ivoryos 0.1.13__tar.gz → 0.1.15__tar.gz

{ivoryos-0.1.13/ivoryos.egg-info → ivoryos-0.1.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.13
+Version: 0.1.15
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/__init__.py

@@ -10,21 +10,17 @@ from ivoryos.routes.control.control import control
 from ivoryos.routes.database.database import database
 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.global_config import GlobalConfig
 from ivoryos.utils.script_runner import ScriptRunner
-from ivoryos.version import __version__ as ivoryos_version
+from version import __version__ as ivoryos_version
 
 global_config = GlobalConfig()
 
 url_prefix = os.getenv('URL_PREFIX', "/ivoryos")
 app = Flask(__name__, static_url_path=f'{url_prefix}/static', static_folder='static')
-app.register_blueprint(main, url_prefix=url_prefix)
-app.register_blueprint(auth, url_prefix=url_prefix)
-app.register_blueprint(design, url_prefix=url_prefix)
-app.register_blueprint(database, url_prefix=url_prefix)
-app.register_blueprint(control, url_prefix=url_prefix)
 
 
 def create_app(config_class=None):
@@ -70,6 +66,7 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
         config: Config = None,
         logger: Union[str, list] = None,
         logger_output_name: str = None,
+        enable_design=True, stream_address=None
         ):
     """
     Start ivoryOS app server.
@@ -83,9 +80,29 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     :param config: config class, defaults to None
     :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:
+    :param stream_address:
     """
     app = create_app(config_class=config or get_config())  # Create app instance using factory function
+    enable_monitor = stream_address is not None
+
+    def inject_nav_config():
+        """Make NAV_CONFIG available globally to all templates."""
+        return dict(
+            enable_design=enable_design,
+            enable_monitor=enable_monitor,
+        )
+
+    # todo modular page
+    app.context_processor(inject_nav_config)
+    app.register_blueprint(main, url_prefix=url_prefix)
+    app.register_blueprint(auth, url_prefix=url_prefix)
+    if enable_design:
+        app.register_blueprint(design, url_prefix=url_prefix)
+        app.register_blueprint(database, url_prefix=url_prefix)
+    if enable_monitor:
+        app.register_blueprint(monitor, url_prefix=url_prefix)
+    app.register_blueprint(control, url_prefix=url_prefix)
 
     port = port or int(os.environ.get("PORT", 8000))
     debug = debug if debug is not None else app.config.get('DEBUG', True)

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/routes/control/templates/control/controllers.html

@@ -16,6 +16,7 @@
             {% 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}}">
@@ -38,7 +39,9 @@
                                 </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>

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/routes/design/design.py

@@ -100,22 +100,25 @@ def experiment_builder(instrument=None):
 
     deck_list = utils.available_pseudo_deck(current_app.config["DUMMY_DECK"])
 
-    functions = []
+    functions = {}
     if deck:
         deck_variables = global_config.deck_snapshot.keys()
     else:
         deck_variables = list(pseudo_deck.keys()) if pseudo_deck else []
         deck_variables.remove("deck_name") if len(deck_variables) > 0 else deck_variables
-    edit_action = session.get("edit_action")
-    if instrument:
+    edit_action_info = session.get("edit_action")
+    if edit_action_info:
+        forms = create_form_from_action(edit_action_info, script=script)
+    elif instrument:
         if instrument in ['if', 'while', 'variable', 'wait', 'repeat']:
-            forms = create_builtin_form(instrument, autofill=autofill, script=script)
+            forms = create_builtin_form(instrument, script=script)
         else:
             if deck:
-                function_metadata = global_config.deck_snapshot.get(instrument, {})
+                functions = global_config.deck_snapshot.get(instrument, {})
             elif pseudo_deck:
-                function_metadata = pseudo_deck.get(instrument, {})
-            functions = {key: data.get('signature', {}) for key, data in function_metadata.items()}
+                functions = pseudo_deck.get(instrument, {})
+            # print(function_metadata)
+            # functions = {key: data.get('signature', {}) for key, data in function_metadata.items()}
             forms = create_form_from_pseudo(pseudo=functions, autofill=autofill, script=script)
         if request.method == 'POST' and "hidden_name" in request.form:
             # all_kwargs = request.form.copy()
@@ -128,21 +131,14 @@ def experiment_builder(instrument=None):
                 function_name = kwargs.pop("hidden_name")
                 save_data = kwargs.pop('return', '')
 
-
-
                 primitive_arg_types = utils.get_arg_type(kwargs, functions[function_name])
 
