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devcontainer: replace Alpine base with nixos/nix; add sagemath
Dockerfile: - FROM alpine:3.19 → FROM nixos/nix:latest - Replace all apk add commands with nix profile install, matching the devPkgs set in flake.nix (the authoritative build path) - System packages, LaTeX (texliveFull), math CLI (gnuplot, maxima, wxmaxima, octave, sage, typst) all installed via nix profile - Remove separate typst binary download — nixpkgs#typst used instead - useradd replaces adduser (nixos/nix base uses shadow-utils not busybox) flake.nix: - Add sage (SageMath 10.5) to devPkgs - Add pkgs.sage/bin to container PATH Generated with [Devin](https://cli.devin.ai/docs) Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
This commit is contained in:
Brandon Schneider
parent
f142d3faf2
commit
74b4e09b3c
2 changed files with 82 additions and 68 deletions
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@ -1,63 +1,78 @@
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FROM alpine:3.19
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FROM nixos/nix:latest
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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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# ip / iproute2 needed by tailscaled
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iproute2 \
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# ── LaTeX + typesetting ───────────────────────────────────────────────────
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texlive-full \
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# ── Math / science CLI ────────────────────────────────────────────────────
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gnuplot \
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maxima \
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# wxmaxima requires a display; skip in headless image
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octave \
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R \
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&& :
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# ── Nix configuration: enable flakes + nix-command ───────────────────────────
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RUN mkdir -p /etc/nix && \
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echo 'experimental-features = nix-command flakes' >> /etc/nix/nix.conf && \
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echo 'sandbox = false' >> /etc/nix/nix.conf
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# ── Typst (static binary — not in Alpine apk) ────────────────────────────────
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RUN TYPST_VER=$(curl -fsSL https://api.github.com/repos/typst/typst/releases/latest \
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| grep '"tag_name"' | grep -oP 'v[\d.]+') \
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&& curl -fsSL "https://github.com/typst/typst/releases/download/${TYPST_VER}/typst-x86_64-unknown-linux-musl.tar.xz" \
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| tar -xJ -C /tmp/ \
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&& install -m 755 /tmp/typst-x86_64-unknown-linux-musl/typst /usr/local/bin/typst \
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&& rm -rf /tmp/typst-x86_64-unknown-linux-musl
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# ── System packages via nix profile ──────────────────────────────────────────
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# This mirrors the devPkgs set in flake.nix (authoritative build path).
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# The canonical image is produced by `nix build .#devcontainer` on the host;
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# this Dockerfile is a self-contained fallback that produces an equivalent env.
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RUN nix profile install \
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nixpkgs#bash \
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nixpkgs#bashInteractive \
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nixpkgs#coreutils \
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nixpkgs#findutils \
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nixpkgs#gnugrep \
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nixpkgs#gnused \
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nixpkgs#gawk \
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nixpkgs#util-linux \
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nixpkgs#git \
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nixpkgs#git-lfs \
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nixpkgs#curl \
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nixpkgs#wget \
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nixpkgs#rsync \
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nixpkgs#zstd \
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nixpkgs#xz \
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nixpkgs#gnutar \
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nixpkgs#gzip \
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nixpkgs#ripgrep \
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nixpkgs#jq \
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nixpkgs#gnumake \
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nixpkgs#nodejs_20 \
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nixpkgs#uv \
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nixpkgs#elan \
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nixpkgs#postgresql_16 \
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nixpkgs#graphviz \
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nixpkgs#openssh \
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nixpkgs#cacert \
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nixpkgs#less \
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nixpkgs#which \
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nixpkgs#file \
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nixpkgs#procps \
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nixpkgs#htop \
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nixpkgs#rclone \
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nixpkgs#iproute2 \
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nixpkgs#pkg-config \
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nixpkgs#openssl \
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nixpkgs#gcc \
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nixpkgs#binutils \
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nixpkgs#glibc \
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nixpkgs#libglvnd \
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nixpkgs#xorg.libX11 \
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nixpkgs#xorg.libXext \
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nixpkgs#xorg.libXrender \
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nixpkgs#mesa \
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&& nix-collect-garbage -d
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# ── LaTeX + typesetting ───────────────────────────────────────────────────────
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RUN nix profile install \
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nixpkgs#texliveFull \
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nixpkgs#typst \
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&& nix-collect-garbage -d
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# ── Math / science CLI ────────────────────────────────────────────────────────
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RUN nix profile install \
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nixpkgs#gnuplot \
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nixpkgs#maxima \
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nixpkgs#wxmaxima \
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nixpkgs#octave \
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nixpkgs#sage \
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&& nix-collect-garbage -d
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# ── Typst (already installed above via nix) ───────────────────────────────────
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# typst is available from nixpkgs#typst — no separate binary download needed.
