ivoryos 1.3.5a0__tar.gz → 1.3.7__tar.gz

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.5a0
+Version: 1.3.7
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -9,6 +9,7 @@ Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: bcrypt
+Requires-Dist: Flask[async]
 Requires-Dist: Flask-Login
 Requires-Dist: Flask-Session
 Requires-Dist: Flask-SocketIO
@@ -17,9 +18,21 @@ Requires-Dist: Flask-WTF
 Requires-Dist: SQLAlchemy-Utils
 Requires-Dist: python-dotenv
 Requires-Dist: astor; python_version < "3.9"
+Provides-Extra: optimizer-ax
+Requires-Dist: ax-platform; extra == "optimizer-ax"
+Provides-Extra: optimizer-baybe
+Requires-Dist: baybe; extra == "optimizer-baybe"
+Provides-Extra: optimizer-nimo
+Requires-Dist: nimo; extra == "optimizer-nimo"
 Provides-Extra: optimizer
-Requires-Dist: ax-platform; extra == "optimizer"
+Requires-Dist: ax-platform>=1.1.2; extra == "optimizer"
 Requires-Dist: baybe; extra == "optimizer"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-rtd-theme; extra == "doc"
+Requires-Dist: sphinxcontrib-httpdomain; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/__init__.py

@@ -1,8 +1,8 @@
-from ivoryos.server import run
+from ivoryos.server import run, global_config
 from ivoryos.optimizer.registry import OPTIMIZER_REGISTRY
 from ivoryos.version import __version__ as ivoryos_version
 from ivoryos.utils.decorators import block, BUILDING_BLOCKS
-from ivoryos.app import app
+from ivoryos.app import app, create_app, socketio, db
 
 __all__ = [
     "block",
@@ -11,4 +11,8 @@ __all__ = [
     "run",
     "app",
     "ivoryos_version",
+    "create_app",
+    "socketio",
+    "global_config",
+    "db"
 ]

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/optimizer/ax_optimizer.py

@@ -30,7 +30,7 @@ class AxOptimizer(OptimizerBase):
     @staticmethod
     def _create_generator_mapping():
         """Create a mapping from string values to Generator enum members."""
-        from ax.modelbridge import Generators
+        from ax.adapter import Generators
         return {member.value: member for member in Generators}
 
     def _convert_parameter_to_ax_format(self, parameter_space):
@@ -96,8 +96,8 @@ class AxOptimizer(OptimizerBase):
         step_2 = optimizer_config.get("step_2", {})
         step_1_generator = step_1.get("model", "Sobol")
         step_2_generator = step_2.get("model", "BOTorch")
-        generator_1 = GenerationStep(model=generators.get(step_1_generator), num_trials=step_1.get("num_samples", 5))
-        generator_2 = GenerationStep(model=generators.get(step_2_generator), num_trials=step_2.get("num_samples", -1))
+        generator_1 = GenerationStep(generator=generators.get(step_1_generator), num_trials=step_1.get("num_samples", 5))
+        generator_2 = GenerationStep(generator=generators.get(step_2_generator), num_trials=step_2.get("num_samples", -1))
         return GenerationStrategy(steps=[generator_1, generator_2])
 
     def suggest(self, n=1):

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/optimizer/base_optimizer.py

@@ -5,7 +5,7 @@ from abc import ABC, abstractmethod
 
 
 class OptimizerBase(ABC):
-    def __init__(self, experiment_name:str, parameter_space: list, objective_config: dict, optimizer_config: dict):
+    def __init__(self, experiment_name:str, parameter_space: list, objective_config: dict, optimizer_config: dict, datapath:str=None):
         """
         :param experiment_name: arbitrary name
         :param parameter_space: list of parameter names
@@ -29,6 +29,7 @@ class OptimizerBase(ABC):
         self.parameter_space = parameter_space
         self.objective_config = objective_config
         self.optimizer_config = optimizer_config
+        self.datapath = datapath
 
