KeyError when trying to run code is still present in 6.0.3

[mbassalbioinformatics]

Description

What steps will reproduce the problem?

pasted code into spyder and tried to run, then crash

Traceback

Traceback (most recent call last):
  File "/Users/mahmoud/Library/spyder-6/envs/spyder-runtime/lib/python3.11/site-packages/spyder/plugins/run/container.py", line 214, in run_file
    self.edit_run_configurations(
  File "/Users/mahmoud/Library/spyder-6/envs/spyder-runtime/lib/python3.11/site-packages/spyder/plugins/run/container.py", line 232, in edit_run_configurations
    self.dialog.setup()
  File "/Users/mahmoud/Library/spyder-6/envs/spyder-runtime/lib/python3.11/site-packages/spyder/plugins/run/widgets.py", line 760, in setup
    self.run_conf_model.get_initial_index())
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mahmoud/Library/spyder-6/envs/spyder-runtime/lib/python3.11/site-packages/spyder/plugins/run/models.py", line 192, in get_initial_index
    return self.inverted_index[self.current_configuration]
           ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: None

Versions

• Spyder version: 6.0.3 (standalone)
• Python version: 3.11.10 64-bit
• Qt version: 5.15.8
• PyQt5 version: 5.15.9
• Operating System: macOS-15.1.1-arm64-arm-64bit

Dependencies

# Mandatory:
aiohttp >=3.9.3                  :  3.11.10 (OK)
asyncssh >=2.14.0,<3.0.0         :  2.18.0 (OK)
atomicwrites >=1.2.0             :  1.4.1 (OK)
chardet >=2.0.0                  :  5.2.0 (OK)
cloudpickle >=0.5.0              :  3.1.0 (OK)
cookiecutter >=1.6.0             :  2.6.0 (OK)
diff_match_patch >=20181111      :  20241021 (OK)
github >=2.3.0                   :  2.5.0 (OK)
importlib_metadata >=4.6.0       :  8.5.0 (OK)
intervaltree >=3.0.2             :  3.1.0 (OK)
IPython >=8.13.0,<9.0.0,!=8.17.1 :  8.30.0 (OK)
jedi >=0.17.2,<0.20.0            :  0.19.2 (OK)
jellyfish >=0.7                  :  1.1.2 (OK)
jsonschema >=3.2.0               :  4.23.0 (OK)
keyring >=17.0.0                 :  25.5.0 (OK)
nbconvert >=4.0                  :  7.16.4 (OK)
numpydoc >=0.6.0                 :  1.8.0 (OK)
parso >=0.7.0,<0.9.0             :  0.8.4 (OK)
pexpect >=4.4.0                  :  4.9.0 (OK)
pickleshare >=0.4                :  0.7.5 (OK)
psutil >=5.3                     :  6.1.0 (OK)
pygments >=2.0                   :  2.18.0 (OK)
pylint >=3.1,<4                  :  3.3.2 (OK)
pylint_venv >=3.0.2              :  3.0.4 (OK)
pyls_spyder >=0.4.0              :  0.4.0 (OK)
pylsp >=1.12.0,<1.13.0           :  1.12.0 (OK)
pylsp_black >=2.0.0,<3.0.0       :  2.0.0 (OK)
pyuca >=1.2                      :  1.2 (OK)
qdarkstyle >=3.2.0,<3.3.0        :  3.2.3 (OK)
qstylizer >=0.2.2                :  0.2.4 (OK)
qtawesome >=1.3.1,<1.4.0         :  1.3.1 (OK)
qtconsole >=5.6.1,<5.7.0         :  5.6.1 (OK)
qtpy >=2.4.0                     :  2.4.2 (OK)
rtree >=0.9.7                    :  1.3.0 (OK)
setuptools >=49.6.0              :  75.6.0 (OK)
sphinx >=0.6.6                   :  8.1.3 (OK)
spyder_kernels >=3.0.2,<3.1.0    :  3.0.2 (OK)
superqt >=0.6.2,<1.0.0           :  0.6.7 (OK)
textdistance >=4.2.0             :  4.6.2 (OK)
three_merge >=0.1.1              :  0.1.1 (OK)
watchdog >=0.10.3                :  6.0.0 (OK)
yarl >=1.9.4                     :  1.18.3 (OK)
zmq >=24.0.0                     :  26.2.0 (OK)

