Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[Bug-gmx_MMPBSA_ana]: pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'" #468

Open
camattelaer opened this issue Mar 7, 2024 · 3 comments
Open

[Bug-gmx_MMPBSA_ana]: pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'" #468

camattelaer opened this issue Mar 7, 2024 · 3 comments

Comments

@camattelaer
Copy link

Bug summary

when trying to plot the timeseries of dH or -TdS the program quits unexpectedly with pandas error pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'"

Terminal output

Traceback (most recent call last):
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/customitem.py", line 371, in fn_btn_group
    self.plotting_line(checked)
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/customitem.py", line 398, in plotting_line
    self.lp_subw = LineChart(line_plot_data, self.line_chart_action, options=options, item_parent=self)
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/plots.py", line 215, in __init__
    self.line_plot_ax = sns.lineplot(data=self.data, color=rgb2rgbf(options[('Line Plot', 'line-color')]),
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/_decorators.py", line 46, in inner_f
    return f(**kwargs)
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/relational.py", line 710, in lineplot
    p.plot(ax, kwargs)
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/relational.py", line 471, in plot
    for sub_vars, sub_data in self.iter_data(grouping_vars, from_comp_data=True):
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/_core.py", line 983, in iter_data
    data = self.comp_data
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/seaborn/_core.py", line 1054, in comp_data
    with pd.option_context('mode.use_inf_as_null', True):
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/_config/config.py", line 478, in __enter__
    self.undo = [(pat, _get_option(pat)) for pat, val in self.ops]
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/_config/config.py", line 478, in <listcomp>
    self.undo = [(pat, _get_option(pat)) for pat, val in self.ops]
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/_config/config.py", line 146, in _get_option
    key = _get_single_key(pat, silent)
  File "/home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/_config/config.py", line 132, in _get_single_key
    raise OptionError(f"No such keys(s): {repr(pat)}")
pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'"
Aborted (core dumped)

