ivoryos 1.2.0b1__py3-none-any.whl → 1.2.1__py3-none-any.whl

ivoryos/__init__.py

@@ -1,8 +1,11 @@
 import os
 import sys
+import uuid
 from typing import Union
 
-from flask import Flask, redirect, url_for, g, Blueprint
+from flask import Flask, redirect, url_for, g, Blueprint, session
+from flask_login import AnonymousUserMixin
+
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 
 from ivoryos.config import Config, get_config
@@ -90,6 +93,23 @@ def create_app(config_class=None):
         """
         g.logger = logger
         g.socketio = socketio
+        session.permanent = False
+        # DEMO_MODE: Simulate logged-in user per session
+        if app.config.get("DEMO_MODE", False):
+            if "demo_user_id" not in session:
+                session["demo_user_id"] = f"demo_{str(uuid.uuid4())[:8]}"
+
+            class SessionDemoUser(AnonymousUserMixin):
+                @property
+                def is_authenticated(self):
+                    return True
+
+                def get_id(self):
+                    return session.get("demo_user_id")
+
+            login_manager.anonymous_user = SessionDemoUser
+
+
 
     @app.route('/')
     def redirect_to_prefix():
@@ -101,6 +121,7 @@ def create_app(config_class=None):
         text = ' '.join(word for word in name.split('_'))
         return text.capitalize()
 
+    # app.config.setdefault("DEMO_MODE", False)
     return app
 
 

ivoryos/config.py

@@ -43,6 +43,7 @@ class TestingConfig(Config):
 
 class DemoConfig(Config):
     DEBUG = False
+    DEMO_MODE = True
     SQLALCHEMY_DATABASE_URI = 'sqlite:///:memory:'
     OUTPUT_FOLDER = os.path.join(os.path.abspath(os.curdir), '/tmp/ivoryos_data')
     CSV_FOLDER = os.path.join(OUTPUT_FOLDER, 'config_csv/')

ivoryos/routes/auth/auth.py

@@ -5,6 +5,7 @@ import bcrypt
 from ivoryos.utils.db_models import Script, User, db
 from ivoryos.utils.utils import post_script_file
 login_manager = LoginManager()
+# from flask import g
 
 auth = Blueprint('auth', __name__, template_folder='templates')
 
@@ -37,7 +38,8 @@ def login():
             # password.encode("utf-8")
             # user = User(username, password.encode("utf-8"))
             login_user(user)
-            session['user'] = username
+            # g.user = user
+            # session['user'] = username
             script_file = Script(author=username)
             session["script"] = script_file.as_dict()
             session['hidden_functions'], session['card_order'], session['prompt'] = {}, {}, {}

ivoryos/routes/data/data.py

@@ -10,6 +10,7 @@ data = Blueprint('data', __name__, template_folder='templates')
 
 
 @data.route('/executions/records')
+@login_required
 def list_workflows():
     """
     .. :quickref: Workflow Execution Database; list all workflow execution records
@@ -113,6 +114,7 @@ def delete_workflow_record(workflow_id: int):
 
 
 @data.route('/files/execution-data/<string:filename>')
+@login_required
 def download_results(filename:str):
     """
     .. :quickref: Workflow data; download a workflow data file (.CSV)

ivoryos/routes/design/design.py

@@ -1,7 +1,7 @@
 import os
 
 from flask import Blueprint, redirect, url_for, flash, jsonify, request, render_template, session, current_app
-from flask_login import login_required
+from flask_login import login_required, current_user
 
 from ivoryos.routes.library.library import publish
 from ivoryos.utils import utils
@@ -64,7 +64,7 @@ def experiment_builder():
     if deck and script.deck is None:
         script.deck = os.path.splitext(os.path.basename(deck.__file__))[
             0] if deck.__name__ == "__main__" else deck.__name__
-
+        utils.post_script_file(script)
     pseudo_deck_name = session.get('pseudo_deck', '')
     pseudo_deck_path = os.path.join(current_app.config["DUMMY_DECK"], pseudo_deck_name)
     off_line = current_app.config["OFF_LINE"]
@@ -238,7 +238,7 @@ def clear_draft():
             0] if deck.__name__ == "__main__" else deck.__name__
     else:
         deck_name = session.get("pseudo_deck", "")
-    script = Script(deck=deck_name, author=session.get('username'))
+    script = Script(deck=deck_name, author=current_user.get_id())
     utils.post_script_file(script)
     exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
     session['python_code'] = exec_string
@@ -265,7 +265,7 @@ def submit_script():
     """
     deck = global_config.deck
     deck_name = os.path.splitext(os.path.basename(deck.__file__))[0] if deck.__name__ == "__main__" else deck.__name__
-    script = Script(author=session.get('user'), deck=deck_name)
+    script = Script(author=current_user.get_id(), deck=deck_name)
     script_collection = request.get_json()
     workflow_name = script_collection.pop("workflow_name")
     script.python_script = script_collection

ivoryos/routes/library/library.py

@@ -1,5 +1,5 @@
 from flask import Blueprint, redirect, url_for, flash, request, render_template, session, current_app, jsonify
-from flask_login import login_required
+from flask_login import login_required, current_user
 
 from ivoryos.utils.db_models import Script, db, WorkflowRun, WorkflowStep
 from ivoryos.utils.utils import get_script_file, post_script_file
@@ -66,14 +66,14 @@ def publish():
     script = get_script_file()
 
     if script.author is None:
-        script.author = session.get('user')
+        script.author = current_user.get_id()
     if not script.name or not script.deck:
         return {"success": False, "error": "Deck cannot be empty, try to re-submit deck configuration on the left panel"}
     row = Script.query.get(script.name)
     if row and row.status == "finalized":
         return {"success": False, "error": "This is a protected script, use save as to rename."}
 