-                # print(script.get_added_variables(), script.get_output_variables())
-                arg_types = {}
-                # arg_types.update(variable_kwargs_types)
-                arg_types.update(primitive_arg_types)
-                # all_kwargs.update(variable_kwargs)
-                script.eval_list(kwargs, arg_types)
-                kwargs = script.eval_variables(kwargs)
+                script.eval_list(kwargs, primitive_arg_types)
+                kwargs = script.validate_variables(kwargs)
                 action = {"instrument": instrument, "action": function_name,
-                          "args": {name: arg for (name, arg) in kwargs.items()},
+                          "args": kwargs,
                           "return": save_data,
-                          'arg_types': arg_types}
+                          'arg_types': primitive_arg_types}
                 script.add_action(action=action)
             else:
                 flash(form.errors)
@@ -167,14 +163,13 @@ def experiment_builder(instrument=None):
             autofill = not autofill
             forms = create_form_from_pseudo(functions, autofill=autofill, script=script)
             session['autofill'] = autofill
-    elif edit_action:
-        forms = create_form_from_action(edit_action, script=script)
+
     utils.post_script_file(script)
     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,
                            local_variables=global_config.defined_variables,
-                           functions=functions, forms=forms, buttons=design_buttons, format_name=format_name,
+                           forms=forms, buttons=design_buttons, format_name=format_name,
                            use_llm=enable_llm)
 
 
@@ -505,7 +500,7 @@ def edit_action(uuid: str):
             # print(kwargs)
             if forms and forms.validate_on_submit():
                 save_as = kwargs.pop('return', '')
-                kwargs = script.eval_variables(kwargs)
+                kwargs = script.validate_variables(kwargs)
             # try:
                 script.update_by_uuid(uuid=uuid, args=kwargs, output=save_as)
             # except Exception as e:

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/routes/design/templates/design/experiment_builder.html

@@ -150,12 +150,12 @@
                                             {{ format_name(name) }}
                                         </button>
                                     </h2>
+
                                     <div id="{{name}}" class="accordion-collapse collapse" data-bs-parent="#accordionActions">
                                         <div class="accordion-body">
                                             <form role="form" method='POST' name="add" id="add">
                                                 <div class="form-group">
                                                     {{ form.hidden_tag() }}
-{#                                                    {{ form.hidden_name() }}#}
                                                     {% for field in form %}
                                                         {% if field.type not in ['CSRFTokenField', 'HiddenField'] %}
                                                             <div class="input-group mb-3">
@@ -172,6 +172,8 @@
                                                     {% endfor %}
                                                 </div>
                                                 <button type="submit" class="btn btn-dark">Add </button>
+                                                <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>
+
                                             </form>
 
 

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/routes/main/main.py

@@ -1,6 +1,6 @@
 from flask import Blueprint, render_template, current_app
 from flask_login import login_required
-from ivoryos.version import __version__ as ivoryos_version
+from version import __version__ as ivoryos_version
 
 main = Blueprint('main', __name__, template_folder='templates/main')
 

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/routes/main/templates/main/home.html

@@ -9,32 +9,32 @@
         </h1>
         <p>Version: {{ version }}</p>
         <div class="row">
-
-            <div class="col-lg-6 mb-4 d-flex align-items-stretch">
-                <div class="card rounded shadow-sm flex-fill">
-                    <div class="card-body">
-                        <h5 class="card-title">Browse designs</h5>
-                        <p class="card-text">Browse all workflows saved in the database.</p>
-                        <a href="{{ url_for('database.load_from_database') }}" class="stretched-link"></a>
+            {% if enable_design %}
+                <div class="col-lg-6 mb-4 d-flex align-items-stretch">
+                    <div class="card rounded shadow-sm flex-fill">
+                        <div class="card-body">
+                            <h5 class="card-title">Browse designs</h5>
+                            <p class="card-text">Browse all workflows saved in the database.</p>
+                            <a href="{{ url_for('database.load_from_database') }}" class="stretched-link"></a>
+                        </div>
                     </div>
                 </div>
-            </div>
-            <div class="col-lg-6 mb-4 d-flex align-items-stretch">
-                <div class="card rounded shadow-sm flex-fill">
-                    <div class="card-body">
-                        <h5 class="card-title">Edit designs</h5>
-                        <p class="card-text">Build your workflow from current deck functions.</p>
-                        <a href="{{ url_for('design.experiment_builder') }}" class="stretched-link"></a>
+                <div class="col-lg-6 mb-4 d-flex align-items-stretch">
+                    <div class="card rounded shadow-sm flex-fill">
+                        <div class="card-body">
+                            <h5 class="card-title">Edit designs</h5>
+                            <p class="card-text">Build your workflow from current deck functions.</p>
+                            <a href="{{ url_for('design.experiment_builder') }}" class="stretched-link"></a>
+                        </div>
                     </div>
                 </div>
-            </div>
+            {% endif %}
         </div>
 
