Module 'logging' requires separate import of 'logging.config' when using --log option in CLI #1839
Description
Describe the bug
Running the openfe CLI with the --log option causes an AttributeError because logging.config is used but never imported. The code imports only the module logging, which does not include the module logging.conf.
To Reproduce
Run the cli with with any command, e.g. openfe --log debug_logging.conf quickrun path/to/transformation.json -o results.json -d working-directory similar to one of the tutorials but including the --log flag.
The error can also be reproduced by just running the following in a Python console:
import logging
logging.conf
Software versions
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OS Version: Debian 14.2.0
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Installation via the conda-lock file
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Output of
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Name Version Build Channel _openmp_mutex 4.5 7_kmp_llvm conda-forge _python_abi3_support 1.0 hd8ed1ab_2 conda-forge adjusttext 1.3.0 pyhd8ed1ab_0 conda-forge adwaita-icon-theme 49.0 unix_0 conda-forge ambertools 24.8 cuda_None_nompi_py312hbe1986e_101 conda-forge annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge anyio 4.12.1 pyhcf101f3_0 conda-forge argon2-cffi 25.1.0 pyhd8ed1ab_0 conda-forge argon2-cffi-bindings 25.1.0 py312h4c3975b_2 conda-forge arpack 3.9.1 nompi_hf03ea27_102 conda-forge arrow 1.4.0 pyhcf101f3_0 conda-forge asttokens 3.0.1 pyhd8ed1ab_0 conda-forge async-lru 2.1.0 pyhcf101f3_0 conda-forge at-spi2-atk 2.38.0 h0630a04_3 conda-forge at-spi2-core 2.40.3 h0630a04_0 conda-forge atk-1.0 2.38.0 h04ea711_2 conda-forge attrs 25.4.0 pyhcf101f3_1 conda-forge babel 2.17.0 pyhd8ed1ab_0 conda-forge backports.zstd 1.3.0 py312h90b7ffd_0 conda-forge beautifulsoup4 4.14.3 pyha770c72_0 conda-forge biopython 1.86 py312h4c3975b_1 conda-forge bleach 6.3.0 pyhcf101f3_0 conda-forge bleach-with-css 6.3.0 h5f6438b_0 conda-forge blosc 1.21.6 he440d0b_1 conda-forge brotli 1.2.0 hed03a55_1 conda-forge brotli-bin 1.2.0 hb03c661_1 conda-forge brotli-python 1.2.0 py312hdb49522_1 conda-forge bson 0.5.10 pyhd8ed1ab_0 conda-forge bzip2 1.0.8 hda65f42_8 conda-forge c-ares 1.34.6 hb03c661_0 conda-forge c-blosc2 2.23.0 hc31b594_0 conda-forge ca-certificates 2026.1.4 hbd8a1cb_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge cachetools 7.0.0 pyhd8ed1ab_0 conda-forge cairo 1.18.4 h3394656_0 conda-forge certifi 2026.1.4 pyhd8ed1ab_0 conda-forge cffi 2.0.0 py312h460c074_1 conda-forge cftime 1.6.5 py312h4f23490_1 conda-forge charset-normalizer 3.4.4 pyhd8ed1ab_0 conda-forge cinnabar 0.5.0 pyhd8ed1ab_0 conda-forge click 8.3.1 pyh8f84b5b_1 conda-forge click-option-group 0.5.6 pyhd8ed1ab_0 conda-forge colorama 0.4.6 pyhd8ed1ab_1 conda-forge comm 0.2.3 pyhe01879c_0 conda-forge contourpy 1.3.3 py312h0a2e395_4 conda-forge cpython 3.12.12 py312hd8ed1ab_2 conda-forge cuda-nvrtc 12.9.86 hecca717_1 conda-forge cuda-version 12.9 h4f385c5_3 conda-forge cycler 0.12.1 pyhcf101f3_2 conda-forge cyrus-sasl 2.1.28 hd9c7081_0 conda-forge dbus 1.16.2 h24cb091_1 conda-forge debugpy 1.8.20 py312h8285ef7_0 conda-forge decorator 5.2.1 pyhd8ed1ab_0 