Hugging Face's logo

Spaces:
LudwigO
/
chemprop_example
Paused

App Files Community
1
chemprop_example
File size: 5,061 Bytes
230b005
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
FROM nvidia/cuda:11.3.1-base-ubuntu20.04

ENV DEBIAN_FRONTEND=noninteractive \
        TZ=Europe/Paris

# Remove any third-party apt sources to avoid issues with expiring keys.
# Install some basic utilities
RUN rm -f /etc/apt/sources.list.d/*.list && \
    apt-get update && apt-get install -y --no-install-recommends \
    curl \
    ca-certificates \
    sudo \
    git \
    wget \
    procps \
    git-lfs \
    zip \
    unzip \
    htop \
    vim \
    nano \
    bzip2 \
    libx11-6 \
    build-essential \
    libsndfile-dev \
    software-properties-common \
 && rm -rf /var/lib/apt/lists/*

RUN add-apt-repository ppa:flexiondotorg/nvtop && \
    apt-get upgrade -y && \
    apt-get install -y --no-install-recommends nvtop

RUN curl -sL https://deb.nodesource.com/setup_14.x  | bash - && \
    apt-get install -y nodejs && \
    npm install -g configurable-http-proxy

# Create a working directory
WORKDIR /app

# Create a non-root user and switch to it
RUN adduser --disabled-password --gecos '' --shell /bin/bash user \
 && chown -R user:user /app
RUN echo "user ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/90-user
USER user

# All users can use /home/user as their home directory
ENV HOME=/home/user
RUN mkdir $HOME/.cache $HOME/.config \
 && chmod -R 777 $HOME

# Set up the Conda environment
ENV CONDA_AUTO_UPDATE_CONDA=false \
    PATH=$HOME/miniconda/bin:$PATH
RUN curl -sLo ~/miniconda.sh https://repo.continuum.io/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh \
 && chmod +x ~/miniconda.sh \
 && ~/miniconda.sh -b -p ~/miniconda \
 && rm ~/miniconda.sh \
 && conda clean -ya

WORKDIR $HOME/app

#######################################
# Start root user section
#######################################

USER root

# User Debian packages
## Security warning : Potential user code executed as root (build time)
RUN --mount=target=/root/packages.txt,source=packages.txt \
    apt-get update && \
    xargs -r -a /root/packages.txt apt-get install -y --no-install-recommends \
    && rm -rf /var/lib/apt/lists/*

RUN --mount=target=/root/on_startup.sh,source=on_startup.sh,readwrite \
        bash /root/on_startup.sh

RUN mkdir /data && chown user:user /data

#######################################
# End root user section
#######################################

USER user

# Pull chemprop from github
RUN git clone https://github.com/chemprop/chemprop.git
RUN cd chemprop

# build an empty conda environment with appropriate Python version
RUN conda create --name chemprop_env python=3.11*

SHELL ["conda", "run", "--no-capture-output", "-n", "chemprop_env", "/bin/bash", "-c"]



# Python packages
RUN --mount=target=requirements.txt,source=requirements.txt \
    pip install --no-cache-dir --upgrade -r requirements.txt



# Copy the current directory contents into the container at $HOME/app setting the owner to the user
COPY --chown=user . $HOME/app

RUN chmod +x start_server.sh

COPY --chown=user login.html /home/user/miniconda/lib/python3.9/site-packages/jupyter_server/templates/login.html

ENV PYTHONUNBUFFERED=1 \
        GRADIO_ALLOW_FLAGGING=never \
        GRADIO_NUM_PORTS=1 \
        GRADIO_SERVER_NAME=0.0.0.0 \
        GRADIO_THEME=huggingface \
        SYSTEM=spaces \
        SHELL=/bin/bash

CMD ["./start_server.sh"]
####################################################### FROM CHEMPROP DOCKERFILE ##########################################################
# Dockerfile
#
# Builds a Docker image containing Chemprop and its required dependencies.
#
# Build this image with:
#  git clone https://github.com/chemprop/chemprop.git
#  cd chemprop
#  docker build --tag=chemprop:latest .
#
# Run the built image with:
#  docker run --name chemprop_container -it chemprop:latest
#
# Note:
# This image only runs on CPU - we do not provide a Dockerfile
# for GPU use (see installation documentation). 

# Parent Image
#FROM continuumio/miniconda3:latest

# Install libxrender1 (required by RDKit) and then clean up
#RUN apt-get update && \
#    apt-get install -y \
#    libxrender1 && \
#    apt-get autoremove -y && \
#    apt-get clean -y

#WORKDIR /opt/chemprop

# build an empty conda environment with appropriate Python version
RUN conda create --name chemprop_env python=3.11*

# This runs all subsequent commands inside the chemprop_env conda environment
#
# Analogous to just activating the environment, which we can't actually do here
# since that requires running conda init and restarting the shell (not possible
# in a Dockerfile build script)
SHELL ["conda", "run", "--no-capture-output", "-n", "chemprop_env", "/bin/bash", "-c"]

# Follow the installation instructions then clear the cache
ADD chemprop chemprop
ENV PYTHONPATH /opt/chemprop
ADD LICENSE.txt pyproject.toml README.md ./
RUN conda install pytorch cpuonly -c pytorch && \
    conda clean --all --yes && \
    python -m pip install . && \
    python -m pip cache purge

# when running this image, open an interactive bash terminal inside the conda environment
RUN echo "conda activate chemprop_env" > ~/.bashrc
ENTRYPOINT ["/bin/bash", "--login"]