ivoryos 0.1.5__tar.gz → 0.1.7__tar.gz

ivoryos-0.1.7/PKG-INFO

@@ -0,0 +1,166 @@
+Metadata-Version: 2.1
+Name: ivoryos
+Version: 0.1.7
+Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
+Home-page: https://gitlab.com/heingroup/ivoryos
+Author: Ivory Zhang
+Author-email: ivoryzhang@chem.ubc.ca
+License: MIT
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: bcrypt
+Requires-Dist: Flask-Login
+Requires-Dist: Flask-Session
+Requires-Dist: Flask-SocketIO
+Requires-Dist: Flask-SQLAlchemy
+Requires-Dist: Flask-WTF
+Requires-Dist: SQLAlchemy-Utils
+Requires-Dist: python-dotenv
+
+![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/ivoryos.png)
+# ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
+"plug and play" web UI extension for flexible SDLs.
+
+## Table of Contents
+- [Description](#description)
+- [System requirements](#system-requirements)
+- [Installation](#installation)
+- [Instructions for use](#instructions-for-use)
+- [Demo](#demo)
+- [License](#license)
+
+## Description
+Granting SDLs flexibility and modularity makes it almost impossible to design a UI, yet it's a necessity for allowing more people to interact with it (democratisation). 
+This web UI aims to ease up the control of any Python-based SDLs by displaying functions and parameters for initialized modules dynamically. 
+The modules can be hardware API, high-level functions, or experiment workflow.
+With the least modification of the current workflow, user can design, manage and execute their experimental designs and monitor the execution process. 
+
+## System requirements
+This software is developed and tested using Windows. This software and its dependencies are compatible across major platforms: Linux, macOS, and Windows. Some dependencies (Flask-SQLAlchemy) may require additional setup.
+
+### Python Version
+Python >=3.7 for best compatibility.
+### Python dependencies
+This software is compatible with the latest versions of all dependencies. 
+- bcrypt~=4.0
+- Flask-Login~=0.6
+- Flask-Session~=0.8
+- Flask-SocketIO~=5.3
+- Flask-SQLAlchemy~=3.1
+- SQLAlchemy-Utils~=0.41
+- Flask-WTF~=1.2
+- python-dotenv==1.0.1
+- openai (optional ~=1.53)
+- ax-platform (optional ~=0.3 or ~=0.4 for Python>=3.9)
+
+## Installation
+```bash
+pip install ivoryos
+```
+or
+```bash
+git clone https://gitlab.com/heingroup/ivoryos.git
+cd ivoryos
+pip install -e .
+```
+
+The installation may take 10 to 30 seconds to install. The installation time may vary and take up to several minutes, depending on the network speed, computer performance, and virtual environment settings.
+
+## Instructions for use
+### Quick start
+In your SDL script, use `ivoryos(__name__)`. 
+```python
+import ivoryos
+
+ivoryos.run(__name__)
+```
+### Login
+Create an account and login (local database)
+### Features
+- **Direct control**: direct function calling _Device_ tab
+- **Workflow design and iteration**:
+  - **Design**: add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution page
