switchcraft: include model weights by default; add missing README.container.md

[pansapiens]

Problem

The published switchcraft:67ffc0d image cannot run any real design out of the box.

The Dockerfile defaulted to ARG DOWNLOAD_WEIGHTS=false, so the image ships with only the CCD ligand database (ccd.pkl) and is missing the required Boltz-1 checkpoint boltz1_conf.ckpt. switchcraft.py hardcodes:

Boltz1.load_from_checkpoint("boltz/boltz1_conf.ckpt", ...)

with no runtime download, so every design run fails at model load.

Reproduction

$ apptainer run --nv switchcraft_67ffc0d.img \
    python3 switchcraft.py --config tasks/pos_allostery.yaml --out /output
...
File ".../torch/serialization.py", in _deserialize
    return obj.to(device=device)
torch.OutOfMemoryError / FileNotFoundError: ... boltz/boltz1_conf.ckpt

I confirmed the image lacks the checkpoint (ls /app/boltz/ → only ccd.pkl symlink). A pos_allostery run only succeeded once the 3.5 GB checkpoint was downloaded from Hugging Face and bind-mounted into /app/boltz/boltz1_conf.ckpt — it then completed a full design (~9 min, valid holo/apo structures with correct ligand placement and confidence metrics).

Fix

This PR makes two changes to dockerfiles/switchcraft/67ffc0d/:

1. Dockerfile — include weights by default

• ARG DOWNLOAD_WEIGHTS=false → ARG DOWNLOAD_WEIGHTS=true
• Updated the build-comment header accordingly.

This matches the convention already used by the boltz containers in this repo (e.g. boltz/v2.2.1-2), which bake model weights into the image unconditionally. The weight-download logic (DOWNLOAD_WEIGHTS=true branch) is pre-existing, downloading boltz1_conf.ckpt and LigandMPNN params from public URLs (Hugging Face, files.ipd.uw.edu). A slim ~3.5 GB-smaller build is still available via --build-arg DOWNLOAD_WEIGHTS=false (weights then bind-mounted at runtime).

2. Add the missing README.container.md

The Dockerfile does COPY README.container.md /README.md, but that file was never committed (only one commit 44f61b4 "Add SwitchCraft" added this container, without the README). As a result docker build from current HEAD fails at the COPY step. The engens and cf-random containers each ship their own README.container.md next to the Dockerfile; this adds the equivalent for switchcraft, documenting source, weights, GPU usage (apptainer --pwd /app --nv and docker --gpus), the example tasks, and output layout.

Validation

• docker build --check on the edited Dockerfile → no warnings.
• End-to-end run of the published image with the checkpoint bind-mounted completed a full pos_allostery design successfully (correct holo ligand placement, sensible Boltz confidence metrics), confirming the only thing the published image was missing is exactly what this PR bakes in.

Trade-off

Image size grows by ~3.5–4 GB (Boltz-1 checkpoint + LigandMPNN params). This is consistent with the other weight-bearing images in this repo and is the price of a self-contained, runnable image. Users who want the smaller image can build with --build-arg DOWNLOAD_WEIGHTS=false.

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