@moldesk/registry 0.0.1 → 0.0.2

package/dist/errors.d.ts

@@ -0,0 +1,14 @@
+export interface MoldeskErrorData {
+    code: string;
+    message: string;
+    remediation?: string;
+    cause?: unknown;
+    details?: Record<string, unknown>;
+}
+export declare class MoldeskError extends Error {
+    readonly code: string;
+    readonly remediation?: string;
+    readonly cause?: unknown;
+    readonly details?: Record<string, unknown>;
+    constructor(data: MoldeskErrorData);
+}

package/dist/errors.js

@@ -0,0 +1,14 @@
+export class MoldeskError extends Error {
+    code;
+    remediation;
+    cause;
+    details;
+    constructor(data) {
+        super(data.message);
+        this.name = "MoldeskError";
+        this.code = data.code;
+        this.remediation = data.remediation;
+        this.cause = data.cause;
+        this.details = data.details;
+    }
+}

package/dist/index.d.ts

@@ -1,14 +1,7 @@
-export interface ModelManifest {
-    name: string;
-    displayName: string;
-    version: string;
-    description: string;
-    homepage?: string;
-    license?: string;
-    compatibility?: {
-        cpu?: boolean;
-        gpu?: "required" | "recommended" | "unsupported";
-    };
-}
-export declare function listAvailableModels(): ModelManifest[];
-export declare function listInstalledModels(): ModelManifest[];
+export { MoldeskError } from "./errors.js";
+export type { MoldeskErrorData } from "./errors.js";
+export { allowedCommandTokens, commandSpecSchema, modelManifestV1Schema, } from "./schema.js";
+export type { AssetSpec, CommandSpec, HardwareRequirements, InputSpec, ModelCategory, ModelManifestV1, ModelStatus, OutputSpec, PlatformId, PostInstallHook, PythonRequirement, PythonRuntimeSpec, DockerRuntimeSpec, RequirementLevel, RuntimeKind, RuntimeSpec, SourceSpec, } from "./schema.js";
+export type { LegacyModelManifest } from "./types.js";
+export { getModelsDir, listAvailableModels, loadManifestFile, parseManifest, } from "./loader.js";
+export { detectHostPlatformId, effectiveRuntimeSource, selectPythonRuntime, } from "./runtime-selection.js";

package/dist/index.js

@@ -1,29 +1,4 @@
-import fs from "node:fs";
-import path from "node:path";
-import { fileURLToPath } from "node:url";
-import YAML from "yaml";
-const __dirname = path.dirname(fileURLToPath(import.meta.url));
-function repoModelsDir() {
-    // packages/registry/src -> repo root -> models
-    return path.resolve(__dirname, "../../../models");
-}
-export function listAvailableModels() {
-    const modelsDir = repoModelsDir();
-    if (!fs.existsSync(modelsDir))
-        return [];
-    return fs
-        .readdirSync(modelsDir, { withFileTypes: true })
-        .filter((entry) => entry.isDirectory())
-        .map((entry) => {
-        const manifestPath = path.join(modelsDir, entry.name, "manifest.yaml");
-        if (!fs.existsSync(manifestPath))
-            return null;
-        const raw = fs.readFileSync(manifestPath, "utf-8");
-        return YAML.parse(raw);
-    })
-        .filter((manifest) => manifest !== null);
-}
-export function listInstalledModels() {
-    // No models are installed yet — installation support lands with `moldesk install`.
-    return [];
-}
+export { MoldeskError } from "./errors.js";
+export { allowedCommandTokens, commandSpecSchema, modelManifestV1Schema, } from "./schema.js";
+export { getModelsDir, listAvailableModels, loadManifestFile, parseManifest, } from "./loader.js";
+export { detectHostPlatformId, effectiveRuntimeSource, selectPythonRuntime, } from "./runtime-selection.js";