     @abstractmethod
     def suggest(self, n=1):

ivoryos-1.3.7/ivoryos/optimizer/nimo_optimizer.py

@@ -0,0 +1,162 @@
+### ivoryos/optimizers/nimo_optimizer.py
+import itertools
+import os
+
+
+from ivoryos.optimizer.base_optimizer import OptimizerBase
+
+
+class NIMOOptimizer(OptimizerBase):
+    def __init__(self, experiment_name:str, parameter_space: list, objective_config: list, optimizer_config: dict, datapath:str):
+        """
+        :param experiment_name: arbitrary name
+        :param parameter_space: list of parameter names
+        [
+            {"name": "param_1", "type": "range", "bounds": [1.0, 2.0], "value_type": "float"},
+            {"name": "param_2", "type": "choice", "bounds": ["a", "b", "c"], "value_type": "str"},
+            {"name": "param_3", "type": "range", "bounds": [0 10], "value_type": "int"},
+        ]
+        :param objective_config: objective configuration
+                [
+            {"name": "obj_1", "minimize": True, "weight": 1},
+            {"name": "obj_2", "minimize": False, "weight": 1}
+        ]
+        :param optimizer_config: optimizer configuration
+        optimizer_config={
+            "step_1": {"model": "Random", "num_samples": 10},
+            "step_2": {"model": "BOTorch"}
+        }
+        """
+        self.current_step = 0
+        self.experiment_name = experiment_name
+        self.parameter_space = parameter_space
+        self.objective_config = objective_config
+        self.optimizer_config = optimizer_config
+
+        super().__init__(experiment_name, parameter_space, objective_config, optimizer_config, datapath)
+
+        step_1 = optimizer_config.get("step_1", {})
+        step_2 = optimizer_config.get("step_2", {})
+        self.step_1_generator = step_1.get("model", "RE")
+        self.step_1_batch_num = step_1.get("num_samples", 1)
+        self.step_2_generator = step_2.get("model", "PDC")
+        self.candidates = os.path.join(self.datapath, f"{self.experiment_name}_candidates.csv")
+        self.proposals = os.path.join(self.datapath, f"{self.experiment_name}_proposals.csv")
+        self.n_objectives = len(self.objective_config)
+        self._create_candidates_csv()
+
+
+    def _create_candidates_csv(self):
+        # Extract parameter names and their possible values
+        import pandas as pd
+        import nimo
+        if os.path.exists(self.candidates) and nimo.history(self.candidates, self.n_objectives):
+            return
+        param_names = [p["name"] for p in self.parameter_space]
+
+        param_values = []
+        for p in self.parameter_space:
+            if p["type"] == "choice" and isinstance(p["bounds"], list):
+                param_values.append(p["bounds"])
+            elif p["type"] == "range" and len(p["bounds"]) == 2:
+                low, high = p["bounds"]
+                num_points = 10  # you can customize this granularity
+                step = (high - low) / (num_points - 1)
+                param_values.append([round(low + i * step, 4) for i in range(num_points)])
+            else:
+                raise ValueError(f"Unsupported parameter format: {p}")
+
+        # Generate all possible combinations
+        combos = list(itertools.product(*param_values))
+
+        # Create a DataFrame with parameter columns
+        df = pd.DataFrame(combos, columns=param_names)
+
+        # Add empty objective columns
+        for obj in self.objective_config:
+            df[obj["name"]] = ""
+
+        # Save to CSV
