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Browse files- README.md +6 -4
- docker/.env +0 -29
- docker/DESCRIPTION +0 -18
- docker/Dockerfile.jupyter +0 -146
- docker/Dockerfile.rstudio +0 -83
- docker/dl_module/.devcontainer/.devcontainer.json +0 -62
- docker/docker-compose.yml +0 -88
- docker/entrypoint-rstudio.sh +0 -25
- docker/entrypoint.sh +0 -10
- docker/environment.yml +0 -73
- docker/get_jupyter_token.sh +0 -7
- docker/ipython_config.py +0 -1
- docker/jupyter_build.logs +0 -0
- docker/jupyter_config/lab/user-settings/@jupyterlab/notebook-extension/tracker.jupyterlab-settings +0 -5
- docker/jupyter_config/lab/user-settings/@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings +0 -90
- docker/jupyter_config/lab/user-settings/@parente/jupyterlab-quickopen/plugin.jupyterlab-settings +0 -23
- docker/port +0 -1
- docker/postBuild +0 -1
- docker/requirements.txt +0 -1
- requirements.txt +3 -0
- run.sh +7 -0
- static/index.html +1 -0
README.md
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---
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<<<<<<< HEAD
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title: Deepvats
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emoji: 🐢
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colorFrom: red
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sdk: docker
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pinned: false
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license: mit
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title: DeepVATS 2024
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emoji:
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colorFrom: green
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colorTo: blue
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sdk: docker
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pinned: false
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>>>>>>> b61f6e4 (initial commit)
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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---
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title: Deepvats
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emoji: 🐢
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colorFrom: red
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sdk: docker
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pinned: false
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license: mit
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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---
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title: DeepVATS 2024
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emoji: 🐨
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colorFrom: green
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colorTo: blue
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sdk: docker
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pinned: false
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---
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Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
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docker/.env
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# The name of the docker-compose project
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COMPOSE_PROJECT_NAME=dvats
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# The user ID you are using to run docker-compose
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USER_ID=1004
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# The group ID you are using to run docker-compose (you can get it with id -g in a terminal)
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GROUP_ID=1004
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# The user name assigned to the user id
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USER_NAME=yourusername
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# The port from which you want to access Jupyter lab
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JUPYTER_PORT=7861
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# The token used to access (like a password)
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JUPYTER_TOKEN=password
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# The path toz your data files to train/test the models
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LOCAL_DATA_PATH=/home/yourusername/work_dir
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# The W&B entity
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WANDB_ENTITY=youruser
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# The W&B project
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WANDB_PROJECT=deepvats
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# The W&B personal API key (see https://wandb.ai/authorize)
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WANDB_API_KEY=yourkey
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# List of comma separated GPU indices that will be available in the container (by default only 0, the first one)
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CUDA_VISIBLE_DEVICES=0,1,2,3
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# Github PAT (see https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and>
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GH_TOKEN=yourtoken
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# Port in which you want Rstudio server to be deployed (for developing in the front end)
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RSTUDIO_PORT=7862
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# Password to access the Rstudio server
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RSTUDIO_PASSWD=password
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docker/DESCRIPTION
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Depends:
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R (>= 3.6.0),
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shiny,
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pals,
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shinyWidgets,
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dygraphs,
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shinycssloaders,
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shinyjs,
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Rcpp,
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reactlog,
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feather,
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fasttime,
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zoo,
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reticulate,
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xts
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Remotes:
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r-lib/later,
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apache/arrow/r
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docker/Dockerfile.jupyter
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#############################
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# JUPYTER VOLUME DOCKERFILE #
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#***************************#
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# Set up a jupyter-lab for #
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# developing using deepvats #
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#############################
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##############
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# Base image #
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##############
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##--- Setup Ubuntu
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ARG CUDA_VERSION
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FROM nvidia/cuda:${CUDA_VERSION}
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#--- Tags
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LABEL maintainer="vrodriguezf <victor.rfernandez@upm.es>"
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LABEL cuda_version=${CUDA_VERSION}
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LABEL log_path=${log_path}
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##---Initialize bash
