ivoryos 1.3.5__py3-none-any.whl → 1.3.6__py3-none-any.whl

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/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/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/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/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/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/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/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/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/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/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/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/version.py

@@ -1 +1 @@
-__version__ = "1.3.5"
+__version__ = "1.3.6"

{ivoryos-1.3.5.dist-info → ivoryos-1.3.6.dist-info}/METADATA

@@ -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.dist-info → ivoryos-1.3.6.dist-info}/RECORD

@@ -1,13 +1,13 @@
 ivoryos/__init__.py,sha256=gEvBO2y5TRq06Itjjej3iAcq73UsihqKPWcb2HykPwM,463
 ivoryos/app.py,sha256=G6kzEOVzCduj7Fc2r1rMbMFHgDzZQV0lC20Oxps7RSM,4839
 ivoryos/config.py,sha256=y3RxNjiIola9tK7jg-mHM8EzLMwiLwOzoisXkDvj0gA,2174
-ivoryos/server.py,sha256=5tXrgG16lm6Fl-Q-ZHxiGQQoyZQFxRhdDf6idNYqhNg,6985
+ivoryos/server.py,sha256=Idr41Boa8rPsh3bVJ8xy2Flwfxa1Xu6f2T0oMp4qBEk,7121
 ivoryos/socket_handlers.py,sha256=VWVWiIdm4jYAutwGu6R0t1nK5MuMyOCL0xAnFn06jWQ,1302
-ivoryos/version.py,sha256=tdqvkGH0OryRjjXzO3HS5DyYol-VTO9fC8m43nB2PgI,22
-ivoryos/optimizer/ax_optimizer.py,sha256=PoSu8hrDFFpqyhRBnaSMswIUsDfEX6sPWt8NEZ_sobs,7112
-ivoryos/optimizer/base_optimizer.py,sha256=JTbUharZKn0t8_BDbAFuwZIbT1VOnX1Xuog1pJuU8hY,1992
+ivoryos/version.py,sha256=5ZbAQtod5QalTI1C2N07edlxplzG_Q2XvGOSyOok4uA,22
+ivoryos/optimizer/ax_optimizer.py,sha256=k7RzhNMjh3MseOE-_FADVX72lYLDyXz-XE3juSBRWTk,7116
+ivoryos/optimizer/base_optimizer.py,sha256=gNBX9m3RxoYklwEBkqeDGZlU7c6e9e5kN0ZeTtnxnCE,2044
 ivoryos/optimizer/baybe_optimizer.py,sha256=EdrrRiYO-IOx610cPXiQhH4qG8knUP0uiZ0YoyaGIU8,7954
-ivoryos/optimizer/registry.py,sha256=lr0cqdI2iEjw227ZPRpVkvsdYdddjeJJRzawDv77cEc,219
+ivoryos/optimizer/registry.py,sha256=dLMo5cszcwa06hfBxdINQIGpkHtRe5-J3J7t76Jq6X0,306
 ivoryos/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ivoryos/routes/api/api.py,sha256=97Y7pqTwOaWgZgI5ovEPxEBm6Asrt0Iy0VhBkVp2xqA,2304
 ivoryos/routes/auth/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -27,9 +27,9 @@ ivoryos/routes/data/templates/workflow_database.html,sha256=ofvHcovpwmJXo1SFiSrL
