ivoryos 1.0.3__tar.gz → 1.0.5__tar.gz

{ivoryos-1.0.3/ivoryos.egg-info → ivoryos-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 1.0.3
+Version: 1.0.5
 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-1.0.3 → ivoryos-1.0.5}/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-1.0.3 → ivoryos-1.0.5}/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.
@@ -101,10 +110,11 @@ 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
+    os.makedirs(app.config["OUTPUT_FOLDER"], exist_ok=True)
 
     # plugins = load_installed_plugins(app, socketio)
     plugins = []
@@ -153,6 +163,13 @@ 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 +192,7 @@ 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-1.0.3 → ivoryos-1.0.5}/ivoryos/config.py

@@ -10,7 +10,6 @@ class Config:
     OPENAI_API_KEY = os.getenv('OPENAI_API_KEY', None)
 
     OUTPUT_FOLDER = os.path.join(os.path.abspath(os.curdir), 'ivoryos_data')
-    os.makedirs(OUTPUT_FOLDER, exist_ok=True)
     CSV_FOLDER = os.path.join(OUTPUT_FOLDER, 'config_csv/')
     SCRIPT_FOLDER = os.path.join(OUTPUT_FOLDER, 'scripts/')
     DATA_FOLDER = os.path.join(OUTPUT_FOLDER, 'results/')
@@ -38,10 +37,17 @@ class TestingConfig(Config):
     DEBUG = True
     TESTING = True
 
+class DemoConfig(Config):
+    DEBUG = False
+    SQLALCHEMY_DATABASE_URI = 'sqlite:///:memory:'
+    OUTPUT_FOLDER = "/tmp/ivoryos_data"
+
 
 def get_config(env='dev'):
     if env == 'production':
         return ProductionConfig()
     elif env == 'testing':
         return TestingConfig()
+    elif env == 'demo':
+        return DemoConfig()
     return DevelopmentConfig()

{ivoryos-1.0.3 → ivoryos-1.0.5}/ivoryos/routes/auth/auth.py

@@ -69,16 +69,18 @@ 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')
 
 
@@ -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-1.0.3 → ivoryos-1.0.5}/ivoryos/routes/database/database.py

@@ -20,7 +20,7 @@ def edit_workflow(script_name:str):
 
     :param script_name: script name
     :type script_name: str
-    :status 302: redirect to :http:get:`/ivoryos/experiment/build/`
+    :status 302: redirect to :http:get:`/ivoryos/design/script/`
     """
     row = Script.query.get(script_name)
     script = Script(**row.as_dict())
@@ -244,7 +244,7 @@ def get_workflow_steps(workflow_id:int):
     .. http:get:: /database/workflows/<int:workflow_id>
 
     """
-    workflow = WorkflowRun.query.get_or_404(workflow_id)
+    workflow = db.session.get(WorkflowRun, workflow_id)
     steps = WorkflowStep.query.filter_by(workflow_id=workflow_id).order_by(WorkflowStep.start_time).all()
 
     # Use full objects for template rendering

{ivoryos-1.0.3 → ivoryos-1.0.5}/ivoryos/routes/design/design.py

@@ -120,7 +120,7 @@ def experiment_builder(instrument=None):
     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__
-    script.sort_actions()
+    # script.sort_actions()
 
     pseudo_deck_name = session.get('pseudo_deck', '')
     pseudo_deck_path = os.path.join(current_app.config["DUMMY_DECK"], pseudo_deck_name)
@@ -202,11 +202,11 @@ def experiment_builder(instrument=None):
                 logic_type = kwargs.pop('builtin_name')
                 if 'variable' in kwargs:
                     try:
-                        script.add_variable(**kwargs, insert_position=insert_position)
+                        script.add_variable(insert_position=insert_position, **kwargs)
                     except ValueError:
                         flash("Invalid variable type")
                 else:
-                    script.add_logic_action(logic_type=logic_type, **kwargs, insert_position=insert_position)
+                    script.add_logic_action(logic_type=logic_type, insert_position=insert_position, **kwargs)
             else:
                 flash(form.errors)
         elif request.method == 'POST' and "workflow_name" in request.form:
@@ -240,6 +240,10 @@ def experiment_builder(instrument=None):
                 forms = create_form_from_pseudo(functions, autofill=autofill, script=script)
 