+        df.to_csv(self.candidates, index=False)
+
+
+    def suggest(self, n=1):
+        import pandas as pd
+        import nimo
+        method = self.step_1_generator if self.current_step <= self.step_1_batch_num else self.step_2_generator
+        nimo.selection(method = method,
+                       input_file = self.candidates,
+                       output_file = self.proposals,
+                       num_objectives = self.n_objectives,
+                       num_proposals = n)
+        self.current_step += 1
+        # Read proposals from CSV file
+        proposals_df = pd.read_csv(self.proposals)
+        # Get parameter names
+        param_names = [p["name"] for p in self.parameter_space]
+        # Convert proposals to list of parameter dictionaries
+        proposals = []
+        for _, row in proposals_df.iterrows():
+            proposal = {name: row[name] for name in param_names}
+            proposals.append(proposal)
+        return proposals[0] if n == 1 else proposals
+
+    def _convert_observation_to_list(self, obs: dict) -> list:
+        obj_names = [o["name"] for o in self.objective_config]
+        return [obs.get(name, None) for name in obj_names]
+
+    def observe(self, results: dict):
+        """
+        observe single output, nimo obj input is [1,2,3] or [[1, 2], [1, 2], [1, 2]] for MO
+        :param results: {"objective_name": "value"}
+        """
+        import nimo
+        nimo_objective_values = [self._convert_observation_to_list(results)]
+
+        nimo.output_update(input_file=self.proposals,
+                           output_file=self.candidates,
+                           num_objectives=self.n_objectives,
+                           objective_values=nimo_objective_values)
+
+    def append_existing_data(self, existing_data):
+        # TODO, history is part of the candidate file, we probably won't need this
+        pass
+
+
+    @staticmethod
+    def get_schema():
+        return {
+            "parameter_types": ["choice"],
+            "multiple_objectives": True,
+            "optimizer_config": {
+                "step_1": {"model": ["RE", "ES", "PDC"], "num_samples": 5},
+                "step_2": {"model": ["PHYSBO", "BLOX", "PTR", "SLESA", "BOMP", "COMBI"]}
+            },
+        }
+
+
+
+
+if __name__ == "__main__":
+    parameter_space = [
+        {"name": "silica", "type": "choice", "bounds": [100], "value_type": "float"},
+        {"name": "water", "type": "choice", "bounds": [900, 800, 750, 700, 650, 600, 550, 500], "value_type": "float"},
+        {"name": "PVA", "type": "choice", "bounds": [0, 0.005, 0.0075, 0.01, 0.05, 0.075, 0.1], "value_type": "float"},
+        {"name": "SDS", "type": "choice", "bounds": [0], "value_type": "float"},
+        {"name": "DTAB", "type": "choice", "bounds": [0, 0.005, 0.0075, 0.01, 0.05, 0.075, 0.1], "value_type": "float"},
+        {"name": "PVP", "type": "choice", "bounds": [0], "value_type": "float"},
+    ]
+    objective_config = [
+        {"name": "objective", "minimize": False, "weight": 1},
+
+    ]
+    optimizer_config = {
+        "step_1": {"model": "RE", "num_samples": 10},
+        "step_2": {"model": "PDC"}
+    }
+
+    nimo_optimizer = NIMOOptimizer(experiment_name="example_experiment", optimizer_config=optimizer_config, parameter_space=parameter_space, objective_config=objective_config)
+    nimo_optimizer.suggest(n=1)
+    nimo_optimizer.observe(
+        results={"objective": 1.0}
+    )