# Optional:
cython >=0.21                    :  3.0.11 (OK)
matplotlib >=3.0.0               :  3.9.3 (OK)
numpy >=1.7                      :  2.2.0 (OK)
pandas >=1.1.1                   :  2.2.3 (OK)
scipy >=0.17.0                   :  1.14.1 (OK)
sympy >=0.7.3                    :  1.13.3 (OK)

Environment

Environment

# packages in environment at /Users/mahmoud/miniforge3/envs/scRNA:
#
# Name                    Version                   Build  Channel
anndata                   0.10.9             pyhd8ed1ab_0    conda-forge
appnope                   0.1.4                    pypi_0    pypi
array-api-compat          1.9                pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1                    pypi_0    pypi
bedtools                  2.31.1               he85ad4a_3    bioconda
biopython                 1.84                     pypi_0    pypi
brotli                    1.1.0                hd74edd7_2    conda-forge
brotli-bin                1.1.0                hd74edd7_2    conda-forge
bzip2                     1.0.8                h99b78c6_7    conda-forge
c-ares                    1.34.2               h7ab814d_0    conda-forge
ca-certificates           2024.12.14           hf0a4a13_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
cellphonedb               5.0.1                    pypi_0    pypi
certifi                   2024.8.30          pyhd8ed1ab_0    conda-forge
cffi                      1.17.1                   pypi_0    pypi
cfgv                      3.4.0                    pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.1.0                    pypi_0    pypi
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.0           py311h2c37856_2    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
debugpy                   1.8.7                    pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
distlib                   0.3.9                    pypi_0    pypi
docrep                    0.3.2                    pypi_0    pypi
exceptiongroup            1.2.2              pyhd8ed1ab_0    conda-forge
executing                 2.1.0                    pypi_0    pypi
fbpca                     1.0                      pypi_0    pypi
filelock                  3.16.1                   pypi_0    pypi
fonttools                 4.54.1          py311h460d6c5_0    conda-forge
freetype                  2.12.1               hadb7bae_2    conda-forge
geosketch                 1.2                      pypi_0    pypi
get-annotations           0.1.2              pyhd8ed1ab_0    conda-forge
gseapy                    1.1.3                    pypi_0    pypi
h5py                      3.11.0          nompi_py311h0fa3d65_103    conda-forge
hdf5                      1.14.3          nompi_hec07895_105    conda-forge
icu                       75.1                 hfee45f7_0    conda-forge
identify                  2.6.1                    pypi_0    pypi
idna                      3.10                     pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
ipykernel                 6.29.5                   pypi_0    pypi
ipython                   8.28.0                   pypi_0    pypi
jedi                      0.19.1                   pypi_0    pypi
jinja2                    3.1.4                    pypi_0    pypi
joblib                    1.4.2              pyhd8ed1ab_0    conda-forge
jupyter-client            8.6.3                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
kiwisolver                1.4.7           py311h2c37856_0    conda-forge
krb5                      1.21.3               h237132a_0    conda-forge
ktplotspy                 0.2.4                    pypi_0    pypi
lcms2                     2.16                 ha0e7c42_0    conda-forge
legacy-api-wrap           1.4                pyhd8ed1ab_1    conda-forge
lerc                      4.0.0                h9a09cb3_0    conda-forge
liana                     1.4.0                    pypi_0    pypi
libaec                    1.1.3                hebf3989_0    conda-forge
libblas                   3.9.0           24_osxarm64_openblas    conda-forge
libbrotlicommon           1.1.0                hd74edd7_2    conda-forge
libbrotlidec              1.1.0                hd74edd7_2    conda-forge
libbrotlienc              1.1.0                hd74edd7_2    conda-forge
libcblas                  3.9.0           24_osxarm64_openblas    conda-forge
libcurl                   8.10.1               h13a7ad3_0    conda-forge
libcxx                    19.1.2               ha82da77_0    conda-forge
libdeflate                1.22                 hd74edd7_0    conda-forge
libedit                   3.1.20191231         hc8eb9b7_2    conda-forge
libev                     4.33                 h93a5062_2    conda-forge
libexpat                  2.6.3                hf9b8971_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           13_2_0_hd922786_3    conda-forge
libgfortran5              13.2.0               hf226fd6_3    conda-forge
libhwloc                  2.11.1          default_h7685b71_1000    conda-forge
libiconv                  1.17                 h0d3ecfb_2    conda-forge
libjpeg-turbo             3.0.0                hb547adb_1    conda-forge
liblapack                 3.9.0           24_osxarm64_openblas    conda-forge
libllvm14                 14.0.6               hd1a9a77_4    conda-forge
liblzma                   5.6.3                h39f12f2_1    conda-forge
libnghttp2                1.58.0               ha4dd798_1    conda-forge
libopenblas               0.3.27          openmp_h517c56d_1    conda-forge
libpng                    1.6.44               hc14010f_0    conda-forge
libsqlite                 3.46.1               hc14010f_0    conda-forge
libssh2                   1.11.0               h7a5bd25_0    conda-forge
libtiff                   4.7.0                hfce79cd_1    conda-forge
