ivoryos 1.0.8__py3-none-any.whl → 1.1.0__py3-none-any.whl

ivoryos/utils/bo_campaign.py

@@ -1,7 +1,7 @@
 from ivoryos.utils.utils import install_and_import
 
 
-def ax_init_form(data, arg_types):
+def ax_init_form(data, arg_types, previous_data_len=0):
     """
     create Ax campaign from the web form input
     :param data:
@@ -9,7 +9,11 @@ def ax_init_form(data, arg_types):
     install_and_import("ax", "ax-platform")
     parameter, objectives = ax_wrapper(data, arg_types)
     from ax.service.ax_client import AxClient
-    ax_client = AxClient()
+    if previous_data_len > 0:
+        gs = exisitng_data_gs(previous_data_len)
+        ax_client = AxClient(generation_strategy=gs)
+    else:
+        ax_client = AxClient()
     ax_client.create_experiment(parameter, objectives=objectives)
     return ax_client
 
@@ -84,4 +88,40 @@ def ax_init_opc(bo_args):
     bo_args["objectives"] = objectives_formatted
     ax_client.create_experiment(**bo_args)
 
-    return ax_client
+    return ax_client
+
+
+def exisitng_data_gs(data_len):
+    """
+    temporal generation strategy for existing data
+    """
+    from ax.generation_strategy.generation_node import GenerationStep
+    from ax.generation_strategy.generation_strategy import GenerationStrategy
+    from ax.modelbridge.registry import Generators
+    if data_len > 4:
+        gs = GenerationStrategy(
+            steps=[
+                GenerationStep(
+                    model=Generators.BOTORCH_MODULAR,
+                    num_trials=-1,
+                    max_parallelism=3,
+                ),
+            ]
+        )
+    else:
+        gs = GenerationStrategy(
+            steps=[
+                GenerationStep(
+                    model=Generators.SOBOL,
+                    num_trials=5-data_len,  # how many sobol trials to perform (rule of thumb: 2 * number of params)
+                    max_parallelism=5,
+                    model_kwargs={"seed": 999},
+                ),
+                GenerationStep(
+                    model=Generators.BOTORCH_MODULAR,
+                    num_trials=-1,
+                    max_parallelism=3,
+                ),
+            ]
+        )
+    return gs

ivoryos/utils/form.py

@@ -321,6 +321,7 @@ def create_add_form(attr, attr_name, autofill: bool, script=None, design: bool =
     """
     signature = attr.get('signature', {})
     docstring = attr.get('docstring', "")
+    # print(signature, docstring)
     dynamic_form = create_form_for_method(signature, autofill, script, design)
     if design:
         return_value = StringField(label='Save value as', render_kw={"placeholder": "Optional"})

