default text improvements + some design options

theislab · Feb 17, 2025 · 2149d6a · 2149d6a
1 parent 29f6bed
commit 2149d6a
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diff --git a/jupyter-book/_static/default_text_env_setup.md b/jupyter-book/_static/default_text_env_setup.md
@@ -1,16 +1,20 @@
-1. **Save the yml content**:
+1. **Install conda**:
+
+   - Before creating the environment, ensure that [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) is installed on your system.
+
+2. **Save the yml content**:
 
    - Copy the content from the yml tab into a file named `environment.yml`.
 
-2. **Create the environment**:
+3. **Create the environment**:
 
    - Open a terminal or command prompt.
    - Run the following command:
      ```bash
      conda env create -f environment.yml
      ```
 
-3. **Activate the environment**:
+4. **Activate the environment**:
 
    - After the environment is created, activate it using:
      ```bash
@@ -21,7 +25,7 @@
      name: <environment_name>
      ```
 
-4. **Verify the installation**:
+5. **Verify the installation**:
    - Check that the environment was created successfully by running:
      ```bash
      conda env list

diff --git a/jupyter-book/conditions/gsea_pathway.ipynb b/jupyter-book/conditions/gsea_pathway.ipynb
@@ -4,25 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "``````{admonition} How do I set up an environment with the yml file used in this chapter?\n",
-    ":class: dropdown\n",
-    "\n",
-    "`````{tab-set}\n",
-    "   \n",
-    "````{tab-item} Steps\n",
-    "```{include} ../_static/default_text_env_setup.md\n",
-    "```\n",
-    "````\n",
-    "\n",
-    "````{tab-item} yml\n",
-    "```{literalinclude} gsea_pathway.yml\n",
-    ":language: yaml\n",
-    "```\n",
-    "````\n",
-    "\n",
-    "`````\n",
-    "\n",
-    "``````"
+    "{bdg-link-primary-line}`Env Setup <#this-is-a-test>`"
    ]
   },
   {
@@ -32,7 +14,7 @@
    "source": [
     "(enrichment-analysis)=\n",
     "\n",
-    "# Gene set enrichment and pathway analysis "
+    "# Gene set enrichment and pathway analysis"
    ]
   },
   {
@@ -2116,6 +2098,33 @@
     "session_info.show()"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "(this-is-a-test)=\n",
+    "## Environment setup\n",
+    "\n",
+    "``````{admonition} How do I set up an environment with the yml file used in this chapter?\n",
+    "\n",
+    "`````{tab-set}\n",
+    "   \n",
+    "````{tab-item} Steps\n",
+    "```{include} ../_static/default_text_env_setup.md\n",
+    "```\n",
+    "````\n",
+    "\n",
+    "````{tab-item} yml\n",
+    "```{literalinclude} gsea_pathway.yml\n",
+    ":language: yaml\n",
+    "```\n",
+    "````\n",
+    "\n",
+    "`````\n",
+    "\n",
+    "``````"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/jupyter-book/conditions/perturbation_modeling.ipynb b/jupyter-book/conditions/perturbation_modeling.ipynb
@@ -2,7 +2,15 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "cc96c027",
+   "id": "understanding-memory",
+   "metadata": {},
+   "source": [
+    "# Perturbation modeling"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d9e767e9",
    "metadata": {},
    "source": [
     "``````{admonition} How do I set up an environment with the yml file used in this chapter?\n",
@@ -26,14 +34,6 @@
     "``````"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "understanding-memory",
-   "metadata": {},
-   "source": [
-    "# Perturbation modeling"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "5e1ff7c8",