complexa-setup

name	complexa-setup
description	First-time setup, environment configuration, and model-weight installation for Proteina-Complexa. Reach for this skill whenever the user says "set up complexa", "install complexa", "configure my .env", "first-time setup", "what models do I have installed", "what's in my .env", "download model weights", "download Complexa / AF2 / RF3 / ProteinMPNN / LigandMPNN / ESM2 / ESMFold checkpoints", "preflight my GPU", "verify environment", "complexa init", "complexa download", "complexa download --status", "complexa validate env", or any time a fresh checkout needs to be made runnable. This is the first skill to run on a new clone — it drives `complexa init`, `complexa download`, and `complexa validate env` end-to-end, edits the required `.env` keys, picks the right runtime (UV vs Docker), and emits a replayable setup artifact.
compatibility	complexa CLI installed (pip install -e .); bash 4+; nvidia-smi optional
allowed-tools	Bash, Read, Write, AskUserQuestion

Complexa Setup Skill

Drive the three steps a fresh Proteina-Complexa checkout needs before any design run: create .env, fetch model weights, and sanity-check the env. Probe the host for GPU / disk / tool binaries first so the user does not discover a missing dependency mid-pipeline. End with a JSON setup artifact the user (or a future agent) can re-read instead of re-deriving state.

CLI vs direct file-edit — pick the cheapest path per step

Step	Preferred path	Why
.env creation (Step 2)	CLI (complexa init <runtime>)	complexa init copies .env_example → .env and swaps the runtime lines (_swap_runtime_in_env in cli_runner.py). Use the CLI: it is the supported entry point and guarantees the .env the rest of the toolchain expects. A bare cp .env_example .env is a fragile re-implementation — prefer complexa init.
.env value edits (Step 3)	File edit (StrReplace LOCAL_CODE_PATH=… etc.)	No CLI for this — the values are user-specific paths.
Download model weights (Step 4)	CLI (complexa download --…)	Dispatches to env/download_startup.sh (~1000 lines of bash with NGC URLs, retries, checksum-style skip-if-present). Don't try to replicate.
Validate env (Step 5)	CLI (complexa validate env) or test -f .env && test -d $DATA_PATH	They check the same thing — .env exists + DATA_PATH is an existing dir. Shallow smoke test only; for real readiness use preflight.sh.
Validate full design config (after picking a pipeline)	CLI (complexa validate design CONFIG)	Hydra defaults traversal + ckpt + reward/eval-weight checks worth not replicating. Caveat: reads the config YAML as-is — it rejects ++ overrides and does not validate overridden values.

What this skill enables

• A correctly-shaped .env for either UV or Docker runtime.
• Model checkpoints (Complexa protein/ligand/AME plus community models) downloaded to known paths.
• A preflight.json snapshot of the host (GPU, disk, .env, ckpts, tool binaries).
• A run_manifest.json capturing exactly which complexa init + complexa download invocations were used (replay-friendly).
• A pass/fail report from complexa validate env with clear next-step hints.

Step 1: Pre-flight check

Always run the shared preflight before touching the environment. It does not require .env to exist — it falls back to defaults — and it tells you whether the host can run Complexa at all.

bash .claude/skills/_shared/scripts/preflight.sh

The script writes ./complexa_setup/preflight.json. Read it and surface:

• gpu.available — if false, design / evaluate steps will fail; warn the user.
• gpu.vram_gb — Complexa needs ≥40 GB (A100/H100/L40S).
• disk.free_gb at CKPT_PATH — minimum ~50 GB for the full Complexa + community model set.
• env.missing_required — anything listed here must be edited in .env before validation passes.
• tools.{foldseek,mmseqs,dssp,hbplus,sc}.exists — missing tools degrade evaluation but do not block generation.

Step 1b: Build the Python environment (only if .venv/ is missing)

The complexa CLI is installed inside the project's Python environment, not on the system path by default. On a fresh clone, the .venv/ directory does not yet exist and complexa init will fail with command not found.

First, probe for the system (OS-level) build dependencies. env/build_uv_env.sh is silent about these — on a bare cloud VM (e.g. a fresh Brev / Lambda image) they are usually missing, and the build dies deep inside a wheel compile (cpdb-protein fails without cc/make; later atomworks → openbabel → pybel fails to import without libxrender1). The errors at that depth are confusing, so check up front and install before building:

# C toolchain (build-essential = cc + make + headers) and the libXrender shared
# library that OpenBabel/pybel dlopen at import time.
missing=()
command -v cc   >/dev/null 2>&1 || missing+=(build-essential)
command -v make >/dev/null 2>&1 || missing+=(build-essential)
ldconfig -p 2>/dev/null | grep -q libXrender || missing+=(libxrender1)
if [ ${#missing[@]} -gt 0 ]; then
    echo "Missing system packages: ${missing[*]}"
    echo "Install with: sudo apt-get update && sudo apt-get install -y $(printf '%s ' "${missing[@]}" | tr ' ' '\n' | sort -u | tr '\n' ' ')"
    # On Debian/Ubuntu:
    #   sudo apt-get update && sudo apt-get install -y build-essential libxrender1
fi

Install anything flagged (sudo apt-get install -y build-essential libxrender1), then build the UV venv:

test -d .venv || ./env/build_uv_env.sh   # first-time UV build
source .venv/bin/activate
which complexa                            # sanity check: should point inside .venv

Skip this step if which complexa already resolves — that means a previous build is still good. The Docker runtime skips it entirely; the venv lives inside the container image instead. If the user said "I just cloned" or you see no .venv/ next to pyproject.toml, run the build script — complexa init without a venv produces a confusing command not found rather than an obvious "build the venv first" error.