     utils.post_script_file(script)
+
+    exec_string = script.python_script if script.python_script else script.compile(current_app.config['SCRIPT_FOLDER'])
+    session['python_code'] = exec_string
+
     design_buttons = create_action_button(script)
     return render_template('experiment_builder.html', off_line=off_line, instrument=instrument, history=deck_list,
                            script=script, defined_variables=deck_variables,
@@ -313,7 +317,8 @@ def experiment_run():
     """
     deck = global_config.deck
     script = utils.get_script_file()
-    script.sort_actions()
+
+    # script.sort_actions() # handled in update list
     off_line = current_app.config["OFF_LINE"]
     deck_list = utils.import_history(os.path.join(current_app.config["OUTPUT_FOLDER"], 'deck_history.txt'))
     # if not off_line and deck is None:
@@ -345,7 +350,7 @@ def experiment_run():
     if filename:
         # config_preview = list(csv.DictReader(open(os.path.join(current_app.config['CSV_FOLDER'], filename))))
         config = list(csv.DictReader(open(os.path.join(current_app.config['CSV_FOLDER'], filename))))
-        config_preview = config[1:6]
+        config_preview = config[1:]
         arg_type = config.pop(0)  # first entry is types
     try:
         for key, func_str in exec_string.items():
@@ -439,14 +444,24 @@ def toggle_script_type(stype=None):
     return redirect(url_for('design.experiment_builder'))
 
 
-@design.route("/updateList", methods=['GET', 'POST'])
+@design.route("/updateList", methods=['POST'])
 @login_required
 def update_list():
     order = request.form['order']
     script = utils.get_script_file()
     script.currently_editing_order = order.split(",", len(script.currently_editing_script))
+    script.sort_actions()
+    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
     utils.post_script_file(script)
-    return jsonify('Successfully Updated')
+    session['python_code'] = exec_string
+
+    return jsonify({'success': True})
+
+
+@design.route("/toggle_show_code", methods=["POST"])
+def toggle_show_code():
+    session["show_code"] = not session.get("show_code", False)
+    return redirect(request.referrer or url_for("design.experiment_builder"))
 
 
 # --------------------handle all the import/export and download/upload--------------------------

{ivoryos-1.0.3 → ivoryos-1.0.5}/ivoryos/routes/design/templates/design/experiment_builder.html

@@ -3,6 +3,23 @@
 
 {% block body %}
     {# overlay block for text-to-code gen #}
+    <style>
+    .code-overlay {
+        position: absolute;
+        top: 0;
+        right: -50%;
+        height: 100%;
+        width: 50%;
+        z-index: 100;
+        background: #f8f9fa;
+        box-shadow: -2px 0 6px rgba(0, 0, 0, 0.1);
+        transition: right 0.3s ease;
+        overflow-y: auto;
+    }
+    .code-overlay.show {
+        right: 0;
+    }
+</style>
     <div id="overlay" class="overlay">
         <div>
             <h3 id="overlay-text">Generating design, please wait...</h3>
@@ -252,6 +269,13 @@
                     <li class="nav-item"><a class="{{'nav-link active' if script.editing_type=='script' else 'nav-link'}}" aria-current="page" href="{{url_for('design.toggle_script_type', stype='script') }}">Experiment</a></li>
                     <li class="nav-item"><a class="{{'nav-link active' if script.editing_type=='cleanup' else 'nav-link'}}" aria-current="page" href="{{url_for('design.toggle_script_type', stype='cleanup') }}">Clean up</a></li>
                 </ul>
+                <form method="POST" action="{{ url_for('design.toggle_show_code') }}" class="ms-3">
+                    <div class="form-check form-switch">
+                        <input class="form-check-input" type="checkbox" id="showPythonCodeSwitch" name="show_code"
+                               onchange="this.form.submit()" {% if session.get('show_code') %}checked{% endif %}>
+                        <label class="form-check-label" for="showPythonCodeSwitch">Show Python Code</label>
+                    </div>
+                </form>
 
