Plugins added (#45)

* plugins --------- Co-authored-by: Phil Downey <[email protected]> Co-authored-by: Brian Duenas <[email protected]>
acceleratedscience · May 31, 2024 · 7eed012 · 7eed012
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diff --git a/README.md b/README.md
@@ -118,29 +118,29 @@ If you get an error when running `init_magic`, you may first need to setup the d
 
 ## Table of Contents <!-- omit from toc -->
 
-<a href="#openad-beta">OpenAD Beta</a>
-
-<a href="#installation">Installation</a>
-<li><a href="#getting-started---cli">Getting Started - CLI</a></li>
-<li><a href="#getting-started---jupyter">Getting Started - Jupyter</a></li>
-<li><a href="#Setting up Jupyter">#setting-up-jupyter</a><br></li>
-<li><a href="#launching-openad-in-jupyter">Launching OpenAD in Jupyter</a><br></li>
-<a href="#interacting-with-the-toolkits">Interacting with the Toolkits</a>
-<li><a href="#registration">Registration</a></li>
-<li><a href="#adding-a-toolkit">Adding a Toolkit</a></li>
-<li><a href="#sample-commands">Sample Commands</a></li>
-<li><a href="#running-bash-commands-cli">Running Bash Commands (CLI)</a></li>
-<a href="#ai-assistant">AI AssistantL</a>
-<a href="#for-developers">For Developer</a>
-<li><a href="#installation-for-development">Installation for Development</a></li>
-<li><a href="#testing-a-branch">Testing a branch</a></li>
-<a href="#installing-on-windows">Installing on Windows</a>
-<li><a href="#before-you-start">Before you start</a></li>
-<li><a href="#installing-wsl">Installing WSL</a></li>
-<a href="#linux-notes">Linux Notes</a>
-
-
----
+<!-- toc -->
+
+- [OpenAD Beta](#openad-beta)
+- [Installation](#installation)
+- [Getting Started - CLI](#getting-started---cli)
+- [Getting Started - Jupyter](#getting-started---jupyter)
+  - [Setting up Jupyter](#setting-up-jupyter)
+  - [Launching OpenAD in Jupyter](#launching-openad-in-jupyter)
+- [Interacting with the Toolkits](#interacting-with-the-toolkits)
+    - [Registration](#registration)
+    - [Adding a Toolkit](#adding-a-toolkit)
+    - [Sample Commands](#sample-commands)
+    - [Running Bash Commands (CLI)](#running-bash-commands-cli)
+- [AI Assistant](#ai-assistant)
+- [For Developers](#for-developers)
+  - [Installation for Development](#installation-for-development)
+  - [Testing a branch](#testing-a-branch)
+- [Installing on Windows](#installing-on-windows)
+  - [Before you start](#before-you-start)
+  - [Installing WSL](#installing-wsl)
+- [Linux Notes](#linux-notes)
+
+<!-- tocstop -->
 
 <br>
 
@@ -160,7 +160,7 @@ Ensure you're running Python 3.10 or 3.11. There's multiple ways of updating Pyt
 
 1.  **Step 1: Set up your virtual environment** (optional)<br>
 
-        python -m venv ~/ad-venv
+        python3.11 -m venv ~/ad-venv
         source ~/ad-venv/bin/activate
 
     > **Note:** To exit the virtual environment, you can run `deactivate`
@@ -169,16 +169,12 @@ Ensure you're running Python 3.10 or 3.11. There's multiple ways of updating Pyt
 
         pip install openad
 
-    if you are going to use the model services you will need to have an AWS CLI enabled on your machine and follow the below steps to install and check skypilot is enabled on your machine:
-
-        A. Install Sky  with `pip install "skypilot-nightly[aws]"`
-
-        B. setup your aws command line
+    if you are going to use the model services you will need to have an AWS CLI enabled on your machine and follow the below steps to  check skypilot is enabled to deploy on aws on your machine:
 
-        C. run `sky check`
+        A. run `sky check`
 
         
-    Services will take about 10 minutes to deploy it can be monitored through the controllers logs.
+    If you launch Model Services will take about 10 minutes to deploy it can be monitored through the controllers logs.
         e.g. `sky serve logs sky-service-0af4  --controller`
 