-    elif row and session.get('user') != row.author:
+    elif row and current_user.get_id() != row.author:
         return {"success": False, "error": "You are not the author, use save as to rename."}
     else:
         db.session.merge(script)
@@ -145,7 +145,7 @@ def save_as():
         script = get_script_file()
         script.save_as(run_name)
         script.registered = register_workflow == "on"
-        script.author = session.get('user')
+        script.author = current_user.get_id()
         post_script_file(script)
         status = publish()
         if request.accept_mimetypes.best_match(['application/json', 'text/html']) == 'application/json':

ivoryos/utils/script_runner.py

@@ -66,7 +66,7 @@ class ScriptRunner:
         global deck
         if deck is None:
             deck = global_config.deck
-        print("history", history)
+        # print("history", history)
         if self.current_app is None:
             self.current_app = current_app
         # time.sleep(1)  # Optional: may help ensure deck readiness

ivoryos/utils/utils.py

@@ -11,6 +11,7 @@ from collections import Counter
 
 import flask
 from flask import session
+from flask_login import current_user
 from flask_socketio import SocketIO
 
 from ivoryos.utils.db_models import Script
@@ -24,7 +25,7 @@ def get_script_file():
         s.__dict__.update(**session_script)
         return s
     else:
-        return Script(author=session.get('user'))
+        return Script(author=current_user.get_id(),)
 
 
 def post_script_file(script, is_dict=False):

ivoryos/version.py

@@ -1 +1 @@
-__version__ = "1.2.0b1"
+__version__ = "1.2.1"

{ivoryos-1.2.0b1.dist-info → ivoryos-1.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 1.2.0b1
+Version: 1.2.1
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -48,7 +48,7 @@ With the least modification of the current workflow, user can design, manage and
 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 >=3.10 for best compatibility. Python >=3.7 without Ax.
+Python >=3.10 for the best compatibility. Python >=3.7 without Ax.
 ### Python dependencies
 This software is compatible with the latest versions of all dependencies. 
 - bcrypt~=4.0
@@ -59,7 +59,9 @@ This software is compatible with the latest versions of all dependencies.
 - SQLAlchemy-Utils~=0.41
 - Flask-WTF~=1.2
 - python-dotenv==1.0.1
-- ax-platform (optional ~=0.4 for Python>=3.9)
+- ax-platform (optional 1.0 for Python>=3.10)
+- baybe (optional)
+
 
 ## Installation
 ```bash
@@ -83,43 +85,60 @@ import ivoryos
 ivoryos.run(__name__)
 ```
 ### Login
-Create an account and login (local database)
+Create an account and login (local database with bcrypt password)
 ### 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.
+- **Direct control**: direct function calling _Devices_ tab
+- **Workflows**:
+  - **Design Editor**: drag/add function to canvas in _Design_ tab. click `Compile and Run` button to go to the execution configuration page
+  - **Execution Config**: configure iteration methods and parameters in _Compile/Run_ tab. 
+  - **Design Library**: manage workflow scripts in _Library_ tab.
+  - **Workflow Data**: Execution records are in _Data_ tab.
 
 [//]: # (![Discord](https://img.shields.io/discord/1313641159356059770))
 
 [//]: # (![PyPI - Downloads](https://img.shields.io/pypi/dm/ivoryos))
 
 
-### Additional settings (not actively maintained)
-#### 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.
+### Additional settings
+[//]: # (#### AI assistant)
 
-#### 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.
+[//]: # (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.)
 
-```python
-ivoryos.run(__name__, model="gpt-3.5-turbo")
-```
+[//]: # ()
+[//]: # (#### Enable LLMs with [OpenAI API](https://github.com/openai/openai-python))
 
-#### 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.
+[//]: # (1. Create a `.env` file for `OPENAI_API_KEY`)
 
-```python
-ivoryos.run(__name__, llm_server="localhost", model="llama3.1")
-```
+[//]: # (```)
+
+[//]: # (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
@@ -144,7 +163,7 @@ 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
+ * Running on http://0.0.0.0:8000
 
 ### Deck function and web form 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/demo.gif)
@@ -172,6 +191,8 @@ When you run the application for the first time, it will automatically create th
 - [x] dropdown input ✅  
 - [x] show line number option ✅  
 - [ ] snapshot version control
+- [ ] optimizer-agnostic
+- [ ] check batch-config file compatibility
 