 ivoryos/routes/data/templates/workflow_view.html,sha256=Ti17kzlPlYTmzx5MkdsPlXJ1_k6QgMYQBM6FHjG50go,12491
 ivoryos/routes/data/templates/components/step_card.html,sha256=XWsr7qxAY76RCuQHETubWjWBlPgs2HkviH4ju6qfBKo,1923
 ivoryos/routes/design/__init__.py,sha256=zS3HXKaw0ALL5n6t_W1rUz5Uj5_tTQ-Y1VMXyzewvR0,113
-ivoryos/routes/design/design.py,sha256=8xWsJxs-jg3r1yszzvHWK0mccYoYlgzhO_dTV7aEA_w,18567
+ivoryos/routes/design/design.py,sha256=HPjjoGH9mzSP6TxVNUYWgwhfzkpRt5BF38agL_tJvXk,18760
 ivoryos/routes/design/design_file.py,sha256=MVIc5uGSaGxZhs86hfPjX2n0iy1OcXeLq7b9Ucdg4VQ,2115
-ivoryos/routes/design/design_step.py,sha256=maDaR-CFK6UY_ajbQeYJ_onwYW0e9nMD-HgrhsSU6JY,5874
+ivoryos/routes/design/design_step.py,sha256=M3l37kP1kU4_bolLBU1MWJgEW0LUXojo9UdQgysZyXs,5943
 ivoryos/routes/design/templates/experiment_builder.html,sha256=hh-d2tOc_40gww5WfUYIf8sM3qBaALZnR8Sx7Ja4tpU,1623
 ivoryos/routes/design/templates/components/action_form.html,sha256=kXJOrJLbFsMHHWVSuMQHpt1xFrUMnwgzTG8e6Qfn0Cg,3042
 ivoryos/routes/design/templates/components/actions_panel.html,sha256=jHTR58saTUIZInBdC-vLc1ZTbStLiULeWbupjB4hQzo,977
@@ -39,7 +39,7 @@ ivoryos/routes/design/templates/components/canvas_footer.html,sha256=5VRRacMZbzx
 ivoryos/routes/design/templates/components/canvas_header.html,sha256=7iIzLDGHX7MnmBbf98nWtLDprbeIgoNV4dJUO1zE4Tc,3598
 ivoryos/routes/design/templates/components/canvas_main.html,sha256=nLEtp3U2YtfJwob1kR8ua8-UVdu9hwc6z1L5UMNVz8c,1524
 ivoryos/routes/design/templates/components/deck_selector.html,sha256=ryTRpljYezo0AzGLCJu_qOMokjjnft3GIxddmNGtBA0,657
-ivoryos/routes/design/templates/components/edit_action_form.html,sha256=Dz7FnnOK4PYptAHNy9_WFCU1RZTSV61-1lNHHOSRJNs,1876
+ivoryos/routes/design/templates/components/edit_action_form.html,sha256=idhUKOqewIxgqMKYKLutqOjopKQVLvddB6uufoBA3Lo,1912
 ivoryos/routes/design/templates/components/instruments_panel.html,sha256=tRKd-wOqKjaMJCLuGgRmHtxIgSjklhBkuX8arm5aTCU,4268
 ivoryos/routes/design/templates/components/modals.html,sha256=6Dl8I8oD4ln7kK8C5e92pFVVH5KDte-vVTL0U_6NSTg,306
 ivoryos/routes/design/templates/components/python_code_overlay.html,sha256=GUHgsmUWQf0P1Fbg5W0OJC34TXCUIMQVUkS7KDoauyI,1264
@@ -74,7 +74,7 @@ ivoryos/static/logo.webp,sha256=lXgfQR-4mHTH83k7VV9iB54-oC2ipe6uZvbwdOnLETc,1497
 ivoryos/static/style.css,sha256=zQVx35A5g6JMJ-K84-6fSKtzXGjp_p5ZVG6KLHPM2IE,4021
 ivoryos/static/gui_annotation/Slide1.png,sha256=Lm4gdOkUF5HIUFaB94tl6koQVkzpitKj43GXV_XYMMc,121727
 ivoryos/static/gui_annotation/Slide2.PNG,sha256=z3wQ9oVgg4JTWVLQGKK_KhtepRHUYP1e05XUWGT2A0I,118761