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/optimizer/registry.py

@@ -2,8 +2,10 @@
 
 from ivoryos.optimizer.ax_optimizer import AxOptimizer
 from ivoryos.optimizer.baybe_optimizer import BaybeOptimizer
+from ivoryos.optimizer.nimo_optimizer import NIMOOptimizer
 
 OPTIMIZER_REGISTRY = {
     "ax": AxOptimizer,
-    "baybe": BaybeOptimizer
+    "baybe": BaybeOptimizer,
+    "nimo": NIMOOptimizer,
 }

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/routes/design/design.py

@@ -87,8 +87,11 @@ def experiment_builder():
 
     # edit_action_info = session.get("edit_action")
 
-
-    exec_string = script.python_script if script.python_script else script.compile(current_app.config['SCRIPT_FOLDER'])
+    try:
+        exec_string = script.python_script if script.python_script else script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        flash(f"Error in Python script: {e}")
     session['python_code'] = exec_string
 
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
@@ -382,7 +385,13 @@ def methods_handler(instrument: str = ''):
                 success = False
                 msg = [f"{field}: {', '.join(messages)}" for field, messages in form.errors.items()]
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    #TODO
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        msg = f"Compilation failed: {str(e)}"
+    # exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
     session['python_code'] = exec_string
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
     html = render_template("components/canvas_main.html", script=script, buttons_dict=design_buttons)

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/routes/design/design_step.py

@@ -23,12 +23,16 @@ def get_step(uuid: int):
     """
     script = utils.get_script_file()
     action = script.find_by_uuid(uuid)
-    if request.method == 'GET':
-        # forms = create_form_from_action(action, script=script)
+    if action is None:
+        return jsonify({"warning": "Step not found, please refresh the page."}), 404
+
+    elif request.method == 'GET':
+        forms = create_form_from_action(action, script=script)
         # session['edit_action'] = action
         return render_template("components/edit_action_form.html",
                                action=action,
-                               forms=create_form_from_action(action, script=script))
+                               forms=forms)
+
 
 
 @steps.post("/draft/steps/<int:uuid>")
@@ -47,6 +51,7 @@ def save_step(uuid: int):
     """
     script = utils.get_script_file()
     action = script.find_by_uuid(uuid)
+    warning = None
     if action is not None:
         forms = create_form_from_action(action, script=script)
         kwargs = {field.name: field.data for field in forms if field.name != 'csrf_token'}
@@ -55,14 +60,19 @@ def save_step(uuid: int):
             kwargs = script.validate_variables(kwargs)
             script.update_by_uuid(uuid=uuid, args=kwargs, output=save_as)
         else:
-            flash(forms.errors)
+            warning = f"Compilation failed: {str(forms.errors)}"
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
     return render_template("components/canvas_main.html",
-                               script=script,
-                               buttons_dict=design_buttons)
+                           script=script,
+                           buttons_dict=design_buttons,
+                           warning=warning)
 
 @steps.delete("/draft/steps/<int:uuid>")
 def delete_step(uuid: int):
@@ -82,12 +92,17 @@ def delete_step(uuid: int):
     if request.method == 'DELETE':
         script.delete_action(uuid)
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    warning = None
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
     return render_template("components/canvas_main.html",
                                script=script,
-                               buttons_dict=design_buttons)
+                               buttons_dict=design_buttons, warning=warning)
 
 
 @steps.route("/draft/steps/<int:uuid>/duplicate", methods=["POST"], strict_slashes=False,)
@@ -107,13 +122,18 @@ def duplicate_action(uuid: int):
     script = utils.get_script_file()
     script.duplicate_action(uuid)
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    warning = None
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
 
     return render_template("components/canvas_main.html",
                          script=script,
-                         buttons_dict=design_buttons)
+                         buttons_dict=design_buttons, warning=warning)
 
 
 @steps.route("/draft/steps/order", methods=['POST'])
@@ -133,13 +153,18 @@ def update_list():
     script = utils.get_script_file()
     script.currently_editing_order = order.split(",", len(script.currently_editing_script))
     script.sort_actions()
+    warning = None
 
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
 
     # Return the updated canvas HTML instead of JSON
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
     return render_template("components/canvas_main.html",
                            script=script,
-                           buttons_dict=design_buttons)
+                           buttons_dict=design_buttons, warning=warning)

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/routes/design/templates/components/canvas_main.html

@@ -31,4 +31,9 @@
 </div>
 <div class="python-code-wrapper" id="python-code-wrapper">
     {% include 'components/python_code_overlay.html' %}
-</div>
+</div>
+
+
+{% if warning %}
+<div id="warning" style="display:none;">{{ warning }}</div>
+{% endif %}

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/routes/design/templates/components/edit_action_form.html