package/dist/loader.d.ts

@@ -0,0 +1,5 @@
+import { type ModelManifestV1 } from "./schema.js";
+export declare function parseManifest(raw: unknown, manifestPath: string): ModelManifestV1;
+export declare function loadManifestFile(manifestPath: string): ModelManifestV1;
+export declare function listAvailableModels(modelsDir?: string): ModelManifestV1[];
+export declare function getModelsDir(): string;

package/dist/loader.js

@@ -0,0 +1,128 @@
+import fs from "node:fs";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import YAML from "yaml";
+import { z } from "zod";
+import { MoldeskError } from "./errors.js";
+import { modelManifestV1Schema } from "./schema.js";
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+function packagedModelsDir() {
+    return path.resolve(__dirname, "models");
+}
+function sourceModelsDir() {
+    // packages/registry/src -> repo root -> models (dev fallback only)
+    return path.resolve(__dirname, "../../../models");
+}
+function resolveModelsDir() {
+    const override = process.env["MOLDESK_MODELS_DIR"];
+    if (override && fs.existsSync(override))
+        return override;
+    if (fs.existsSync(packagedModelsDir()))
+        return packagedModelsDir();
+    if (fs.existsSync(sourceModelsDir()))
+        return sourceModelsDir();
+    throw new MoldeskError({
+        code: "REGISTRY_NOT_FOUND",
+        message: "MoleculeDesk model registry is missing from this installation.",
+        remediation: "Reinstall @moldesk/cli. Package maintainers should verify that @moldesk/registry includes dist/models.",
+        details: { packagedModelsDir: packagedModelsDir(), sourceModelsDir: sourceModelsDir() },
+    });
+}
+function toMoldeskError(manifestPath, error) {
+    if (error instanceof z.ZodError) {
+        const first = error.issues[0];
+        const field = first && first.path.length > 0 ? first.path.join(".") : "(root)";
+        return new MoldeskError({
+            code: "INVALID_MANIFEST",
+            message: `Invalid manifest ${manifestPath}: ${field}: ${first?.message ?? "validation failed"}`,
+            remediation: "Fix the manifest field and re-run the registry build. See docs/v0.1-implementation-spec.md Step 1.",
+            details: { manifestPath, field, issues: error.issues },
+        });
+    }
+    return new MoldeskError({
+        code: "INVALID_MANIFEST",
+        message: `Invalid manifest ${manifestPath}: ${error instanceof Error ? error.message : String(error)}`,
+        remediation: "Ensure the file is valid YAML matching ModelManifestV1.",
+        details: { manifestPath },
+        cause: error,
+    });
+}
+export function parseManifest(raw, manifestPath) {
+    if (typeof raw !== "object" || raw === null) {
+        throw new MoldeskError({
+            code: "INVALID_MANIFEST",
+            message: `Invalid manifest ${manifestPath}: root must be a mapping`,
+            remediation: "Ensure the manifest is a YAML mapping with schemaVersion: 1.",
+            details: { manifestPath },
+        });
+    }
+    const record = raw;
+    if (record["schemaVersion"] !== 1) {
+        throw new MoldeskError({
+            code: "UNKNOWN_SCHEMA_VERSION",
+            message: `Unknown schema version in ${manifestPath}: ${String(record["schemaVersion"])}`,
+            remediation: "Set schemaVersion: 1. Only v1 manifests are supported in v0.1.",
+            details: { manifestPath, schemaVersion: record["schemaVersion"] },
+        });
+    }
+    if ("version" in record && !("modelVersion" in record)) {
+        throw new MoldeskError({
+            code: "INVALID_MANIFEST",
+            message: `Invalid manifest ${manifestPath}: ambiguous top-level "version" field; use modelVersion + adapterVersion`,
+            remediation: "Rename version to modelVersion and add adapterVersion.",
+            details: { manifestPath, field: "version" },
+        });
+    }
+    try {
+        return modelManifestV1Schema.parse(raw);
+    }
+    catch (error) {
+        throw toMoldeskError(manifestPath, error);
+    }
+}
+export function loadManifestFile(manifestPath) {
+    let raw;
+    try {
+        raw = YAML.parse(fs.readFileSync(manifestPath, "utf-8"));
+    }
+    catch (error) {
+        throw new MoldeskError({
+            code: "INVALID_MANIFEST",
+            message: `Invalid manifest ${manifestPath}: YAML parse failed`,
+            remediation: "Fix YAML syntax.",
+            details: { manifestPath },
+            cause: error,
+        });
+    }
+    return parseManifest(raw, manifestPath);
+}
+export function listAvailableModels(modelsDir) {
+    const dir = modelsDir ?? resolveModelsDir();
+    if (!fs.existsSync(dir))
+        return [];
+    const manifests = [];
+    const seen = new Set();
+    for (const entry of fs.readdirSync(dir, { withFileTypes: true })) {
+        if (!entry.isDirectory())
+            continue;
+        const manifestPath = path.join(dir, entry.name, "manifest.yaml");
+        if (!fs.existsSync(manifestPath))
+            continue;
+        const manifest = loadManifestFile(manifestPath);
+        if (seen.has(manifest.name)) {
+            throw new MoldeskError({
+                code: "DUPLICATE_MODEL_ID",
+                message: `Duplicate model id "${manifest.name}" in ${manifestPath}`,
+                remediation: "Rename one model so every manifest name is unique.",
+                details: { manifestPath, name: manifest.name },
+            });
+        }
+        seen.add(manifest.name);
+        manifests.push(manifest);
+    }
+    manifests.sort((a, b) => a.name.localeCompare(b.name));
+    return manifests;
+}
+export function getModelsDir() {
+    return resolveModelsDir();
+}