+  - **Execution**: configure iteration methods and parameters in _Compile/Run_ tab. 
+  - **Database**: manage workflows in _Library_ tab.
+- **Info page**: additional info in _About_ tab.
+
+
+### Additional settings
+#### AI assistant
+To streamline the experimental design on SDLs, we also integrate Large Language Models (LLMs) to interpret the inspected functions and generate code according to task descriptions.
+
+#### Enable LLMs with [OpenAI API](https://github.com/openai/openai-python)
+1. Create a `.env` file for `OPENAI_API_KEY`
+```
+OPENAI_API_KEY="Your API Key"
+```
+2. In your SDL script, define model, you can use any GPT models.
+
+```python
+ivoryos.run(__name__, model="gpt-3.5-turbo")
+```
+
+#### Enable local LLMs with [Ollama](https://ollama.com/)
+1. Download Ollama.
+2. pull models from Ollama
+3. In your SDL script, define LLM server and model, you can use any models available on Ollama.
+
+```python
+ivoryos.run(__name__, llm_server="localhost", model="llama3.1")
+```
+
+#### Add additional logger(s)
+```python
+ivoryos.run(__name__, logger="logger name")
+```
+or
+```python
+ivoryos.run(__name__, logger=["logger 1", "logger 2"])
+```
+#### Offline (design without hardware connection)
+After one successful connection, a blueprint will be automatically saved and made accessible without hardware connection. In a new Python script in the same directory, use `ivoryos.run()` to start offline mode.
+
+```python
+ivoryos.run()
+```
+## Demo
+In the [abstract_sdl.py](https://gitlab.com/heingroup/ivoryos/-/blob/main/example/sdl_example/abstract_sdl.py), where instances of `AbstractSDL` is created as `sdl`,
+addresses will be available on terminal.
+```Python
+ivoryos.run(__name__)
+```
+
+ * Running on all addresses (0.0.0.0)
+ * Running on http://127.0.0.1:8000
+ * Running on http://xxx.xx.xx.xxx:8000
+
+### Deck function and web form 
+![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/demo.gif)
+
+### Directory structure
+
+When you run the application for the first time, it will automatically create the following folders and files in the same directory:
+
+- **`ivoryos_data/`**: Main directory for application-related data.
+  - **`ivoryos_data/config_csv/`**: Contains iteration configuration files in CSV format.
+  - **`ivoryos_data/llm_output/`**: Stores raw prompt generated for the large language model.
+  - **`ivoryos_data/pseudo_deck/`**: Contains pseudo-deck `.pkl` files for offline access.
+  - **`ivoryos_data/results/`**: Used for storing results or outputs during workflow execution.
+  - **`ivoryos_data/scripts/`**: Holds Python scripts compiled from the visual programming script design.
+
+- **`default.log`**: Log file that captures application logs.
+- **`ivoryos.db`**: Database file that stores application data locally.
+
+
+### Demo video
+Intro + Tutorial + Demo with PurPOSE platform
+https://youtu.be/dFfJv9I2-1g 
+
+
+## Authors and Acknowledgement
+Ivory Zhang, Lucy Hao
+
+Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+
+## License
+[LICENSE](LICENSE)

