mirror of
https://github.com/allaunthefox/Research-Stack.git
synced 2026-07-31 03:05:21 +00:00
ac4e23dc9b
- .devcontainer/Dockerfile: add PostgreSQL client libs, OpenSSL/libffi headers, gfortran/BLAS for scipy, rclone; install full Python dependency set (boto3, psycopg2-binary, fastapi, uvicorn, notion-client, httpx, pytest, numpy, scipy, etc.) in uv-managed venv; add rclone S3 gateway init script as ENTRYPOINT - .devcontainer/devcontainer.json: switch from build to pre-built image (localhost/research
113 lines
3.8 KiB
Docker
113 lines
3.8 KiB
Docker
FROM alpine:3.19
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# ── System packages ───────────────────────────────────────────────────────────
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# Core build + dev tools
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RUN apk add --no-cache \
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bash \
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build-base \
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git \
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curl \
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wget \
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openssh-client \
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rsync \
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zstd \
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jq \
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ripgrep \
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# Graphviz for visualisation helpers
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graphviz \
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# Node / npm for JS tooling
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nodejs \
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npm \
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# Python runtime + package managers
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python3 \
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py3-pip \
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pipx \
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# PostgreSQL client libs (needed by psycopg2 --no-binary build)
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postgresql16-client \
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postgresql16-dev \
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libpq-dev \
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# SSL / crypto headers (boto3, requests, psycopg2)
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openssl-dev \
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# CFFI / ffi headers
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libffi-dev \
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# Needed for some science packages (scipy, etc.)
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gfortran \
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openblas-dev \
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lapack-dev \
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# Misc compression
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xz \
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bzip2-dev \
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# rclone (Google Drive / S3 / etc.)
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rclone \
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&& :
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# ── uv package manager ────────────────────────────────────────────────────────
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RUN pipx install uv && cp /root/.local/bin/uv /usr/local/bin/uv && cp /root/.local/bin/uvx /usr/local/bin/uvx
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# ── Non-root developer user 'researcher' (UID 1000) ──────────────────────────
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RUN adduser -D -u 1000 researcher
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ENV PYTHONUNBUFFERED=1 \
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XDG_CACHE_HOME=/home/researcher/.cache \
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UV_LINK_MODE=copy
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USER researcher
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WORKDIR /home/researcher/stack
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# ── Python 3.11 venv + all repo-required packages ────────────────────────────
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RUN uv python install 3.11.15 \
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&& uv venv --clear --python 3.11.15 /home/researcher/venv
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# Core infrastructure / ingestion dependencies
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RUN uv pip install --python /home/researcher/venv/bin/python3 \
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# AWS + RDS IAM auth
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boto3 \
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botocore \
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# Postgres
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psycopg2-binary \
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# HTTP clients
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requests \
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httpx \
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# API server (swarm API, credential server)
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fastapi \
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"uvicorn[standard]" \
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pydantic \
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# Notion + Linear clients
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notion-client \
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# Data / serialisation
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python-dotenv \
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pyyaml \
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rich \
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# Science / math baseline (from requirements-optional-science.txt)
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biopython \
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networkx \
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pycryptodome \
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zstandard \
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z3-solver \
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PyWavelets \
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# galois>=0.4 needs numba->llvmlite which requires LLVM; install separately on host if needed
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# Numerics
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numpy \
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scipy \
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# Search / web
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beautifulsoup4 \
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lxml \
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# Lean / symbolic
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sympy \
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# Testing
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pytest \
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&& :
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# ── elan (Lean 4 Version Manager) ────────────────────────────────────────────
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RUN curl https://raw.githubusercontent.com/leanprover/elan/master/elan-init.sh -sSf \
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| sh -s -- -y --default-toolchain leanprover/lean4:stable
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# ── PATH ──────────────────────────────────────────────────────────────────────
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ENV PATH="/home/researcher/.elan/bin:/home/researcher/venv/bin:/home/researcher/.local/bin:${PATH}"
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# ── rclone S3 gateway init script ─────────────────────────────────────────────
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COPY --chown=researcher:researcher .devcontainer/init-rclone-s3.sh /home/researcher/init-rclone-s3.sh
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RUN chmod +x /home/researcher/init-rclone-s3.sh
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ENTRYPOINT ["/home/researcher/init-rclone-s3.sh"]
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CMD ["/bin/bash"]
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