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GBRSA import error: Module 'pandas' has no attribute 'Panel'#515
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@salilabwfu
salilabwfu
opened on Jun 13, 2022

I am attempting to follow the tutorial for GBRSA here: https://github.com/brainiak/brainiak/blob/master/examples/reprsimil/bayesian_rsa_example.ipynb but I receive an error that the module 'pandas' has no attribute 'Panel.'

I've followed the installation instructions using Conda. Does GBRSA require an older version of pandas? Thanks in advance!

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  1. mihaic commented on Jun 13, 2022

    @mihaic
    mihaic
    on Jun 13, 2022
    Member

    Hello, @salilabwfu! Yes, please try a version older than 0.25.

  2. mihaic
    added
    examples
    bug
    on Jun 13, 2022

  3. salilabwfu commented on Jun 13, 2022

    @salilabwfu
    salilabwfu
    on Jun 13, 2022
    Author

    Thanks for your quick response! I tried running conda install -c conda-forge pandas=0.24 and trying again, but it is still giving me the same error. I'm likely doing something wrong with conda. Could you point me to how to use an older version? Thanks again!

  4. mihaic commented on Jun 14, 2022

    @mihaic
    mihaic
    on Jun 14, 2022
    Member

    That install command should have been enough, if you ran it in the same environment where you installed BrainIAK. Could you please paste here the whole error output?

  5. salilabwfu commented on Jun 23, 2022

    @salilabwfu
    salilabwfu
    on Jun 23, 2022
    Author

    Sorry for my slow response. Here is what I have run:
    conda create -n venv
    condo activate venv
    conda install -c brainiak -c defaults -c conda-forge brainiak
    conda install -c conda-forge pandas=0.24

    When I then start python and attempt to load GBRSA, I get this error message

    from brainiak.reprsimil.brsa import GBRSA

    Traceback (most recent call last):
    File "", line 1, in
    File "/Users/anthonysali/miniconda3/envs/venv2/lib/python3.7/site-packages/brainiak/reprsimil/brsa.py", line 53, in
    import brainiak.utils.utils as utils
    File "/Users/anthonysali/miniconda3/envs/venv2/lib/python3.7/site-packages/brainiak/utils/utils.py", line 19, in
    from .fmrisim import generate_stimfunction, _double_gamma_hrf, convolve_hrf
    File "/Users/anthonysali/miniconda3/envs/venv2/lib/python3.7/site-packages/brainiak/utils/fmrisim.py", line 81, in
    from statsmodels.tsa.arima_model import ARMA
    File "/Users/anthonysali/miniconda3/envs/venv2/lib/python3.7/site-packages/statsmodels/tsa/arima_model.py", line 22, in
    import statsmodels.tsa.base.tsa_model as tsbase
    File "/Users/anthonysali/miniconda3/envs/venv2/lib/python3.7/site-packages/statsmodels/tsa/base/tsa_model.py", line 2, in
    from statsmodels.compat.pandas import is_numeric_dtype, Float64Index
    File "/Users/anthonysali/miniconda3/envs/venv2/lib/python3.7/site-packages/statsmodels/compat/pandas.py", line 49, in
    data_klasses = (pandas.Series, pandas.DataFrame, pandas.Panel)
    File "/Users/anthonysali/.local/lib/python3.7/site-packages/pandas/init.py", line 244, in getattr
    raise AttributeError(f"module 'pandas' has no attribute '{name}'")
    AttributeError: module 'pandas' has no attribute 'Panel'

    Thank you again!
    Anthony

  6. mihaic commented on Jun 23, 2022

    @mihaic
    mihaic
    on Jun 23, 2022
    Member

    I tried reproducing the error on Ubuntu 20.04, but I could not. (I don't have access to MacOS right now.) Installing in a new Conda environment like you did and importing GBRSA works. It works both immediately after installing BrainIAK and after downgrading Pandas.

    Can you please try again in a new environment and paste here all the output from your terminal, including the installation commands output?

  7. salilabwfu commented on Jun 24, 2022

    @salilabwfu
    salilabwfu
    on Jun 24, 2022
    Author

    Thanks for your help. I am running MacOS 10.15.5. Here are the commands with the corresponding outputs. Please let me know if I can provide any additional information.

    conda create -n venv

    Collecting package metadata (current_repodata.json): done
    Solving environment: done

    Package Plan

    environment location: /Users/anthonysali/miniconda3/envs/NewEnv

    Proceed ([y]/n)? y

    Preparing transaction: done
    Verifying transaction: done
    Executing transaction: done

    To activate this environment, use

     $ conda activate NewEnv

    To deactivate an active environment, use

     $ conda deactivate

    condo activate NewEnv

    conda install -c brainiak -c defaults -c conda-forge brainiak

    Collecting package metadata (current_repodata.json): done
    Solving environment: done