ivoryos-0.1.7/README.md

@@ -0,0 +1,147 @@
+![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/ivoryos.png)
+# ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
+"plug and play" web UI extension for flexible SDLs.
+
+## Table of Contents
+- [Description](#description)
+- [System requirements](#system-requirements)
+- [Installation](#installation)
+- [Instructions for use](#instructions-for-use)
+- [Demo](#demo)
+- [License](#license)
+
+## Description
+Granting SDLs flexibility and modularity makes it almost impossible to design a UI, yet it's a necessity for allowing more people to interact with it (democratisation). 
+This web UI aims to ease up the control of any Python-based SDLs by displaying functions and parameters for initialized modules dynamically. 
+The modules can be hardware API, high-level functions, or experiment workflow.
+With the least modification of the current workflow, user can design, manage and execute their experimental designs and monitor the execution process. 
+
+## System requirements
+This software is developed and tested using Windows. This software and its dependencies are compatible across major platforms: Linux, macOS, and Windows. Some dependencies (Flask-SQLAlchemy) may require additional setup.
+
+### Python Version
+Python >=3.7 for best compatibility.
+### Python dependencies
+This software is compatible with the latest versions of all dependencies. 
+- bcrypt~=4.0
+- Flask-Login~=0.6
+- Flask-Session~=0.8
+- Flask-SocketIO~=5.3
+- Flask-SQLAlchemy~=3.1
+- SQLAlchemy-Utils~=0.41
+- Flask-WTF~=1.2
+- python-dotenv==1.0.1
+- openai (optional ~=1.53)
+- ax-platform (optional ~=0.3 or ~=0.4 for Python>=3.9)
+
+## Installation
+```bash
+pip install ivoryos
+```
+or
+```bash
+git clone https://gitlab.com/heingroup/ivoryos.git
+cd ivoryos
+pip install -e .
+```
+
+The installation may take 10 to 30 seconds to install. The installation time may vary and take up to several minutes, depending on the network speed, computer performance, and virtual environment settings.
+
+## Instructions for use
+### Quick start
+In your SDL script, use `ivoryos(__name__)`. 
+```python
+import ivoryos
+
+ivoryos.run(__name__)
+```
+### Login
+Create an account and login (local database)
+### Features
+- **Direct control**: direct function calling _Device_ tab
+- **Workflow design and iteration**:
+  - **Design**: add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution page
+  - **Execution**: configure iteration methods and parameters in _Compile/Run_ tab. 
+  - **Database**: manage workflows in _Library_ tab.
+- **Info page**: additional info in _About_ tab.
+
+
+### Additional settings
+#### AI assistant
+To streamline the experimental design on SDLs, we also integrate Large Language Models (LLMs) to interpret the inspected functions and generate code according to task descriptions.
+
+#### Enable LLMs with [OpenAI API](https://github.com/openai/openai-python)
+1. Create a `.env` file for `OPENAI_API_KEY`
+```
+OPENAI_API_KEY="Your API Key"
+```
+2. In your SDL script, define model, you can use any GPT models.
+
+```python
+ivoryos.run(__name__, model="gpt-3.5-turbo")
+```
+
+#### Enable local LLMs with [Ollama](https://ollama.com/)
+1. Download Ollama.
+2. pull models from Ollama
+3. In your SDL script, define LLM server and model, you can use any models available on Ollama.
+
+```python
+ivoryos.run(__name__, llm_server="localhost", model="llama3.1")
+```
+
+#### Add additional logger(s)
+```python
+ivoryos.run(__name__, logger="logger name")
+```
+or
+```python
+ivoryos.run(__name__, logger=["logger 1", "logger 2"])
+```
+#### Offline (design without hardware connection)
+After one successful connection, a blueprint will be automatically saved and made accessible without hardware connection. In a new Python script in the same directory, use `ivoryos.run()` to start offline mode.
+
+```python
+ivoryos.run()
+```
+## Demo
+In the [abstract_sdl.py](https://gitlab.com/heingroup/ivoryos/-/blob/main/example/sdl_example/abstract_sdl.py), where instances of `AbstractSDL` is created as `sdl`,
+addresses will be available on terminal.
+```Python
+ivoryos.run(__name__)
+```
+
+ * Running on all addresses (0.0.0.0)
+ * Running on http://127.0.0.1:8000
+ * Running on http://xxx.xx.xx.xxx:8000
+
+### Deck function and web form 
+![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/demo.gif)
+
+### Directory structure
+
+When you run the application for the first time, it will automatically create the following folders and files in the same directory:
+
+- **`ivoryos_data/`**: Main directory for application-related data.
+  - **`ivoryos_data/config_csv/`**: Contains iteration configuration files in CSV format.
+  - **`ivoryos_data/llm_output/`**: Stores raw prompt generated for the large language model.
+  - **`ivoryos_data/pseudo_deck/`**: Contains pseudo-deck `.pkl` files for offline access.
+  - **`ivoryos_data/results/`**: Used for storing results or outputs during workflow execution.
+  - **`ivoryos_data/scripts/`**: Holds Python scripts compiled from the visual programming script design.
+
+- **`default.log`**: Log file that captures application logs.
+- **`ivoryos.db`**: Database file that stores application data locally.
+
+
+### Demo video
+Intro + Tutorial + Demo with PurPOSE platform
+https://youtu.be/dFfJv9I2-1g 
+
+
+## Authors and Acknowledgement
+Ivory Zhang, Lucy Hao
+
+Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+
+## License
+[LICENSE](LICENSE)