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LABEL cuda_version=${CUDA_VERSION}
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RUN echo "Cuda version: $CUDA_VERSION"
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##---Initialize bash
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SHELL [ "/bin/bash", "--login", "-c" ]
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##################
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# Packages setup #
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##################
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#TODO: Automatizar que lo coja de /etc/timezone
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#Only neccesary for libarchive & libtiff if error appears
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ARG TZ=Etc/UTC
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RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone \
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&& apt-get update --fix-missing \
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#if errors with libtiff library
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#&& apt-get install -y wget bzip2 curl git sudo libarchive-dev libtiff5-dev \
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&& apt-get install -y wget bzip2 curl git sudo libarchive-dev libtiff5-dev zsh\
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#Otherwise
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# && apt-get install -y wget bzip2 curl git sudo \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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-
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#-- Environmental variables for wandb
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ENV LC_ALL=C.UTF-8 \
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LANG=C.UTF-8
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-
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########################
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# Create non-root user #
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########################
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ARG username=user\
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uid=1000 \
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gid=1000
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ENV USER=$username \
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UID=$uid \
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GID=$gid
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ENV HOME=/home/$USER
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#-- Passwordless sudo (TODO: mv to root section)
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RUN addgroup --gid $GID $USER \
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&& adduser --disabled-password \
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--gecos "Non-root user" \
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--uid $UID \
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--gid $GID \
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--home $HOME $USER\
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&& echo "$USER ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
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#-- Move to user
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USER $USER
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# Add the jupyterlab settings
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COPY --chown=$uid:$gid docker/jupyter_config $HOME/.jupyter
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#####################
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# Install miniconda #
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#####################
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ENV MINICONDA_VERSION=4.10.3 \
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#ENV MINICONDA_VERSION=23.9.0 \
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CONDA_DIR=$HOME/miniconda3 \
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# Make non-activate conda commands available
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PATH=$CONDA_DIR/bin:$PATH \
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PROJECT_DIR=$HOME
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RUN echo "HOME: ${HOME} | CONDA_DIR = ${CONDA_DIR}" \
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#-- Install MINICONDA
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&& wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh -O ~/miniconda.sh \
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&& chmod +x ~/miniconda.sh \
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&& ~/miniconda.sh -b -p $CONDA_DIR \
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&& rm ~/miniconda.sh
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# Make conda activate command available from /bin/bash --login shells
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RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile
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# make conda activate command available from /bin/bash --interative shells
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RUN conda init bash \
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# create a project directory inside user home
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&& mkdir -p $PROJECT_DIR
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WORKDIR $PROJECT_DIR
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##########################
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# Install & update MAMBA #
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##########################
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ENV ENV_PREFIX $PROJECT_DIR/env
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RUN conda install --name base --channel conda-forge mamba \
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&& mamba update --name base --channel defaults conda
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#-- Build the mamba environment
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RUN mamba install conda-lock -c conda-forge
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COPY --chown=$UID:$GID docker/environment.yml docker/requirements.txt /tmp/
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#RUN mamba lock -f /tmp/environment.yml --lockfile /tmp/environment.lock
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#RUN mamba create --prefix ${ENV_PREFIX} --file /tmp/environment.lock
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RUN mamba env create --prefix ${ENV_PREFIX} --file /tmp/environment.yml
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RUN conda clean --all --yes
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# run the postBuild script to install the JupyterLab extensions
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COPY --chown=$UID:$GID docker/postBuild /usr/local/bin
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RUN chmod u+x /usr/local/bin/postBuild \
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&& conda activate $ENV_PREFIX \
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&& /usr/local/bin/postBuild \
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&& conda deactivate \
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# Make bash automatically activate the conda environment
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&& echo "conda activate $ENV_PREFIX" >> ~/.bashrc
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RUN chmod u+x /usr/local/bin/postBuild \
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&& conda activate $ENV_PREFIX \
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&& /usr/local/bin/postBuild \
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&& conda deactivate \
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# Make bash automatically activate the conda environment
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&& echo "conda activate $ENV_PREFIX" >> ~/.bashrc
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#####################################################
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# Install external libraries not available in conda #