                 <div class="form-check form-switch ms-auto">
                     <input class="form-check-input" type="checkbox" id="toggleLineNumbers" onchange="toggleLineNumbers()">
@@ -259,54 +283,74 @@
                 </div>
 
             </div>
-
-            <div class="canvas" droppable="true">
-                <div class="collapse" id="info">
-                    <table class="table script-table">
-                        <tbody>
-                            <tr><th scope="row">Deck Name</th><td>{{script.deck}}</td></tr>
-                            <tr><th scope="row">Script Name</th><td>{{ script.name }}</td></tr>
-                            <tr>
-                                <th scope="row">Editing status <a role="button" data-bs-toggle="popover" data-bs-title="How to use:" data-bs-content="You can choose to disable editing, so the script is finalized and cannot be edited. Use save as to rename the script"><i class="bi bi-info-circle"></i></a></th>
-                                <td>{{script.status}}</td>
-                            </tr>
-                            <tr>
-                                <th scope="row">Output Values <a role="button" data-bs-toggle="popover" data-bs-title="How to use:" data-bs-content="This will be your output data. If the return data is not a value, it will save as None is the result file"><i class="bi bi-info-circle"></i></a></th>
-                                <td>
-                                    {% for i in script.config_return()[1] %}
-                                        <input type="checkbox">{{i}}
-                                    {% endfor %}
-                                </td>
-                            </tr>
-                            <tr>
-                                <th scope="row">Config Variables <a role="button" data-bs-toggle="popover" data-bs-title="How to use:" data-bs-content="This shows variables you want to configure later using .csv file"><i class="bi bi-info-circle"></i></a></th>
-                                <td>
-                                    <ul>
-                                        {% for i in script.config("script")[0] %}
-                                            <li>{{i}}</li>
+            <div class="canvas-wrapper position-relative">
+                <div class="canvas" droppable="true">
+                    <div class="collapse" id="info">
+                        <table class="table script-table">
+                            <tbody>
+                                <tr><th scope="row">Deck Name</th><td>{{script.deck}}</td></tr>
+                                <tr><th scope="row">Script Name</th><td>{{ script.name }}</td></tr>
+                                <tr>
+                                    <th scope="row">Editing status <a role="button" data-bs-toggle="popover" data-bs-title="How to use:" data-bs-content="You can choose to disable editing, so the script is finalized and cannot be edited. Use save as to rename the script"><i class="bi bi-info-circle"></i></a></th>
+                                    <td>{{script.status}}</td>
+                                </tr>
+                                <tr>
+                                    <th scope="row">Output Values <a role="button" data-bs-toggle="popover" data-bs-title="How to use:" data-bs-content="This will be your output data. If the return data is not a value, it will save as None is the result file"><i class="bi bi-info-circle"></i></a></th>
+                                    <td>
+                                        {% for i in script.config_return()[1] %}
+                                            <input type="checkbox">{{i}}
                                         {% endfor %}
-                                    </ul>
-                                </td>
-                            </tr>
-                        </tbody>
-                    </table>
-                </div>
-                <div class="list-group" id="list" style="margin-top: 20px">
-                    <ul class="reorder">
-                    {% for button in buttons %}
-                        <li id="{{ button['id'] }}" style="list-style-type: none;">
-                            <span class="line-number d-none">{{ button['id'] }}.</span>
-                            <a href="{{ url_for('design.edit_action', uuid=button['uuid']) }}" type="button" class="btn btn-light" style="{{ button['style'] }}">{{ button['label'] }}</a>
-                            {% if not button["instrument"] in ["if","while","repeat"] %}
-                                <a href="{{ url_for('design.duplicate_action', id=button['id']) }}" type="button" class="btn btn-light"><span class="bi bi-copy"></span></a>
-                            {% endif %}
-                            <a href="{{ url_for('design.delete_action', id=button['id']) }}" type="button" class="btn btn-light"><span class="bi bi-trash"></span></a>
-                        </li>
-                    {% endfor %}
-                    </ul>
+                                    </td>
+                                </tr>
+                                <tr>
+                                    <th scope="row">Config Variables <a role="button" data-bs-toggle="popover" data-bs-title="How to use:" data-bs-content="This shows variables you want to configure later using .csv file"><i class="bi bi-info-circle"></i></a></th>
+                                    <td>
+                                        <ul>
+                                            {% for i in script.config("script")[0] %}
+                                                <li>{{i}}</li>
+                                            {% endfor %}
+                                        </ul>
+                                    </td>
+                                </tr>
+                            </tbody>
+                        </table>
+                    </div>
+
+                    <div class="list-group" id="list" style="margin-top: 20px">
+                        <ul class="reorder">
+                        {% for button in buttons %}
+                            <li id="{{ button['id'] }}" style="list-style-type: none;">
+                                <span class="line-number d-none">{{ button['id'] }}.</span>
+                                <a href="{{ url_for('design.edit_action', uuid=button['uuid']) }}" type="button" class="btn btn-light" style="{{ button['style'] }}">{{ button['label'] }}</a>
+                                {% if not button["instrument"] in ["if","while","repeat"] %}
+                                    <a href="{{ url_for('design.duplicate_action', id=button['id']) }}" type="button" class="btn btn-light"><span class="bi bi-copy"></span></a>
+                                {% endif %}
+                                <a href="{{ url_for('design.delete_action', id=button['id']) }}" type="button" class="btn btn-light"><span class="bi bi-trash"></span></a>
+                            </li>
+                        {% endfor %}
+                        </ul>
 