@@ -6,6 +6,7 @@
             <i class="bi bi-arrow-return-left"></i>
         </a>
     </div>
+    {% if action %}
     <h5> {{ action['action'] | format_name }} </h5>
     <form role="form" method='POST' name="{{instrument}}" 
           action="{{ url_for('design.design_steps.get_step', uuid=action['uuid']) }}"
@@ -36,3 +37,4 @@
         <button type="submit" class="btn btn-primary">Save</button>
         <button type="button" class="btn btn-primary" id="back">Back</button>
     </form>
+    {% endif %}

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/server.py

@@ -50,6 +50,7 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
         blueprint_plugins: Union[list, Blueprint] = [],
         exclude_names: list = [],
         notification_handler=None,
+        optimizer_registry: dict = None,
         ):
     """
     Start ivoryOS app server.
@@ -91,7 +92,10 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     app.config["LOGGERS_PATH"] = logger_output_name or app.config["LOGGERS_PATH"]  # default.log
     logger_path = os.path.join(app.config["OUTPUT_FOLDER"], app.config["LOGGERS_PATH"])
     dummy_deck_path = os.path.join(app.config["OUTPUT_FOLDER"], app.config["DUMMY_DECK"])
-    global_config.optimizers = OPTIMIZER_REGISTRY
+    if optimizer_registry:
+        global_config.optimizers = optimizer_registry
+    else:
+        global_config.optimizers = OPTIMIZER_REGISTRY
     if module:
         app.config["MODULE"] = module
         app.config["OFF_LINE"] = False

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/static/js/action_handlers.js

@@ -103,6 +103,12 @@ function submitEditForm(event) {
                 document.getElementById('instrument-panel').innerHTML = previousHtmlState;
                 previousHtmlState = null;  // Clear the stored state
             }
+            const parser = new DOMParser();
+            const doc = parser.parseFromString(html, 'text/html');
+            const warningDiv = doc.querySelector('#warning');
+            if (warningDiv && warningDiv.textContent.trim()) {
+                alert(warningDiv.textContent.trim()); // or use a nicer toast
+            }
         }
     })
     .catch(error => {
@@ -149,6 +155,13 @@ function duplicateAction(uuid) {
     .then(response => response.text())
     .then(html => {
         updateActionCanvas(html);
+
+        const parser = new DOMParser();
+        const doc = parser.parseFromString(html, 'text/html');
+        const warningDiv = doc.querySelector('#warning');
+        if (warningDiv && warningDiv.textContent.trim()) {
+            alert(warningDiv.textContent.trim()); // or use a nicer toast
+        }
     })
     .catch(error => console.error('Error:', error));
 }
@@ -159,33 +172,50 @@ function editAction(uuid) {
         return;
     }
 
-    // Save current state before fetching new content
     previousHtmlState = document.getElementById('instrument-panel').innerHTML;
 
     fetch(scriptStepUrl.replace('0', uuid), {
-        method: 'GET',
+        method: 'GET',  // no need for Content-Type on GET
         headers: {
             'Content-Type': 'application/json'
         }
     })
-    .then(response => response.text())
+    .then(response => {
+        if (!response.ok) {
+            return response.json().then(err => {
+                if (err.warning) {
+                    alert(err.warning);  // <-- should fire now
+                }
+                // restore panel so user isn't stuck
+                if (previousHtmlState) {
+                    document.getElementById('instrument-panel').innerHTML = previousHtmlState;
+                    previousHtmlState = null;
+                }
+                throw new Error("Step fetch failed: " + response.status);
+            });
+        }
+        return response.text();
+    })
     .then(html => {
         document.getElementById('instrument-panel').innerHTML = html;
 
-        // Add click handler for back button
-        document.getElementById('back').addEventListener('click', function(e) {
-            e.preventDefault();
-            if (previousHtmlState) {
-                document.getElementById('instrument-panel').innerHTML = previousHtmlState;
-                previousHtmlState = null;  // Clear the stored state
-            }
-        });
+        const backButton = document.getElementById('back');
+        if (backButton) {
+            backButton.addEventListener('click', function(e) {
+                e.preventDefault();
+                if (previousHtmlState) {
+                    document.getElementById('instrument-panel').innerHTML = previousHtmlState;
+                    previousHtmlState = null;
+                }
+            });
+        }
     })
     .catch(error => console.error('Error:', error));
 }
 