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#####################################################
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RUN chmod u+x /usr/local/bin/postBuild \
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&& conda activate $ENV_PREFIX \
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&& pip install zennit==0.5.1 \
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&& conda deactivate
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RUN conda list --prefix ${ENV_PREFIX}
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COPY --chown=$UID:$GID docker/entrypoint.sh /usr/local/bin
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RUN chmod u+x /usr/local/bin/entrypoint.sh
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ENTRYPOINT [ "/usr/local/bin/entrypoint.sh" ]
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ARG JUPYTER_TOKEN
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ENV JUPYTER_TOKEN=${JUPYTER_TOKEN}
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# default command will be to launch JupyterLab server for development
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CMD ["sh", "-c", "jupyter lab --no-browser --ip 0.0.0.0 --ContentsManager.allow_hidden=True --NotebookApp.token=$JUPYTER_TOKEN"]
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docker/Dockerfile.rstudio
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#############################
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# RSTUDIO-SERVER #
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# VOLUME DOCKERFILE #
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#***************************#
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# Set up a jupyter-lab for #
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# developing using deepvats #
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#############################
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##############
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# Base image #
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##############
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#FROM vrodriguezf/rstudio-server-shiny-development
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# Adds rstudio server, tiyverse, devtools to rocker/cuda
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FROM rocker/ml:4.2
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SHELL [ "/bin/bash", "--login", "-c" ]
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RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC
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RUN apt-get update
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RUN apt-get install -y python3-pip
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RUN python3 -m pip install --upgrade pip
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RUN apt-get install -y python3-venv libxt-dev
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## Install R packages
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#COPY docker/DESCRIPTION /tmp/
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COPY --chown=${UID}:${GID} docker/DESCRIPTION /tmp/
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RUN ls -la /tmp/ && sleep 5
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#RUN R -e "install.packages(deps_path = '/tmp/DESCRIPTION', remotes::dev_package_deps(dependencies = TRUE), repos = NULL)"
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RUN R -e "devtools::install_deps('/tmp/', dependencies = TRUE)"
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#RUN R -e "install.packages(c('shiny', 'pals', 'shinyWidgets', 'dygraphs', 'shinycssloaders', 'shinyjs', 'Rcpp', 'reactlog', 'pals', 'feather', 'fasttime', 'zoo', 'shinyWidgets'))"
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#RUN R -e "remotes::install_github('r-lib/later')"
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#RUN R -e "remotes::install_github('apache/arrow/r')"
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## Install reticulate and create virtual environment using default Ubuntu installed Python
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#RUN R -e "install.packages('reticulate')"
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-
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ARG USER=user
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ARG UID=1000
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ARG GID=1000
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ENV HOME /home/$USER
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ENV ENV_PREFIX $HOME/env
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-
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RUN addgroup --gid $GID $USER
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RUN adduser --disabled-password \
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--gecos "Non-root user" \
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--uid $UID \
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--gid $GID \
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--home $HOME \
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$USER
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-
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RUN adduser $USER sudo
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RUN echo "$USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
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-
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-
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ARG RETICULATE_MINICONDA_PATH=/usr/local/share/r-miniconda
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ARG RETICULATE_PYTHON_ENV=/usr/virtualenvs/venv_shiny_app
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ENV RETICULATE_PYTHON=${RETICULATE_PYTHON_ENV}/bin/python/
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-
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#RUN R -e "reticulate::virtualenv_create(envname='${RETICULATE_PYTHON_ENV}', python='/usr/bin/python3')"
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#RUN R -e "reticulate::virtualenv_install(c('numpy', 'pandas', 'wandb', 'hdbscan'), envname='${RETICULATE_PYTHON_ENV}')"
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-
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RUN echo "RETICULATE_PYTHON_ENV=${RETICULATE_PYTHON_ENV}" >> ${HOME}/.Renviron
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RUN echo "RETICULATE_PYTHON=${RETICULATE_PYTHON}" >> ${HOME}/.Renviron
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-
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## Export W&B environment variable to Rstudio
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-
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ARG WANDB_API_KEY
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RUN echo "WANDB_API_KEY=${WANDB_API_KEY}" >> /${HOME}/.Renviron
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-
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# use an entrypoint script to insure conda environment is properly activated at runtime
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-
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75 |
-
COPY --chown=${UID}:${GID} docker/entrypoint-rstudio.sh /usr/local/bin
|
76 |
-
RUN chmod u+x /usr/local/bin/entrypoint-rstudio.sh
|
77 |
-
ENTRYPOINT [ "/usr/local/bin/entrypoint-rstudio.sh" ]
|
78 |
-
|
79 |
-
# Rewrite the miniconda path environment in case it has been redefined in the compose file
|
80 |
-
RUN echo "RETICULATE_MINICONDA_PATH=${RETICULATE_MINICONDA_PATH}" >> ${HOME}/.Renviron
|
81 |
-
|
82 |
-
# make non-activate conda commands available
|
83 |
-
ENV PATH=${RETICULATE_MINICONDA_PATH}/bin:${PATH}
|
|
|
|
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|
|
|
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|
docker/dl_module/.devcontainer/.devcontainer.json
DELETED
@@ -1,62 +0,0 @@
|
|
1 |
-
// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
|
2 |
-
// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/python-3
|
3 |
-
{
|
4 |
-
"name": "Deep Learning Module (backend)",
|
5 |
-
"dockerComposeFile": ["../../docker-compose.yml"],
|
6 |
-
"service": "jupyter",
|
7 |
-
//"workspaceFolder": "/workspace/frontend", // TODO: What does this do?
