updating install instructions

Author: borisbolliet

README.md

@@ -32,11 +32,24 @@ Our project is funded by the [Cambridge Centre for Data-Driven Discovery Acceler
 
 If you plan to modify the code, follow these steps:
 
-Clone and install our package from `PyPi`:
+An old version of `cmbagent` is available on `PyPi`, however we are not maintaining it at this time due to intensive development on the new version.
+
+Thus, we recommend cloning the repository and installing it from source. You need `cmbagent` and our fork of `ag2` to get things working.
 
 ```bash
-pip install cmbagent
-```
+git clone https://github.com/CMBAgents/cmbagent.git
+git clone https://github.com/CMBAgents/ag2.git
+cd cmbagent
+pip install -e .
+cd ..
+cd ag2
+pip install -e .
+```   
+
+We apologize for some bugs that you may encounter we hope to release a stable version before the end of 2025.
+
+
+
 
 Before pip installing cmbagent, creating a virual environment is encouraged: 
 ```bash

docs/README.md

@@ -1,20 +1,23 @@
 ## Installation
 
-To install cmbagent, follow these steps:
 
-Clone and install our package PyPi:
+An old version of `cmbagent` is available on `PyPi`, however we are not maintaining it at this time due to intensive development on the new version.
 
-```bash
-pip install cmbagent
-```
-
-Or clone the repository and install it locally (advised if you want to develop the package, or if you have issues with the installation):
+Thus, we recommend cloning the repository and installing it from source. You need `cmbagent` and our fork of `ag2` to get things working.
 
 ```bash
 git clone https://github.com/CMBAgents/cmbagent.git
+git clone https://github.com/CMBAgents/ag2.git
 cd cmbagent
 pip install -e .
-```
+cd ..
+cd ag2
+pip install -e .
+```   
+
+We apologize for some bugs that you may encounter we hope to release a stable version before the end of 2025.
+
+
 
 Creating a virual environment is envouraged: 
 ```bash

docs/notebooks/1_getting_started.ipynb

@@ -33,7 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "582f8e04-11ff-43f5-ae7c-681233f7fe8c",
+   "id": "a1a9f668",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,6 +42,26 @@
     "!pip install -e ."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "65c3e1cd",
+   "metadata": {},
+   "source": [
+    "## Clone and install our fork of ag2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "582f8e04-11ff-43f5-ae7c-681233f7fe8c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!git clone https://github.com/CMBAgents/ag2.git\n",
+    "%cd ag2\n",
+    "!pip install -e ."
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "01402b0f-8098-4416-b83c-300a694d9691",

docs/notebooks/4_your_rag.ipynb

@@ -885,7 +885,7 @@
      ]
     },
     {
-     "name": "stdin",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Provide feedback to cmbagent. Type 'proceed' to continue as suggested or type your suggestion, or type 'exit' to end the conversation:  proceed\n"
@@ -999,7 +999,7 @@
      ]
     },
     {
-     "name": "stdin",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Provide feedback to cmbagent. Type 'proceed' to continue as suggested or type your suggestion, or type 'exit' to end the conversation:  Provide more detailed statistical information from the documents\n"
@@ -1113,7 +1113,7 @@
      ]
     },
     {
-     "name": "stdin",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Provide feedback to cmbagent. Type 'proceed' to continue as suggested or type your suggestion, or type 'exit' to end the conversation:  Collect extensive information, which we can summarize into a plot. Your answer should be several paragraphs long\n"
@@ -1237,7 +1237,7 @@
      ]
     },
     {
-     "name": "stdin",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Provide feedback to cmbagent. Type 'proceed' to continue as suggested or type your suggestion, or type 'exit' to end the conversation:  now ask engineer to provide a plot that summarizes this\n"
@@ -1385,7 +1385,7 @@
      ]
     },
     {
-     "name": "stdin",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Provide feedback to cmbagent. Type 'proceed' to continue as suggested or type your suggestion, or type 'exit' to end the conversation:  execute\n"
@@ -1499,7 +1499,7 @@
      ]
     },
     {
-     "name": "stdin",
+     "name": "stdout",
      "output_type": "stream",
      "text": [
       "Provide feedback to cmbagent. Type 'proceed' to continue as suggested or type your suggestion, or type 'exit' to end the conversation:  exit\n"