libwebp-base              1.4.0                h93a5062_0    conda-forge
libxcb                    1.17.0               hdb1d25a_0    conda-forge
libxml2                   2.12.7               h01dff8b_4    conda-forge
libzlib                   1.3.1                h8359307_2    conda-forge
llvm-openmp               19.1.1               hb52a8e5_1    conda-forge
llvmlite                  0.43.0          py311hc367efa_1    conda-forge
loompy                    3.0.7                    pypi_0    pypi
markupsafe                3.0.1                    pypi_0    pypi
matplotlib-base           3.9.2           py311hbe3227e_1    conda-forge
matplotlib-inline         0.1.7                    pypi_0    pypi
mizani                    0.9.3                    pypi_0    pypi
mousipy                   0.1.5                    pypi_0    pypi
mudata                    0.3.1                    pypi_0    pypi
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
natsort                   8.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.5                  h7bae524_1    conda-forge
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.4.1              pyhd8ed1ab_0    conda-forge
nodeenv                   1.9.1                    pypi_0    pypi
numba                     0.60.0          py311h9506ed5_0    conda-forge
numpy                     1.26.4                   pypi_0    pypi
numpy-groupies            0.11.2                   pypi_0    pypi
openjpeg                  2.5.2                h9f1df11_0    conda-forge
openssl                   3.4.0                h39f12f2_0    conda-forge
packaging                 24.1               pyhd8ed1ab_0    conda-forge
pandas                    2.2.3           py311h9cb3ce9_1    conda-forge
parso                     0.8.4                    pypi_0    pypi
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0                    pypi_0    pypi
pillow                    10.4.0          py311hc903d1b_1    conda-forge
pip                       24.2               pyh8b19718_1    conda-forge
platformdirs              4.3.6                    pypi_0    pypi
plotnine                  0.12.4                   pypi_0    pypi
pluggy                    1.5.0                    pypi_0    pypi
polars                    1.9.0                    pypi_0    pypi
pre-commit                4.0.1                    pypi_0    pypi
prompt-toolkit            3.0.48                   pypi_0    pypi
psutil                    6.0.0                    pypi_0    pypi
pthread-stubs             0.4               hd74edd7_1002    conda-forge
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.3                    pypi_0    pypi
pybedtools                0.10.0                   pypi_0    pypi
pycparser                 2.22                     pypi_0    pypi
pygments                  2.18.0                   pypi_0    pypi
pynndescent               0.5.13             pyhff2d567_0    conda-forge
pyparsing                 3.2.0              pyhd8ed1ab_1    conda-forge
pysam                     0.22.1                   pypi_0    pypi
pytest                    8.3.3                    pypi_0    pypi
python                    3.11.10         hc51fdd5_3_cpython    conda-forge
python-circos             0.3.0                    pypi_0    pypi
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-tzdata             2024.2             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    5_cp311    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.0                   pypi_0    pypi
qhull                     2020.2               h420ef59_5    conda-forge
readline                  8.2                  h92ec313_1    conda-forge
requests                  2.32.3                   pypi_0    pypi
rpy2                      3.5.16                   pypi_0    pypi
scanpy                    1.10.3             pyhd8ed1ab_0    conda-forge
scikit-learn              1.5.2           py311h9e23f0f_1    conda-forge
scipy                     1.14.1          py311h2929bc6_0    conda-forge
scvelo                    0.3.2                    pypi_0    pypi
seaborn                   0.13.2               hd8ed1ab_2    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_2    conda-forge
session-info              1.0.0              pyhd8ed1ab_0    conda-forge
setuptools                75.1.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
spyder-kernels            3.0.0                    pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
statsmodels               0.14.4          py311h0f07fe1_0    conda-forge
stdlib-list               0.10.0             pyhd8ed1ab_0    conda-forge
tbb                       2021.13.0            h7b3277c_0    conda-forge
threadpoolctl             3.5.0              pyhc1e730c_0    conda-forge
tk                        8.6.13               h5083fa2_1    conda-forge
tornado                   6.4.1                    pypi_0    pypi
tqdm                      4.66.5             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3                   pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2024b                hc8b5060_0    conda-forge
tzlocal                   5.2                      pypi_0    pypi
umap-learn                0.5.6           py311h267d04e_1    conda-forge
urllib3                   2.2.3                    pypi_0    pypi
virtualenv                20.26.6                  pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
wurlitzer                 3.1.1                    pypi_0    pypi
xorg-libxau               1.0.11               hd74edd7_1    conda-forge
xorg-libxdmcp             1.1.5                hd74edd7_0    conda-forge
xz                        5.2.6                h57fd34a_0    conda-forge
zstd                      1.5.6                hb46c0d2_0    conda-forge

