ivoryos 1.0.1__tar.gz → 1.0.4__tar.gz

{ivoryos-1.0.1/ivoryos.egg-info → ivoryos-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 1.0.1
+Version: 1.0.4
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -168,6 +168,42 @@ When you run the application for the first time, it will automatically create th
 - [x] show line number option ✅  
 - [ ] snapshot version control
 
+## Citing
+
+If you find this project useful, please consider citing the following manuscript:
+
+> Zhang, W., Hao, L., Lai, V. et al. [IvoryOS: an interoperable web interface for orchestrating Python-based self-driving laboratories.](https://www.nature.com/articles/s41467-025-60514-w) Nat Commun 16, 5182 (2025).
+
+```bibtex
+@article{zhang_et_al_2025,
+  author       = {Wenyu Zhang and Lucy Hao and Veronica Lai and Ryan Corkery and Jacob Jessiman and Jiayu Zhang and Junliang Liu and Yusuke Sato and Maria Politi and Matthew E. Reish and Rebekah Greenwood and Noah Depner and Jiyoon Min and Rama El-khawaldeh and Paloma Prieto and Ekaterina Trushina and Jason E. Hein},
+  title        = {{IvoryOS}: an interoperable web interface for orchestrating {Python-based} self-driving laboratories},
+  journal      = {Nature Communications},
+  year         = {2025},
+  volume       = {16},
+  number       = {1},
+  pages        = {5182},
+  doi          = {10.1038/s41467-025-60514-w},
+  url          = {https://doi.org/10.1038/s41467-025-60514-w}
+}
+```
+
+For an additional perspective related to the development of the tool, please see:
+
+> Zhang, W., Hein, J. [Behind IvoryOS: Empowering Scientists to Harness Self-Driving Labs for Accelerated Discovery](https://communities.springernature.com/posts/behind-ivoryos-empowering-scientists-to-harness-self-driving-labs-for-accelerated-discovery). Springer Nature Research Communities (2025).
+
+```bibtex
+@misc{zhang_hein_2025,
+  author       = {Wenyu Zhang and Jason Hein},
+  title        = {Behind {IvoryOS}: Empowering Scientists to Harness Self-Driving Labs for Accelerated Discovery},
+  howpublished = {Springer Nature Research Communities},
+  year         = {2025},
+  month        = {Jun},
+  day          = {18},
+  url          = {https://communities.springernature.com/posts/behind-ivoryos-empowering-scientists-to-harness-self-driving-labs-for-accelerated-discovery}
+}
+```
+
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao
 

{ivoryos-1.0.1 → ivoryos-1.0.4}/README.md

@@ -156,6 +156,42 @@ When you run the application for the first time, it will automatically create th
 - [x] show line number option ✅  
 - [ ] snapshot version control
 
+## Citing
+
+If you find this project useful, please consider citing the following manuscript:
+
+> Zhang, W., Hao, L., Lai, V. et al. [IvoryOS: an interoperable web interface for orchestrating Python-based self-driving laboratories.](https://www.nature.com/articles/s41467-025-60514-w) Nat Commun 16, 5182 (2025).
+
+```bibtex
+@article{zhang_et_al_2025,
+  author       = {Wenyu Zhang and Lucy Hao and Veronica Lai and Ryan Corkery and Jacob Jessiman and Jiayu Zhang and Junliang Liu and Yusuke Sato and Maria Politi and Matthew E. Reish and Rebekah Greenwood and Noah Depner and Jiyoon Min and Rama El-khawaldeh and Paloma Prieto and Ekaterina Trushina and Jason E. Hein},
+  title        = {{IvoryOS}: an interoperable web interface for orchestrating {Python-based} self-driving laboratories},
+  journal      = {Nature Communications},
+  year         = {2025},
+  volume       = {16},
+  number       = {1},
+  pages        = {5182},
+  doi          = {10.1038/s41467-025-60514-w},
+  url          = {https://doi.org/10.1038/s41467-025-60514-w}
+}
+```
+
+For an additional perspective related to the development of the tool, please see:
+
+> Zhang, W., Hein, J. [Behind IvoryOS: Empowering Scientists to Harness Self-Driving Labs for Accelerated Discovery](https://communities.springernature.com/posts/behind-ivoryos-empowering-scientists-to-harness-self-driving-labs-for-accelerated-discovery). Springer Nature Research Communities (2025).
+
+```bibtex
+@misc{zhang_hein_2025,
+  author       = {Wenyu Zhang and Jason Hein},
+  title        = {Behind {IvoryOS}: Empowering Scientists to Harness Self-Driving Labs for Accelerated Discovery},
+  howpublished = {Springer Nature Research Communities},
+  year         = {2025},
+  month        = {Jun},
+  day          = {18},
+  url          = {https://communities.springernature.com/posts/behind-ivoryos-empowering-scientists-to-harness-self-driving-labs-for-accelerated-discovery}
+}
+```
+
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao
 