-ivoryos/static/js/action_handlers.js,sha256=DnNYV5mITADKp14I6NaByNRzHco0dDPP2fuSM43x2hY,6119
+ivoryos/static/js/action_handlers.js,sha256=MdYfXLRNSMAkfO_lkDb8Mr--MlZA7SluEQ5AB3Jqw7k,6704
 ivoryos/static/js/db_delete.js,sha256=l67fqUaN_FVDaL7v91Hd7LyRbxnqXx9nyjF34-7aewY,561
 ivoryos/static/js/overlay.js,sha256=dPxop19es0E0ZUSY3d_4exIk7CJuQEnlW5uTt5fZfzI,483
 ivoryos/static/js/script_metadata.js,sha256=m8VYZ8OGT2oTx1kXMXq60bKQI9WCbJNkzcFDzLvRuGc,1188
@@ -84,20 +84,20 @@ ivoryos/static/js/sortable_design.js,sha256=ASc9P6_423Mczeg6QH6LVtyxLyWhpxWJP2nE
 ivoryos/static/js/ui_state.js,sha256=XYsOcfGlduqLlqHySvPrRrR50CiAsml51duqneigsRY,3368
 ivoryos/templates/base.html,sha256=cl5w6E8yskbUzdiJFal6fZjnPuFNKEzc7BrrbRd6bMI,8581
 ivoryos/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/utils/bo_campaign.py,sha256=Fil-zT7JexL_p9XqyWByjAk42XB1R9XUKN8CdV5bi6c,9714
+ivoryos/utils/bo_campaign.py,sha256=AqTE4aIUWL26P0-o1qvL2ms4MjYzNQABNxZFisxBsyg,9712
 ivoryos/utils/client_proxy.py,sha256=74G3HAuq50iEHkSvlMZFmQaukm613FbRgOdzO_T3dMg,10191
-ivoryos/utils/db_models.py,sha256=i1fLiWFnese2xqAfWipN9eUDHeuy6eIYE9_cY6YZ6NU,31553
+ivoryos/utils/db_models.py,sha256=TbOydX7rC1jGfei2mVYaexlE3lyq1Igb1VQuHJlMRKQ,31945
 ivoryos/utils/decorators.py,sha256=p1Bdl3dCeaHNv6-cCCUOZMiFu9kRaqqQnkFJUkzPoJE,991
-ivoryos/utils/form.py,sha256=Ej9tx06KZZ5fPQm1ho1byotNocF3u24aatc2ZyI0rK4,22301
+ivoryos/utils/form.py,sha256=f1yXHlOQX1YnJ2j_UW6iHmh4pTAGAs9sAlhyQB8yBIo,22505
 ivoryos/utils/global_config.py,sha256=leYoEXvAS0AH4xQpYsqu4HI9CJ9-wiLM-pIh_bEG4Ak,3087
 ivoryos/utils/llm_agent.py,sha256=-lVCkjPlpLues9sNTmaT7bT4sdhWvV2DiojNwzB2Lcw,6422
 ivoryos/utils/py_to_json.py,sha256=ZtejHgwdEAUCVVMYeVNR8G7ceLINue294q6WpiJ6jn0,9734
-ivoryos/utils/script_runner.py,sha256=qozSrlpnsk5rZzui8WT59cMaw41ZfsYKvofAXdDiC5A,20747
+ivoryos/utils/script_runner.py,sha256=gIYdTEFNWZFmPf9cf31y3wAUKUeJk_qnjohYDKevWNw,20749
 ivoryos/utils/serilize.py,sha256=lkBhkz8r2bLmz2_xOb0c4ptSSOqjIu6krj5YYK4Nvj8,6784
 ivoryos/utils/task_runner.py,sha256=xiMzK8gQ0mHsg0A1Ah8fmXe3azpaJh4hJiQJLHA11ZQ,3682
 ivoryos/utils/utils.py,sha256=dIc4BO55eS3lCA0nhbIncS5d7sLaKZy5hJS1I_Sm45o,14949
-ivoryos-1.3.5.dist-info/licenses/LICENSE,sha256=p2c8S8i-8YqMpZCJnadLz1-ofxnRMILzz6NCMIypRag,1084
-ivoryos-1.3.5.dist-info/METADATA,sha256=z3rNHhq2GaCBN6bWwi6JtUXn8fWzkigMR-_PuKHgFtc,8403
-ivoryos-1.3.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-ivoryos-1.3.5.dist-info/top_level.txt,sha256=FRIWWdiEvRKqw-XfF_UK3XV0CrnNb6EmVbEgjaVazRM,8
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