Cleaned up jupyter container, fixed PATH
parent
41ee2dc5b7
commit
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GPG Key ID:
AD62BB059C2AAEE4
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@ -8,11 +8,24 @@ This directory contains build files for a complete jupyter environment. It is ba
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The images these files produce contain everything you could possibly want in a jupyter notebook. Additional packages can be installed in notebooks with `%%bash` magic.
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## Building the Image
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To build this image, run `build/build.fish.` Edit the script to customize the image.
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## Image contents
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- jupyter + all dependencies
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- Python + many packages
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- Octave
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- R
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- Julia
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## TODO
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- Fix sage
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- Haskell ([source](https://github.com/IHaskell/ihaskell-notebook))
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- Maxima Kernel
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## Configuration
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Change the permissions on the configuration volume (see `docker-compose.yml`) if you get errors.
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@ -34,30 +47,21 @@ The first sets `0.0.0.0` to the allowed local hostname list. This prevents a pos
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The second line sets a persistent token. If this config value is unset, jupyter will generate a new one on each run, making it hard to make a one-click bookmark.
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## Image contents
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- jupyterlab, jupyterhub, notebook
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- latex + pandoc for exporting
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- mamba for packages
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- Python
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- Scrape tools (bs4, requests)
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- scipy, scikit-learn, scikit-image
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- tensorflow
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- sympy
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- numpy
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- matplotlib
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- pandas
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- manim
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- Octave
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- R
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- Julia
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### As a Server
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Add the following lines and remove ``c.ServerApp.token``. This allows remote access and enables password authentication. **Warning:** be careful. Anyone with access to this server has a shell in your system.
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## TODO
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- Auto dark theme
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- Fix sage
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- GPU support ([source](https://github.com/iot-salzburg/gpu-jupyter))
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- Haskell ([source](https://github.com/IHaskell/ihaskell-notebook))
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- Rust Kernel
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- C++ Kernel
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- Perl Kernel
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- Maxima Kernel
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```python
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c.NotebookApp.allow_remote_access = True
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c.NotebookApp.allow_origin = "*"
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c.ServerApp.ip = "*"
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c.ServerApp.password = u"pwd_str"
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c.ServerApp.open_browser = False
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```
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Passwords can be generated with
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```python
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from jupyter_server.auth import passwd
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passwd()
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```
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@ -75,14 +75,15 @@ ENV CONDA_DIR=/opt/conda \
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ENV PATH="${CONDA_DIR}/bin:${PATH}" \
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HOME="/home/${NB_USER}"
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# Copy a script that we will use to correct permissions after running certain commands
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# A script that we will use to correct permissions after running certain commands
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COPY fix-permissions.sh /usr/local/bin/fix-permissions
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RUN chmod a+rx /usr/local/bin/fix-permissions
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# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
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RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
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# Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
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echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc
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echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc && \
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echo "export PATH=${CONDA_DIR}/bin:\$PATH" >> /etc/skel/.bashrc
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# Create user
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RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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@ -103,7 +104,6 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
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USER ${NB_UID}
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# Pin python version here, or set it to "default"
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ARG PYTHON_VERSION=3.10
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@ -184,14 +184,6 @@ RUN mkdir -p "${HOME}/.jupyter" && \
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chmod u+rwx "${HOME}/.jupyter"
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VOLUME "${HOME}/.jupyter"
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# Legacy for Jupyter Notebook Server, see: [#1205](https://github.com/jupyter/docker-stacks/issues/1205)
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#RUN sed -re "s/c.ServerApp/c.NotebookApp/g" \
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# /etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && \
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# fix-permissions /etc/jupyter/
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# HEALTHCHECK documentation: https://docs.docker.com/engine/reference/builder/#healthcheck
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# This healtcheck works well for `lab`, `notebook`, `nbclassic`, `server` and `retro` jupyter commands
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# https://github.com/jupyter/docker-stacks/issues/915#issuecomment-1068528799
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HEALTHCHECK --interval=15s --timeout=3s --start-period=5s --retries=3 \
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CMD wget -O- --no-verbose --tries=1 --no-check-certificate \
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http${GEN_CERT:+s}://localhost:8888${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1
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@ -2,9 +2,8 @@ import os
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import stat
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import subprocess
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from jupyter_core.paths import jupyter_data_dir
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c = get_config() # noqa: F821
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c.ServerApp.ip = "0.0.0.0"
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c.ServerApp.port = 8888
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c.ServerApp.open_browser = False
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@ -16,42 +15,6 @@ c.InlineBackend.figure_formats = {"png", "jpeg", "svg", "pdf"}
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# https://github.com/jupyter/notebook/issues/3130
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c.FileContentsManager.delete_to_trash = False
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# Generate a self-signed certificate
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OPENSSL_CONFIG = """\
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[req]
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distinguished_name = req_distinguished_name
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[req_distinguished_name]