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/__init__.py

@@ -2,7 +2,7 @@ import os
 import sys
 from typing import Union
 
-from flask import Flask
+from flask import Flask, redirect, url_for
 
 from ivoryos.config import Config, get_config
 from ivoryos.routes.auth.auth import auth, login_manager
@@ -19,7 +19,8 @@ global_config = GlobalConfig()
 
 
 def create_app(config_class=None):
-    app = Flask(__name__)
+    url_prefix = os.getenv('URL_PREFIX', None)
+    app = Flask(__name__, static_url_path=f'{url_prefix}/static', static_folder='static')
     app.config.from_object(config_class or 'config.get_config()')
 
     # Initialize extensions
@@ -45,11 +46,15 @@ def create_app(config_class=None):
         g.logger = logger
         g.socketio = socketio
 
-    app.register_blueprint(main)
-    app.register_blueprint(auth)
-    app.register_blueprint(design)
-    app.register_blueprint(database)
-    app.register_blueprint(control)
+    app.register_blueprint(main, url_prefix=url_prefix)
+    app.register_blueprint(auth, url_prefix=url_prefix)
+    app.register_blueprint(design, url_prefix=url_prefix)
+    app.register_blueprint(database, url_prefix=url_prefix)
+    app.register_blueprint(control, url_prefix=url_prefix)
+
+    @app.route('/')
+    def redirect_to_prefix():
+        return redirect(url_for('main.index'))  # Assuming 'index' is a route in your blueprint
 
     return app
 
@@ -72,7 +77,7 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
         app.config["MODULE"] = module
         app.config["OFF_LINE"] = False
         global_config.deck = sys.modules[module]
-        global_config.deck_variables = utils.parse_deck(global_config.deck, output_path=app.config["DUMMY_DECK"], save=True)
+        global_config.deck_snapshot = utils.create_deck_snapshot(global_config.deck, output_path=app.config["DUMMY_DECK"], save=True)
         # global_config.runner = ScriptRunner(globals())
     else:
         app.config["OFF_LINE"] = True

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/config.py

@@ -15,6 +15,7 @@ class Config:
     SCRIPT_FOLDER = os.path.join(OUTPUT_FOLDER, 'scripts/')
     DATA_FOLDER = os.path.join(OUTPUT_FOLDER, 'results/')
     DUMMY_DECK = os.path.join(OUTPUT_FOLDER, 'pseudo_deck/')
+    LLM_OUTPUT = os.path.join(OUTPUT_FOLDER, 'llm_output/')
     DECK_HISTORY = os.path.join(OUTPUT_FOLDER, 'deck_history.txt')
     LOGGERS_PATH = "default.log"
 

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/routes/control/control.py

@@ -1,8 +1,6 @@
 import os
-import pickle
-import sys
 
-from flask import Blueprint, redirect, url_for, flash, request, render_template, session, current_app
+from flask import Blueprint, redirect, url_for, flash, request, render_template, session, current_app, jsonify
 from flask_login import login_required
 
 from ivoryos.utils.global_config import GlobalConfig
@@ -17,7 +15,7 @@ control = Blueprint('control', __name__, template_folder='templates/control')
 @control.route("/my_deck")
 @login_required
 def deck_controllers():
-    deck_variables = global_config.deck_variables.keys()
+    deck_variables = global_config.deck_snapshot.keys()
     deck_list = utils.import_history(os.path.join(current_app.config["OUTPUT_FOLDER"], 'deck_history.txt'))
     return render_template('controllers_home.html', defined_variables=deck_variables, deck=True, history=deck_list)
 
