Implement full_build orchestration with manifest, domestication, assembly_lvl1, transformation, and plating

notebooks/full_build_quickstart.ipynb

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+{
+  "cells": [
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "# BuildCompiler `full_build(...)` Quickstart\n",
+        "\n",
+        "This notebook shows how to run the high-level `BuildCompiler.full_build(...)` workflow end-to-end.\n",
+        "\n",
+        "The orchestrated stages are:\n",
+        "1. domestication (only when missing parts are detected)\n",
+        "2. assembly level 1\n",
+        "3. transformation\n",
+        "4. plating\n",
+        "\n",
+        "`assembly_lvl2` is intentionally skipped for now and recorded as skipped in the output manifest."
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## 1) Imports and setup"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "from pathlib import Path\n",
+        "import sbol2\n",
+        "\n",
+        "from buildcompiler.buildcompiler import BuildCompiler"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## 2) Load an SBOL design document\n",
+        "\n",
+        "Replace the path below with your own SBOL file containing one or more abstract designs."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "doc = sbol2.Document()\n",
+        "# Example: doc.read(\"path/to/your/designs.xml\")"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## 3) Construct the compiler\n",
+        "\n",
+        "Provide one or more SynBioHub collections that contain available parts/backbones/implementations."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "compiler = BuildCompiler(\n",
+        "    collections=[\n",
+        "        # \"https://synbiohub.org/public/example_collection\",\n",
+        "    ],\n",
+        "    sbh_registry=\"https://synbiohub.org\",\n",
+        "    auth_token=\"\",\n",
+        "    sbol_doc=doc,\n",
+        ")"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## 4) Full build with concrete designs (list of `ComponentDefinition`)"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "# Example lookup by displayId (adjust to your document)\n",
+        "# design_1 = doc.getComponentDefinition(\"design_1\")\n",
+        "# design_2 = doc.getComponentDefinition(\"design_2\")\n",
+        "# designs = [design_1, design_2]\n",
+        "\n",
+        "# result = compiler.full_build(\n",
+        "#     designs=designs,\n",
+        "#     results_dir=Path(\"results/full_build\"),\n",
+        "#     chassis_name=\"E_coli_DH5alpha\",\n",
+        "#     protocol_type=\"manual\",\n",
+        "#     plating_params={\n",
+        "#         \"incubation_temperature_c\": 37,\n",
+        "#         \"incubation_time_h\": 16,\n",
+        "#     },\n",
+        "#     product_name_prefix=\"build\",\n",
+        "#     overwrite=True,\n",
+        "# )\n",
+        "\n",
+        "# print(result[\"status\"])\n",
+        "# print(result[\"manifest_path\"])\n",
+        "# print(result[\"zip_path\"])"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## 5) Full build with a `CombinatorialDerivation`\n",
+        "\n",
+        "Use this when your input is combinatorial. `full_build(...)` expands the derivation into concrete variants automatically."
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "# derivation = doc.combinatorialderivations[0]\n",
+        "\n",
+        "# combo_result = compiler.full_build(\n",
+        "#     designs=derivation,\n",
+        "#     results_dir=Path(\"results/full_build_combinatorial\"),\n",
+        "#     chassis_name=\"E_coli_DH5alpha\",\n",
+        "#     protocol_type=\"automated\",\n",
+        "#     plating_params={\n",
+        "#         \"replicates\": 1,\n",
+        "#         \"number_dilutions\": 1,\n",
+        "#         \"volume_colony\": 6,\n",
+        "#         \"thermocycler_starting_well\": 0,\n",
+        "#     },\n",
+        "#     product_name_prefix=\"combo_build\",\n",
+        "#     overwrite=True,\n",
+        "# )\n",
+        "\n",
+        "# print(combo_result[\"status\"])\n",
+        "# print(combo_result[\"manifest_path\"])"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "## 6) Return shape and generated files"
+      ]
+    },
+    {
+      "cell_type": "code",
+      "execution_count": null,
+      "metadata": {},
+      "outputs": [],
+      "source": [
+        "# Top-level keys in returned result:\n",
+        "# stage, status, results_dir, zip_path, manifest_path, sbol_path,\n",
+        "# inputs, domestication, assembly_lvl1, transformation, plating, skipped, errors\n",
+        "\n",
+        "# Files written under <results_dir>:\n",
+        "# - full_build_manifest.json\n",
+        "# - full_build_results.zip\n",
+        "# - sbol/full_build.xml\n",
+        "# - domestication/* and assembly_lvl1/* plating/transformation artifacts"
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "name": "python",
+      "version": "3"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 5
+}