 <br>

diff --git a/docs/output/csv/commands.csv b/docs/output/csv/commands.csv
@@ -70,8 +70,8 @@ model service config '<service_name>'|<service_name>;Model
 model catalog list;Model
 uncatalog model service '<service_name>'|<service_name>;Model
 catalog model service from (remote) '<path or github>' as  '<service_name>'|<service_name>;Model
-model service up '<service_name>'|<service_name>;Model
-model service local up '<service_name>'|<service_name>;Model
+model service up '<service_name>'|<service_name> [no_gpu]};Model
+model service local up '<service_name>'|<service_name> ;Model
 model service down '<service_name>'|<service_name>;Model
 search for similar molecules to '<smiles>' [ save as '<filename.csv>' ];Search Molecules
 search for molecules in patents from list ['<patent1>', '<patent2>', ...] | dataframe <dataframe_name> | file '<filename.csv>' [ save as '<filename.csv>' ];Search Molecules

diff --git a/docs/output/markdown/commands.md b/docs/output/markdown/commands.md
@@ -482,25 +482,34 @@ uncatalog a model service  <br>
 `uncatalog model service 'gen'` <br><br>
 
 `catalog model service from (remote) '<path or github>' as  '<service_name>'|<service_name>`{: .cmd }
-catalog a model service from a path or github or remotely from an existing OpenAD service.   <br> 
- Example:  <br> 
+catalog a model service from a path or github or remotely from an existing OpenAD service. <br> 
 
-`catalog model service from '[email protected]:acceleratedscience/generation_inference_service.git' as 'gen'` <br><br>
+Example: <br> 
 
-`model service up '<service_name>'|<service_name>`{: .cmd }
-launch a model service   <br> 
- Examples:  <br> 
-`model service up gen`  <br> 
-`model service up 'gen'` <br><br>
+-`catalog model service from '[email protected]:acceleratedscience/generation_inference_service.git' as 'gen'` <br> 
+
+or to catalog a remote service shared with you: <br> 
+-`catalog model service from remote 'http://54.235.3.243:30001' as gen` <br><br>
+
+`model service up '<service_name>'|<service_name> [no_gpu]}`{: .cmd }
+launches a cataloged model service. <br> 
+If you do not want to launch a service with GPU you should specify `no_gpu` at the end of the command. <br> 
+Examples: <br> 
+
+-`model service up gen` <br> 
+
+-`model service up 'gen'` <br> 
+
+-`model service up gen no_gpu` <br><br>
 
 `model service local up '<service_name>'|<service_name>`{: .cmd }
-launch a model service locally  <br> 
+launch a model service locally. <br> 
 
-Example: <br> 
- ` model service local up gen` <br><br>
+            Example: <br> 
+              ` model service local up gen` <br><br>
 
 `model service down '<service_name>'|<service_name>`{: .cmd }
-bring down a model service   <br> 
+Bring down a model service   <br> 
  Examples:  <br> 
 
 `model service down gen`  <br> 

diff --git a/docs/output/markdown/installation.md b/docs/output/markdown/installation.md
@@ -28,6 +28,10 @@ Get started with Jupyter:
     init_examples
     jupyter lab ~/openad_notebooks/Table_of_Contents.ipynb
 
+If you get an error when running `init_magic`, you may first need to setup the default iPython profile for magic commands.
+
+    ipython profile create
+
 <br>
 
 ---
@@ -60,8 +64,6 @@ Get started with Jupyter:
   - [Installing WSL](#installing-wsl)
 - [Linux Notes](#linux-notes)
 
----
-
 <br>
 
 # Installation
@@ -80,7 +82,7 @@ Ensure you're running Python 3.10 or 3.11. There's multiple ways of updating Pyt
 
 1.  **Step 1: Set up your virtual environment** (optional)<br>
 
-        python -m venv ~/ad-venv
+        python3.11 -m venv ~/ad-venv
         source ~/ad-venv/bin/activate
 