@@ -77,12 +75,15 @@ def controllers_home():
 def controllers(instrument):
     inst_object = find_instrument_by_name(instrument)
     _forms = create_form_from_module(sdl_module=inst_object, autofill=False, design=False)
-    card_order = session.get('card_order')
-    order = card_order.get(instrument, _forms.keys())
-    if instrument not in card_order:
-        card_order[instrument] = list(order)
-        session['card_order'] = card_order
-        # print(session['card_order'])
+    functions = list(_forms.keys())
+
+    order = get_session_by_instrument('card_order', instrument)
+    hidden_functions = get_session_by_instrument('hide_function', instrument)
+
+    for function in functions:
+        if function not in hidden_functions and function not in order:
+            order.append(function)
+    post_session_by_instrument('card_order', instrument, order)
     forms = {name: _forms[name] for name in order if name in _forms}
     if request.method == 'POST':
         all_kwargs = request.form.copy()
@@ -103,6 +104,32 @@ def controllers(instrument):
     return render_template('controllers.html', instrument=instrument, forms=forms, format_name=format_name)
 
 
+@control.route("/backend_control/<instrument>", methods=['GET', 'POST'])
+@login_required
+def backend_control(instrument):
+    inst_object = find_instrument_by_name(instrument)
+    forms = create_form_from_module(sdl_module=inst_object, autofill=False, design=False)
+    if request.method == 'POST':
+        all_kwargs = request.form.copy()
+        method_name = all_kwargs.pop("hidden_name", None)
+        # if method_name is not None:
+        form = forms.get(method_name, None)
+        kwargs = {field.name: field.data for field in form if field.name != 'csrf_token'}
+        function_executable = getattr(inst_object, method_name)
+        if form:
+            # print(kwargs)
+            try:
+                kwargs.pop("hidden_name")
+                output = function_executable(**kwargs)
+                json_output = jsonify(output)
+            except Exception as e:
+                json_output = jsonify(e.__str__())
+                return json_output, 400
+        else:
+            return "instrument not exist", 400
+    return json_output, 200
+
+
 @control.route("/import_api", methods=['GET', 'POST'])
 def import_api():
     filepath = request.form.get('filepath')
@@ -164,12 +191,12 @@ def import_deck():
     try:
         module = utils.import_module_by_filepath(filepath=filepath, name=name)
         utils.save_to_history(filepath, current_app.config["DECK_HISTORY"])
-        module_sigs = utils.parse_deck(module, save=update, output_path=current_app.config["DUMMY_DECK"])
+        module_sigs = utils.create_deck_snapshot(module, save=update, output_path=current_app.config["DUMMY_DECK"])
         if not len(module_sigs) > 0:
             flash("Invalid hardware deck, connect instruments in deck script", "error")
             return redirect(url_for("control.deck_controllers"))
         global_config.deck = module
-        global_config.deck_variables = module_sigs
+        global_config.deck_snapshot = module_sigs
 
         if script.deck is None:
             script.deck = module.__name__
@@ -183,47 +210,59 @@ def import_deck():
 def save_order(instrument):
     # Save the new order for the specified group to session
     data = request.json
-    card_order = session.get("card_order", {})
-    card_order[instrument] = data['order']
-    session['card_order'] = card_order
+    post_session_by_instrument('card_order', instrument, data['order'])
     return '', 204
 
 
 @control.route('/hide_function/<instrument>/<function>')
 def hide_function(instrument, function):
     back = request.referrer
-    hidden_functions = session.get("hidden_functions")
-    functions = hidden_functions.get(instrument, [])
-    card_order = session.get("card_order")
-    order = card_order.get(instrument)
+    functions = get_session_by_instrument("hidden_functions", instrument)
+    order = get_session_by_instrument("card_order", instrument)
     if function not in functions:
         functions.append(function)
         order.remove(function)
-    hidden_functions[instrument] = functions
-    card_order[instrument] = order
-    session['hidden_functions'] = hidden_functions
-    session['card_order'] = card_order
+    post_session_by_instrument('hidden_functions', instrument, functions)
+    post_session_by_instrument('card_order', instrument, order)
     return redirect(back)
 