         <br><br><br>
         {% if not off_line %}
-{#            <h5>Only available in online mode</h5>#}
-{#            <hr>#}
             <div class="row">
+                {% if enable_design %}
                 <div class="col-lg-6 mb-4 d-flex align-items-stretch">
                     <div class="card rounded shadow-sm flex-fill">
                         <div class="card-body">
@@ -44,6 +44,8 @@
                         </div>
                     </div>
                 </div>
+                {% endif %}
+
                 <div class="col-lg-6 mb-4 d-flex align-items-stretch">
                     <div class="card rounded shadow-sm flex-fill">
                         <div class="card-body">

ivoryos-0.1.15/ivoryos/routes/monitor/monitor.py

@@ -0,0 +1,21 @@
+from flask import Blueprint, flash, render_template
+from flask_login import login_required
+
+from ivoryos.utils.global_config import GlobalConfig
+
+global_config = GlobalConfig()
+
+monitor = Blueprint('monitor', __name__, template_folder='templates/monitor')
+
+
+@monitor.route("/stream_feed")
+@login_required
+def stream_feed():
+    """
+    .. :quickref: Monitor; stream feed
+
+    display feed by ip address
+    e.g. HeinSight output feed
+    .. http:get:: /my_deck
+    """
+    return render_template('monitor.html', stream_address="http://127.0.0.1:8001/frame")

ivoryos-0.1.15/ivoryos/routes/monitor/templates/monitor/monitor.html

@@ -0,0 +1,24 @@
+{% extends 'base.html' %}
+{% block title %}IvoryOS | Monitor {% endblock %}
+
+{% block body %}
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/socket.io/4.4.1/socket.io.js"></script>
+
+    <h1>Live Stream</h1>
+    <img src="{{ stream_address }}" width="800" height="600">
+
+    {% if no_deck_warning and not dismiss %}
+{#      auto pop import when there is no deck#}
+        <script type="text/javascript">
+            function OpenBootstrapPopup() {
+                $("#importModal").modal('show');
+            }
+            window.onload = function () {
+                OpenBootstrapPopup();
+            };
+        </script>
+    {% endif %}
+
+    <script src="{{ url_for('static', filename='js/socket_handler.js') }}"></script>
+
+{% endblock %}

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/templates/base.html

@@ -23,7 +23,7 @@
 <body>
     <nav class="navbar navbar-expand-lg navbar-light bg-light fixed-top">
         <div class= "container">
-
+{#            {{ module_config }}#}
             <a class="navbar-brand" href="{{ url_for('main.index') }}">
                 <img src="{{url_for('static', filename='logo.webp')}}" alt="Logo" height="60" class="d-inline-block align-text-bottom">
             </a>
@@ -36,15 +36,22 @@
                     <li class="nav-item">
                         <a class="nav-link" href="{{ url_for('main.index') }}" aria-current="page">Home</a>
                     </li>
-                    <li class="nav-item">
-                        <a class="nav-link" href="{{ url_for('database.load_from_database') }}" aria-current="page">Library</a>
-                    </li>
-                    <li class="nav-item">
-                        <a class="nav-link" href="{{ url_for('design.experiment_builder') }}">Design</a>
-                    </li>
-                    <li class="nav-item">
-                        <a class="nav-link" href="{{ url_for('design.experiment_run') }}">Compile/Run</a>
-                    </li>
+                    {% if enable_design %}
+                        <li class="nav-item">
+                            <a class="nav-link" href="{{ url_for('database.load_from_database') }}" aria-current="page">Library</a>
+                        </li>
+                        <li class="nav-item">
+                            <a class="nav-link" href="{{ url_for('design.experiment_builder') }}">Design</a>
+                        </li>
+                        <li class="nav-item">
+                            <a class="nav-link" href="{{ url_for('design.experiment_run') }}">Compile/Run</a>
+                        </li>
+                    {% endif %}
+                    {% if enable_monitor %}
+                        <li class="nav-item">
+                            <a class="nav-link" href="{{ url_for('monitor.stream_feed') }}">Monitor</a></li>
+                        </li>
+                    {% endif %}
                     <li class="nav-item">
                         <a class="nav-link" href="{{ url_for('control.deck_controllers') }}">Devices</a></li>
                     </li>