 
 
+
 function deleteAction(uuid) {
     if (!uuid) {
         console.error('Invalid UUID');
@@ -202,6 +232,13 @@ function deleteAction(uuid) {
     .then(html => {
         // Find the first list element's content and replace it
         updateActionCanvas(html);
+        // Optionally, check if a warning element exists
+        const parser = new DOMParser();
+        const doc = parser.parseFromString(html, 'text/html');
+        const warningDiv = doc.querySelector('#warning');
+        if (warningDiv && warningDiv.textContent.trim()) {
+            alert(warningDiv.textContent.trim()); // or use a nicer toast
+        }
     })
     .catch(error => console.error('Error:', error));
 }

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/utils/bo_campaign.py

@@ -209,7 +209,7 @@ def parse_optimization_form(form_data: Dict[str, str]):
                         parameter["bounds"] = bounds
 
             elif value == "choice":
-                choices_field = f"{param_name}_choices"
+                choices_field = f"{param_name}_value"
                 if choices_field in form_data and form_data[choices_field]:
                     # Split choices by comma and clean whitespace
                     choices = [choice.strip() for choice in form_data[choices_field].split(',')]

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/utils/db_models.py

@@ -644,12 +644,21 @@ class Script(db.Model):
                 args_str = args_str.replace(f"'#{args[arg][1:]}'", args[arg][1:])
             elif isinstance(args[arg], dict):
                 # print(args[arg])
-                variables = self.get_variables()
+                if not args[arg]:
+                    continue
+                # Extract the variable name (first key in the dict)
                 value = next(iter(args[arg]))
-                if value not in variables:
-                    raise ValueError(f"Variable ({value}) is not defined.")
-                args_str = args_str.replace(f"{args[arg]}", next(iter(args[arg])))
-            # elif self._is_variable(arg):
+                var_type = args[arg].get(value)
+
+                # Only process if it's a function_output variable reference
+                if var_type == "function_output":
+                    variables = self.get_variables()
+                    if value not in variables:
+                        raise ValueError(f"Variable ({value}) is not defined.")
+                    # Replace the dict string representation with just the variable name
+                    args_str = args_str.replace(f"{args[arg]}", value)
+
+        # elif self._is_variable(arg):
             #     print("is variable")
             #     args_str = args_str.replace(f"'{args[arg]}'", args[arg])
         return args_str

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/utils/form.py

@@ -405,7 +405,7 @@ def create_form_from_action(action: dict, script=None, design=True):
     for name, param_type in arg_types.items():
         # formatted_param_name = format_name(name)
         value = args.get(name, "")
-        if type(value) is dict:
+        if type(value) is dict and value:
             value = next(iter(value))
         field_kwargs = {
             "label": name,
@@ -556,9 +556,13 @@ def _action_button(action: dict, variables: dict):
                 arg_list = []
                 for k, v in action['args'].items():
                     if isinstance(v, dict):
-                        value = next(iter(v))  # Extract the first key if it's a dict
-                        # show warning color for variable calling when there is no definition
-                        style = "background-color: khaki" if value not in variables.keys() else ""
+                        if not v:
+                            value = v  # Keep the original value if not a dict
+                        else:
+                            value = next(iter(v))  # Extract the first key if it's a dict
+                            # show warning color for variable calling when there is no definition
+
+                            style = "background-color: khaki" if v.get(value) == "function_output" and value not in variables.keys() else ""
                     else:
                         value = v  # Keep the original value if not a dict
                     arg_list.append(f"{k} = {value}")  # Format the key-value pair

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos/utils/script_runner.py

@@ -195,11 +195,12 @@ class ScriptRunner:
 
