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Commit 1cd399a

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author
Javier Garcia Ordonez
committedMar 14, 2025·
fixed issue git-lfs and pysonic lookups
1 parent 2f5fe06 commit 1cd399a

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6 files changed

+156
-162
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6 files changed

+156
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‎docker/python/Dockerfile

+5-2
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@@ -28,11 +28,12 @@ ENV INPUT_FOLDER="/input" \
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WORKDIR /home/${SC_USER_NAME}
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RUN apt-get update && apt-get install -y --no-install-recommends git-lfs && git lfs install && \
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apt-get clean && rm -rf /var/lib/apt/lists/*
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RUN pip install -e git+https://github.com/tjjlemaire/PySONIC.git@6ee5e571edba358dbfa8436c066846fc5d787632#egg=PySONIC
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RUN pip install -e git+https://github.com/tjjlemaire/MorphoSONIC.git@19c86216da7939065bc6e719c03d41024a21c3ca#egg=MorphoSONIC
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RUN cd /home/scu/src/morphosonic/MorphoSONIC/nmodl && \
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nrnivmodl
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RUN cd /home/scu/src/morphosonic/MorphoSONIC/nmodl && nrnivmodl
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# copy docker bootup scripts
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COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} docker/python/*.sh docker/
@@ -44,6 +45,8 @@ COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} service.cli/ service.cli/
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ENV PATH="/home/${SC_USER_NAME}/service.cli:${PATH}"
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RUN pip install -r src/pymorphosonic/requirements.txt
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ENTRYPOINT [ "/bin/sh", "docker/entrypoint.sh", "/bin/sh", "-c" ]
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## only for computational (also the "/bin/sh", "-c" above)
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CMD ["run"]

‎src/pymorphosonic/requirements.txt

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@@ -1,9 +1,151 @@
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tqdm>=4.3
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lockfile>=0.1.2
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multiprocess>=0.70
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boltons>=20.1.0
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openpyxl
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jupyterlab
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# matplotlib requirements
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contourpy==1.3.0
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matplotlib==3.7.3
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anyio==4.2.0
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argon2-cffi==23.1.0
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argon2-cffi-bindings==21.2.0
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arrow==1.3.0
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astroid==3.0.2
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asttokens==2.4.1
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async-lru==2.0.4
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attrs==23.1.0
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autopep8==2.0.4
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Babel==2.14.0
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beautifulsoup4==4.12.2
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bleach==6.1.0
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boltons==23.1.1
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build==1.0.3
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certifi==2023.11.17
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cffi==1.16.0
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charset-normalizer==3.3.2
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click==8.1.7
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colorama==0.4.6
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colorlog==6.8.0
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comm==0.2.0
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cycler==0.12.1
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debugpy==1.8.0
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decorator==5.1.1
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defusedxml==0.7.1
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dill==0.3.7
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docstring-to-markdown==0.13
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et-xmlfile==1.1.0
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exceptiongroup==1.2.0
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executing==2.0.1
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fastjsonschema==2.19.0
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flake8==6.1.0
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fqdn==1.5.1
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gitdb==4.0.11
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GitPython==3.1.40
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idna==3.6
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importlib-metadata==7.0.0
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ipyevents==2.0.2
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ipykernel==6.27.1
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ipython==8.18.1
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ipywidgets==8.1.1
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isoduration==20.11.0
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isort==5.13.2
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jedi==0.19.1
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Jinja2==3.1.2
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json5==0.9.14
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jsonpointer==2.4
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jsonschema==4.20.0
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jsonschema-specifications==2023.11.2
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jupyter-events==0.9.0
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jupyter-lsp==2.2.1
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jupyter-server-mathjax==0.2.6
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jupyter_client==8.6.0
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jupyter_core==5.5.1
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jupyter_server==2.12.1
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jupyter_server_terminals==0.5.0
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jupyterlab==4.0.9
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jupyterlab-latex==3.0.0
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jupyterlab-lsp==5.0.1
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jupyterlab-widgets==3.0.9
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jupyterlab_git==0.50.0
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jupyterlab_pygments==0.3.0
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jupyterlab_server==2.25.2
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kiwisolver==1.4.5
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lockfile==0.12.2
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MarkdownPP==1.5.1
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MarkupSafe==2.1.3
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matplotlib==2.2.5
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matplotlib-inline==0.1.6
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mccabe==0.7.0
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mistune==3.0.2
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multiprocess==0.70.15
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nbclient==0.7.4
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nbconvert==7.13.0
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nbdime==4.0.1
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nbformat==5.9.2
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nest-asyncio==1.5.8
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NEURON==8.2.3
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notebook==7.0.6
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notebook_shim==0.2.3
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numpy==1.26.2
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openpyxl==3.1.2
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overrides==7.4.0
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packaging==23.2
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pandas==2.1.4
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pandocfilters==1.5.0
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parso==0.8.3
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pexpect==4.9.0
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pip-tools==7.3.0
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platformdirs==4.1.0
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pluggy==1.3.0
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prometheus-client==0.19.0
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prompt-toolkit==3.0.43
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psutil==5.9.7
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ptyprocess==0.7.0
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pure-eval==0.2.2
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pycodestyle==2.11.1
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pycparser==2.21
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pydocstyle==6.3.0
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pyflakes==3.1.0
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Pygments==2.17.2
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pylint==3.0.3
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pyparsing==3.1.1
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pyproject_hooks==1.0.0
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python-dateutil==2.8.2
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python-json-logger==2.0.7
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python-lsp-jsonrpc==1.1.2
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python-lsp-server==1.9.0
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pytoolconfig==1.2.6
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pytz==2023.3.post1
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PyYAML==6.0.1
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pyzmq==25.1.2
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referencing==0.32.0
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requests==2.31.0
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rfc3339-validator==0.1.4
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rfc3986-validator==0.1.1
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rope==1.11.0
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rpds-py==0.15.2
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scipy==1.11.4
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seaborn==0.11.2
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Send2Trash==1.8.2
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six==1.16.0
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smmap==5.0.1
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sniffio==1.3.0
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snowballstemmer==2.2.0
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soupsieve==2.5
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stack-data==0.6.3
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terminado==0.18.0
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tinycss2==1.2.1
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tomli==2.0.1
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tomlkit==0.12.3
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tornado==6.4
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tqdm==4.66.1
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traitlets==5.14.0
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types-python-dateutil==2.8.19.14
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typing_extensions==4.9.0
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tzdata==2023.3
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ujson==5.9.0
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uri-template==1.3.0
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urllib3==2.1.0
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voila==0.5.5
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watchdog==3.0.0
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wcwidth==0.2.12
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webcolors==1.13
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webencodings==0.5.1
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websocket-client==1.7.0
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websockets==12.0
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whatthepatch==1.0.5
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widgetsnbextension==4.0.9
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yapf==0.40.2
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zipp==3.17.0

‎validation/input/axon_details

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‎validation/input/gamma_dicts

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‎validation/input/requirements.txt

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‎validation/input/weird_zip_name.zip

-1.49 KB
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