|
8 |
-
// Configure tool-specific properties.
|
9 |
-
"customizations": {
|
10 |
-
// Configure properties specific to VS Code.
|
11 |
-
"vscode": {
|
12 |
-
// Set *default* container specific settings.json values on container create.
|
13 |
-
"settings": {
|
14 |
-
"python.defaultInterpreterPath": "/usr/local/bin/python",
|
15 |
-
"python.linting.enabled": true,
|
16 |
-
"python.linting.pylintEnabled": true,
|
17 |
-
"python.formatting.autopep8Path": "/usr/local/py-utils/bin/autopep8",
|
18 |
-
"python.formatting.blackPath": "/usr/local/py-utils/bin/black",
|
19 |
-
"python.formatting.yapfPath": "/usr/local/py-utils/bin/yapf",
|
20 |
-
"python.linting.banditPath": "/usr/local/py-utils/bin/bandit",
|
21 |
-
"python.linting.flake8Path": "/usr/local/py-utils/bin/flake8",
|
22 |
-
"python.linting.mypyPath": "/usr/local/py-utils/bin/mypy",
|
23 |
-
"python.linting.pycodestylePath": "/usr/local/py-utils/bin/pycodestyle",
|
24 |
-
"python.linting.pydocstylePath": "/usr/local/py-utils/bin/pydocstyle",
|
25 |
-
"python.linting.pylintPath": "/usr/local/py-utils/bin/pylint"
|
26 |
-
},
|
27 |
-
|
28 |
-
// Add the IDs of extensions you want installed when the container is created.
|
29 |
-
"extensions": [
|
30 |
-
"ms-python.python",
|
31 |
-
"ms-python.vscode-pylance",
|
32 |
-
"ms-toolsai.jupyter",
|
33 |
-
"github.copilot",
|
34 |
-
"genieai.chatgpt-vscode",
|
35 |
-
"run-ai.vscode-genv"
|
36 |
-
]
|
37 |
-
}
|
38 |
-
},
|
39 |
-
|
40 |
-
// Use 'forwardPorts' to make a list of ports inside the container available locally.
|
41 |
-
// "forwardPorts": [],
|
42 |
-
|
43 |
-
// Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root.
|
44 |
-
"remoteUser": "victor",
|
45 |
-
"features": {
|
46 |
-
"git": "latest",
|
47 |
-
"ghcr.io/meaningful-ooo/devcontainer-features/fish:1": {},
|
48 |
-
"ghcr.io/devcontainers/features/python:1": {
|
49 |
-
"installTools": false, // TODO: Enabling this causes the container to fail to build
|
50 |
-
"installJupyterlab": true
|
51 |
-
}
|
52 |
-
// This should be by default given by the compose file
|
53 |
-
// "ghcr.io/devcontainers/features/nvidia-cuda:1": {
|
54 |
-
// "installCudnn": true
|
55 |
-
// }
|
56 |
-
},
|
57 |
-
"runArgs": ["--env-file", "../.env"]
|
58 |
-
//"runArgs": ["--env-file", ".devcontainer/devcontainer.env", "--gpus", "all"] // For machines with GPUs
|
59 |
-
|
60 |
-
// Use 'postCreateCommand' to run commands after the container is created.