Step 2: Create .env

Pick the runtime. UV is the default and faster to start; Docker is required on Ubuntu 20.04 or systems with GLIBC mismatches.

Use AskUserQuestion if it is not obvious from context:

"Which runtime do you want to configure? uv (recommended, faster) or docker (use if you do not have a UV venv built locally)?"

Run complexa init (recommended — do not hand-roll this)

complexa init                    # UV runtime (default)
complexa init --runtime docker   # Docker runtime
complexa init --force            # Recreate .env from .env_example (drops any edits)

Always create .env with complexa init. Downstream commands (complexa design, complexa target add, …) refuse to run until .env exists, and complexa init is the only path guaranteed to produce the .env they expect. Do not substitute a bare cp .env_example .env — that is a fragile re-implementation that has caused "env not initialized" failures on fresh VMs.

If .env already exists and --force is not passed, only the runtime-dependent lines are swapped — user edits in Step 3 are preserved across runtime flips.

complexa init copies .env_example → .env, swaps the COMPLEXA_RUNTIME= line plus the UV_* ↔ DOCKER_* prefixes on the tool/data/cache path block, and prepares the runtime activation that downstream commands expect — a bare cp does not, which is why complexa design / complexa target add then abort with "environment not initialized". You will still hand-edit the machine-specific values in Step 3 — init sets the runtime, not your paths.

Verify

test -f .env && echo "OK: .env present" || echo "MISSING"
grep -E '^COMPLEXA_RUNTIME=' .env

Step 3: Edit .env

No CLI for this — Step 2 only set the runtime; you still need to write your machine-specific paths into .env by hand (StrReplace or your editor). The two absolutely-required edits are:

LOCAL_CODE_PATH=/absolute/path/to/protein-foundation-models
LOCAL_DATA_PATH=/absolute/path/to/PFM_data

Everything else (cache, ckpts, community-model dirs, tool binaries) is derived from LOCAL_CODE_PATH by default and only needs editing if you have a non-standard layout. For the full table — every key, what it controls, what fails if it is missing — see reference/env_keys.md.

Quick decision table for the four edits most users make:

Key	Default	Set this if
LOCAL_CODE_PATH	placeholder	Always — required
LOCAL_DATA_PATH	/nvda/data/PFM_data	Always — required, points at target PDBs
HF_TOKEN	placeholder	You need ESMFold or gated HF models
WANDB_API_KEY	placeholder	You want training runs logged to W&B

Step 4: Download checkpoints

Always use the CLI here. complexa download dispatches to env/download_startup.sh (~1000 lines of bash with NGC URLs, retries, and skip-if-present logic across ~6 community-model families). Rolling your own wget loop is a recipe for partial downloads and wrong destination paths.

Ask which models the user actually needs — downloading everything is ~100+ GB. Pick from the three Complexa variants and the community-model set. Each Complexa variant unlocks exactly one complexa design pipeline; AF2 / RF3 inside the community-model set are what evaluate (and reward-guided search) need at run time.

Flag	What it downloads	Unlocks pipeline	Destination	Approx size
--complexa	Complexa protein-binder model + AE (complexa.ckpt, complexa_ae.ckpt)	Protein binder (default) — configs/search_binder_local_pipeline.yaml	./ckpts/	~3 GB
--complexa-ligand	Ligand-binder model + AE (complexa_ligand.ckpt, complexa_ligand_ae.ckpt)	Ligand binder — configs/search_ligand_binder_local_pipeline.yaml	./ckpts/	~3 GB
--complexa-ame	AME motif-scaffolding model + AE (complexa_ame.ckpt, complexa_ame_ae.ckpt)	AME (enzyme) — configs/search_ame_local_pipeline.yaml	./ckpts/	~3 GB
--complexa-all	All three Complexa variants	All three pipelines	./ckpts/	~9 GB
--all	All community models (ProteinMPNN + LigandMPNN + AF2 + ESM2 + ESMFold + RF3)	Needed by evaluate / reward: AF2 (protein binder), RF3 (ligand binder + AME), MPNNs (inverse folding for every pipeline).	./community_models/	~50 GB
--everything	Complexa + community + optional (Boltz2 / Protenix)	Everything plus alternative refold backends	both	~100+ GB
--status	Show install state — does not download	(none)	(none)	n/a

Minimum download per pipeline:

• Protein binder (default): complexa download --complexa --all
• Ligand binder: complexa download --complexa-ligand --all
• AME / enzyme: complexa download --complexa-ame --all
• All three: complexa download --everything

For the full per-model destination breakdown and the ORD rsync fallback, see reference/downloads.md.