ivoryos/utils/py_to_json.py

@@ -0,0 +1,225 @@
+import ast
+import json
+import uuid
+
+def generate_uuid():
+    return int(str(uuid.uuid4().int)[:15])
+
+def infer_type(value):
+    if isinstance(value, bool):
+        return "bool"
+    elif isinstance(value, int):
+        return "int"
+    elif isinstance(value, float):
+        return "float"
+    elif isinstance(value, str):
+        return "str"
+    elif isinstance(value, (ast.Name, str)) and str(value).startswith("#"):
+        return "float"  # default fallback for variables
+    else:
+        return "unknown"
+
+def convert_to_cards(source_code: str):
+    tree = ast.parse(source_code)
+    cards = []
+    card_id = 1
+    block_stack = []  # to track control flow UUIDs
+
+    def new_id():
+        nonlocal card_id
+        val = card_id
+        card_id += 1
+        return val
+
+    def add_card(card):
+        cards.append(card)
+
+    def is_supported_assignment(node):
+        return (
+            isinstance(node.targets[0], ast.Name) and
+            isinstance(node.value, (ast.Constant, ast.Num, ast.Str, ast.NameConstant))
+        )
+
+    class CardVisitor(ast.NodeVisitor):
+        def visit_FunctionDef(self, node):
+            self.defined_types = {
+                arg.arg: ast.unparse(arg.annotation) if arg.annotation else "float"
+                for arg in node.args.args
+            }
+            for stmt in node.body:
+                self.visit(stmt)
+
+        def visit_If(self, node):
+            uuid_ = generate_uuid()
+            block_stack.append(("if", uuid_))
+
+            add_card({
+                "action": "if",
+                "arg_types": {"statement": ""},
+                "args": {"statement": ast.unparse(node.test)},
+                "id": new_id(),
+                "instrument": "if",
+                "return": "",
+                "uuid": uuid_
+            })
+
+            for stmt in node.body:
+                self.visit(stmt)
+
+            if node.orelse:
+                add_card({
+                    "action": "else",
+                    "args": {},
+                    "id": new_id(),
+                    "instrument": "if",
+                    "return": "",
+                    "uuid": uuid_
+                })
+                for stmt in node.orelse:
+                    self.visit(stmt)
+
+            _, block_uuid = block_stack.pop()
+            add_card({
+                "action": "endif",
+                "args": {},
+                "id": new_id(),
+                "instrument": "if",
+                "return": "",
+                "uuid": block_uuid
+            })
+
+        def visit_While(self, node):
+            uuid_ = generate_uuid()
+            block_stack.append(("while", uuid_))
+
+            add_card({
+                "action": "while",
+                "arg_types": {"statement": ""},
+                "args": {"statement": ast.unparse(node.test)},
+                "id": new_id(),
+                "instrument": "while",
+                "return": "",
+                "uuid": uuid_
+            })
+
+            for stmt in node.body:
+                self.visit(stmt)
+
+            _, block_uuid = block_stack.pop()
+            add_card({
+                "action": "endwhile",
+                "args": {},
+                "id": new_id(),
+                "instrument": "while",
+                "return": "",
+                "uuid": block_uuid
+            })
+
+        def visit_Assign(self, node):
+            if is_supported_assignment(node):
+                var_name = node.targets[0].id
+                value = node.value.value
+                add_card({
+                    "action": var_name,
+                    "arg_types": {"statement": infer_type(value)},
+                    "args": {"statement": value},
+                    "id": new_id(),
+                    "instrument": "variable",
+                    "return": "",
+                    "uuid": generate_uuid()
+                })
+            elif isinstance(node.value, ast.Call):
+                self.handle_call(node.value, ret_var=node.targets[0].id)
+
+        def visit_Expr(self, node):
+            if isinstance(node.value, ast.Call):
+                self.handle_call(node.value)
+
+        def handle_call(self, node, ret_var=""):
+            func_parts = []
+            f = node.func
+            while isinstance(f, ast.Attribute):
+                func_parts.insert(0, f.attr)
+                f = f.value
+            if isinstance(f, ast.Name):
+                func_parts.insert(0, f.id)
+            if not func_parts or not func_parts[0].startswith("deck"):
+                return
+
+            instrument = ".".join(func_parts[:-1])
+            action = func_parts[-1]
+
+            args = {}
+            arg_types = {}
+
+            for kw in node.keywords:
+                if kw.arg is None and isinstance(kw.value, ast.Dict):
+                    for k_node, v_node in zip(kw.value.keys, kw.value.values):
+                        key = k_node.s if isinstance(k_node, ast.Constant) else ast.unparse(k_node)
+                        if isinstance(v_node, ast.Constant):
+                            value = v_node.value
+                        elif isinstance(v_node, ast.Name):
+                            value = f"#{v_node.id}"
+                        else:
+                            value = ast.unparse(v_node)
+                        args[key] = value
+                        arg_types[key] = infer_type(value)
+                else:
+                    if isinstance(kw.value, ast.Constant):
+                        value = kw.value.value
+                    elif isinstance(kw.value, ast.Name):
+                        value = f"#{kw.value.id}"
+                    else:
+                        value = ast.unparse(kw.value)
+                    args[kw.arg] = value
+                    arg_types[kw.arg] = (
+                        self.defined_types.get(kw.value.id, "float")
+                        if isinstance(kw.value, ast.Name)
+                        else infer_type(value)
+                    )
+
+            add_card({
+                "action": action,
+                "arg_types": arg_types,
+                "args": args,
+                "id": new_id(),
+                "instrument": instrument,
+                "return": ret_var,
+                "uuid": generate_uuid()
+            })
+
+    CardVisitor().visit(tree)
+    return cards
+
+
+if __name__ == "__main__":
+    test = '''def workflow_dynamic(solid_amount_mg, methanol_amount_ml):
+    """
+    SDL workflow: dose solid, add methanol, equilibrate, and analyze
+    
+    Args:
+        solid_amount_mg (float): Amount of solid to dose in mg
+        methanol_amount_ml (float): Amount of methanol to dose in ml
+    
+    Returns:
+        dict: Results containing analysis data
+    """
+    # Step 1: Dose solid material
+    deck.sdl.dose_solid(amount_in_mg=solid_amount_mg)
+    
+    # Step 2: Add methanol solvent
+    deck.sdl.dose_solvent(solvent_name='Methanol', amount_in_ml=methanol_amount_ml)
+    
+    # Step 3: Equilibrate at room temperature (assuming ~23°C) for 20 seconds
+    deck.sdl.equilibrate(temp=23.0, duration=20.0)
+    
+    # Step 4: Analyze the sample
+    analysis_results = deck.sdl.analyze(param_1=1, param_2=2)
+    
+    # Brief pause for system stability
+    time.sleep(1.0)
+    
+    # Return only analysis results
+    return {'analysis_results': analysis_results}
+    '''
+    print(json.dumps(convert_to_cards(test)))