|
61 |
-
//"postCreateCommand": "pip install --user -r requirements.txt"
|
62 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
docker/docker-compose.yml
DELETED
@@ -1,88 +0,0 @@
|
|
1 |
-
services:
|
2 |
-
jupyter:
|
3 |
-
build:
|
4 |
-
args:
|
5 |
-
- username=${USER_NAME}
|
6 |
-
- uid=${USER_ID}
|
7 |
-
- gid=${GROUP_ID}
|
8 |
-
- CUDA_VERSION=12.2.0-devel-ubuntu20.04
|
9 |
-
- JUPYTER_TOKEN=${JUPYTER_TOKEN}
|
10 |
-
context: ../
|
11 |
-
dockerfile: docker/Dockerfile.jupyter
|
12 |
-
image: dvats-jupyter:12.2.0-devel-ubuntu20.04
|
13 |
-
ports:
|
14 |
-
- "${JUPYTER_PORT}:8888"
|
15 |
-
environment:
|
16 |
-
- WANDB_ENTITY=${WANDB_ENTITY}
|
17 |
-
- WANDB_PROJECT=${WANDB_PROJECT}
|
18 |
-
- WANDB_API_KEY=${WANDB_API_KEY}
|
19 |
-
- GH_TOKEN=${GH_TOKEN}
|
20 |
-
- CUDA_VISIBLE_DEVICES=${CUDA_VISIBLE_DEVICES}
|
21 |
-
- WANDB_DIR=/home/${USER_NAME}/work
|
22 |
-
- JUPYTER_TOKEN=${JUPYTER_TOKEN}
|
23 |
-
volumes:
|
24 |
-
- ../:/home/${USER}/work
|
25 |
-
- ${LOCAL_DATA_PATH}:/home/${USER_NAME}/data/
|
26 |
-
- conda-env:/home/${USER_NAME}/env
|
27 |
-
- miniconda:/home/${USER_NAME}/miniconda3
|
28 |
-
- lib:/home/${USER_NAME}/lib
|
29 |
-
init: true
|
30 |
-
stdin_open: true
|
31 |
-
tty: true
|
32 |
-
deploy:
|
33 |
-
resources:
|
34 |
-
reservations:
|
35 |
-
devices:
|
36 |
-
- driver: nvidia
|
37 |
-
count: all
|
38 |
-
capabilities: [gpu]
|
39 |
-
|
40 |
-
rstudio-server:
|
41 |
-
build:
|
42 |
-
context: ../
|
43 |
-
dockerfile: docker/Dockerfile.rstudio
|
44 |
-
args:
|
45 |
-
- WANDB_API_KEY=${WANDB_API_KEY} #
|
46 |
-
- RETICULATE_PYTHON_ENV=/home/${USER_NAME}/env
|
47 |
-
- RETICULATE_MINICONDA_PATH=/home/${USER_NAME}/miniconda3
|
48 |
-
- USER=${USER_NAME} #*
|
49 |
-
- UID=${USER_ID} #*
|
50 |
-
- GID=${GROUP_ID} #*
|
51 |
-
image: dvats-r:rocker-ml_4.2
|
52 |
-
ports:
|
53 |
-
- "${RSTUDIO_PORT}:8787" #*
|
54 |
-
environment:
|
55 |
-
- WANDB_ENTITY=${WANDB_ENTITY}
|
56 |
-
- WANDB_PROJECT=${WANDB_PROJECT}
|
57 |
-
- USER=${USER_NAME} #*
|
58 |
-
- USERID=${USER_ID} #*
|
59 |
-
- GROUPID=${GROUP_ID} #*
|
60 |
-
- PASSWORD=${RSTUDIO_PASSWD} #*
|
61 |
-
- ROOT=FALSE
|
62 |
-
- CUDA_VISIBLE_DEVICES=0,1,2
|
63 |
-
#- CUDA_VISIBLE_DEVICES=1
|
64 |
-
# - CUDA_VISIBLE_DEVICES=${CUDA_VISIBLE_DEVICES}
|
65 |
-
- GH_TOKEN=${GH_TOKEN} #*
|
66 |
-
# TODO (28/03/2023): I don't know why it is not working without this
|
67 |
-
- ENV_VARS=WANDB_ENTITY,WANDB_PROJECT,USER,USERID,GROUPID,PASSWORD,ROOT,CUDA_VISIBLE_DEVICES
|
68 |
-
volumes:
|
69 |
-
- ../r_shiny_app:/home/${USER_NAME}/app #*
|
70 |
-
- ${LOCAL_DATA_PATH}:/home/${USER_NAME}/data/ #*
|
71 |
-
- ../dvats:/home/${USER_NAME}/dvats
|
72 |
-
- conda-env:/home/${USER_NAME}/env
|
73 |
-
- miniconda:/home/${USER_NAME}/miniconda3 #:ro
|
74 |
-
- lib:/home/${USER_NAME}/lib
|
75 |
-
deploy:
|
76 |
-
resources:
|
77 |
-
#limits:
|
78 |
-
#cpus: '0.75'
|
79 |
-
reservations:
|
80 |
-
devices:
|
81 |
-
- driver: nvidia
|
82 |
-
count: all
|
83 |
-
capabilities: [gpu]
|
84 |
-
|
85 |
-
volumes:
|
86 |
-
conda-env:
|
87 |
-
miniconda:
|
88 |
-
lib:
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
docker/entrypoint-rstudio.sh
DELETED
@@ -1,25 +0,0 @@
|
|
1 |
-
#!/bin/bash --login
|
2 |
-
set -e
|
3 |
-
|
4 |
-
echo ". ${HOME}/miniconda3/etc/profile.d/conda.sh" >> ${HOME}/.bashrc
|
5 |
-
# Make bash automatically activate the conda environment
|
6 |
-
echo "conda activate ${ENV_PREFIX}" >> ~/.bashrc
|
7 |
-
#echo "export WANDB_ENTITY=${WANDB_ENTITY:-default}" >> ${HOME}/.bashrc
|
8 |
-
# echo "WANDB_ENTITY=${WANDB_ENTITY:-default}" >> ${HOME}/.Renviron
|
9 |
-
|
10 |
-
# Define an array of environment variable names from the ENV_VARS Compose variable
|
11 |
-
IFS=',' read -ra ENV_VAR_NAMES <<< "$ENV_VARS"
|
12 |
-
|
13 |
-
echo "ENV_VAR_NAMES=${ENV_VAR_NAMES[@]}"
|
14 |
-
|
15 |
-
# Loop through the array of environment variable names and set the variables
|
16 |
-
for ENV_VAR_NAME in "${ENV_VAR_NAMES[@]}"; do
|
17 |
-
ENV_VAR_VALUE="${!ENV_VAR_NAME:-default}"
|
18 |
-
echo "$ENV_VAR_NAME=$ENV_VAR_VALUE" >> ${HOME}/.Renviron
|
19 |
-
done
|
20 |
-
|
21 |
-
ulimit -s 16384
|
22 |
-
|
23 |
-
# start rstudio server
|
24 |
-
/init
|
25 |
-
exec "$@"
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
docker/entrypoint.sh
DELETED
@@ -1,10 +0,0 @@
|
|
1 |
-
#!/bin/bash --login
|
2 |
-
set -e
|
3 |
-
echo $ENV_PREFIX
|
4 |
-
conda activate $ENV_PREFIX
|
5 |
-
conda list
|
6 |
-
pip install -e /home/$USER/work
|
7 |
-
|
8 |
-
|
9 |
-
|
10 |
-
exec "$@"
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
docker/environment.yml
DELETED
@@ -1,73 +0,0 @@
|
|
1 |
-
name: dvats_env
|
2 |
-
channels:
|
3 |
-
#--- Torch & Cuda
|
4 |
-
- pytorch
|
5 |
-
#- nvidia/label/cuda-12.2.0
|
6 |
-
- nvidia
|
7 |
-
#--- Generic
|
8 |
-
- conda-forge
|
9 |
-
- defaults
|
10 |
-
#--- AI
|
11 |
-
- fastai
|
12 |
-
- rapidsai
|
13 |
-
- defaults
|
14 |
-
- conda-forge
|
15 |
-
|
16 |
-
- timeseriesai
|
17 |
-
dependencies:
|
18 |
-
##########################
|
19 |
-
# Generic configurations #
|
20 |
-
##########################
|
21 |
-
- nano=7.2=h8228510_0
|
22 |
-
- git=2.42.0=pl5321h86e50cf_0
|
23 |
-
#--- github
|
24 |
-
- gh=2.37.0=ha8f183a_0
|
25 |
-
#--- Python
|
26 |
-
- python=3.10.13=hd12c33a_0_cpython
|
27 |
-
#WANDB <= 0.15.12 needs this version. See https://github.com/wandb/wandb/issues/6546
|
28 |
-
- ipython=8.16.1=pyh0d859eb_0
|
29 |
-
- pip=23.3.1=pyhd8ed1ab_0
|
30 |
-
- conda-forge::twine=4.0.2=pyhd8ed1ab_0
|
31 |
-
- conda-forge::xeus-python=0.15.10=py310hd41b1e2_1
|
32 |
-
#--- NodeJS
|
33 |
-
- conda-forge::nodejs=20.8.1=h1990674_0
|
34 |
-
#---Jupyter
|
35 |
-