    Package Plan

    environment location: /Users/anthonysali/miniconda3/envs/NewEnv

    added / updated specs:
    - brainiak

    The following packages will be downloaded:

    package                    |            build
---------------------------|-----------------
certifi-2022.6.15          |   py37hecd8cb5_0         153 KB
------------------------------------------------------------
                                       Total:         153 KB

    The following NEW packages will be INSTALLED:

    bottleneck pkgs/main/osx-64::bottleneck-1.3.4-py37h67323c0_0
    brainiak brainiak/osx-64::brainiak-0.11-py37h04f5b5a_0
    brotli pkgs/main/osx-64::brotli-1.0.9-hb1e8313_2
    ca-certificates pkgs/main/osx-64::ca-certificates-2022.4.26-hecd8cb5_0
    cached-property pkgs/main/noarch::cached-property-1.5.2-py_0
    cctools_osx-64 pkgs/main/osx-64::cctools_osx-64-949.0.1-hc7db93f_23
    certifi pkgs/main/osx-64::certifi-2022.6.15-py37hecd8cb5_0
    clang pkgs/main/osx-64::clang-12.0.0-hecd8cb5_2
    clang-12 pkgs/main/osx-64::clang-12-12.0.0-default_hfcad0e5_2
    clang_osx-64 pkgs/main/osx-64::clang_osx-64-12.0.0-h7ad7729_2
    clangxx pkgs/main/osx-64::clangxx-12.0.0-default_hfcad0e5_2
    clangxx_osx-64 pkgs/main/osx-64::clangxx_osx-64-12.0.0-he0c6f94_2
    compiler-rt pkgs/main/osx-64::compiler-rt-12.0.0-hd87ff74_2
    compiler-rt_osx-64 pkgs/main/noarch::compiler-rt_osx-64-12.0.0-hfb26b64_2
    cycler pkgs/main/noarch::cycler-0.11.0-pyhd3eb1b0_0
    cython pkgs/main/osx-64::cython-0.29.28-py37he9d5cce_0
    decorator pkgs/main/noarch::decorator-5.1.1-pyhd3eb1b0_0
    fonttools pkgs/main/noarch::fonttools-4.25.0-pyhd3eb1b0_0
    freetype pkgs/main/osx-64::freetype-2.11.0-hd8bbffd_0
    giflib pkgs/main/osx-64::giflib-5.2.1-haf1e3a3_0
    h5py pkgs/main/osx-64::h5py-3.6.0-py37h4a1dd59_0
    hdf5 pkgs/main/osx-64::hdf5-1.10.6-hdbbcd12_0
    joblib pkgs/main/noarch::joblib-1.1.0-pyhd3eb1b0_0
    jpeg pkgs/main/osx-64::jpeg-9e-hca72f7f_0
    kiwisolver pkgs/main/osx-64::kiwisolver-1.4.2-py37he9d5cce_0
    lcms2 pkgs/main/osx-64::lcms2-2.12-hf1fd2bf_0
    ld64_osx-64 pkgs/main/osx-64::ld64_osx-64-530-h70f3046_23
    ldid pkgs/main/osx-64::ldid-2.1.2-h2d21305_2
    libblas conda-forge/osx-64::libblas-3.9.0-15_osx64_openblas
    libcblas conda-forge/osx-64::libcblas-3.9.0-15_osx64_openblas
    libclang-cpp12 pkgs/main/osx-64::libclang-cpp12-12.0.0-default_hfcad0e5_2
    libcxx pkgs/main/osx-64::libcxx-12.0.0-h2f01273_0
    libffi pkgs/main/osx-64::libffi-3.3-hb1e8313_2
    libgfortran pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
    liblapack conda-forge/osx-64::liblapack-3.9.0-15_osx64_openblas
    libllvm12 pkgs/main/osx-64::libllvm12-12.0.0-h9b2ccf5_3
    libopenblas pkgs/main/osx-64::libopenblas-0.3.20-h9a5756b_0
    libpng pkgs/main/osx-64::libpng-1.6.37-ha441bb4_0
    libtiff pkgs/main/osx-64::libtiff-4.2.0-hdb42f99_1
    libwebp pkgs/main/osx-64::libwebp-1.2.2-h56c3ce4_0
    libwebp-base pkgs/main/osx-64::libwebp-base-1.2.2-hca72f7f_0
    llvm-openmp conda-forge/osx-64::llvm-openmp-8.0.1-h770b8ee_0
    llvm-tools pkgs/main/osx-64::llvm-tools-12.0.0-h9b2ccf5_3
    lz4-c pkgs/main/osx-64::lz4-c-1.9.3-h23ab428_1
    matplotlib-base pkgs/main/osx-64::matplotlib-base-3.5.1-py37hfb0c5b7_1
    mpi pkgs/main/osx-64::mpi-1.0-mpich
    mpi4py pkgs/main/osx-64::mpi4py-3.0.3-py37h77202c6_0
    mpich pkgs/main/osx-64::mpich-3.3.2-hc856adb_0
    munkres pkgs/main/noarch::munkres-1.1.4-py_0
    ncurses pkgs/main/osx-64::ncurses-6.3-hca72f7f_2
    networkx pkgs/main/osx-64::networkx-2.2-py37_1
    nibabel conda-forge/noarch::nibabel-4.0.1-pyhd8ed1ab_0
    nitime conda-forge/osx-64::nitime-0.9-py37h032687b_3
    numexpr conda-forge/osx-64::numexpr-2.8.0-py37h5b83a90_1
    numpy conda-forge/osx-64::numpy-1.20.3-py37hdb226fd_2
    openmp conda-forge/osx-64::openmp-8.0.1-0
    openssl pkgs/main/osx-64::openssl-1.1.1o-hca72f7f_0
    packaging pkgs/main/noarch::packaging-21.3-pyhd3eb1b0_0
    pandas pkgs/main/osx-64::pandas-1.3.5-py37h743cdd8_0
    patsy pkgs/main/osx-64::patsy-0.5.2-py37hecd8cb5_1
    pillow pkgs/main/osx-64::pillow-9.0.1-py37hde71d04_0
    pip pkgs/main/osx-64::pip-21.2.2-py37hecd8cb5_0
    psutil pkgs/main/osx-64::psutil-5.8.0-py37h9ed2024_1
    pybind11 pkgs/main/osx-64::pybind11-2.9.1-py37hc29d2bd_0
    pydicom conda-forge/noarch::pydicom-2.3.0-pyh6c4a22f_0
    pyparsing pkgs/main/noarch::pyparsing-3.0.4-pyhd3eb1b0_0
    python pkgs/main/osx-64::python-3.7.13-hdfd78df_0
    python-dateutil pkgs/main/noarch::python-dateutil-2.8.2-pyhd3eb1b0_0
    python_abi conda-forge/osx-64::python_abi-3.7-2_cp37m
    pytz pkgs/main/osx-64::pytz-2022.1-py37hecd8cb5_0
    readline pkgs/main/osx-64::readline-8.1.2-hca72f7f_1
    scikit-learn conda-forge/osx-64::scikit-learn-0.21.3-py37hd4ffd6c_0
    scipy conda-forge/osx-64::scipy-1.2.1-py37hbd7caa9_1
    setuptools pkgs/main/osx-64::setuptools-61.2.0-py37hecd8cb5_0
    six pkgs/main/noarch::six-1.16.0-pyhd3eb1b0_1
    sqlite pkgs/main/osx-64::sqlite-3.38.3-h707629a_0
    statsmodels conda-forge/osx-64::statsmodels-0.9.0-py37h917ab60_1000
    tapi pkgs/main/osx-64::tapi-1000.10.8-ha1b3eb9_0
    theano pkgs/main/osx-64::theano-1.0.5-py37he9d5cce_1
    tk pkgs/main/osx-64::tk-8.6.12-h5d9f67b_0
    typing_extensions pkgs/main/noarch::typing_extensions-4.1.1-pyh06a4308_0
    wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
    xz pkgs/main/osx-64::xz-5.2.5-hca72f7f_1
    zlib pkgs/main/osx-64::zlib-1.2.12-h4dc903c_2
    zstd pkgs/main/osx-64::zstd-1.5.2-hcb37349_0