{ivoryos-1.0.1 → ivoryos-1.0.4}/ivoryos/__init__.py

@@ -12,7 +12,7 @@ from ivoryos.routes.design.design import design, socketio
 from ivoryos.routes.main.main import main
 # from ivoryos.routes.monitor.monitor import monitor
 from ivoryos.utils import utils
-from ivoryos.utils.db_models import db
+from ivoryos.utils.db_models import db, User
 from ivoryos.utils.global_config import GlobalConfig
 from ivoryos.utils.script_runner import ScriptRunner
 from ivoryos.version import __version__ as ivoryos_version
@@ -40,6 +40,15 @@ app.register_blueprint(control, url_prefix=url_prefix)
 app.register_blueprint(design, url_prefix=url_prefix)
 app.register_blueprint(database, url_prefix=url_prefix)
 
+@login_manager.user_loader
+def load_user(user_id):
+    """
+    This function is called by Flask-Login on every request to get the
+    current user object from the user ID stored in the session.
+    """
+    # The correct implementation is to fetch the user from the database.
+    return db.session.get(User, user_id)
+
 
 def create_app(config_class=None):
     """
@@ -85,8 +94,8 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
         logger: Union[str, list] = None,
         logger_output_name: str = None,
         enable_design: bool = True,
-        blueprint_plugins: Union[list[Blueprint], Blueprint] = [],
-        exclude_names: list[str] = [],
+        blueprint_plugins: Union[list, Blueprint] = [],
+        exclude_names: list = [],
         ):
     """
     Start ivoryOS app server.
@@ -101,8 +110,8 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     :param logger: logger name of list of logger names, defaults to None
     :param logger_output_name: log file save name of logger, defaults to None, and will use "default.log"
     :param enable_design: enable design canvas, database and workflow execution
-    :param blueprint_plugins: custom Blueprint pages
-    :param exclude_names: module names to exclude from parsing
+    :param blueprint_plugins: Union[list[Blueprint], Blueprint] custom Blueprint pages
+    :param exclude_names: list[str] module names to exclude from parsing
     """
     app = create_app(config_class=config or get_config())  # Create app instance using factory function
 
@@ -153,6 +162,13 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     elif type(logger) is list:
         for log in logger:
             utils.start_logger(socketio, log_filename=logger_path, logger_name=log)
+
+    # in case Python 3.12 or higher doesn't log URL
+    if sys.version_info >= (3, 12):
+        ip = utils.get_ip_address()
+        print(f"Server running at http://localhost:{port}")
+        if not ip == "127.0.0.1":
+            print(f"Server running at http://{ip}:{port}")
     socketio.run(app, host=host, port=port, debug=debug, use_reloader=False, allow_unsafe_werkzeug=True)
     # return app
 
@@ -175,7 +191,7 @@ def load_installed_plugins(app, socketio):
     return plugin_names
 
 
-def load_plugins(blueprints: Union[list[Blueprint], Blueprint], app, socketio):
+def load_plugins(blueprints: Union[list, Blueprint], app, socketio):
     """
     Dynamically load installed plugins and attach Flask-SocketIO.
     """