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/utils/db_models.py

@@ -32,16 +32,6 @@ class User(db.Model, UserMixin):
         return self.username
 
 
-class Variable:
-    def __init__(self, name: str = None, data_type=str, value=None):
-        self.name = name
-        self.data_type = data_type
-        self.value = value
-
-    def __str__(self):
-        return self.name
-
-
 class Script(db.Model):
     __tablename__ = 'script'
     # id = db.Column(db.Integer, primary_key=True)
@@ -128,20 +118,8 @@ class Script(db.Model):
         if type(action['args']) is dict:
             # pass
             self.eval_list(args, arg_types)
-
         else:
             pass
-            # """handle"""
-            # args = list(args.values())[0]
-            # if not args.startswith("#"):
-            #     if args in bool_dict.keys():
-            #         args = bool_dict[args]
-            #
-            #     else:
-            #         if 'arg_types' in action:
-            #             arg_types = action['arg_types']
-            #             self._convert_type(args, arg_types)
-
         action['args'] = args
         action['return'] = output
 
@@ -186,14 +164,6 @@ class Script(db.Model):
     def currently_editing_order(self, script):
         self.id_order[self.editing_type] = script
 
-    # @property
-    # def editing_type(self):
-    #     return self.editing_type
-
-    # @editing_type.setter
-    # def editing_type(self, change_type):
-    #     self.editing_type = change_type
-
     def update_time_stamp(self):
         self.last_modified = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
 
@@ -236,6 +206,7 @@ class Script(db.Model):
         self.update_time_stamp()
 
     def add_variable(self, statement, variable, type):
+        variable = self.validate_function_name(variable)
         convert_type = getattr(builtins, type)
         statement = convert_type(statement)
         current_len = len(self.currently_editing_script)
@@ -266,17 +237,20 @@ class Script(db.Model):
 
         return output_variables
 
-    def eval_variables(self, kwargs):
+    def validate_variables(self, kwargs):
+        """
+        Validates the kwargs passed to the Script
+        """
         output_variables: Dict[str, str] = self.get_variables()
         # print(output_variables)
         for key, value in kwargs.items():
             if type(value) is str and value in output_variables:
                 var_type = output_variables[value]
-                kwargs[key] = {value:var_type}
-
+                kwargs[key] = {value: var_type}
+            if isinstance(value, str) and value.startswith("#"):
+                kwargs[key] = f"#{self.validate_function_name(value[1:])}"
         return kwargs
 
-
     def add_logic_action(self, logic_type: str, statement):
         current_len = len(self.currently_editing_script)
         uid = uuid.uuid4().fields[-1]
@@ -294,7 +268,8 @@ class Script(db.Model):
             "while":
                 [
                     {"id": current_len + 1, "instrument": 'while', "action": 'while',
-                     "args": {"statement": 'False' if statement == '' else statement}, "return": '', "uuid": uid, "arg_types": {"statement": ''}},
+                     "args": {"statement": 'False' if statement == '' else statement}, "return": '', "uuid": uid,
+                     "arg_types": {"statement": ''}},
                     {"id": current_len + 2, "instrument": 'while', "action": 'endwhile', "args": {}, "return": '',
                      "uuid": uid},
                 ],
@@ -308,7 +283,8 @@ class Script(db.Model):
             "repeat":
                 [
                     {"id": current_len + 1, "instrument": 'repeat', "action": "repeat",
-                     "args": {"statement": 1 if statement == '' else statement}, "return": '', "uuid": uid, "arg_types": {"statement": "int"}},
+                     "args": {"statement": 1 if statement == '' else statement}, "return": '', "uuid": uid,
+                     "arg_types": {"statement": "int"}},
                     {"id": current_len + 2, "instrument": 'repeat', "action": 'endrepeat',
                      "args": {}, "return": '', "uuid": uid},
                 ],
@@ -319,7 +295,9 @@ class Script(db.Model):
         self.update_time_stamp()
 
     def delete_action(self, id: int):
-
+        """
+        Delete the action by id (step number)
+        """
         uid = next((action['uuid'] for action in self.currently_editing_script if action['id'] == int(id)), None)
         id_to_be_removed = [action['id'] for action in self.currently_editing_script if action['uuid'] == uid]
         order = self.currently_editing_order
@@ -330,6 +308,9 @@ class Script(db.Model):
         self.update_time_stamp()
 
