docs: show example of passing media composition in FBA

Author: pablormier

.gitignore

@@ -6,6 +6,8 @@ my_graph.pkl.gz
 tests/_notebooks/
 .asv/results/
 CLAUDE.md
+benchmarks/
+resources/
 
 
 ########################

.pre-commit-config.yaml

@@ -20,7 +20,7 @@ repos:
     -   id: pre-commit-update
 
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
+    rev: v0.15.13
     hooks:
     -   id: ruff
         args:
@@ -50,7 +50,7 @@ repos:
         stages: [commit-msg]
 
 -   repo: https://github.com/python-poetry/poetry
-    rev: 2.3.2
+    rev: 2.4.1
     hooks:
     -   id: poetry-check
     -   id: poetry-lock

docs/guide/metabolism/flux-balance-analysis.ipynb

@@ -6121,6 +6121,86 @@
     "G.plot(custom_edge_attr=cn.pl.flow_style(P), layout=\"fdp\")"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "custom-media-01",
+   "metadata": {},
+   "source": [
+    "## Passing a custom media composition\n",
+    "\n",
+    "Media composition is represented as sample-specific reaction bounds. In CORNETO, each sample passed to `MultiSampleFBA` can include exchange reactions with `lower_bound` and `upper_bound` values. For exchange reactions in this model, uptake is a negative flux, so a more negative lower bound allows more uptake.\n",
+    "\n",
+    "The same data object can also include the biomass objective, which lets us solve several media conditions in one FBA problem."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "custom-media-02",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "media = {\n",
+    "    \"glucose_rich\": {\n",
+    "        \"EX_glc__D_e\": {\"lower_bound\": -10.0, \"upper_bound\": 1000.0},\n",
+    "        \"EX_o2_e\": {\"lower_bound\": -20.0, \"upper_bound\": 1000.0},\n",
+    "    },\n",
+    "    \"glucose_limited\": {\n",
+    "        \"EX_glc__D_e\": {\"lower_bound\": -2.0, \"upper_bound\": 1000.0},\n",
+    "        \"EX_o2_e\": {\"lower_bound\": -20.0, \"upper_bound\": 1000.0},\n",
+    "    },\n",
+    "}\n",
+    "\n",
+    "media_data = cn.Data.from_cdict(\n",
+    "    {\n",
+    "        condition: {\n",
+    "            \"Biomass_Ecoli_core\": {\"role\": \"objective\"},\n",
+    "            **bounds,\n",
+    "        }\n",
+    "        for condition, bounds in media.items()\n",
+    "    }\n",
+    ")\n",
+    "\n",
+    "media_data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "custom-media-03",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "media_problem = FBA().build(G, media_data)\n",
+    "media_problem.solve(solver=\"scipy\");"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "custom-media-04",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reaction_ids = [\"Biomass_Ecoli_core\", \"EX_glc__D_e\", \"EX_o2_e\"]\n",
+    "reaction_index = {rid: next(iter(G.get_edges_by_attr(\"id\", rid))) for rid in reaction_ids}\n",
+    "\n",
+    "pd.DataFrame(\n",
+    "    {\n",
+    "        condition: {rid: media_problem.expr.flow[reaction_index[rid], i].value for rid in reaction_ids}\n",
+    "        for i, condition in enumerate(media_data.samples)\n",
+    "    }\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "custom-media-05",
+   "metadata": {},
+   "source": [
+    "The custom bounds override the default exchange bounds stored in the graph for the matching sample. Here, glucose-limited medium restricts `EX_glc__D_e` uptake and the optimal biomass flux decreases accordingly."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "3f320215-867e-4882-bd9d-5dc94f629054",