{ivoryos-1.0.1 → ivoryos-1.0.4}/ivoryos/routes/auth/auth.py

@@ -9,7 +9,7 @@ login_manager = LoginManager()
 auth = Blueprint('auth', __name__, template_folder='templates/auth')
 
 
-@auth.route('/login', methods=['GET', 'POST'])
+@auth.route('/auth/login', methods=['GET', 'POST'])
 def login():
     """
     .. :quickref: User; login user
@@ -50,7 +50,7 @@ def login():
     return render_template('login.html')
 
 
-@auth.route('/signup', methods=['GET', 'POST'])
+@auth.route('/auth/signup', methods=['GET', 'POST'])
 def signup():
     """
     .. :quickref: User; signup for a new account
@@ -69,20 +69,22 @@ def signup():
     if request.method == 'POST':
         username = request.form.get('username')
         password = request.form.get('password')
-        salt = bcrypt.gensalt()
-        hashed = bcrypt.hashpw(password.encode('utf-8'), salt)
-        user = User(username, hashed)
-        try:
-            db.session.add(user)
-            db.session.commit()
-            return redirect(url_for('auth.login'))
-        except Exception:
-            flash("username exists :(", "error")
+
+        # Query the database to see if the user already exists.
+        existing_user = User.query.filter_by(username=username).first()
+
+        if existing_user:
+            flash("User already exists :(", "error")
             return render_template('signup.html'), 409
+        hashed = bcrypt.hashpw(password.encode('utf-8'), bcrypt.gensalt())
+        user = User(username, hashed)
+        db.session.add(user)
+        db.session.commit()
+        return redirect(url_for('auth.login'))
     return render_template('signup.html')
 
 
-@auth.route("/logout")
+@auth.route("/auth/logout")
 @login_required
 def logout():
     """
@@ -92,9 +94,4 @@ def logout():
     """
     logout_user()
     session.clear()
-    return redirect(url_for('auth.login'))
-
-
-@login_manager.user_loader
-def load_user(username):
-    return User(username, password=None)
+    return redirect(url_for('auth.login'))

{ivoryos-1.0.1 → ivoryos-1.0.4}/ivoryos/routes/control/control.py

@@ -1,8 +1,10 @@
 import os
 
-from flask import Blueprint, redirect, url_for, flash, request, render_template, session, current_app, jsonify
+from flask import Blueprint, redirect, url_for, flash, request, render_template, session, current_app, jsonify, \
+    send_file
 from flask_login import login_required
 
+from ivoryos.utils.client_proxy import export_to_python, create_function
 from ivoryos.utils.global_config import GlobalConfig
 from ivoryos.utils import utils
 from ivoryos.utils.form import create_form_from_module, format_name
@@ -14,7 +16,7 @@ runner = TaskRunner()
 control = Blueprint('control', __name__, template_folder='templates/control')
 
 
-@control.route("/my_deck")
+@control.route("/control/home/deck", strict_slashes=False)
 @login_required
 def deck_controllers():
     """
@@ -22,15 +24,15 @@ def deck_controllers():
 
     deck control home interface for listing all deck instruments
 
-    .. http:get:: /my_deck
+    .. http:get:: /control/home/deck
     """
     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)
 
 
-@control.route("/new_controller/")
-@control.route("/new_controller/<instrument>", methods=['GET', 'POST'])
+@control.route("/control/new/", strict_slashes=False)
+@control.route("/control/new/<instrument>", methods=['GET', 'POST'])
 @login_required
 def new_controller(instrument=None):
     """
@@ -38,12 +40,12 @@ def new_controller(instrument=None):
 
     interface for connecting a new <instrument>
 
-    .. http:get:: /new_controller
+    .. http:get:: /control/new/
 
     :param instrument: instrument name
     :type instrument: str
 
-    .. http:post:: /new_controller
+    .. http:post:: /control/new/
 
     :form device_name: module instance name (e.g. my_instance = MyClass())
     :form kwargs: dynamic module initialization kwargs fields
@@ -88,7 +90,7 @@ def new_controller(instrument=None):
                            device=device, args=args, defined_variables=global_config.defined_variables)
 