+                        <!-- Python Code Overlay -->
+                        <!-- Right side: Python code (conditionally shown) -->
+                        <!-- Python Code Slide-Over Panel -->
+                        {% if session.get('show_code') %}
+                        <div id="pythonCodeOverlay" class="code-overlay bg-light border-start show">
+                            <div class="overlay-header d-flex justify-content-between align-items-center px-3 py-2 border-bottom">
+                                <strong>Python Code</strong>
+                                <button class="btn btn-sm btn-outline-secondary" onclick="toggleCodeOverlay(false)">
+                                    <i class="bi bi-x-lg"></i>
+                                </button>
+                            </div>
+                            <div class="overlay-content p-3">
+                                {% for stype, script in session['python_code'].items() %}
+                                    <pre><code class="language-python">{{ script }}</code></pre>
+                                {% endfor %}
+                                <a href="{{ url_for('design.download', filetype='python') }}">Download <i class="bi bi-download"></i></a>
+                            </div>
+                        </div>
+                        {% endif %}
+                    </div>
                 </div>
-            </div>
             <div>
                 <a class="btn btn-dark {{ 'disabled' if not script.name or script.status == "finalized" else ''}}" href="{{url_for('database.publish')}}">Quick Save</a>
                 <a class="btn btn-dark " href="{{ url_for('design.experiment_run') }}">Compile and Run</a>
@@ -445,6 +489,17 @@
         }
     }
 
+    function toggleCodeOverlay() {
+        const overlay = document.getElementById("pythonCodeOverlay");
+        const toggleBtn = document.getElementById("codeToggleBtn");
+        overlay.classList.toggle("show");
+
+        // Change arrow icon
+        const icon = toggleBtn.querySelector("i");
+        icon.classList.toggle("bi-chevron-left");
+        icon.classList.toggle("bi-chevron-right");
+    }
+
     // Restore state on page load
     document.addEventListener('DOMContentLoaded', () => {
         const savedState = localStorage.getItem('showLineNumbers');