     > **Note:** To exit the virtual environment, you can run `deactivate`
@@ -89,6 +91,13 @@ Ensure you're running Python 3.10 or 3.11. There's multiple ways of updating Pyt
 
         pip install openad
 
+    if you are going to use the model services you will need to have an AWS CLI enabled on your machine and follow the below steps to  check skypilot is enabled to deploy on aws on your machine:
+
+        A. run `sky check`
+
+    If you launch Model Services will take about 10 minutes to deploy it can be monitored through the controllers logs.
+        e.g. `sky serve logs sky-service-0af4  --controller`
+
 <br>
 
 # Getting Started - CLI
@@ -187,7 +196,7 @@ The following commands only need to be run once after installation:
 
 # Interacting with the Toolkits
 
-OpenAD integrates with `DS4SD`, `RXN`, and has placeholder support for `ST4SD`.
+OpenAD integrates with `DS4SD`, `RXN`, and has placeholder support for  `ST4SD`.
 
 <div class="notice" style="margin-top: 16px;" markdown="block">
 
@@ -277,8 +286,14 @@ To run a command in bash mode, prepend it with `openad` and make sure to escape
 
 To enable our AI assistant, you'll need an account with OpenAI. There is a one month free trial.
 
+This is available for IBM BAM service and Openai.
+
 > **Note:** watsonx coming soon
 
+For IBM BAM simply used your supplied API key if you have BAM access
+
+For OpenAI
+
 1. Go to [platform.openai.com](https://platform.openai.com) and create an account
 
 2. Click on the profile icon in the top right and choose "View API keys"
@@ -287,8 +302,6 @@ To enable our AI assistant, you'll need an account with OpenAI. There is a one m
 
 4. Run `tell me` to be prompted for your OpenAI API credentials
 
-<a href="https://raw.githubusercontent.com/acceleratedscience/open-ad-toolkit/main/assets/openai-api-key.png" target="_blank"><img src="https://raw.githubusercontent.com/acceleratedscience/open-ad-toolkit/main/assets/openai-api-key.png" /></a>
-
 <br>
 
 # For Developers
@@ -378,7 +391,7 @@ Install WSL and create a user called 'openad' or one of your choosing.
 
     wsl --install Ubuntu-22.04
 
-**Optional:** To setup an Ubuntu Python environment from scratch, continue to [Linux Notes](#linux-notes)
+**Optional:** To setup an Ubuntu Python environment from scratch, continue to <a href="#linux-notes">Linux Notes</a>
 
 <br>
 
@@ -393,6 +406,8 @@ If you wish to setup an Ubuntu Python environment from scratch, run:
     sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.11 100
     sudo pip install pip --upgrade
 
+You will need to restart your Linux session before running `pip install openad` so that the python libraries are in your path.
+
 If you get an error when running `init_magic`, you may first need to setup the default iPython profile for magic commands.
 
     ipython profile create
diff --git a/openad/app/main.py b/openad/app/main.py
@@ -52,6 +52,26 @@
 from openad.app.global_var_lib import GLOBAL_SETTINGS
 from openad.app.global_var_lib import MEMORY
 
+# Load available_Plugins modules
+import pkg_resources
+import inspect
+import importlib
+
+
+PLUGIN_CLASS_LIST = []
+installed_packages = pkg_resources.working_set
+installed_packages_list = [
+    i.key for i in installed_packages if i.key.startswith("openad-plugin-") or i.key.startswith("openad_plugin_")
+]
+
+for module_name in installed_packages_list:
+    try:
+        module_name = module_name.replace("-", "_")
+        module = importlib.import_module(f"{module_name}.plugins")
+        PLUGIN_CLASS_LIST.append(getattr(module, "openad_plugins"))
+    except:
+        output_error("ignoring addin, incorrect class definition")
+
 
 sys.ps1 = "\x01\033[31m\x02>>> \x01\033[0m\x02"
 
@@ -100,6 +120,17 @@ class RUNCMD(Cmd):
     llm_model = "gpt-3.5-turbo"
     llm_models = SUPPORTED_TELL_ME_MODELS_SETTINGS
 