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge dill 0.4.1 pyhcf101f3_0 conda-forge epoxy 1.5.10 hb03c661_2 conda-forge exceptiongroup 1.3.1 pyhd8ed1ab_0 conda-forge executing 2.2.1 pyhd8ed1ab_0 conda-forge fftw 3.3.10 nompi_h3b011a4_111 conda-forge filelock 3.20.3 pyhd8ed1ab_0 conda-forge flexcache 0.3 pyhd8ed1ab_1 conda-forge flexparser 0.4 pyhd8ed1ab_1 conda-forge 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 h77eed37_3 conda-forge fontconfig 2.15.0 h7e30c49_1 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 hc364b38_1 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hpack 4.1.0 pyhd8ed1ab_0 conda-forge httpcore 1.0.9 pyh29332c3_0 conda-forge httpx 0.28.1 pyhd8ed1ab_0 conda-forge hyperframe 6.1.0 pyhd8ed1ab_0 conda-forge icu 75.1 he02047a_0 conda-forge idna 3.11 pyhd8ed1ab_0 conda-forge importlib-metadata 8.7.0 pyhe01879c_1 conda-forge importlib_resources 6.5.2 pyhd8ed1ab_0 conda-forge iniconfig 2.3.0 pyhd8ed1ab_0 conda-forge ipycytoscape 1.3.3 pyhd8ed1ab_1 conda-forge ipykernel 7.1.0 pyha191276_0 conda-forge ipython 9.10.0 pyh53cf698_0 conda-forge ipython_pygments_lexers 1.1.1 pyhd8ed1ab_0 conda-forge ipywidgets 8.1.8 pyhd8ed1ab_0 conda-forge isoduration 20.11.0 pyhd8ed1ab_1 conda-forge jax 0.7.2 pyhd8ed1ab_0 conda-forge jaxlib 0.7.2 cpu_py312h9a1a051_2 conda-forge jedi 0.19.2 pyhd8ed1ab_1 conda-forge jinja2 3.1.6 pyhcf101f3_1 conda-forge joblib 1.5.3 pyhd8ed1ab_0 conda-forge jq 1.8.1 h73b1eb8_0 conda-forge json5 0.13.0 pyhd8ed1ab_0 conda-forge jsonpointer 3.0.0 pyhcf101f3_3 conda-forge jsonschema 4.26.0 pyhcf101f3_0 conda-forge jsonschema-specifications 2025.9.1 pyhcf101f3_0 conda-forge jsonschema-with-format-nongpl 4.26.0 hcf101f3_0 conda-forge jupyter-lsp 2.3.0 pyhcf101f3_0 conda-forge jupyter_client 8.8.0 pyhcf101f3_0 conda-forge jupyter_core 5.9.1 pyhc90fa1f_0 conda-forge jupyter_events 0.12.0 pyh29332c3_0 conda-forge jupyter_server 2.17.0 pyhcf101f3_0 conda-forge jupyter_server_terminals 0.5.4 pyhcf101f3_0 conda-forge jupyterlab 4.5.3 pyhd8ed1ab_0 conda-forge jupyterlab_pygments 0.3.0 pyhd8ed1ab_2 conda-forge jupyterlab_server 2.28.0 pyhcf101f3_0 conda-forge jupyterlab_widgets 3.0.16 pyhcf101f3_1 conda-forge kartograf 1.2.0 pyhd8ed1ab_0 conda-forge keyutils 1.6.3 hb9d3cd8_0 conda-forge kiwisolver 1.4.9 py312h0a2e395_2 conda-forge konnektor 0.2.1 pyhcf101f3_0 conda-forge krb5 1.21.3 h659f571_0 conda-forge lark 1.3.1 pyhd8ed1ab_0 conda-forge lcms2 2.18 h0c24ade_0 conda-forge ld_impl_linux-64 2.45.1 default_hbd61a6d_101 conda-forge lerc 4.0.0 h0aef613_1 conda-forge libabseil 20250512.1 cxx17_hba17884_0 conda-forge libaec 1.1.5 h088129d_0 conda-forge libblas 3.11.0 5_h5875eb1_mkl conda-forge libboost 1.86.0 hed09d94_4 conda-forge libboost-python 1.86.0 py312hf890105_5 conda-forge libbrotlicommon 1.2.0 hb03c661_1 conda-forge libbrotlidec 1.2.0 hb03c661_1 conda-forge libbrotlienc 1.2.0 hb03c661_1 conda-forge libcblas 3.11.0 5_hfef963f_mkl conda-forge libcufft 11.4.1.4 hecca717_1 conda-forge libcups 2.3.3 hb8b1518_5 conda-forge libcurl 8.18.0 h4e3cde8_0 conda-forge libdeflate 1.25 h17f619e_0 conda-forge libdrm 2.4.125 hb03c661_1 conda-forge libedit 3.1.20250104 pl5321h7949ede_0 conda-forge libegl 1.7.0 ha4b6fd6_2 conda-forge libegl-devel 1.7.0 