remove sphinx reference anchors from top of notebooks

these weren't being picked up and got rendered instead instead, include sphinx anchor in the nblink prolog so this is programmatically created also rename some section headings in RFE alchemical planners so there aren't duplicated titles, this was automatically creating reference anchors then creating a warning on duplicate references
OpenFreeEnergy · Apr 10, 2024 · 5eabeab · 5eabeab
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diff --git a/cookbook/choose_protocol.ipynb b/cookbook/choose_protocol.ipynb
@@ -1,13 +1,5 @@
 {
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-   "metadata": {},
-   "source": [
-    ".. _cookbook_choose_config_protocol:"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "8efbded0-0b69-4392-b8df-7afbd817d733",

diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
@@ -1,13 +1,5 @@
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  "cells": [
-  {
-   "cell_type": "raw",
-   "id": "9fb7586c",
-   "metadata": {},
-   "source": [
-    ".. _cookbook_create_alchemicalnetwork:"
-   ]
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diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb
@@ -1,13 +1,5 @@
 {
  "cells": [
-  {
-   "cell_type": "raw",
-   "id": "c6a2c302",
-   "metadata": {},
-   "source": [
-    ".. _cookbook_planning_ligandnetwork:"
-   ]
-  },
   {
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    "id": "035c0099-6892-4ed2-b0d6-80b1c247c1e7",

diff --git a/cookbook/hand_write_ligand_network.ipynb b/cookbook/hand_write_ligand_network.ipynb
@@ -1,13 +1,5 @@
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  "cells": [
-  {
-   "cell_type": "raw",
-   "id": "554bc9f7",
-   "metadata": {},
-   "source": [
-    ".. _cookbook_ligandnetworks_by_hand:"
-   ]
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diff --git a/cookbook/ligandnetwork_vis.ipynb b/cookbook/ligandnetwork_vis.ipynb
@@ -1,13 +1,5 @@
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-   "id": "68723119",
-   "metadata": {},
-   "source": [
-    ".. _cookbook_viz_ligandnetworks:"
-   ]
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diff --git a/cookbook/network_from_orion_fepp.ipynb b/cookbook/network_from_orion_fepp.ipynb
@@ -1,13 +1,5 @@
 {
  "cells": [
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-   "cell_type": "raw",
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-   "metadata": {},
-   "source": [
-    ".. _cookbook_network_from_orion_fepp:"
-   ]
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diff --git a/cookbook/rfe_alchemical_planners.ipynb b/cookbook/rfe_alchemical_planners.ipynb
@@ -1,13 +1,5 @@
 {
  "cells": [
-  {
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-   "id": "6cf8c16b",
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-    ".. _cookbook_rfe_network_planners:"
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@@ -135,7 +127,7 @@
    "id": "e96f95fb",
    "metadata": {},
    "source": [
-    "### Building the Network Planner and getting an AlchemicalNetwork\n",
+    "### Building the RBFEAlchemicalNetworkPlanner and getting an AlchemicalNetwork\n",
     "\n",
     "Finally we can use the `RBFEAlchemicalNetworkPlanner` to create an `AlchemicalNetwork`.\n",
     "\n",
@@ -188,7 +180,7 @@
    "id": "dc5f6bcb",
    "metadata": {},
    "source": [
-    "### Building the Network Planner and getting an AlchemicalNetwork\n",
+    "### Building the RHFEAlchemicalNetworkPlanner and getting an AlchemicalNetwork\n",
     "\n",
     "Here we use the same ChemicalComponents, atom mapper, scorer, and network planner as used in the RBFE section above.\n",
     "\n",

diff --git a/cookbook/user_charges.ipynb b/cookbook/user_charges.ipynb
@@ -1,13 +1,5 @@
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