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"""
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if "GEN_CERT" in os.environ:
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dir_name = jupyter_data_dir()
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pem_file = os.path.join(dir_name, "notebook.pem")
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os.makedirs(dir_name, exist_ok=True)
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# Generate an openssl.cnf file to set the distinguished name
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cnf_file = os.path.join(os.getenv("CONDA_DIR", "/usr/lib"), "ssl", "openssl.cnf")
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if not os.path.isfile(cnf_file):
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with open(cnf_file, "w") as fh:
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fh.write(OPENSSL_CONFIG)
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# Generate a certificate if one doesn't exist on disk
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subprocess.check_call(
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[
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"openssl",
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"req",
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"-new",
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"-newkey=rsa:2048",
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"-days=365",
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"-nodes",
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"-x509",
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"-subj=/C=XX/ST=XX/L=XX/O=generated/CN=generated",
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f"-keyout={pem_file}",
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f"-out={pem_file}",
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]
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)
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# Restrict access to the file
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os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
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c.ServerApp.certfile = pem_file
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# Change default umask for all subprocesses of the notebook server if set in
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# the environment
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if "NB_UMASK" in os.environ:
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@ -5,7 +5,8 @@ set is_quiet true
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set root_dir "."
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function build_image
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# First argument: (optional) remove parent image? (true or false)
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# First argument: remove parent image?
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# true or false, optional, default is false
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# Second argument: file name to build
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# Parse arguments
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@ -13,7 +14,7 @@ function build_image
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set remove_previous $argv[1]
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set build_file $argv[2]
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else if test (count $argv) -eq 1
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set remove_previous true
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set remove_previous false
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set build_file $argv[1]
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end
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@ -41,7 +42,7 @@ end
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date "+Build started at %Y-%m-%d %T"
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echo ""
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# Base image MUST be built first
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# Base image must be built first
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printf "Building base image...\n"
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docker build \
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--quiet=$is_quiet \
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@ -52,17 +53,17 @@ printf "Done. \n\n"
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build_image false octave
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build_image false r
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build_image false julia
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#build_image false sage (BROKEN)
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build_image octave
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build_image r
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build_image julia
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#build_image sage (BROKEN)
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build_image false plugins
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build_image false pymodules
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build_image plugins
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build_image pymodules
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# Manim will not install under python 3.10.
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# 3.9 works (see arguments for base above)
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#build_image false manim
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#build_image manim
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@ -13,7 +13,6 @@ RUN mamba install --yes \
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"requests" \
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"schedule" \
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# ML and Data
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"tensorflow" \
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"scikit-image" \
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"scikit-learn" \
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"scipy" \
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@ -54,34 +53,7 @@ RUN mamba install --yes \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Import matplotlib the first time to build the font cache.
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# Import matplotlib once to build the font cache.
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ENV XDG_CACHE_HOME="/home/${NB_USER}/.cache/"
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RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" && \
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fix-permissions "/home/${NB_USER}"
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#FROM pymodules as selenium
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#USER ${NB_UID}
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#
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#RUN mamba install --yes \
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# "selenium" \
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# && \
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# # Cleanup
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# mamba clean --all -f -y && \
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# npm cache clean --force && \
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# jupyter lab clean && \
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# rm -rf "/home/${NB_USER}/.cache/yarn" && \
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# fix-permissions "${CONDA_DIR}" && \
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# fix-permissions "/home/${NB_USER}"
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#
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## Install google chrome
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#RUN wget -q -O - https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add -
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#RUN sh -c 'echo "deb [arch=amd64] http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/#sources.list.d/google-chrome.list'
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#RUN apt-get -y update
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#RUN apt-get install -y google-chrome-stable
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#
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## Install chromedriver
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#RUN apt-get install -yqq unzip
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#RUN wget -O /tmp/chromedriver.zip http://chromedriver.storage.googleapis.com/`curl -sS #chromedriver.storage.googleapis.com/LATEST_RELEASE`/chromedriver_linux64.zip
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#RUN unzip /tmp/chromedriver.zip chromedriver -d /usr/local/bin/
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fix-permissions "/home/${NB_USER}"
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@ -15,7 +15,7 @@ services:
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- "127.0.0.1:8888:8888"
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# Allow GPU access.
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# Requires nvidia-containter-toolkit
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# Requires nvidia-container-toolkit
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deploy:
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resources:
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reservations:
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