Actual outcome

gmx_MMPBSA_ana crashes and closes

Expected outcome

gmx_MMPBSA_ana plots the timeseries

Additional information

No response

Operating system

ubuntu 22.04

gmx_MMPBSA_ana Version

gmx_MMPBSA_ana v1.6.2+30.ga8a326d based on MMPBSA version 16.0

Python version

Python 3.9.15

Installation

conda AmberTools + pip
@Valdes-Tresanco-MS
Copy link
Owner

Please attach the conda list output

@camattelaer
Copy link
Author 

# packages in environment at /home/camattelaer/Programs/anaconda3/envs/gmxMMPBSA:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
acpype                    2023.10.27         pyhd8ed1ab_0    conda-forge
ambertools                21.12            py39hc630cb1_0    conda-forge
amberutils                21.0                     pypi_0    pypi
arpack                    3.7.0                hdefa2d7_2    conda-forge
binutils                  2.39                 hdd6e379_1    conda-forge
binutils_impl_linux-64    2.39                 he00db2b_1    conda-forge
binutils_linux-64         2.39                h5fc0e48_13    conda-forge
boost-cpp                 1.74.0               h75c5d50_8    conda-forge
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.24.0               hd590300_0    conda-forge
c-compiler                1.2.0                h7f98852_0    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cairo                     1.16.0               hb05425b_5  
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
compilers                 1.2.0                ha770c72_0    conda-forge
contourpy                 1.2.0            py39h7633fee_0    conda-forge
curl                      7.87.0               h6312ad2_0    conda-forge
cxx-compiler              1.2.0                h4bd325d_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.7            py39h3d6467e_0    conda-forge
expat                     2.5.0                hcb278e6_1    conda-forge
fftw                      3.3.10          nompi_hc118613_108    conda-forge
fontconfig                2.14.2               h14ed4e7_0    conda-forge
fonttools                 4.47.0           py39hd1e30aa_0    conda-forge
fortran-compiler          1.2.0                h1990efc_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
gcc_impl_linux-64         9.5.0               h99780fb_19    conda-forge
gcc_linux-64              9.5.0               h4258300_13    conda-forge
gettext                   0.21.1               h27087fc_0    conda-forge
gfortran_impl_linux-64    9.5.0               hf1096a2_19    conda-forge
gfortran_linux-64         9.5.0               hdb51d14_13    conda-forge
git                       2.39.1          pl5321ha3eba64_0    conda-forge
glib                      2.78.1               hfc55251_0    conda-forge
glib-tools                2.78.1               hfc55251_0    conda-forge
gmx-mmpbsa                1.6.2+30.ga8a326d          pypi_0    pypi
gromacs                   2022.4          nompi_hca75aac_100    conda-forge
gxx_impl_linux-64         9.5.0               h99780fb_19    conda-forge
gxx_linux-64              9.5.0               h43f449f_13    conda-forge
hdf4                      4.2.15               h9772cbc_5    conda-forge
hdf5                      1.12.2          nompi_h2386368_101    conda-forge
icu                       70.1                 h27087fc_0    conda-forge
importlib-resources       6.1.1              pyhd8ed1ab_0    conda-forge
importlib_resources       6.1.1              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h0b41bf4_3    conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_16    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5            py39h7633fee_1    conda-forge
krb5                      1.20.1               hf9c8cef_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.39                 hcc3a1bd_1    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libaec                    1.1.2                h59595ed_1    conda-forge
libblas                   3.9.0           20_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           20_linux64_openblas    conda-forge
libclang-cpp14            14.0.6          default_h7634d5b_1    conda-forge
libcurl                   7.87.0               h6312ad2_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.5.0                hcb278e6_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-devel_linux-64     9.5.0               h0a57e50_19    conda-forge
libgcc-ng                 13.2.0               h807b86a_3    conda-forge
libgfortran-ng            13.2.0               h69a702a_3    conda-forge
libgfortran5              13.2.0               ha4646dd_3    conda-forge
libglib                   2.78.1               hebfc3b9_0    conda-forge
libgomp                   13.2.0               h807b86a_3    conda-forge
libhwloc                  2.9.0                hd6dc26d_0    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
liblapack                 3.9.0           20_linux64_openblas    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libnetcdf                 4.8.1           nompi_h261ec11_106    conda-forge
libnghttp2                1.51.0               hdcd2b5c_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.25          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsanitizer              9.5.0               h2f262e1_19    conda-forge
libsqlite                 3.44.2               h2797004_0    conda-forge
libssh2                   1.10.0               haa6b8db_3    conda-forge
libstdcxx-devel_linux-64  9.5.0               h0a57e50_19    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_3    conda-forge
libtiff                   4.3.0                h0fcbabc_4    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.10.3               hca2bb57_4    conda-forge
libzip                    1.9.2                hc869a4a_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
matplotlib-base           3.8.2            py39he9076e7_0    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.1.3            py39h32b9844_3    conda-forge
mpich                     4.1.2              h846660c_101    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.4                  h59595ed_2    conda-forge
netcdf-fortran            4.5.4           nompi_hc402ea5_102    conda-forge
numpy                     1.26.2           py39h474f0d3_0    conda-forge
ocl-icd                   2.3.1                h7f98852_0    conda-forge
olefile                   0.47               pyhd8ed1ab_0    conda-forge
openbabel                 3.1.1            py39h80c93ca_5    conda-forge
openjpeg                  2.5.0                h7d73246_0    conda-forge
openssl                   1.1.1w               hd590300_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
packmol                   20.010               h86c2bf4_0    conda-forge
packmol-memgen            1.2.1rc0                 pypi_0    pypi
pandas                    1.2.2                    pypi_0    pypi
parmed                    3.4.3+11.g41cc9ab          pypi_0    pypi
pcre2                     10.40                hc3806b6_0    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
pillow                    8.4.0            py39ha612740_0    conda-forge
pip                       23.3.2             pyhd8ed1ab_0    conda-forge
pixman                    0.42.2               h59595ed_0    conda-forge
pocl                      3.1                  h311816e_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyqt5                     5.15.6                   pypi_0    pypi
pyqt5-qt5                 5.15.2                   pypi_0    pypi
pyqt5-sip                 12.13.0                  pypi_0    pypi
pyqt6                     6.6.1                    pypi_0    pypi
pyqt6-qt6                 6.6.2                    pypi_0    pypi
pyqt6-sip                 13.6.0                   pypi_0    pypi
python                    3.9.15          h47a2c10_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      4_cp39    conda-forge
pytraj                    2.0.6                    pypi_0    pypi
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
sander                    16.0                     pypi_0    pypi
scipy                     1.11.4           py39h474f0d3_0    conda-forge
seaborn                   0.11.2                   pypi_0    pypi
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sysroot_linux-64          2.12                he073ed8_16    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tqdm                      4.66.1                   pypi_0    pypi
tzdata                    2023d                h0c530f3_0    conda-forge
unicodedata2              15.1.0           py39hd1e30aa_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    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               1.8.7                h8ee46fc_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-libxt                1.3.0                hd590300_1    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
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

@marioernestovaldes marioernestovaldes changed the title [Bug-gmx_MMPBSA_ana]: [Bug-gmx_MMPBSA_ana]: pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'" Mar 10, 2024
@derefeq
Copy link

derefeq commented Apr 6, 2024 •
edited
Loading

I have been exactly the same. It seems to be a compatibility problem between the version of pandas and python

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@Valdes-Tresanco-MS @camattelaer @derefeq