ivoryos/utils/script_runner.py

@@ -62,11 +62,11 @@ class ScriptRunner:
 
 
     def run_script(self, script, repeat_count=1, run_name=None, logger=None, socketio=None, config=None, bo_args=None,
-                   output_path="", compiled=False, current_app=None):
+                   output_path="", compiled=False, current_app=None, history=None):
         global deck
         if deck is None:
             deck = global_config.deck
-
+        print("history", history)
         if self.current_app is None:
             self.current_app = current_app
         # time.sleep(1)  # Optional: may help ensure deck readiness
@@ -81,7 +81,8 @@ class ScriptRunner:
 
         thread = threading.Thread(
             target=self._run_with_stop_check,
-            args=(script, repeat_count, run_name, logger, socketio, config, bo_args, output_path, current_app, compiled)
+            args=(script, repeat_count, run_name, logger, socketio, config, bo_args, output_path, current_app, compiled,
+                  history)
         )
         thread.start()
         return thread
@@ -182,7 +183,7 @@ class ScriptRunner:
         return exec_locals  # Return the 'results' variable
 
     def _run_with_stop_check(self, script: Script, repeat_count: int, run_name: str, logger, socketio, config, bo_args,
-                             output_path, current_app, compiled):
+                             output_path, current_app, compiled, history=None):
         time.sleep(1)
         # _func_str = script.compile()
         # step_list_dict: dict = script.convert_to_lines(_func_str)
@@ -205,7 +206,8 @@ class ScriptRunner:
             # Run "script" section multiple times
             if repeat_count:
                 self._run_repeat_section(repeat_count, arg_type, bo_args, output_list, script,
-                                         run_name, return_list, compiled, logger, socketio, run_id=run_id)
+                                         run_name, return_list, compiled, logger, socketio,
+                                         history, output_path, run_id=run_id)
             elif config:
                 self._run_config_section(config, arg_type, output_list, script, run_name, logger,
                                          socketio, run_id=run_id, compiled=compiled)
@@ -262,13 +264,28 @@ class ScriptRunner:
                     output_list.append(output)
 
