Add ref tags to all cookbooks that don't have them

OpenFreeEnergy · Apr 5, 2024 · 21c5884 · 21c5884
1 parent 3d0d024
commit 21c5884
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Showing 10 changed files with 80 additions and 74 deletions.
diff --git a/cookbook/choose_protocol.ipynb b/cookbook/choose_protocol.ipynb
@@ -1,10 +1,17 @@
 {
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+  {
+   "cell_type": "raw",
+   "id": "0765a7c9",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_choose_config_protocol:"
+   ]
+  },
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@@ -35,7 +42,6 @@
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@@ -50,7 +56,6 @@
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@@ -64,7 +69,6 @@
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@@ -89,7 +93,6 @@
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@@ -108,7 +111,6 @@
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@@ -130,7 +132,6 @@
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@@ -145,7 +146,6 @@
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@@ -160,7 +160,6 @@
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@@ -175,7 +174,6 @@
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@@ -250,7 +248,6 @@
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@@ -265,7 +262,6 @@
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@@ -288,7 +284,6 @@
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@@ -303,7 +298,6 @@
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@@ -406,7 +400,6 @@
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@@ -440,7 +433,6 @@
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@@ -476,7 +468,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
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diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "9fb7586c",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_create_alchemicalnetwork:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "b89fdb9a-24fe-4aeb-9390-a359dae6cc9b",
@@ -22,7 +30,6 @@
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@@ -109,7 +116,6 @@
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@@ -265,7 +271,6 @@
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@@ -284,7 +289,6 @@
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@@ -298,7 +302,6 @@
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@@ -315,7 +318,6 @@
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@@ -350,7 +352,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
   },
   "widgets": {
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diff --git a/cookbook/generate_ligand_network.ipynb b/cookbook/generate_ligand_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "c6a2c302",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_planning_ligandnetwork:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "035c0099-6892-4ed2-b0d6-80b1c247c1e7",
@@ -259,7 +267,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.8"
+   "version": "3.11.6"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

diff --git a/cookbook/generate_lomap_network.ipynb b/cookbook/generate_lomap_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "a41f6896",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_ligandnetwork_lomap:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "035c0099-6892-4ed2-b0d6-80b1c247c1e7",

diff --git a/cookbook/hand_write_ligand_network.ipynb b/cookbook/hand_write_ligand_network.ipynb
@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "554bc9f7",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_ligandnetworks_by_hand:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "bf739d70-3249-42b3-a352-8a41f8f8c667",
@@ -266,7 +274,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
   },
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diff --git a/cookbook/ligandnetwork_vis.ipynb b/cookbook/ligandnetwork_vis.ipynb
@@ -1,10 +1,17 @@
 {
  "cells": [
+  {
+   "cell_type": "raw",
+   "id": "68723119",
+   "metadata": {},
+   "source": [
+    ".. _cookbook_viz_ligandnetworks:"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "a2f0ee60-1060-4ca9-b0ff-529348dbc0e6",
    "metadata": {
-    "editable": true,
     "slideshow": {
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@@ -26,7 +33,6 @@
    "cell_type": "markdown",
    "id": "d4fe6c50-3971-4b9d-bc2f-71b5deb58fd4",
    "metadata": {
-    "editable": true,
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     },
@@ -41,7 +47,6 @@
    "execution_count": 1,
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@@ -71,7 +76,6 @@
    "execution_count": 2,
    "id": "594364f7-00ab-4497-bf5e-74cb497802e7",
    "metadata": {
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     },
@@ -430,7 +434,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.5"
+   "version": "3.11.6"
   },
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