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Author SHA1 Message Date
Brandon Schneider
6fd404e20a chore(root): refresh package lock and flake outputs 2026-05-20 18:43:13 -05:00
Brandon Schneider
dbc7980e97 flake.nix: add rs-surface binary + OCI image outputs; fix Dockerfile base 
flake.nix:
- rsSurface: pkgs.rustPlatform.buildRustPackage for
  4-Infrastructure/infra/embedded_surface/rs-surface — uses cargoLock.lockFile
  (no cargoHash/cargoSha256 for Cargo.lock-based fetching).
- rsSurfaceImage: pkgs.dockerTools.buildLayeredImage — pure Nix OCI tarball,
  no Alpine, no musl. Closure: rs-surface binary + cacert + coreutils.
  Healthcheck, ExposedPorts, Env, Labels all set.
- packages.${system}.rs-surface and .rs-surface-image registered.

Build:
  nix build .#rs-surface          # binary only
  nix build .#rs-surface-image    # OCI tarball → docker load < result

Dockerfile:
- Switch fallback runtime from alpine:3.20 → debian:bookworm-slim (glibc,
  no musl compat issues). Builder stage debian:bookworm-slim with libssl-dev.
- Added comment directing users to `nix build .#rs-surface-image` as the
  canonical build path on NixOS.

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Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
 2026-05-19 14:14:17 +00:00
Brandon Schneider
74b4e09b3c 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>
 2026-05-19 09:40:14 +00:00
Brandon Schneider
f142d3faf2 devcontainer: add LaTeX, typst, math CLI tools, and Python math packages 
flake.nix (authoritative — Nix-built OCI image):
- pythonEnv: add mpmath, matplotlib, seaborn, pandas, polars, scikit-learn
- New rEnv binding: R via rWrapper with tidyverse, ggplot2, dplyr, tidyr,
  readr, purrr, stringr, forcats, lubridate, MASS, Matrix, survival,
  knitr, rmarkdown
- devPkgs: add texliveFull, gnuplot, maxima, wxmaxima, octave, rEnv, typst
- PATH env: expose texliveFull, typst, gnuplot, maxima, octave, rEnv bins

Dockerfile (Alpine reference — kept in sync):
- apk: add texlive-full, gnuplot, maxima, octave, R
- New RUN layer: typst static binary from GitHub releases (musl build)
- uv pip install: add mpmath, matplotlib, seaborn, pandas, polars, scikit-learn

Note: sage is not packaged in nixpkgs 24.11; mpmath covers
arbitrary-precision arithmetic needs. wxmaxima omitted from Dockerfile
(requires display server; headless image).

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Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
 2026-05-19 09:35:35 +00:00
Brandon Schneider
bd2786818d Add OpenGL/X11, pkg-config, and openssl to devcontainer flake 
- libglvnd, xorg.libX11, xorg.libXext, xorg.libXrender, mesa:
  enables build123d/OCP/VTK CAD dependencies inside the container
- pkg-config, openssl: enables Rust workspace builds with openssl-sys
- Update PATH and LD_LIBRARY_PATH env vars to include new packages

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Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
 2026-05-19 08:05:40 +00:00
Brandon Schneider
09cfe00eec Expand ene-rds Rust workspace and refine devcontainer 
- Add ene-node, ene-rds-chat, ene-rds-ephemeral, ene-rds-wiki,
  ene-storage, ene-sync crates to the ene-rds workspace
- Extend ene-rds-core with shared types and cluster messaging
- Add review doc and wiki page for the RDS Rust workspace
- Fix devcontainer: custom /etc/passwd with researcher user,
  add gcc/glibc/binutils for VS Code server compatibility,
  include util-linux, gnutar, gzip; add LD_LIBRARY_PATH
- Ignore Nix build output (`result`) and Rust artifacts

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Co-Authored-By: Devin <158243242+devin-ai-integration[bot]@users.noreply.github.com>
 2026-05-19 07:52:39 +00:00
Brandon Schneider
ac4e23dc9b Expand devcontainer with full Python stack, add MCP servers (Notion/AWS), strengthen Lean theorems 
- .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
 2026-05-19 01:52:14 -05:00