     def _run_repeat_section(self, repeat_count, arg_types, bo_args, output_list, script, run_name, return_list, compiled,
-                            logger, socketio, run_id):
+                            logger, socketio, history, output_path, run_id):
         if bo_args:
             logger.info('Initializing optimizer...')
             if compiled:
                 ax_client = bo_campaign.ax_init_opc(bo_args)
             else:
-                ax_client = bo_campaign.ax_init_form(bo_args, arg_types)
+                if history:
+                    import pandas as pd
+                    file_path = os.path.join(output_path, history)
+                    previous_runs = pd.read_csv(file_path).to_dict(orient='records')
+                    ax_client = bo_campaign.ax_init_form(bo_args, arg_types, len(previous_runs))
+                    for row in previous_runs:
+                        parameter = {key: value for key, value in row.items() if key in arg_types.keys()}
+                        raw_data = {key: value for key, value in row.items() if key in return_list}
+                        _, trial_index = ax_client.attach_trial(parameter)
+                        ax_client.complete_trial(trial_index=trial_index, raw_data=raw_data)
+                        output_list.append(row)
+                else:
+                    ax_client = bo_campaign.ax_init_form(bo_args, arg_types)
+
+
+
         for i_progress in range(int(repeat_count)):
             if self.stop_pending_event.is_set():
                 logger.info(f'Stopping execution during {run_name}: {i_progress + 1}/{int(repeat_count)}')
@@ -298,6 +315,12 @@ class ScriptRunner:
             if output:
                 output_list.append(output)
                 logger.info(f'Output value: {output}')
+
+        if bo_args:
+            ax_client.save_to_json_file(os.path.join(output_path, f"{run_name}_ax_client.json"))
+        logger.info(
+            f'Optimization complete. Results saved to {os.path.join(output_path, f"{run_name}_ax_client.json")}'
+        )
         return output_list
 
     @staticmethod

ivoryos/version.py

@@ -1 +1 @@
-__version__ = "1.0.8"
+__version__ = "1.1.0"

{ivoryos-1.0.8.dist-info → ivoryos-1.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 1.0.8
+Version: 1.1.0
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -48,7 +48,7 @@ With the least modification of the current workflow, user can design, manage and
 This software is developed and tested using Windows. This software and its dependencies are compatible across major platforms: Linux, macOS, and Windows. Some dependencies (Flask-SQLAlchemy) may require additional setup.
 
 ### Python Version
-Python >=3.7 for best compatibility.
+Python >=3.10 for best compatibility. Python >=3.7 without Ax.
 ### Python dependencies
 This software is compatible with the latest versions of all dependencies. 
 - bcrypt~=4.0
@@ -59,8 +59,7 @@ This software is compatible with the latest versions of all dependencies.
 - SQLAlchemy-Utils~=0.41
 - Flask-WTF~=1.2
 - python-dotenv==1.0.1
-- openai (optional ~=1.53)
-- ax-platform (optional ~=0.3 or ~=0.4 for Python>=3.9)
+- ax-platform (optional ~=0.4 for Python>=3.9)
 