ha4b6fd6_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.7.3 hecca717_0 conda-forge libffi 3.5.2 h3435931_0 conda-forge libfreetype 2.14.1 ha770c72_0 conda-forge libfreetype6 2.14.1 h73754d4_0 conda-forge libgcc 15.2.0 he0feb66_17 conda-forge libgcc-ng 15.2.0 h69a702a_17 conda-forge libgd 2.3.3 h6f5c62b_11 conda-forge libgfortran 15.2.0 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pyhd8ed1ab_1 conda-forge typing_extensions 4.15.0 pyhcf101f3_0 conda-forge typing_utils 0.1.0 pyhd8ed1ab_1 conda-forge tzdata 2025c hc9c84f9_1 conda-forge unicodedata2 17.0.0 py312h4c3975b_1 conda-forge uri-template 1.3.0 pyhd8ed1ab_1 conda-forge urllib3 2.6.3 pyhd8ed1ab_0 conda-forge validators 0.35.0 pyhd8ed1ab_0 conda-forge wayland 1.24.0 hd6090a7_1 conda-forge wcwidth 0.5.3 pyhd8ed1ab_0 conda-forge webcolors 25.10.0 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pyhd8ed1ab_3 conda-forge websocket-client 1.9.0 pyhd8ed1ab_0 conda-forge wheel 0.46.3 pyhd8ed1ab_0 conda-forge widgetsnbextension 4.0.15 pyhd8ed1ab_0 conda-forge xkeyboard-config 2.46 hb03c661_0 conda-forge xmltodict 1.0.2 pyhcf101f3_0 conda-forge xorg-libice 1.1.2 hb9d3cd8_0 conda-forge xorg-libsm 1.2.6 he73a12e_0 conda-forge xorg-libx11 1.8.12 h4f16b4b_0 conda-forge xorg-libxau 1.0.12 hb03c661_1 conda-forge xorg-libxcomposite 0.4.7 hb03c661_0 conda-forge xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge xorg-libxdamage 1.1.6 hb9d3cd8_0 conda-forge xorg-libxdmcp 1.1.5 hb03c661_1 conda-forge xorg-libxext 1.3.7 hb03c661_0 conda-forge xorg-libxfixes 6.0.2 hb03c661_0 conda-forge xorg-libxi 1.8.2 hb9d3cd8_0 conda-forge xorg-libxinerama 1.1.6 hecca717_0 conda-forge xorg-libxrandr 1.5.5 hb03c661_0 conda-forge xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge xorg-libxt 1.3.1 hb9d3cd8_0 conda-forge xorg-libxtst 1.2.5 hb9d3cd8_3 conda-forge xorg-libxxf86vm 1.1.7 hb03c661_0 conda-forge xorg-xorgproto 2025.1 hb03c661_0 conda-forge yaml 0.2.5 h280c20c_3 conda-forge zeromq 4.3.5 h387f397_9 conda-forge zipp 3.23.0 pyhcf101f3_1 conda-forge zlib 1.3.1 hb9d3cd8_2 conda-forge zlib-ng 2.3.3 hceb46e0_1 conda-forge zstandard 0.25.0 py312h5253ce2_1 conda-forge zstd 1.5.7 hb78ec9c_6 conda-forge
Output
Traceback (most recent call last):
File "/programs/openfe/bin/openfe", line 8, in <module>
sys.exit(main())
^^^^^^
File "/programs/openfe/lib/python3.12/site-packages/click/core.py", line 1485, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/programs/openfe/lib/python3.12/site-packages/click/core.py", line 1406, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/programs/openfe/lib/python3.12/site-packages/click/core.py", line 1870, in invoke
super().invoke(ctx)
File "/programs/openfe/lib/python3.12/site-packages/click/core.py", line 1269, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/programs/openfe/lib/python3.12/site-packages/click/core.py", line 824, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/programs/openfe/lib/python3.12/site-packages/openfecli/cli.py", line 47, in main
logging.config.fileConfig(log, disable_existing_loggers=False)
^^^^^^^^^^^^^^
AttributeError: module 'logging' has no attribute 'config'
Suggestion
Just importing logging.config should solve the problem.
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