package/dist/loader.test.d.ts

@@ -0,0 +1 @@
+export {};

package/dist/loader.test.js

@@ -0,0 +1,72 @@
+import fs from "node:fs";
+import os from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import YAML from "yaml";
+import { MoldeskError } from "./errors.js";
+import { listAvailableModels } from "./loader.js";
+const tempDirs = [];
+function makeTempDir(prefix) {
+    const dir = fs.mkdtempSync(path.join(os.tmpdir(), prefix));
+    tempDirs.push(dir);
+    return dir;
+}
+afterEach(() => {
+    for (const dir of tempDirs.splice(0))
+        fs.rmSync(dir, { recursive: true, force: true });
+});
+function writeManifest(dir, name, overrides = {}) {
+    const base = {
+        schemaVersion: 1,
+        name,
+        displayName: name,
+        modelVersion: "1.0.0",
+        adapterVersion: "0.1.0",
+        description: `${name} model`,
+        category: "other",
+        status: "beta",
+        runtimes: [{ kind: "python", python: "3.11", installer: "uv", requirements: [{ name: "torch" }] }],
+        hardware: {},
+        input: { formats: [".pdb"], required: true },
+        outputs: [{ id: "out", glob: "*.txt", required: true }],
+        ...overrides,
+    };
+    const modelDir = path.join(dir, name);
+    fs.mkdirSync(modelDir, { recursive: true });
+    fs.writeFileSync(path.join(modelDir, "manifest.yaml"), YAML.stringify(base));
+}
+describe("listAvailableModels", () => {
+    it("discovers validated manifests sorted by name", () => {
+        const dir = makeTempDir("moldesk-registry-");
+        writeManifest(dir, "zebra");
+        writeManifest(dir, "alpha");
+        const models = listAvailableModels(dir);
+        expect(models.map((m) => m.name)).toEqual(["alpha", "zebra"]);
+    });
+    it("throws DUPLICATE_MODEL_ID on duplicate names", () => {
+        const dir = makeTempDir("moldesk-dup-");
+        writeManifest(dir, "dir-a", { name: "same" });
+        writeManifest(dir, "dir-b", { name: "same" });
+        try {
+            listAvailableModels(dir);
+            expect.unreachable();
+        }
+        catch (error) {
+            expect(error).toBeInstanceOf(MoldeskError);
+            expect(error.code).toBe("DUPLICATE_MODEL_ID");
+        }
+    });
+    it("loads default manifests relative to the module, not cwd", () => {
+        const originalCwd = process.cwd();
+        const unrelatedCwd = makeTempDir("moldesk-unrelated-cwd-");
+        try {
+            process.chdir(unrelatedCwd);
+            const models = listAvailableModels();
+            const names = models.map((m) => m.name).sort();
+            expect(names).toEqual(["bindcraft2", "boltz", "diffdock", "ligandmpnn", "opendde", "proteinmpnn"]);
+        }
+        finally {
+            process.chdir(originalCwd);
+        }
+    });
+});