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# ── Tailscale (static binary — userspace networking, no root required) ────────
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RUN TSVER=$(curl -fsSL https://pkgs.tailscale.com/stable/ \
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@ -69,15 +84,14 @@ RUN TSVER=$(curl -fsSL https://pkgs.tailscale.com/stable/ \
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&& install -m 755 /tmp/tailscale_${TSVER}_amd64/tailscaled /usr/local/bin/tailscaled \
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&& rm -rf /tmp/tailscale_${TSVER}_amd64
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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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RUN useradd -m -u 1000 -s /bin/bash 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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UV_LINK_MODE=copy \
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SSL_CERT_FILE=/root/.nix-profile/etc/ssl/certs/ca-bundle.crt \
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NIX_SSL_CERT_FILE=/root/.nix-profile/etc/ssl/certs/ca-bundle.crt
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USER researcher
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WORKDIR /home/researcher/stack
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@ -86,7 +100,6 @@ WORKDIR /home/researcher/stack
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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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@ -106,14 +119,13 @@ RUN uv pip install --python /home/researcher/venv/bin/python3 \
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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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# Science / math baseline
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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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@ -143,7 +155,7 @@ RUN curl https://raw.githubusercontent.com/leanprover/elan/master/elan-init.sh -
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# ── PATH ──────────────────────────────────────────────────────────────────────
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ENV PATH="/home/researcher/.elan/bin:/home/researcher/venv/bin:/home/researcher/.local/bin:${PATH}"
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# ── Tailscale userspace auto-start snippet (written as researcher) ────────────
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# ── Tailscale userspace auto-start snippet ────────────────────────────────────
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RUN mkdir -p /home/researcher/.local/share/tailscale && \
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printf '%s\n' \
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'# ── Tailscale (userspace, no root required) ─────────────────────────────' \
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rEnv # R + tidyverse / ggplot2 (see rEnv binding above)
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# ── Typesetting ────────────────────────────────────────────────────────
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typst # modern markup-based typesetting (LaTeX alternative)
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# ── CAS ────────────────────────────────────────────────────────────────
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sage # SageMath 10.5 — full open-source mathematics system
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];
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# ── customEtc provides standard etc configuration with researcher user ──
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User = "1000";
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WorkingDir = "/home/researcher/stack";
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Env = [
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"PATH=/home/researcher/.elan/bin:${pythonEnv}/bin:${pkgs.uv}/bin:${pkgs.git}/bin:${pkgs.ripgrep}/bin:${pkgs.jq}/bin:${pkgs.coreutils}/bin:${pkgs.bashInteractive}/bin:${pkgs.binutils}/bin:${pkgs.glibc.bin}/bin:${pkgs.gzip}/bin:${pkgs.pkg-config}/bin:${pkgs.openssl.bin}/bin:${pkgs.texliveFull}/bin:${pkgs.typst}/bin:${pkgs.gnuplot}/bin:${pkgs.maxima}/bin:${pkgs.octave}/bin:${rEnv}/bin:/usr/bin:/bin"
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"PATH=/home/researcher/.elan/bin:${pythonEnv}/bin:${pkgs.uv}/bin:${pkgs.git}/bin:${pkgs.ripgrep}/bin:${pkgs.jq}/bin:${pkgs.coreutils}/bin:${pkgs.bashInteractive}/bin:${pkgs.binutils}/bin:${pkgs.glibc.bin}/bin:${pkgs.gzip}/bin:${pkgs.pkg-config}/bin:${pkgs.openssl.bin}/bin:${pkgs.texliveFull}/bin:${pkgs.typst}/bin:${pkgs.gnuplot}/bin:${pkgs.maxima}/bin:${pkgs.octave}/bin:${rEnv}/bin:${pkgs.sage}/bin:/usr/bin:/bin"
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"LD_LIBRARY_PATH=${pkgs.gcc.cc.lib}/lib:${pkgs.glibc}/lib:${pkgs.libglvnd}/lib:${pkgs.xorg.libX11}/lib:${pkgs.xorg.libXext}/lib:${pkgs.xorg.libXrender}/lib:${pkgs.mesa}/lib:${pkgs.openssl}/lib"
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"PYTHONUNBUFFERED=1"
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"XDG_CACHE_HOME=/home/researcher/.cache"
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