[athompson673]

@ccordoba12 perhaps #22607 not fully fixed in 6.0.3?

[mbassalbioinformatics]

This occurred in 6.0.3 On 18 Dec 2024, at 10:55 am, Aaron ***@***.***> wrote:  @ccordoba12<https://github.com/ccordoba12> perhaps #22607<#22607> not fully fixed in 6.0.3? — Reply to this email directly, view it on GitHub<#23299 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKDMV6AQCZF7WYXJ3ZCIJ432GGLFXAVCNFSM6AAAAABTW7666SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNJRGY4TGMZYG4>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[ccordoba12]

@ccordoba12 perhaps #22607 not fully fixed in 6.0.3?

It seems it's not, but I don't understand why.

@mbassalbioinformatics, please post a series of clear steps that always lead to generating the error. That way we'll be able to reproduce and fix it in a future version.

[mbassalbioinformatics]

@ccordoba12
I copied the code into spyder. Pasted with CMD+V. Attempted to run the first line of code with F9. Then Spyder crashed.

I tried again, relaunching, pasting, running line 1. Crash again.

[ccordoba12]

@mbassalbioinformatics, I can't reproduce this with your instructions, sorry.

Please post a video of what you're doing so I can follow it on my side.

[ccordoba12]

@mbassalbioinformatics, any luck with the video? We really need it to be able to reproduce this problem.

[mbassalbioinformatics]

Not really, i closed the windows ages ago and so cant get back to the same crash.
Could it be to do with invisible characters that were copied across causing it to crash?

[ccordoba12]

Could it be to do with invisible characters that were copied across causing it to crash?

Perhaps. Do you have at hand the contents of the file you were copy/pasting to Spyder?