package/dist/models/bindcraft2/manifest.yaml

@@ -0,0 +1,178 @@
+schemaVersion: 1
+name: bindcraft2
+displayName: BindCraft2
+modelVersion: 1.0.3
+adapterVersion: 0.1.0
+description: Bounded local protein-binder campaigns with AlphaFold and ProteinMPNN/HyperMPNN.
+category: sequence-design
+status: planned
+license: BindCraft2 Source-Available License (Hosting-Restricted)
+homepage: https://github.com/PacesaLab/BindCraft2
+source:
+  repository: https://github.com/PacesaLab/BindCraft2
+  revision: 5bac63cd2d4e7ed3d5077ba4fc5966e0352038e4
+# Linux dependency resolution passed; no live accelerator verification yet.
+runtimes:
+  - kind: python
+    python: "3.12"
+    installer: uv
+    platforms: [linux-x64]
+    estimatedDownloadBytes: 10000000000
+    estimatedDiskBytes: 20000000000
+    nvidiaGpu: required
+    cuda:
+      level: required
+      minDriverCudaVersion: "12.1"
+    binaryOnly: [jaxlib, jax-cuda12-plugin, jax-cuda12-pjrt, cuequivariance-ops-cu12]
+    requirements:
+      - name: bindcraft
+        source: https://github.com/PacesaLab/BindCraft2
+        revision: 5bac63cd2d4e7ed3d5077ba4fc5966e0352038e4
+        extras: [cuda12]
+      - name: absl-py
+        version: "2.5.0"
+      - name: biotite
+        version: "1.7.1"
+      - name: biotraj
+        version: "1.2.2"
+      - name: certifi
+        version: "2026.7.22"
+      - name: charset-normalizer
+        version: "3.5.2"
+      - name: contourpy
+        version: "1.4.0"
+      - name: cuequivariance
+        version: "0.11.1"
+      - name: cuequivariance-jax
+        version: "0.11.1"
+      - name: cuequivariance-ops-cu12
+        version: "0.11.1"
+        hashes: ["dfb05a8a87ba657e5aa0019a27ceaccfd0152c69646ce5039bcc9eafc9fc0c33"]
+      - name: cycler
+        version: "0.12.1"
+      - name: dm-haiku
+        version: "0.0.17"
+      - name: einops
+        version: "0.8.2"
+      - name: fonttools
+        version: "4.66.1"
+      - name: idna
+        version: "3.20"
+      - name: jax
+        version: "0.11.2"
+      - name: jax-cuda12-pjrt
+        version: "0.11.2"
+        hashes: ["2133b3afc63307c016ae4980f166b2b3de199759363ead74f7d550eaae953463"]
+      - name: jax-cuda12-plugin
+        version: "0.11.2"
+        hashes: ["ae67a4cc49b34c575713a8311f7597f6700ec5a2b6afbdbc3db5550fb022873c"]
+      - name: jaxlib
+        version: "0.11.2"
+        hashes: ["6338a1f0956f60d02529404ac33a8070015a52635cdb6bbb15d0d199757077bb"]
+      - name: jmp
+        version: "0.0.4"
+      - name: kiwisolver
+        version: "1.5.1"
+      - name: matplotlib
+        version: "3.11.2"
+      - name: ml-collections
+        version: "1.1.0"
+      - name: ml-dtypes
+        version: "0.6.0"
+      - name: mpmath
+        version: "1.3.0"
+      - name: msgpack
+        version: "1.2.3"
+      - name: networkx
+        version: "3.7"
+      - name: numpy
+        version: "2.5.3"
+      - name: nvidia-cublas-cu12