 
-@control.route("/controllers")
+@control.route("/control/home/temp", strict_slashes=False)
 @login_required
 def controllers_home():
     """
@@ -96,14 +98,15 @@ def controllers_home():
 
     temporarily connected devices home interface for listing all instruments
 
-    .. http:get:: /controllers
+    .. http:get:: /control/home/temp
 
     """
     # defined_variables = parse_deck(deck)
-    return render_template('controllers_home.html', defined_variables=global_config.defined_variables)
+    defined_variables = global_config.defined_variables.keys()
+    return render_template('controllers_home.html', defined_variables=defined_variables)
 
 
-@control.route("/controllers/<instrument>", methods=['GET', 'POST'])
+@control.route("/control/<instrument>/methods", methods=['GET', 'POST'])
 @login_required
 def controllers(instrument: str):
     """
@@ -111,12 +114,12 @@ def controllers(instrument: str):
 
     control interface for selected <instrument>
 
-    .. http:get:: /controllers
+    .. http:get:: /control/<instrument>/methods
 
     :param instrument: instrument name
     :type instrument: str
 
-    .. http:post:: /controllers
+    .. http:post:: /control/<instrument>/methods
 
     :form hidden_name: function name (hidden field)
     :form kwargs: dynamic kwargs field
@@ -154,24 +157,50 @@ def controllers(instrument: str):
             flash(form.errors)
     return render_template('controllers.html', instrument=instrument, forms=forms, format_name=format_name)
 
+@control.route("/control/download", strict_slashes=False)
+@login_required
+def download_proxy():
+    """
+    .. :quickref: Direct Control; download proxy interface
+
+    download proxy interface
 
-@control.route("/backend_control/<instrument>", methods=['POST'])
+    .. http:get:: /control/download
+    """
+    snapshot = global_config.deck_snapshot.copy()
+    class_definitions = {}
+    # 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'])
+        class_name = instrument_key.split('.')[-1]  # Extracting the class name from the path
+        class_definitions[class_name.capitalize()] = create_function(request.url_root, class_name, instrument_data)
+    # Export the generated class definitions to a .py script
+    export_to_python(class_definitions, current_app.config["OUTPUT_FOLDER"])
+    filepath = os.path.join(current_app.config["OUTPUT_FOLDER"], "generated_proxy.py")
+    return send_file(os.path.abspath(filepath), as_attachment=True)
+
+@control.route("/api/control/", strict_slashes=False, methods=['GET'])
+@control.route("/api/control/<instrument>", methods=['POST'])
 def backend_control(instrument: str=None):
     """
     .. :quickref: Backend Control; backend control
 
     backend control through http requests
 
-    .. http:get:: /backend_control
+    .. http:get:: /api/control/
 
     :param instrument: instrument name
     :type instrument: str
 
-    .. http:post:: /backend_control
+    .. http:post:: /api/control/
 
     """
-    inst_object = find_instrument_by_name(instrument)
-    forms = create_form_from_module(sdl_module=inst_object, autofill=False, design=False)
+    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)
@@ -183,42 +212,48 @@ def backend_control(instrument: str=None):
                                             current_app=current_app._get_current_object())
             return jsonify(output), 200
 
-
-@control.route("/backend_control", methods=['GET'])
-def backend_client():
-    """
-    .. :quickref: Backend Control; get snapshot
-
-    backend control through http requests
-
-    .. http:get:: /backend_control
-    """
-    # Create a snapshot of the current deck configuration
     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
 
-    json_output = jsonify(snapshot)
-    return json_output, 200
+# @control.route("/api/control", strict_slashes=False, methods=['GET'])
+# def backend_client():
+#     """
+#     .. :quickref: Backend Control; get snapshot
+#
+#     backend control through http requests
+#
+#     .. http:get:: /api/control/summary
+#     """
+#     # Create a snapshot of the current deck configuration
+#     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
 
