ivoryos 1.3.5__tar.gz → 1.3.6__tar.gz

{ivoryos-1.3.5 → ivoryos-1.3.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.5
+Version: 1.3.6
 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
@@ -21,8 +22,10 @@ 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"

{ivoryos-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/ivoryos/routes/design/design.py

@@ -385,7 +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-1.3.5 → ivoryos-1.3.6}/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>")

{ivoryos-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/ivoryos/static/js/action_handlers.js

@@ -172,33 +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');

{ivoryos-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/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-1.3.5 → ivoryos-1.3.6}/ivoryos/utils/script_runner.py

@@ -198,7 +198,7 @@ class ScriptRunner:
 
 
                     else:
-                        print("just exec synchronously")
+                        # print("just exec synchronously")
                         exec(line, exec_globals, exec_locals)
                         exec_globals.update(exec_locals)
                         # return locals_dict

ivoryos-1.3.6/ivoryos/version.py

@@ -0,0 +1 @@
+__version__ = "1.3.6"

{ivoryos-1.3.5 → ivoryos-1.3.6}/ivoryos.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.5
+Version: 1.3.6
 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
@@ -21,8 +22,10 @@ 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"

{ivoryos-1.3.5 → ivoryos-1.3.6}/ivoryos.egg-info/requires.txt

@@ -1,4 +1,5 @@
 bcrypt
+Flask[async]
 Flask-Login
 Flask-Session
 Flask-SocketIO
@@ -19,7 +20,7 @@ sphinx-rtd-theme
 sphinxcontrib-httpdomain
 
 [optimizer]
-ax-platform
+ax-platform>=1.1.2
 baybe
 
 [optimizer-ax]
@@ -27,3 +28,6 @@ ax-platform
 
 [optimizer-baybe]
 baybe
+
+[optimizer-nimo]
+nimo

{ivoryos-1.3.5 → ivoryos-1.3.6}/pyproject.toml

@@ -14,6 +14,7 @@ authors = [
 ]
 dependencies = [
     "bcrypt",
+    "Flask[async]",
     "Flask-Login",
     "Flask-Session",
     "Flask-SocketIO",
@@ -27,8 +28,9 @@ dependencies = [
 [project.optional-dependencies]
 optimizer-ax = ["ax-platform"]
 optimizer-baybe = ["baybe"]
+optimizer-nimo = ["nimo"]
 optimizer = [
-    "ax-platform",
+    "ax-platform>=1.1.2",
     "baybe"
 ]
 doc = [

ivoryos-1.3.5/ivoryos/version.py

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