    Proceed ([y]/n)? y

    Downloading and Extracting Packages
    certifi-2022.6.15 | 153 KB | ################################################################################################################## | 100%
    Preparing transaction: done
    Verifying transaction: done
    Executing transaction: done

    conda install -c conda-forge pandas=0.24

    Collecting package metadata (current_repodata.json): done
    Solving environment: done

    Package Plan

    environment location: /Users/anthonysali/miniconda3/envs/NewEnv

    added / updated specs:
    - pandas=0.24

    The following packages will be UPDATED:

    ca-certificates pkgs/main::ca-certificates-2022.4.26-~ --> conda-forge::ca-certificates-2022.6.15-h033912b_0
    openssl pkgs/main::openssl-1.1.1o-hca72f7f_0 --> conda-forge::openssl-1.1.1p-hfe4f2af_0

    The following packages will be SUPERSEDED by a higher-priority channel:

    certifi pkgs/main::certifi-2022.6.15-py37hecd~ --> conda-forge::certifi-2022.6.15-py37hf985489_0
    pandas pkgs/main::pandas-1.3.5-py37h743cdd8_0 --> conda-forge::pandas-0.24.2-py37h4f17bb1_1
    setuptools pkgs/main::setuptools-61.2.0-py37hecd~ --> conda-forge::setuptools-59.8.0-py37hf985489_1