 
-@control.route("/import_api", methods=['POST'])
+@control.route("/control/import/module", methods=['POST'])
 def import_api():
     """
     .. :quickref: Advanced Features; Manually import API module(s)
 
     importing other Python modules
 
-    .. http:post:: /import_api
+    .. http:post:: /control/import/module
 
     :form filepath: API (Python class) module filepath
 
-    import the module and redirect to :http:get:`/ivoryos/new_controller/`
+    import the module and redirect to :http:get:`/ivoryos/control/new/`
 
     """
     filepath = request.form.get('filepath')
@@ -266,12 +301,12 @@ def import_api():
 #     return redirect(url_for('control.deck_controllers'))
 
 
-@control.route("/import_deck", methods=['POST'])
+@control.route("/control/import/deck", methods=['POST'])
 def import_deck():
     """
     .. :quickref: Advanced Features; Manually import a deck
 
-    .. http:post:: /import_deck
+    .. http:post:: /control/import_deck
 
     :form filepath: deck module filepath
 
@@ -304,12 +339,12 @@ def import_deck():
     return redirect(back)
 
 
-@control.route('/save-order/<instrument>', methods=['POST'])
+@control.route('/control/<instrument>/save-order', methods=['POST'])
 def save_order(instrument: str):
     """
     .. :quickref: Control Customization; Save functions' order
 
-    .. http:post:: /save-order
+    .. http:post:: /control/save-order
 
     save function drag and drop order for the given <instrument>
 
@@ -320,12 +355,12 @@ def save_order(instrument: str):
     return '', 204
 
 
-@control.route('/hide_function/<instrument>/<function>')
+@control.route('/control/<instrument>/<function>/hide')
 def hide_function(instrument, function):
     """
     .. :quickref: Control Customization; Hide function
 
-    .. http:get:: /hide_function
+    .. http:get:: //control/<instrument>/<function>/hide
 
     Hide the given <instrument> and <function>
 
@@ -341,12 +376,12 @@ def hide_function(instrument, function):
     return redirect(back)
 
 
-@control.route('/remove_hidden/<instrument>/<function>')
+@control.route('/control/<instrument>/<function>/unhide')
 def remove_hidden(instrument: str, function: str):
     """
     .. :quickref: Control Customization; Remove a hidden function
 
-    .. http:get:: /remove_hidden
+    .. http:get:: /control/<instrument>/<function>/unhide
 
     Un-hide the given <instrument> and <function>
 

{ivoryos-1.0.1 → ivoryos-1.0.4}/ivoryos/routes/control/templates/control/controllers_home.html

@@ -6,21 +6,21 @@
         {% for instrument in defined_variables %}
             <div class="col-xl-3 col-lg-4 col-md-6 mb-4 ">
                 <div class="bg-white rounded shadow-sm position-relative">
-{#                    {% if not deck %}#}
+                    {% if deck %}
 {#                        <a href="{{ url_for('control.disconnect', instrument=instrument) }}" class="stretched-link controller-card" style="float: right;color: red; position: relative;">Disconnect <i class="bi bi-x-square"></i></a>#}
                         <div class="p-4 controller-card">
                             <h5 class=""><a href="{{ url_for('control.controllers', instrument=instrument) }}" class="text-dark stretched-link">{{instrument.split(".")[1]}}</a></h5>
                         </div>
-{#                    {% else %}#}
-{#                        <div class="p-4 controller-card">#}
-{#                            <h5 class=""><a href="{{ url_for('control.controllers', instrument=instrument) }}" class="text-dark stretched-link">{{instrument}}</a></h5>#}
-{#                        </div>#}
-{#                    {% endif %}#}
+                    {% else %}
+                        <div class="p-4 controller-card">
+                            <h5 class=""><a href="{{ url_for('control.controllers', instrument=instrument) }}" class="text-dark stretched-link">{{instrument}}</a></h5>
+                        </div>
+                    {% endif %}
                 </div>
             </div>
         {% endfor %}
         <div class="d-flex mb-3">
-            <a href="{{ url_for('design.download', filetype='proxy') }}" class="btn btn-outline-primary">
+            <a href="{{ url_for('control.download_proxy', filetype='proxy') }}" class="btn btn-outline-primary">
                 <i class="bi bi-download"></i> Download remote control script
             </a>
         </div>