045648/work
hdmf==3.4.7
identify==2.5.9
idna==3.4
image-classifiers==1.0.0
imageio==2.15.0
imagesize==1.4.1
imgaug==0.4.0
imgstore==0.2.9
importlib-metadata==5.1.0
iniconfig==1.1.1
ipykernel==6.19.2
ipython==8.7.0
ipython-genutils==0.2.0
ipywidgets==7.7.2
jaraco.classes==3.2.3
jedi==0.17.2
Jinja2==3.1.2
joblib==1.2.0
jsmin==3.0.1
json5==0.9.10
jsonpickle==1.2
jsonschema==4.17.3
jupyter-cache==0.4.3
jupyter-server==1.13.5
jupyter-server-mathjax==0.2.6
jupyter-sphinx==0.3.2
jupyter_client==7.4.8
jupyter_core==5.1.0
jupyterlab==3.3.4
jupyterlab-pygments==0.2.2
jupyterlab-widgets==1.1.1
jupyterlab_server==2.16.3
keras==2.9.0
Keras-Applications==1.0.8
Keras-Preprocessing==1.1.2
keyring==23.11.0
kiwisolver==1.4.4
libclang==14.0.6
linkify-it-py==2.0.0
livereload==2.6.3
lxml==4.9.1
Markdown==3.4.1
markdown-it-py==1.1.0
MarkupSafe==2.1.1
matplotlib==3.6.2
matplotlib-inline==0.1.6
mdit-py-plugins==0.2.8
mistune==0.8.4
more-itertools==9.0.0
mypy-extensions==0.4.3
myst-nb==0.13.2
myst-parser==0.15.2
nbclassic==0.4.8
nbclient==0.5.13
nbconvert==6.5.4
nbdime==3.1.1
nbformat==5.1.3
ndx-pose==0.1.1
nest-asyncio==1.5.6
networkx==2.8.8
nodeenv==1.7.0
notebook==6.5.2
notebook_shim==0.2.2
numpy @ file:///Users/runner/miniforge3/conda-bld/numpy_1651020584890/work
oauthlib==3.2.2
opencv-python==4.6.0
opt-einsum==3.3.0
packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1670530880680/work
pandas==1.5.2
pandocfilters==1.5.0
parso==0.7.1
pathspec==0.10.3
pexpect==4.8.0
pickleshare==0.7.5
Pillow==8.4.0
pkginfo==1.9.2
platformdirs==2.6.0
pluggy==1.0.0
pre-commit==2.20.0
prometheus-client==0.15.0
prompt-toolkit==3.0.36
protobuf==3.19.6
psutil==5.9.4
ptyprocess==0.7.0
pure-eval==0.2.2
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycparser==2.21
pydata-sphinx-theme==0.8.1
PyGithub==1.57
Pygments==2.13.0
PyJWT==2.6.0
pykalman==0.9.5
PyNaCl==1.5.0
pynwb==2.2.0
pyparsing==3.0.9
pyrsistent==0.19.2
PySide2==5.15.5
pytest==7.2.0
pytest-cov==3.0.0
pytest-qt==4.2.0
pytest-xvfb==2.0.0
python-dateutil==2.8.2
python-rapidjson==1.9
pytz==2022.6
pytz-deprecation-shim==0.1.0.post0
PyVirtualDisplay==3.0
PyWavelets==1.4.1
PyYAML==6.0
pyzmq==24.0.1
qimage2ndarray==1.9.0
QtPy @ file:///home/conda/feedstock_root/build_artifacts/qtpy_1667873092748/work
readme-renderer==37.3
regex==2022.10.31
requests==2.28.1
requests-oauthlib==1.3.1
requests-toolbelt==0.10.1
rfc3986==2.0.0
rich==10.16.1
rsa==4.9
ruamel.yaml==0.17.21
ruamel.yaml.clib==0.2.7
scikit-image==0.19.3
scikit-learn==1.0.2
scikit-video==1.1.11
SciPy @ file:///Users/runner/miniforge3/conda-bld/scipy_1667960661844/work
seaborn==0.12.1
segmentation-models==1.0.1
Send2Trash==1.8.0
Shapely @ file:///Users/runner/miniforge3/conda-bld/shapely_1622660864412/work
shiboken2==5.15.5
six==1.15.0
-e git+https://github.com/talmolab/sleap/@846ce932479085cbec128b235a1172f12404abc8#egg=sleap
smmap==5.0.0
sniffio==1.3.0
snowballstemmer==2.2.0
soupsieve==2.3.2.post1
Sphinx==4.5.0
sphinx-autobuild==2021.3.14
sphinx-book-theme==0.3.3
sphinx-copybutton==0.5.1
sphinx-togglebutton==0.3.2
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
SQLAlchemy==1.4.45
stack-data==0.6.2
tensorboard==2.9.1
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorflow-estimator==2.9.0
tensorflow-macos==2.9.2
tensorflow-metal==0.5.0
termcolor==2.1.1
terminado==0.17.1
threadpoolctl==3.1.0
tifffile==2022.10.10
tinycss2==1.2.1
toml==0.10.2
tomli==2.0.1
tornado==6.2
tqdm==4.64.1
traitlets==5.7.1
twine==3.3.0
typing_extensions==4.4.0
tzdata==2022.7
tzlocal==4.2
uc-micro-py==1.0.1
urllib3==1.26.13
virtualenv==20.17.1
wcwidth==0.2.5
webencodings==0.5.1
websocket-client==1.4.2
Werkzeug==2.2.2
widgetsnbextension==3.6.1
wrapt==1.14.1
zipp==3.11.0

==========NVIDIA==========

unable to locate nvidia-smi
roomrys commented 1 year ago

Hi @shwan19, @kdquine,

So it looks like you have PySide2 installed (PySide6 is not installed).

Can you try the sleap-label --reset command and let me know if that works?

Why?

I suspect that your /Users/sleapuser/.sleap/1.2.9/preferences.yaml lists PySide6 in the window_state parameter where is should list PySide2 as shown below:

window state: !!python/object/apply:PySide2.QtCore.QByteArray

Using the --reset option will reset preferences which should hopefully fix things.

Thanks, Liezl

kdquine commented 1 year ago

Success!

We had almost gotten sleap running through a lot of fiddling with library versions at an earlier point, and as you suspected, one of the preference files then referenced QtCore6. After deleting preferences, we can now load sleap without issue!

Thank you so much!