 ## Citing
 
@@ -212,4 +233,4 @@ For an additional perspective related to the development of the tool, please see
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao
 
-Authors acknowledge all former and current Hein Lab members for their valuable suggestions. 
+Authors acknowledge Telescope Innovations, Hein Lab members for their valuable suggestions and contributions.

ivoryos-1.2.1.dist-info/RECORD

@@ -0,0 +1,51 @@
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ivoryos/routes/api/api.py

@@ -1,56 +0,0 @@
-import os
-from flask import Blueprint, jsonify, request, current_app
-
-from ivoryos.routes.control.control import find_instrument_by_name
-from ivoryos.utils.form import create_form_from_module
-from ivoryos.utils.global_config import GlobalConfig
-from ivoryos.utils.db_models import Script, WorkflowRun, SingleStep, WorkflowStep
-
-from ivoryos.socket_handlers import abort_pending, abort_current, pause, retry, runner
-from ivoryos.utils.task_runner import TaskRunner
-
-api = Blueprint('api', __name__)
-global_config = GlobalConfig()
-task_runner = TaskRunner()
-
-#TODO: add authentication and authorization to the API endpoints
-
-
-@api.route("/control/", strict_slashes=False, methods=['GET'])
-@api.route("/control/<string:instrument>", methods=['POST'])
-def backend_control(instrument: str=None):
-    """
-    .. :quickref: Backend Control; backend control
-
-    backend control through http requests
-
-    .. http:get:: /api/control/
-
-    :param instrument: instrument name
-    :type instrument: str
-
-    .. http:post:: /api/control/
-
-    """
-    if 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':
-        method_name = request.form.get("hidden_name", None)
-        form = forms.get(method_name, None)
-        if form:
-            kwargs = {field.name: field.data for field in form if field.name not in ['csrf_token', 'hidden_name']}
-            wait = request.form.get("hidden_wait", "true") == "true"
-            output = task_runner.run_single_step(component=instrument, method=method_name, kwargs=kwargs, wait=wait,
-                                            current_app=current_app._get_current_object())
-            return jsonify(output), 200
-
-    snapshot = global_config.deck_snapshot.copy()
-    # Iterate through each instrument in the snapshot
-    for instrument_key, instrument_data in snapshot.items():
-        # Iterate through each function associated with the current instrument
-        for function_key, function_data in instrument_data.items():
-            # Convert the function signature to a string representation
-            function_data['signature'] = str(function_data['signature'])
-    return jsonify(snapshot), 200

ivoryos/routes/auth/templates/login.html

@@ -1,25 +0,0 @@
-{% extends 'base.html' %}
-{% block title %}IvoryOS | Login{% endblock %}
-
-
-{% block body %}
-    <div class= "login">
-        <div class="bg-white rounded shadow-sm flex-fill">
-            <div class="p-4" style="align-items: center">
-                <h5>Log in</h5>
-                <form role="form" method='POST' name="login" action="{{ url_for('auth.login') }}">
-                    <div class="input-group mb-3">
-                        <label class="input-group-text" for="username">Username</label>
-                        <input class="form-control" type="text" id="username" name="username">
-                    </div>
-                    <div class="input-group mb-3">
-                        <label class="input-group-text" for="password">Password</label>
-                        <input class="form-control" type="password" id="password" name="password">
-                    </div>
-                    <button type="submit" class="btn btn-secondary" name="login" style="width: 100%;">login</button>
-                </form>
-                <p class="message">Not registered? <a href="{{ url_for('auth.signup') }}">Create a new account</a>
-            </div>
-        </div>
-    </div>
-{% endblock %}

ivoryos/routes/auth/templates/signup.html

@@ -1,32 +0,0 @@
-{% extends 'base.html' %}
-{% block title %}IvoryOS | Signup{% endblock %}
-
-
-{% block body %}
-<div class= "login">
-    <div class="bg-white rounded shadow-sm flex-fill">
-        <div class="p-4" style="align: center">
-            <h5>Create a new account</h5>
-            <form role="form" method='POST' name="signup" action="{{ url_for('auth.signup') }}">
-
-                <div class="input-group mb-3">
-                    <label class="input-group-text" for="username">Username</label>
-                    <input class="form-control" type="text" id="username" name="username" required>
-                </div>
-                <div class="input-group mb-3">
-                    <label class="input-group-text" for="password">Password</label>
-                    <input class="form-control" type="password" id="password" name="password" required>
-                </div>
-{#                <div class="input-group mb-3">#}
-{#                    <label class="input-group-text" for="confirm_password">Confirm Password</label>#}
-{#                    <input class="form-control" type="confirm_password" id="confirm_password" name="confirm_password">#}
-{#                </div>#}
-
-                <button type="submit" class="btn btn-secondary" name="login" style="width: 100%;">Sign up</button>
-            </form>
-            <p class="message" >Already registered? <a href="{{ url_for('auth.login') }}">Sign In</a></p>
-        </div>
-    </div>
-</div>
-
-{% endblock %}