Pick the smallest invocation that covers the user's goal, then run:

# A runnable protein-binder pipeline needs BOTH the Complexa weights AND the
# community models — AF2 is used as the generation-time reward (not just the
# eval refold), so '--complexa' alone crashes at sample 0.
complexa download --complexa --all      # protein binder (Complexa + community)
complexa download --complexa-ligand --all   # ligand binder
complexa download --complexa-ame --all      # AME / enzyme
complexa download --everything          # all three Complexa variants + community + optional

Do not download --complexa on its own and expect the protein-binder pipeline to run. It fetches only the Complexa model; generation then fails immediately because the AF2 reward weights (part of --all) are missing. --all (community models) is required for every pipeline.

Without arguments, complexa download launches an interactive wizard — prefer explicit flags in agent mode.

Verify what landed:

complexa download --status

The status output groups by family (Complexa / community / optional) and prints "Installed" or "Missing" per ckpt. Re-run the specific flag if a ckpt is flagged missing.

Step 5: Validate

Smoke-check that .env is loadable:

complexa validate env

Treat validate env as a shallow smoke test, not a guarantee. It checks exactly two things: (1) .env exists, and (2) DATA_PATH is set and points at some directory that exists. That is all — it does not verify the directory is the correct PFM_data (DATA_PATH=/tmp passes), does not check ckpt files, tool binaries, AF2/RF3 weights, or GPU. A green validate env does not mean a design run will succeed.

For the checks that actually predict whether a run works, use:

• bash .claude/skills/_shared/scripts/preflight.sh — GPU, disk, ckpt presence, tool binaries (Step 1).
• complexa validate design <config> — ckpts + reward/eval weights for a specific pipeline (see complexa-design Step 4). Note its limits there too: it reads the config YAML as-is and does not apply ++ overrides.

Common failures and fixes:

Symptom	Cause	Fix
.env file: No .env file found	complexa init not run	Run complexa init first
DATA_PATH: Not set in .env	Placeholder not edited	Edit LOCAL_DATA_PATH in .env
DATA_PATH: Directory not found	Path edited but does not exist on disk	mkdir -p $LOCAL_DATA_PATH or copy target data there
Hydra error InterpolationKeyError: AF2_DIR	Reward/eval config wants AF2 but .env does not define it	Download AF2 weights or remove AF2 from the config

Step 6: Emit setup artifact

Drop a JSON manifest in ./complexa_setup/ so the user has a single file describing the resulting state. The shared helper writes it for you:

mkdir -p ./complexa_setup
python3 .claude/skills/_shared/scripts/write_manifest.py \
    --kind setup \
    --runtime "$(grep -E '^COMPLEXA_RUNTIME=' .env | cut -d= -f2)" \
    --preflight ./complexa_setup/preflight.json \
    --out ./complexa_setup/run_manifest.json

Surface the resulting files to the user:

ls -la ./complexa_setup/

Expected contents:

complexa_setup/
├── preflight.json      # GPU / disk / .env / ckpt / tool snapshot
└── run_manifest.json   # init + download invocations + git SHA + runtime

Hardware requirements

Resource	Minimum	Recommended
GPU	1× CUDA GPU, ≥24 GB VRAM	A100 / H100 / L40S, 40–80 GB VRAM
CUDA	12.0	12.4+
Disk (CKPT_PATH)	50 GB	150 GB (covers --everything)
RAM	16 GB	64 GB+
OS	Ubuntu 22.04+ (UV)	Ubuntu 22.04+ or Docker on any host

Ubuntu 20.04 throws GLIBC errors with the UV runtime — use complexa init --runtime docker on those hosts. See .claude/skills/_shared/reference/hardware.md for per-pipeline (binder vs ligand vs AME) requirements.

Troubleshooting

Symptom	Cause	Fix
complexa: command not found	Package not installed in active env	source .venv/bin/activate then pip install -e .
complexa init says .env_example not found	Running outside repo root	cd to the project root (where .env_example lives)
.env_example not found. Cannot initialize .env.	Not in project root	cd into protein-foundation-models/ and retry
complexa download fails on NGC URL	Behind firewall / no internet	Use the ORD rsync fallback — see reference/downloads.md
complexa download --status shows ckpts present but validate fails	.env CKPT_PATH points elsewhere	Either move ckpts or edit LOCAL_CHECKPOINT_PATH in .env
GLIBC error on import	Ubuntu 20.04 with UV runtime	Re-run complexa init --runtime docker and use ./env/docker-ops.sh run

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For the full .env reference (every key, defaults, failure modes), see reference/env_keys.md.

For the full download flag matrix, NGC URLs, destination layout, and the ORD rsync fallback, see reference/downloads.md.