    Proceed ([y]/n)? y

    Preparing transaction: done
    Verifying transaction: done
    Executing transaction: done

    python

    Python 3.7.13 (default, Mar 28 2022, 07:24:34)
    [Clang 12.0.0 ] :: Anaconda, Inc. on darwin
    Type "help", "copyright", "credits" or "license" for more information.

    from brainiak.reprsimil.brsa import GBRSA

    Traceback (most recent call last):
    File "", line 1, in
    File "/Users/anthonysali/miniconda3/envs/NewEnv/lib/python3.7/site-packages/brainiak/reprsimil/brsa.py", line 53, in
    import brainiak.utils.utils as utils
    File "/Users/anthonysali/miniconda3/envs/NewEnv/lib/python3.7/site-packages/brainiak/utils/utils.py", line 19, in
    from .fmrisim import generate_stimfunction, _double_gamma_hrf, convolve_hrf
    File "/Users/anthonysali/miniconda3/envs/NewEnv/lib/python3.7/site-packages/brainiak/utils/fmrisim.py", line 81, in
    from statsmodels.tsa.arima_model import ARMA
    File "/Users/anthonysali/miniconda3/envs/NewEnv/lib/python3.7/site-packages/statsmodels/tsa/arima_model.py", line 22, in
    import statsmodels.tsa.base.tsa_model as tsbase
    File "/Users/anthonysali/miniconda3/envs/NewEnv/lib/python3.7/site-packages/statsmodels/tsa/base/tsa_model.py", line 2, in
    from statsmodels.compat.pandas import is_numeric_dtype, Float64Index
    File "/Users/anthonysali/miniconda3/envs/NewEnv/lib/python3.7/site-packages/statsmodels/compat/pandas.py", line 49, in
    data_klasses = (pandas.Series, pandas.DataFrame, pandas.Panel)
    File "/Users/anthonysali/.local/lib/python3.7/site-packages/pandas/init.py", line 244, in getattr
    raise AttributeError(f"module 'pandas' has no attribute '{name}'")
    AttributeError: module 'pandas' has no attribute 'Panel'

  8. mihaic commented on Jun 24, 2022

    @mihaic
    mihaic
    on Jun 24, 2022
    Member

    It looks like the Pandas 0.24 installation was successful. The error should not appear. Can you try the following command?

    python -c "import pandas; print(pandas.Panel)"

    And to double check, does Conda show the version 0.24 for Pandas?

    conda list pandas

  9. salilabwfu commented on Jun 24, 2022

    @salilabwfu
    salilabwfu
    on Jun 24, 2022
    Author

    Thanks again! I'm still stumped:

    python -c "import pandas; print(pandas.Panel)"
    Traceback (most recent call last):
    File "", line 1, in
    File "/Users/anthonysali/.local/lib/python3.7/site-packages/pandas/init.py", line 244, in getattr
    raise AttributeError(f"module 'pandas' has no attribute '{name}'")
    AttributeError: module 'pandas' has no attribute 'Panel'

    conda list pandas

    packages in environment at /Users/anthonysali/miniconda3/envs/NewEnv:

    Name Version Build Channel
    pandas 0.24.2 py37h4f17bb1_1 conda-forge

    I appreciate all of the help!

  10. mihaic commented on Jun 24, 2022

    @mihaic
    mihaic
    on Jun 24, 2022
    Member

    On my machine, Pandas 0.24 does not produce that error. Can you try the import command in a new environment with just Pandas 0.24?

  11. yibeichan commented on Aug 22, 2022

    @yibeichan
    yibeichan
    on Aug 22, 2022

    hello, I had the similar error module 'pandas' has no attribute 'Panel' (my conda env is python 3.7) when using from brainiak.isc import isc
    so I uninstalled pandas in my conda env (the same one, I didn't create a new env), then installed pandas 0.24 using conda install -c conda-forge pandas=0.24.
    Now I got ModuleNotFoundError: No module named 'brainiak.isc' when from brainiak.isc import isc
    Thanks in advance for the help.

  12. yibeichan commented on Aug 22, 2022

    @yibeichan
    yibeichan
    on Aug 22, 2022

    okay, I found the solution, create the new conda env with pandas 0.24 specified, then install brainiak

    conda create -n brainiak pandas=0.24
conda activate brainiak
conda install -c brainiak -c defaults -c conda-forge brainiak

    everything works fine from brainiak.isc import isc no more problem

  13. mihaic commented on Aug 22, 2022

    @mihaic
    mihaic
    on Aug 22, 2022
    Member

    Thanks for sharing your workaround, @yibeichan!

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