+        version: "12.9.2.10"
+      - name: nvidia-cuda-cccl-cu12
+        version: "12.9.27"
+      - name: nvidia-cuda-cupti-cu12
+        version: "12.9.79"
+      - name: nvidia-cuda-nvcc-cu12
+        version: "12.9.86"
+      - name: nvidia-cuda-nvrtc-cu12
+        version: "12.9.86"
+      - name: nvidia-cuda-runtime-cu12
+        version: "12.9.79"
+      - name: nvidia-cudnn-cu12
+        version: "9.27.0.42"
+      - name: nvidia-cufft-cu12
+        version: "11.4.1.4"
+      - name: nvidia-cusolver-cu12
+        version: "11.7.5.82"
+      - name: nvidia-cusparse-cu12
+        version: "12.5.10.65"
+      - name: nvidia-ml-py
+        version: "13.615.71"
+      - name: nvidia-nccl-cu12
+        version: "2.32.3"
+      - name: nvidia-nvjitlink-cu12
+        version: "12.9.86"
+      - name: nvidia-nvshmem-cu12
+        version: "3.8.0"
+      - name: opt-einsum
+        version: "3.4.0"
+      - name: optax
+        version: "0.2.8"
+      - name: packaging
+        version: "26.3"
+      - name: pillow
+        version: "12.3.0"
+      - name: platformdirs
+        version: "4.12.3"
+      - name: pyparsing
+        version: "3.3.3"
+      - name: python-dateutil
+        version: "2.9.0.post0"
+      - name: pyyaml
+        version: "6.0.3"
+      - name: requests
+        version: "2.34.2"
+      - name: scipy
+        version: "1.18.1"
+      - name: six
+        version: "1.17.0"
+      - name: sympy
+        version: "1.14.0"
+      - name: tabulate
+        version: "0.10.0"
+      - name: tqdm
+        version: "4.70.1"
+      - name: urllib3
+        version: "2.8.0"
+hardware:
+  platforms: [linux-x64]
+  nvidiaGpu: required
+  cuda:
+    level: required
+    minDriverCudaVersion: "12.1"
+  minRamGb: 24
+  minDiskGb: 25
+assets:
+  - id: alphafold-parameters
+    url: https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar?generation=1670353726160664
+    source: DeepMind AlphaFold parameters 2022-12-06
+    license: CC-BY-4.0
+    sha256: 36d4b0220f3c735f3296d301152b738c9776d16981d054845a68a1370b26cfe3
+    sizeBytes: 5587968000
+    target: alphafold
+    archive: tar
+input:
+  formats: [.json]
+  required: true
+outputs:
+  - { id: campaign, glob: moldesk-campaign.json, required: true }
+  - { id: metadata, glob: campaign_metadata.json, required: true }
+  - { id: trajectories, glob: "1_Trajectories/!_Trajectories.csv", required: true }
+  - { id: trajectory_structures, glob: "1_Trajectories/*/*.cif", required: false }
+  - { id: refolded, glob: "2_Refolded/!_Refolded.csv", required: false }
+  - { id: refolded_structures, glob: "2_Refolded/*.cif", required: false }
+  - { id: ranked, glob: "3_Ranked/!_Ranked.csv", required: false }
+  - { id: accepted_structures, glob: "3_Ranked/*.cif", required: false }
+  - { id: upstream_summary, glob: summary.csv, required: true }
+  - { id: summary, glob: moldesk-summary.json, required: false }

