misantamaria commited on
Commit
2440321
·
1 Parent(s): d01b1f1
README.md CHANGED
@@ -1,5 +1,4 @@
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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
@@ -7,14 +6,17 @@ colorTo: pink
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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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  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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  ---
 
2
  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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+
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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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+ ---
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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
docker/.env DELETED
@@ -1,29 +0,0 @@
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- # The name of the docker-compose project
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- COMPOSE_PROJECT_NAME=dvats
3
- # The user ID you are using to run docker-compose
4
- USER_ID=1004
5
- # The group ID you are using to run docker-compose (you can get it with id -g in a terminal)
6
- GROUP_ID=1004
7
- # The user name assigned to the user id
8
- USER_NAME=yourusername
9
- # The port from which you want to access Jupyter lab
10
- JUPYTER_PORT=7861
11
- # The token used to access (like a password)
12
- JUPYTER_TOKEN=password
13
- # The path toz your data files to train/test the models
14
- LOCAL_DATA_PATH=/home/yourusername/work_dir
15
- # The W&B entity
16
- WANDB_ENTITY=youruser
17
- # The W&B project
18
- WANDB_PROJECT=deepvats
19
- # The W&B personal API key (see https://wandb.ai/authorize)
20
- WANDB_API_KEY=yourkey
21
- # List of comma separated GPU indices that will be available in the container (by default only 0, the first one)
22
- CUDA_VISIBLE_DEVICES=0,1,2,3
23
- # Github PAT (see https://docs.github.com/en/github/authenticating-to-github/keeping-your-account-and>
24
- GH_TOKEN=yourtoken
25
- # Port in which you want Rstudio server to be deployed (for developing in the front end)
26
- RSTUDIO_PORT=7862
27
- # Password to access the Rstudio server
28
- RSTUDIO_PASSWD=password
29
-
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
docker/DESCRIPTION DELETED
@@ -1,18 +0,0 @@
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- Depends:
2
- R (>= 3.6.0),
3
- shiny,
4
- pals,
5
- shinyWidgets,
6
- dygraphs,
7
- shinycssloaders,
8
- shinyjs,
9
- Rcpp,
10
- reactlog,
11
- feather,
12
- fasttime,
13
- zoo,
14
- reticulate,
15
- xts
16
- Remotes:
17
- r-lib/later,
18
- apache/arrow/r
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
docker/Dockerfile.jupyter DELETED
@@ -1,146 +0,0 @@
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- #############################
2
- # JUPYTER VOLUME DOCKERFILE #
3
- #***************************#
4
- # Set up a jupyter-lab for #
5
- # developing using deepvats #
6
- #############################
7
- ##############
8
- # Base image #
9
- ##############
10
- ##--- Setup Ubuntu
11
- ARG CUDA_VERSION
12
- FROM nvidia/cuda:${CUDA_VERSION}
13
-
14
- #--- Tags
15
- LABEL maintainer="vrodriguezf <victor.rfernandez@upm.es>"
16
- LABEL cuda_version=${CUDA_VERSION}
17
- LABEL log_path=${log_path}
18
- ##---Initialize bash
19
- LABEL cuda_version=${CUDA_VERSION}
20
-
21
- RUN echo "Cuda version: $CUDA_VERSION"
22
- ##---Initialize bash
23
- SHELL [ "/bin/bash", "--login", "-c" ]
24
-
25
- ##################
26
- # Packages setup #
27
- ##################
28
- #TODO: Automatizar que lo coja de /etc/timezone
29
- #Only neccesary for libarchive & libtiff if error appears
30
- ARG TZ=Etc/UTC
31
-
32
- RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone \
33
- && apt-get update --fix-missing \