+    # Load OpenAD Plugins into cmd_pointer
+    plugins = PLUGIN_CLASS_LIST.copy()
+    plugin_objects = {}
+    plugins_statements = []
+    plugins_help = []
+    for plugin in plugins:
+        p = plugin()
+        plugin_objects.update(p.PLUGIN_OBJECTS)
+        plugins_statements.extend(p.statements)
+        plugins_help.extend(p.help)
+
     # # Instantiate memory class # Trash
     # memory = Memory()
 

diff --git a/openad/app/main_lib.py b/openad/app/main_lib.py
@@ -314,14 +314,6 @@ def lang_parse(cmd_pointer, parser):
     ]:
         return openad_model_requestor(cmd_pointer, parser)
 
-    # # Show molecules commands
-    # elif parser.getName() == "show_molecules":
-    #     return show_molsgrid(cmd_pointer, parser)
-    # elif parser.getName() == "show_molecules_df":
-    #     return show_molsgrid(cmd_pointer, parser)
-    # elif parser.getName() == "show_molecule":
-    #     return show_mol__TRASH(cmd_pointer, parser)
-
     # Toolkit execution
     elif str(parser.getName()).startswith("toolkit_exec_"):
         try:
@@ -336,6 +328,10 @@ def lang_parse(cmd_pointer, parser):
     elif parser.getName() == "flask_example":
         return flask_example(cmd_pointer, parser)
 
+    # openad Plugin Search for commands
+    elif parser.getName() in cmd_pointer.plugin_objects.keys():
+        return cmd_pointer.plugin_objects[parser.getName()].exec_command(cmd_pointer, parser)
+
     return
 
 

diff --git a/openad/app/metadata.json b/openad/app/metadata.json
@@ -1,7 +1,7 @@
 {
 	"banner": "OPENAD",
 	"title": "Welcome to the Open Accelerated Discovery CLI",
-	"version": "0.3.0",
+	"version": "0.3.1",
 	"commands": {
 		"intro": "If this is your first time, let us help you getting started.",
 		"? toolkits": "Learn about the toolkits.",

diff --git a/openad/core/grammar.py b/openad/core/grammar.py
@@ -901,12 +901,22 @@ def create_statements(cmd_pointer):
     except Exception as e:
         print(e)
         pass
+    # add plugins
+
+    for stmt in cmd_pointer.plugins_statements:
+        cmd_pointer.current_statements.append(stmt)
+
+    cmd_pointer.current_help.help_plugins.extend(cmd_pointer.plugins_help)
+    cmd_pointer.current_help.reset_help()
+
     for i in cmd_pointer.current_statements:
         cmd_pointer.current_statement_defs |= i
+
     if cmd_pointer.toolkit_current is not None:
         for i in cmd_pointer.toolkit_current.methods_grammar:
             cmd_pointer.current_statement_defs |= i
             cmd_pointer.current_statements.append(i)
+
     # statements_zom = ZeroOrMore(statements_def)
 
 

diff --git a/openad/core/help.py b/openad/core/help.py
@@ -224,6 +224,7 @@ class OpenadHelp:
     help_orig = []
     help_current = []
     help_model_services = []
+    help_plugins = []
 
     def add_help(self, help_dict):
         for i in help_dict:
@@ -232,3 +233,4 @@ def add_help(self, help_dict):
     def reset_help(self):
         self.help_current = self.help_orig.copy()
         self.help_current.extend(self.help_model_services)
+        self.help_current.extend(self.help_plugins)
diff --git a/openad/notebooks/media/genai.png b/openad/notebooks/media/genai.png
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "openad"
-version = "0.3.0"
+version = "0.3.1"
 description = "Open Accelerated Discovery Client "
 authors = ["Phil Downey <[email protected]>"]
 readme = "README.md"
@@ -107,7 +107,7 @@ enable_error_code = [
 ]
 
 [tool.pytest.ini_options]
-addopts = "--cov=openad/openad_model_plugin"
+#addopts = "--cov=openad/openad_model_plugin"
 testpaths = ["tests"]
 filterwarnings = ["ignore::DeprecationWarning"]