 
 @control.route('/remove_hidden/<instrument>/<function>')
 def remove_hidden(instrument, function):
     back = request.referrer
-    hidden_functions = session.get("hidden_functions")
-    functions = hidden_functions.get(instrument, [])
-    card_order = session.get("card_order")
-    order = card_order.get(instrument)
+    functions = get_session_by_instrument("hidden_functions", instrument)
+    order = get_session_by_instrument("card_order", instrument)
     if function in functions:
         functions.remove(function)
         order.append(function)
-    hidden_functions[instrument] = functions
-    card_order[instrument] = order
-    session['hidden_functions'] = hidden_functions
-    session['card_order'] = card_order
+    post_session_by_instrument('hidden_functions', instrument, functions)
+    post_session_by_instrument('card_order', instrument, order)
     return redirect(back)
 
 
+def get_session_by_instrument(session_name, instrument):
+    """get data from session by instrument"""
+    session_object = session.get(session_name, {})
+    functions = session_object.get(instrument, [])
+    return functions
+
+
+def post_session_by_instrument(session_name, instrument, data):
+    """
+    save new data to session by instrument
+    :param session_name: "card_order" or "hidden_functions"
+    :param instrument: function name of class object
+    :param data: order list or hidden function list
+    """
+    session_object = session.get(session_name, {})
+    session_object[instrument] = data
+    session[session_name] = session_object
+
+
 def find_instrument_by_name(name: str):
+    """
+    find instrument class object by instance name
+    """
     if name.startswith("deck"):
         name = name.replace("deck.", "")
         return getattr(global_config.deck, name)

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/routes/control/templates/control/controllers.html

@@ -8,9 +8,12 @@
         </div>
     </div>
     <h1>{{instrument}} controller</h1>
+    {% set hidden = session.get('hidden_functions', {}) %}
     <div class="grid-container" id="sortable-grid">
         {% for function, form in forms.items() %}
-            {% if function not in session['hidden_functions'][instrument] %}
+
+            {% set hidden_instrument = hidden.get(instrument, []) %}
+            {% if function not in hidden_instrument %}
                 <div class="card" id="{{function}}">
                     <div class="bg-white rounded shadow-sm flex-fill">
                         <a style="float: right" aria-label="Close" href="{{ url_for('control.hide_function', instrument=instrument, function=function) }}"><i class="bi bi-eye-slash-fill"></i></a>
@@ -53,7 +56,8 @@
         </div>
         <div id="hidden" class="accordion-collapse collapse" data-bs-parent="#accordionActions">
             <div class="accordion-body">
-                {% for function in session['hidden_functions'][instrument] %}
+                {% set hidden_instrument = hidden.get(instrument, []) %}
+                {% for function in hidden_instrument %}
                     <div>
                         {{ function }} <a href="{{ url_for('control.remove_hidden', instrument=instrument, function=function) }}"><i class="bi bi-eye-fill"></i></a>
                     </div>

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/routes/database/database.py

@@ -61,8 +61,9 @@ def publish():
 def finalize():
     script = get_script_file()
     script.finalize()
-    db.session.merge(script)
-    db.session.commit()
+    if script.name:
+        db.session.merge(script)
+        db.session.commit()
     post_script_file(script)
     return redirect(url_for('design.experiment_builder'))
 