34
- #if errors with libtiff library
35
- #&& apt-get install -y wget bzip2 curl git sudo libarchive-dev libtiff5-dev \
36
- && apt-get install -y wget bzip2 curl git sudo libarchive-dev libtiff5-dev zsh\
37
- #Otherwise
38
- # && apt-get install -y wget bzip2 curl git sudo \
39
- && apt-get clean \
40
- && rm -rf /var/lib/apt/lists/*
41
-
42
- #-- Environmental variables for wandb
43
- ENV LC_ALL=C.UTF-8 \
44
- LANG=C.UTF-8
45
-
46
- ########################
47
- # Create non-root user #
48
- ########################
49
- ARG username=user\
50
- uid=1000 \
51
- gid=1000
52
- ENV USER=$username \
53
- UID=$uid \
54
- GID=$gid
55
- ENV HOME=/home/$USER
56
-
57
- #-- Passwordless sudo (TODO: mv to root section)
58
- RUN addgroup --gid $GID $USER \
59
- && adduser --disabled-password \
60
- --gecos "Non-root user" \
61
- --uid $UID \
62
- --gid $GID \
63
- --home $HOME $USER\
64
- && echo "$USER ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
65
- #-- Move to user
66
- USER $USER
67
-
68
- # Add the jupyterlab settings
69
- COPY --chown=$uid:$gid docker/jupyter_config $HOME/.jupyter
70
- #####################
71
- # Install miniconda #
72
- #####################
73
-
74
- ENV MINICONDA_VERSION=4.10.3 \
75
- #ENV MINICONDA_VERSION=23.9.0 \
76
- CONDA_DIR=$HOME/miniconda3 \
77
- # Make non-activate conda commands available
78
- PATH=$CONDA_DIR/bin:$PATH \
79
- PROJECT_DIR=$HOME
80
-
81
- RUN echo "HOME: ${HOME} | CONDA_DIR = ${CONDA_DIR}" \
82
- #-- Install MINICONDA
83
- && wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py38_$MINICONDA_VERSION-Linux-x86_64.sh -O ~/miniconda.sh \
84
- && chmod +x ~/miniconda.sh \
85
- && ~/miniconda.sh -b -p $CONDA_DIR \
86
- && rm ~/miniconda.sh
87
-
88
- # Make conda activate command available from /bin/bash --login shells
89
- RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.profile
90
- # make conda activate command available from /bin/bash --interative shells
91
- RUN conda init bash \
92
- # create a project directory inside user home
93
- && mkdir -p $PROJECT_DIR
94
-
95
- WORKDIR $PROJECT_DIR
96
- ##########################
97
- # Install & update MAMBA #
98
- ##########################
99
- ENV ENV_PREFIX $PROJECT_DIR/env
100
- RUN conda install --name base --channel conda-forge mamba \
101
- && mamba update --name base --channel defaults conda
102
- #-- Build the mamba environment
103
- RUN mamba install conda-lock -c conda-forge
104
- COPY --chown=$UID:$GID docker/environment.yml docker/requirements.txt /tmp/
105
- #RUN mamba lock -f /tmp/environment.yml --lockfile /tmp/environment.lock
106
- #RUN mamba create --prefix ${ENV_PREFIX} --file /tmp/environment.lock
107
- RUN mamba env create --prefix ${ENV_PREFIX} --file /tmp/environment.yml
108
- RUN conda clean --all --yes
109
-
110
- # run the postBuild script to install the JupyterLab extensions
111
- COPY --chown=$UID:$GID docker/postBuild /usr/local/bin
112
- RUN chmod u+x /usr/local/bin/postBuild \
113
- && conda activate $ENV_PREFIX \
114
- && /usr/local/bin/postBuild \
115
- && conda deactivate \
116
- # Make bash automatically activate the conda environment
117
- && echo "conda activate $ENV_PREFIX" >> ~/.bashrc
118
- RUN chmod u+x /usr/local/bin/postBuild \
119
- && conda activate $ENV_PREFIX \
120
- && /usr/local/bin/postBuild \
121
- && conda deactivate \
122
- # Make bash automatically activate the conda environment
123
- && echo "conda activate $ENV_PREFIX" >> ~/.bashrc
124
-
125
-
126
- #####################################################
127
- # Install external libraries not available in conda #
128
- #####################################################
129
- RUN chmod u+x /usr/local/bin/postBuild \
130
- && conda activate $ENV_PREFIX \
131
- && pip install zennit==0.5.1 \
132
- && conda deactivate
133
-
134
- RUN conda list --prefix ${ENV_PREFIX}
135
-
136