                         # Update exec_locals with the returned locals
                         exec_locals.update(result_locals)
-                        exec_locals.pop("__async_exec_wrapper", None)
+
 
                     else:
-                        print("just exec synchronously")
+                        # print("just exec synchronously")
                         exec(line, exec_globals, exec_locals)
+                        exec_globals.update(exec_locals)
                         # return locals_dict
                     # exec(line, exec_globals, exec_locals)
                 # step.run_error = False
@@ -217,6 +218,7 @@ class ScriptRunner:
 
                 step.run_error = True
                 self.toggle_pause()
+            exec_locals.pop("__async_exec_wrapper", None)
             step.end_time = datetime.now()
             step.output = exec_locals
             db.session.commit()

ivoryos-1.3.7/ivoryos/version.py

@@ -0,0 +1 @@
+__version__ = "1.3.7"

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.5a0
+Version: 1.3.7
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -9,6 +9,7 @@ Requires-Python: >=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: bcrypt
+Requires-Dist: Flask[async]
 Requires-Dist: Flask-Login
 Requires-Dist: Flask-Session
 Requires-Dist: Flask-SocketIO
@@ -17,9 +18,21 @@ Requires-Dist: Flask-WTF
 Requires-Dist: SQLAlchemy-Utils
 Requires-Dist: python-dotenv
 Requires-Dist: astor; python_version < "3.9"
+Provides-Extra: optimizer-ax
+Requires-Dist: ax-platform; extra == "optimizer-ax"
+Provides-Extra: optimizer-baybe
+Requires-Dist: baybe; extra == "optimizer-baybe"
+Provides-Extra: optimizer-nimo
+Requires-Dist: nimo; extra == "optimizer-nimo"
 Provides-Extra: optimizer
-Requires-Dist: ax-platform; extra == "optimizer"
+Requires-Dist: ax-platform>=1.1.2; extra == "optimizer"
 Requires-Dist: baybe; extra == "optimizer"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-rtd-theme; extra == "doc"
+Requires-Dist: sphinxcontrib-httpdomain; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos.egg-info/SOURCES.txt

@@ -15,6 +15,7 @@ ivoryos.egg-info/top_level.txt
 ivoryos/optimizer/ax_optimizer.py
 ivoryos/optimizer/base_optimizer.py
 ivoryos/optimizer/baybe_optimizer.py
+ivoryos/optimizer/nimo_optimizer.py
 ivoryos/optimizer/registry.py
 ivoryos/routes/__init__.py
 ivoryos/routes/api/api.py

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/ivoryos.egg-info/requires.txt

@@ -1,4 +1,5 @@
 bcrypt
+Flask[async]
 Flask-Login
 Flask-Session
 Flask-SocketIO
@@ -10,6 +11,23 @@ python-dotenv
 [:python_version < "3.9"]
 astor
 
+[dev]
+pytest
+
+[doc]
+sphinx
+sphinx-rtd-theme
+sphinxcontrib-httpdomain
+
 [optimizer]
+ax-platform>=1.1.2
+baybe
+
+[optimizer-ax]
 ax-platform
+
+[optimizer-baybe]
 baybe
+
+[optimizer-nimo]
+nimo

{ivoryos-1.3.5a0 → ivoryos-1.3.7}/pyproject.toml

@@ -14,6 +14,7 @@ authors = [
 ]
 dependencies = [
     "bcrypt",
+    "Flask[async]",
     "Flask-Login",
     "Flask-Session",
     "Flask-SocketIO",
@@ -25,7 +26,19 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-optimizer = ["ax-platform", "baybe"]
+optimizer-ax = ["ax-platform"]
+optimizer-baybe = ["baybe"]
+optimizer-nimo = ["nimo"]
+optimizer = [
+    "ax-platform>=1.1.2",
+    "baybe"
+]
+doc = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "sphinxcontrib-httpdomain"
+]
+dev = ["pytest"]
 
 [project.urls]
 Homepage = "https://gitlab.com/heingroup/ivoryos"

ivoryos-1.3.5a0/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "1.3.5a0"