package/dist/models/boltz/manifest.yaml

@@ -0,0 +1,155 @@
+schemaVersion: 1
+name: boltz
+displayName: Boltz-2
+modelVersion: 2.2.1
+adapterVersion: 0.2.0
+description: Joint biomolecular structure and binding-affinity prediction (Boltz team, MIT).
+category: structure-prediction
+status: beta
+license: MIT
+homepage: https://github.com/jwohlwend/boltz
+source:
+  repository: https://github.com/jwohlwend/boltz
+  revision: cb04aeccdd480fd4db707f0bbafde538397fa2ac
+# Darwin/MPS was verified end-to-end with a real install + prediction on
+# 2026-09-23 (see models/boltz/README.md for full evidence: process device
+# banner, checksummed outputs, negative-path test). Linux/CUDA is
+# structurally implemented and unit-tested but not live-verified — no NVIDIA
+# hardware was available to run it; do not treat it as verified per rule 13.
+adapterVerification:
+  lastVerifiedAt: "2026-09-23T11:22:33.984Z"
+  platforms:
+    - darwin-arm64
+  notes: >-
+    Real moldesk install + moldesk run on Apple M3 (macOS, Darwin 25.6.0),
+    re-verified after fixing two P1 review findings (checkpoints now
+    populated/checksum-verified at install time via manifest `assets:`, not
+    lazily on first run; CUDA raised from recommended to required to match
+    the mandatory CUDA probe) and three P2 findings (verifyInstallation now
+    asserts the exact pinned boltz-community version, absence of official
+    boltz, and CLI mps-accelerator support; YAML input validation uses a
+    real parser, not a regex; distribution version is explicitly asserted
+    since git-sourced installs don't get PyPI hash enforcement). Installed
+    boltz-community==2.10.12 + torch==2.14.0 (not official boltz), ran
+    boltz-fix-macos-libomp, verifyInstallation's MPS probe passed with a
+    real tensor round-trip plus the strengthened assertions above. A live
+    prediction against examples/boltz/protein.yaml completed in ~88s (all
+    checkpoints already cache-verified, zero network downloads during the
+    run — confirmed via log inspection) with PyTorch Lightning reporting
+    "GPU available: True (mps), used: True". Outputs: a parseable mmCIF and
+    confidence JSON, both checksummed in run.json. Negative tests: (1)
+    --param accelerator=gpu on this CUDA-less install failed closed
+    instantly with an actionable error; (2) a malformed YAML job
+    ("sequences: [") was rejected with a real parser error before any run
+    started. Linux/CUDA path not covered by this verification — no NVIDIA
+    hardware available.
+runtimes:
+  # Linux/CUDA: official `jwohlwend/boltz`. `--accelerator` on this pinned CLI only
+  # accepts gpu|cpu|tpu (no "mps" choice) — verified against src/boltz/main.py at
+  # this revision. `nvidiaGpu`/`cuda` are `required`, not `recommended`: the
+  # adapter's verifyInstallation runs a mandatory CUDA probe on every non-Darwin
+  # install (torch.cuda.is_available(), device count, CUDA build) with no CPU
+  # verification path implemented — declaring CUDA merely "recommended" would
+  # contradict what install actually enforces and let a CPU-only Linux host pass
+  # compatibility checks only to fail install. A genuine CPU-only Linux path is
+  # not implemented in this pass; `--param accelerator=cpu` is exposed by the
+  # pinned CLI but running it still requires this install to pass its CUDA probe.
+  - kind: python
+    python: "3.11"
+    installer: uv
+    platforms:
+      - linux-x64
+    source:
+      repository: https://github.com/jwohlwend/boltz
+      revision: cb04aeccdd480fd4db707f0bbafde538397fa2ac
+    requirements:
+      - name: boltz
+        version: 2.2.1
+        source: https://github.com/jwohlwend/boltz
+        revision: cb04aeccdd480fd4db707f0bbafde538397fa2ac
+        extras:
+          - cuda
+    nvidiaGpu: required
+    cuda:
+      level: required