- COPY --chown=$UID:$GID docker/entrypoint.sh /usr/local/bin
137
- RUN chmod u+x /usr/local/bin/entrypoint.sh
138
-
139
-
140
- ENTRYPOINT [ "/usr/local/bin/entrypoint.sh" ]
141
-
142
- ARG JUPYTER_TOKEN
143
- ENV JUPYTER_TOKEN=${JUPYTER_TOKEN}
144
- # default command will be to launch JupyterLab server for development
145
-
146
- CMD ["sh", "-c", "jupyter lab --no-browser --ip 0.0.0.0 --ContentsManager.allow_hidden=True --NotebookApp.token=$JUPYTER_TOKEN"]
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
docker/Dockerfile.rstudio DELETED
@@ -1,83 +0,0 @@
1
- #############################
2
- # RSTUDIO-SERVER #
3
- # VOLUME DOCKERFILE #
4
- #***************************#
5
- # Set up a jupyter-lab for #
6
- # developing using deepvats #
7
- #############################
8
- ##############
9
- # Base image #
10
- ##############
11
- #FROM vrodriguezf/rstudio-server-shiny-development
12
- # Adds rstudio server, tiyverse, devtools to rocker/cuda
13
- FROM rocker/ml:4.2
14
-
15
- SHELL [ "/bin/bash", "--login", "-c" ]
16
-
17
- RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys A4B469963BF863CC
18
- RUN apt-get update
19
- RUN apt-get install -y python3-pip
20
- RUN python3 -m pip install --upgrade pip
21
- RUN apt-get install -y python3-venv libxt-dev
22
- ## Install R packages
23
-
24
- #COPY docker/DESCRIPTION /tmp/
25
- COPY --chown=${UID}:${GID} docker/DESCRIPTION /tmp/
26
-
27
- RUN ls -la /tmp/ && sleep 5
28
-
29
- #RUN R -e "install.packages(deps_path = '/tmp/DESCRIPTION', remotes::dev_package_deps(dependencies = TRUE), repos = NULL)"
30
-
31
- RUN R -e "devtools::install_deps('/tmp/', dependencies = TRUE)"
32
-
33
- #RUN R -e "install.packages(c('shiny', 'pals', 'shinyWidgets', 'dygraphs', 'shinycssloaders', 'shinyjs', 'Rcpp', 'reactlog', 'pals', 'feather', 'fasttime', 'zoo', 'shinyWidgets'))"
34
- #RUN R -e "remotes::install_github('r-lib/later')"
35
- #RUN R -e "remotes::install_github('apache/arrow/r')"
36
-
37
- ## Install reticulate and create virtual environment using default Ubuntu installed Python
38
- #RUN R -e "install.packages('reticulate')"
39
-
40
- ARG USER=user
41
- ARG UID=1000
42
- ARG GID=1000
43
- ENV HOME /home/$USER
44
- ENV ENV_PREFIX $HOME/env
45
-
46
- RUN addgroup --gid $GID $USER
47
- RUN adduser --disabled-password \
48
- --gecos "Non-root user" \
49
- --uid $UID \
50
- --gid $GID \
51
- --home $HOME \
52
- $USER
53
-
54
- RUN adduser $USER sudo
55
- RUN echo "$USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
56
-
57
-
58
- ARG RETICULATE_MINICONDA_PATH=/usr/local/share/r-miniconda
59
- ARG RETICULATE_PYTHON_ENV=/usr/virtualenvs/venv_shiny_app
60
- ENV RETICULATE_PYTHON=${RETICULATE_PYTHON_ENV}/bin/python/
61
-
62
- #RUN R -e "reticulate::virtualenv_create(envname='${RETICULATE_PYTHON_ENV}', python='/usr/bin/python3')"
63
- #RUN R -e "reticulate::virtualenv_install(c('numpy', 'pandas', 'wandb', 'hdbscan'), envname='${RETICULATE_PYTHON_ENV}')"
64
-
65
- RUN echo "RETICULATE_PYTHON_ENV=${RETICULATE_PYTHON_ENV}" >> ${HOME}/.Renviron
66
- RUN echo "RETICULATE_PYTHON=${RETICULATE_PYTHON}" >> ${HOME}/.Renviron
67
-
68
- ## Export W&B environment variable to Rstudio
69
-
70
- ARG WANDB_API_KEY
71
- RUN echo "WANDB_API_KEY=${WANDB_API_KEY}" >> /${HOME}/.Renviron
72
-
73
- # use an entrypoint script to insure conda environment is properly activated at runtime
74
-
75
- COPY --chown=${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}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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:
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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/"
 
 
 
 
 
 
 
 
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
- }
 
 
 
 
 
 
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
- }
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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