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/routes/design/design.py

@@ -69,7 +69,7 @@ def experiment_builder(instrument=None):
 
     functions = []
     if deck:
-        deck_variables = global_config.deck_variables.keys()
+        deck_variables = global_config.deck_snapshot.keys()
     else:
         deck_variables = list(pseudo_deck.keys()) if pseudo_deck else []
         deck_variables.remove("deck_name") if len(deck_variables) > 0 else deck_variables
@@ -78,7 +78,7 @@ def experiment_builder(instrument=None):
             forms = create_builtin_form(instrument)
         else:
             if deck:
-                function_metadata = global_config.deck_variables.get(instrument, {})
+                function_metadata = global_config.deck_snapshot.get(instrument, {})
             elif pseudo_deck:
                 function_metadata = pseudo_deck.get(instrument, {})
             functions = {key: data.get('signature', {}) for key, data in function_metadata.items()}
@@ -158,7 +158,7 @@ def generate_code():
         prompt = request.form.get("prompt")
         session['prompt'][instrument] = prompt
         # sdl_module = utils.parse_functions(find_instrument_by_name(f'deck.{instrument}'), doc_string=True)
-        sdl_module = global_config.deck_variables.get(instrument, {})
+        sdl_module = global_config.deck_snapshot.get(instrument, {})
         empty_script = Script(author=session.get('user'))
         if enable_llm and agent is None:
             try:
@@ -241,7 +241,7 @@ def experiment_run():
             bo_args = request.form.to_dict()
             # ax_client = utils.ax_initiation(bo_args)
         if "online-config" in request.form:
-            config = utils.process_data(request.form.to_dict(), config_list)
+            config = utils.web_config_entry_wrapper(request.form.to_dict(), config_list)
         repeat = request.form.get('repeat', None)
 
         try:

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/routes/main/templates/main/help.html

@@ -134,9 +134,6 @@
                 <div class="accordion-body">
                     This is project is a work in progress. In case of any bugs or suggestions, reach out to Ivory: ivoryzhang@chem.ubc.ca or create an issue on GitLab:
                     <a href="https://gitlab.com/heingroup/ivoryos">https://gitlab.com/heingroup/ivoryos</a>.
-{#                    <img src="{{url_for('static', filename='gui_annotation/installation_guide.PNG')}}">#}
-
-{#                    <object webui_data="{{ url_for('static', filename='setup-help.pdf')}}" type="application/pdf" style="min-height:80vh;width:100%"></object>#}
                 </div>
             </div>
         </div>

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/static/js/socket_handler.js

@@ -6,7 +6,16 @@ document.addEventListener("DOMContentLoaded", function() {
     socket.on('progress', function(data) {
         var progress = data.progress;
         console.log(progress);
-        $('#progress-bar-inner').css('width', progress + '%')
+        // Update the progress bar's width and appearance
+        var progressBar = document.getElementById('progress-bar-inner');
+        progressBar.style.width = progress + '%';
+        progressBar.setAttribute('aria-valuenow', progress);
+
+        if (progress === 100) {
+            // Remove animation and set green color when 100% is reached
+            progressBar.classList.remove('progress-bar-animated');
+            progressBar.classList.add('bg-success'); // Bootstrap class for green color
+        }
     });
     socket.on('log', function(data) {
         var logMessage = data.message;

{ivoryos-0.1.5 → ivoryos-0.1.7}/ivoryos/templates/base.html

@@ -25,7 +25,7 @@
         <div class= "container">
 
             <a class="navbar-brand" href="{{ url_for('main.index') }}">
-                <img src="{{url_for('static', filename='logo.png')}}" alt="Logo" height="60" class="d-inline-block align-text-bottom">
+                <img src="{{url_for('static', filename='logo.webp')}}" alt="Logo" height="60" class="d-inline-block align-text-bottom">
             </a>
             <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
                 <span class="navbar-toggler-icon"></span>
@@ -33,6 +33,9 @@
 
             <div class="collapse navbar-collapse" id="navbarSupportedContent">
                 <ul class="navbar-nav mr-auto">
+                    <li class="nav-item">
+                        <a class="nav-link" href="{{ url_for('main.index') }}" aria-current="page">Home</a>
+                    </li>
                     <li class="nav-item">
                         <a class="nav-link" href="{{ url_for('database.load_from_database') }}" aria-current="page">Library</a>
                     </li>