- conda-forge::ipywidgets=8.1.1=pyhd8ed1ab_0
|
36 |
-
- conda-forge::jupyterlab=4.0.7=pyhd8ed1ab_0
|
37 |
-
- conda-forge::jupyterlab-git=0.41.0=pyhd8ed1ab_1
|
38 |
-
- conda-forge::nbclassic=1.0.0=pyhb4ecaf3_1
|
39 |
-
- conda-forge::nbdev=2.2.10=pyhd8ed1ab_0
|
40 |
-
- nbformat>=5.1.3
|
41 |
-
#--- passwords & files
|
42 |
-
- keyrings.alt
|
43 |
-
- platformdirs=2.5.2
|
44 |
-
- conda-forge::keyrings.alt=4.2.0=pyhd8ed1ab_0
|
45 |
-
- psutil>=5.4.8
|
46 |
-
##############
|
47 |
-
# CUDA & GPU #
|
48 |
-
##############
|
49 |
-
- nvidia::cuda-toolkit=11.6=0
|
50 |
-
- rapidsai::cudf=23.02=cuda_11_py310_g5ad4a85b9d_0
|
51 |
-
- rapidsai::cuml=23.02=cuda11_py310_g3356f05bd_0
|
52 |
-
- conda-forge::genv=1.2.0=pyhd8ed1ab_0
|
53 |
-
############
|
54 |
-
# Specific #
|
55 |
-
############
|
56 |
-
#--- Torch
|
57 |
-
- pytorch=1.13=py3.10_cuda11.7_cudnn8.5.0_0
|
58 |
-
#---Graphs & imgs
|
59 |
-
- conda-forge::plotly=5.18.0=pyhd8ed1ab_0
|
60 |
-
- conda-forge::jpeg=9e=h166bdaf_2
|
61 |
-
- conda-forge::seaborn=0.13.0=hd8ed1ab_0
|
62 |
-
- conda-forge::matplotlib=3.8.1=py310hff52083_0
|
63 |
-
#--- IA
|
64 |
-
- conda-forge::hdbscan=0.8.33=py310h1f7b6fc_4
|
65 |
-
- conda-forge::imbalanced-learn>= 0.8.0
|
66 |
-
- conda-forge::pyts >= 0.12.0
|
67 |
-
- conda-forge::umap-learn=0.5.4=py310hff52083_0
|
68 |
-
- conda-forge::scikit-learn=1.2.2=py310hf7d194e_2
|
69 |
-
- conda-forge::wandb=0.14.2=pyhd8ed1ab_0
|
70 |
-
- fastai::fastai>=2.7.9
|
71 |
-
- timeseriesai::tsai
|
72 |
-
- conda-forge::feather-format
|
73 |
-
- conda-forge::python-kaleido #0.2.1
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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docker/get_jupyter_token.sh
DELETED
@@ -1,7 +0,0 @@
|
|
1 |
-
#Para obtener url si no va la contraseña del token
|
2 |
-
ip="127.0.0.1"
|
3 |
-
port=$(hostname | sed -e "s/.*-//")
|
4 |
-
nombre=$port".etsisi.upm.es"
|
5 |
-
puerto_original="8888"
|
6 |
-
puerto_final="8866"
|
7 |
-
docker compose logs jupyter | grep "token=" | tail -n 1 | sed -e "s/$ip/$nombre/" -e "s/$puerto_original/$puerto_final/" | sed "s/.*\(http\)/\1/"
|
|
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docker/ipython_config.py
DELETED
@@ -1 +0,0 @@
|
|
1 |
-
c.Completer.use_jedi = False
|
|
|
|
docker/jupyter_build.logs
DELETED
File without changes
|
docker/jupyter_config/lab/user-settings/@jupyterlab/notebook-extension/tracker.jupyterlab-settings
DELETED
@@ -1,5 +0,0 @@
|
|
1 |
-
{
|
2 |
-
"codeCellConfig": {
|
3 |
-
"rulers": [80]
|
4 |
-
}
|
5 |
-
}
|
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|
docker/jupyter_config/lab/user-settings/@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings
DELETED
@@ -1,90 +0,0 @@
|
|
1 |
-
{
|
2 |
-
"shortcuts": [
|
3 |
-
{
|
4 |
-
"command": "quickopen:activate",
|
5 |
-
"keys": [
|
6 |
-
"Accel ."