+  # Darwin/MPS: `Novel-Therapeutics/boltz-community` fork, which adds an "mps"
+  # `--accelerator` choice (verified against src/boltz/main.py at this revision) and
+  # ships the `boltz-fix-macos-libomp` console script this runtime entry's
+  # `postInstall` runs after dependency install. No `nvidiaGpu`/`cuda` here: this
+  # platform-runtime entry genuinely has no CUDA requirement.
+  - kind: python
+    python: "3.11"
+    installer: uv
+    platforms:
+      - darwin-arm64
+    source:
+      repository: https://github.com/Novel-Therapeutics/boltz-community
+      revision: 401f18150cc7184b7e1bb37239a25035ef6b3a57
+    requirements:
+      - name: boltz-community
+        version: 2.10.12
+        source: https://github.com/Novel-Therapeutics/boltz-community
+        revision: 401f18150cc7184b7e1bb37239a25035ef6b3a57
+      # Newest stable PyPI torch as of 2026-09-23, satisfies boltz-community's own
+      # `torch>=2.2` pyproject constraint and its README's documented "PyTorch 2.6+"
+      # compatibility statement. cp311 wheel to match this entry's `python: "3.11"`.
+      # No credible MPS-blocking regression found for 2.14.0 on shipping macOS
+      # versions (see models/boltz/README.md for research notes).
+      - name: torch
+        version: "2.14.0"
+        hashes:
+          - ae530ddd3f3b94248b77f1fd3313c4f3405bd0d17283d505b81574816767133a
+    postInstall:
+      - boltz-fix-macos-libomp
+# Boltz-2's own CLI (both distributions, identical logic) lazily downloads these
+# from HuggingFace's *mutable* `resolve/main/...` URLs on first prediction — that
+# both defers download past install time and has no fixed content to verify
+# against. Since upstream provides no immutable/checksum-pinned download itself,
+# these assets are instead pinned here to an exact HuggingFace repo commit
+# (boltz-community/boltz-2 @ 6fdef46d763fee7fbb83ca5501ccceff43b85607) with sha256
+# digests read from that commit's `X-Linked-ETag` (HF's convention for an LFS
+# file's sha256) and independently confirmed by hashing a real download of each
+# file byte-for-byte. Materialized by the existing checksum-verified asset
+# pipeline into `assets/boltz-cache/`, which is what the adapter passes as
+# `--cache` — so by the time a prediction runs, Boltz's own downloader finds
+# every file already present and verified, and performs no network access.
+assets:
+  - id: boltz2-ccd
+    url: https://huggingface.co/boltz-community/boltz-2/resolve/6fdef46d763fee7fbb83ca5501ccceff43b85607/mols.tar
+    source: https://huggingface.co/boltz-community/boltz-2
+    sha256: 39e076d96dbec6b4e86982bbda16f3a53a2a60c9bdc17828d88f6f9a0c7d1fd7
+    sizeBytes: 1855662080
+    archive: tar
+    target: boltz-cache
+  - id: boltz2-conf-checkpoint
+    url: https://huggingface.co/boltz-community/boltz-2/resolve/6fdef46d763fee7fbb83ca5501ccceff43b85607/boltz2_conf.ckpt
+    source: https://huggingface.co/boltz-community/boltz-2
+    sha256: 090e82ac8c92f5e943fa1b39e7410a44027bea7243c0bbb3caa67a77fc1428e1
+    sizeBytes: 2286561469
+    target: boltz-cache/boltz2_conf.ckpt
+  - id: boltz2-affinity-checkpoint
+    url: https://huggingface.co/boltz-community/boltz-2/resolve/6fdef46d763fee7fbb83ca5501ccceff43b85607/boltz2_aff.ckpt
+    source: https://huggingface.co/boltz-community/boltz-2
+    sha256: dcc5cd3722b1c9eaa34267e4ae32f55cbbf1963f4c19319381ccfa30fdd2ca9e
+    sizeBytes: 2062139170
+    target: boltz-cache/boltz2_aff.ckpt
+hardware:
+  platforms:
+    - darwin-arm64
+    - linux-x64
+input:
+  formats:
+    - .yaml
+    - .yml
+    - .fasta
+  required: true
+outputs:
+  - id: structures
+    glob: "boltz_results_*/predictions/*/*.cif"
+    required: true
+  - id: confidence
+    glob: "boltz_results_*/predictions/*/confidence_*.json"
+    required: true
+  - id: affinity
+    glob: "boltz_results_*/predictions/*/affinity_*.json"
+    required: false