 ## Installation
 ```bash
@@ -70,7 +69,7 @@ or
 ```bash
 git clone https://gitlab.com/heingroup/ivoryos.git
 cd ivoryos
-pip install -e .
+pip install .
 ```
 
 The installation may take 10 to 30 seconds to install. The installation time may vary and take up to several minutes, depending on the network speed, computer performance, and virtual environment settings.
@@ -98,7 +97,7 @@ Create an account and login (local database)
 [//]: # (![PyPI - Downloads](https://img.shields.io/pypi/dm/ivoryos))
 
 
-### Additional settings
+### Additional settings (not actively maintained)
 #### AI assistant
 To streamline the experimental design on SDLs, we also integrate Large Language Models (LLMs) to interpret the inspected functions and generate code according to task descriptions.
 
@@ -150,8 +149,6 @@ ivoryos.run(__name__)
 ### Deck function and web form 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/demo.gif)
 
-### Text-to-code demo
-![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/text-to-code.gif)
 
 ### Directory structure
 

ivoryos-1.1.0.dist-info/RECORD

@@ -0,0 +1,102 @@
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+ivoryos/config.py,sha256=sk4dskm-K_Nv4uaA3QuE6xtew8wL6q3HmIoLgRm7p8U,2153
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ivoryos/routes/control/templates/control/controllers.html

@@ -1,78 +0,0 @@
-{% extends 'base.html' %}
-{% block title %}IvoryOS | Controller for {{instrument}}{% endblock %}
-{% block body %}
-    <div id="overlay" class="overlay">
-        <div>
-            <h3 id="overlay-text"></h3>
-            <div class="spinner-border" role="status"></div>
-        </div>
-    </div>
-    <h1>{{instrument}} controller</h1>
-    {% set hidden = session.get('hidden_functions', {}) %}
-    <div class="grid-container" id="sortable-grid">
-        {% for function, form in forms.items() %}
-
-            {% set hidden_instrument = hidden.get(instrument, []) %}
-            {% if function not in hidden_instrument %}
-                <div class="card" id="{{function}}">
-                    <div class="bg-white rounded shadow-sm flex-fill">
-                        <i class="bi bi-info-circle ms-2" data-bs-toggle="tooltip" data-bs-placement="top" title='{{ form.hidden_name.description or "Docstring is not available" }}' ></i>
-                        <a style="float: right" aria-label="Close" href="{{ url_for('control.hide_function', instrument=instrument, function=function) }}"><i class="bi bi-eye-slash-fill"></i></a>
-                        <div class="form-control" style="border: none">
-                            <form role="form" method='POST' name="{{function}}" id="{{function}}">
-                                <div class="form-group">
-                                    {{ form.hidden_tag() }}
-                                    {% for field in form %}
-                                        {% if field.type not in ['CSRFTokenField', 'HiddenField'] %}
-                                            <div class="input-group mb-3">
-                                                <label class="input-group-text">{{ field.label.text }}</label>
-                                                {% if field.type == "SubmitField" %}
-                                                    {{ field(class="btn btn-dark") }}
-                                                {% elif field.type == "BooleanField" %}
-                                                    {{ field(class="form-check-input") }}
-                                                {% else %}
-                                                    {{ field(class="form-control") }}
-                                                {% endif %}
-                                            </div>
-                                        {% endif %}
-                                    {% endfor %}
-                                </div>
-                                <div class="input-group mb-3">
-                                    <button type="submit" name="{{ function }}" id="{{ function }}" class="form-control" style="background-color: #a5cece;">{{format_name(function)}} </button>
-
-                                </div>
-
-                            </form>
-                        </div>
-                    </div>
-                </div>
-            {% endif %}
-        {% endfor %}
-    </div>
-    <div class="accordion accordion-flush" id="accordionActions" >
-        <div class="accordion-item">
-            <h4 class="accordion-header">
-                <button class="accordion-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#hidden">
-                    Hidden functions
-                </button>
-            </h4>
-        </div>
-        <div id="hidden" class="accordion-collapse collapse" data-bs-parent="#accordionActions">
-            <div class="accordion-body">
-                {% set hidden_instrument = hidden.get(instrument, []) %}
-                {% for function in hidden_instrument %}
-                    <div>
-                        {{ function }} <a href="{{ url_for('control.remove_hidden', instrument=instrument, function=function) }}"><i class="bi bi-eye-fill"></i></a>
-                    </div>
-                {% endfor %}
-            </div>
-        </div>
-    </div>
-
-    <script>
-        const saveOrderUrl = `{{ url_for('control.save_order', instrument=instrument) }}`;
-        const buttonIds = {{ session['card_order'][instrument] | tojson }};
-    </script>
-    <script src="{{ url_for('static', filename='js/sortable_card.js') }}"></script>
-    <script src="{{ url_for('static', filename='js/overlay.js') }}"></script>
-{% endblock %}