|
7 |
-
],
|
8 |
-
"selector": "body",
|
9 |
-
"title": "Activate Quick Open",
|
10 |
-
"category": "Main Area"
|
11 |
-
},
|
12 |
-
{
|
13 |
-
"command": "application:activate-next-tab",
|
14 |
-
"keys": [
|
15 |
-
"Alt ArrowRight"
|
16 |
-
],
|
17 |
-
"selector": "body"
|
18 |
-
},
|
19 |
-
{
|
20 |
-
"command": "application:activate-previous-tab",
|
21 |
-
"keys": [
|
22 |
-
"Alt ArrowLeft"
|
23 |
-
],
|
24 |
-
"selector": "body"
|
25 |
-
},
|
26 |
-
{
|
27 |
-
"command": "notebook:run-all-above",
|
28 |
-
"keys": [
|
29 |
-
"Accel F8"
|
30 |
-
],
|
31 |
-
"selector": ".jp-Notebook:focus"
|
32 |
-
},
|
33 |
-
{
|
34 |
-
"command": "notebook:run-all-below",
|
35 |
-
"keys": [
|
36 |
-
"Accel F10"
|
37 |
-
],
|
38 |
-
"selector": ".jp-Notebook:focus"
|
39 |
-
},
|
40 |
-
{
|
41 |
-
"command": "notebook:run-all-cells",
|
42 |
-
"keys": [
|
43 |
-
"Accel F9"
|
44 |
-
],
|
45 |
-
"selector": ".jp-Notebook:focus"
|
46 |
-
},
|
47 |
-
{
|
48 |
-
"command": "kernelmenu:restart-and-clear",
|
49 |
-
"keys": [
|
50 |
-
"0 0"
|
51 |
-
],
|
52 |
-
"selector": "[data-jp-kernel-user]:focus"
|
53 |
-
},
|
54 |
-
{
|
55 |
-
"command": "notebook:clear-cell-output",
|
56 |
-
"keys": [
|
57 |
-
"Accel o"
|
58 |
-
],
|
59 |
-
"selector": ".jp-Notebook:focus"
|
60 |
-
},
|
61 |
-
{
|
62 |
-
"command": "console:run-forced",
|
63 |
-
"keys": [
|
64 |
-
"Enter"
|
65 |
-
],
|
66 |
-
"selector": ".jp-CodeConsole[data-jp-interaction-mode='notebook'] .jp-CodeConsole-promptCell"
|
67 |
-
},
|
68 |
-
{
|
69 |
-
"command": "console:run-forced",
|
70 |
-
"keys": [
|
71 |
-
"Enter"
|
72 |
-
],
|
73 |
-
"selector": ".jp-CodeConsole[data-jp-interaction-mode='terminal'] .jp-CodeConsole-promptCell"
|
74 |
-
},
|
75 |
-
{
|
76 |
-
"command": "console:linebreak",
|
77 |
-
"keys": [
|
78 |
-
"Accel Enter"
|
79 |
-
],
|
80 |
-
"selector": ".jp-CodeConsole[data-jp-interaction-mode='notebook'] .jp-CodeConsole-promptCell"
|
81 |
-
},
|
82 |
-
{
|
83 |
-
"command": "console:linebreak",
|
84 |
-
"keys": [
|
85 |
-
"Accel Enter"
|
86 |
-
],
|
87 |
-
"selector": ".jp-CodeConsole[data-jp-interaction-mode='terminal'] .jp-CodeConsole-promptCell"
|
88 |
-
}
|
89 |
-
]
|
90 |
-
}
|
|
|
|
|
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|
|
|
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|
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|
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|
|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
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|
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|
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|
|
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|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
docker/jupyter_config/lab/user-settings/@parente/jupyterlab-quickopen/plugin.jupyterlab-settings
DELETED
@@ -1,23 +0,0 @@
|
|
1 |
-
{
|
2 |
-
// Quick Open
|
3 |
-
// @parente/jupyterlab-quickopen:plugin
|
4 |
-
// Quick open panel settings
|
5 |
-
// ************************************
|
6 |
-
|
7 |
-
// Exclude Patterns
|
8 |
-
// File and directory patterns to exclude from the list
|
9 |
-
"excludes": [
|
10 |
-
"env",
|
11 |
-
"miniconda3",
|
12 |
-
"data",
|
13 |
-
"wandb",
|
14 |
-
".*",
|
15 |
-
"node_modules",
|
16 |
-
"__pycache__",
|
17 |
-
"*.egg-info"
|
18 |
-
],
|
19 |
-
|
20 |
-
// Relative Search
|
21 |
-
// Whether to search from currently selected directory
|
22 |
-
"relativeSearch": false
|
23 |
-
}
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
docker/port
DELETED
@@ -1 +0,0 @@
|
|
1 |
-
g4
|
|
|
|
docker/postBuild
DELETED
@@ -1 +0,0 @@
|
|
1 |
-
#jupyter lab build --dev-build=False --minimize=False
|
|
|
|
docker/requirements.txt
DELETED
@@ -1 +0,0 @@
|
|
1 |
-
|
|
|
|
requirements.txt
ADDED
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
1 |
+
gradio==3.23.0
|
2 |
+
uvicorn
|
3 |
+
fastapi
|
run.sh
ADDED
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
#!/bin/bash
|
2 |
+
|
3 |
+
service nginx start
|
4 |
+
python -m http.server --directory ./static --bind 0.0.0.0 8000 & echo $! > http_server.pid
|
5 |
+
uvicorn "app:app" --port 7860 --host 0.0.0.0
|
6 |
+
pkill -F http_server.pid
|
7 |
+
rm http_server.pid
|
static/index.html
ADDED
@@ -0,0 +1 @@
|
|
|
|
|
1 |
+
hello
|