     def duplicate_action(self, id: int):
+        """
+        duplicate action by id (step number), available only for non logic actions
+        """
         action_to_duplicate = next((action for action in self.currently_editing_script if action['id'] == int(id)),
                                    None)
         insert_id = action_to_duplicate.get("id")
@@ -392,15 +373,18 @@ class Script(db.Model):
         return output_str, return_list
 
     def finalize(self):
+        """finalize script, disable editing"""
         self.status = "finalized"
         self.update_time_stamp()
 
     def save_as(self, name):
+        """resave script, enable editing"""
         self.name = name
         self.status = "editing"
         self.update_time_stamp()
 
     def indent(self, unit=0):
+        """helper: create _ unit of indent in code string"""
         string = "\n"
         for _ in range(unit):
             string += "\t"
@@ -489,7 +473,6 @@ class Script(db.Model):
             return f"{self.indent(indent_unit)}time.sleep({statement})", indent_unit
         elif instrument == 'repeat':
             return self._process_repeat(indent_unit, action_name, statement, next_action)
-
         else:
             return self._process_instrument_action(indent_unit, instrument, action_name, args, save_data)
 
@@ -578,7 +561,7 @@ class Script(db.Model):
             if isinstance(args[arg], str) and args[arg].startswith("#"):
                 args_str = args_str.replace(f"'#{args[arg][1:]}'", args[arg][1:])
             elif isinstance(args[arg], dict):
-                print(args[arg])
+                # print(args[arg])
                 variables = self.get_variables()
                 value = next(iter(args[arg]))
                 if value not in variables:

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/utils/form.py

@@ -7,24 +7,17 @@ from flask_wtf import FlaskForm
 from wtforms import StringField, FloatField, HiddenField, BooleanField, IntegerField
 import inspect
 
-from ivoryos.utils.db_models import Variable, Script
-
 
 def find_variable(data, script):
-    # TODO: needs to check for valid order of variables, important when editting
-    # variable name: variable type
-    added_variables: dict[str, str] = script.get_added_variables()
-    output_variables: dict[str, str] = script.get_output_variables()
-    # [action for action in script.currently_editing_script if
-    #                                          action["instrument"] == "variable"
-    #                                          # or action["return"] # TODO find returns
-    #                                          ]
-    added_variables.update(output_variables)
-    for variable_name, variable_type in added_variables.items():
+    """
+    find user defined variables and return values in the script:Script
+    :param data: string of input variable name
+    :param script:Script object
+    """
+    variables: dict[str, str] = script.get_variables()
+    for variable_name, variable_type in variables.items():
         if variable_name == data:
             return data, variable_type  # variable_type int float str or "function_output"
-        # if added_variable["return"] == data:
-        #     return data, None
     return None, None
 
 
@@ -45,7 +38,7 @@ class VariableOrStringField(Field):
         if self.script:
             variable, variable_type = find_variable(self.data, self.script)
             if variable:
-                return Variable(variable, variable_type)
+                return variable
 
         return str(self.data) if self.data is not None else ""
 
@@ -61,7 +54,7 @@ class VariableOrFloatField(Field):
         if self.script:
             variable, variable_type = find_variable(self.data, self.script)
             if variable:
-                return Variable(variable, variable_type)
+                return variable
 
         if self.raw_data:
             return self.raw_data[0]
@@ -109,7 +102,7 @@ class VariableOrIntField(Field):
         if self.script:
             variable, variable_type = find_variable(self.data, self.script)
             if variable:
-                return Variable(variable, variable_type)
+                return variable
 
         if self.raw_data:
             return self.raw_data[0]
@@ -158,7 +151,7 @@ class VariableOrBoolField(BooleanField):
             if variable:
                 if not variable_type == "function_output":
                     raise ValueError("Not accepting boolean variables")
-                return Variable(variable, variable_type)
+                return variable
 
         self.data = bool(value)
 
@@ -183,7 +176,7 @@ class VariableOrBoolField(BooleanField):
         if self.script:
             variable, variable_type = find_variable(self.raw_data, self.script)
             if variable:
-                return Variable(variable, variable_type)
+                return variable
 
         if self.raw_data:
             return str(self.raw_data[0])
@@ -197,7 +190,15 @@ def format_name(name):
     return text.capitalize()
 
 
-def create_form_for_method(method, method_name, autofill, script=None, design=True):
+def create_form_for_method(method, autofill, script=None, design=True):
+    """
+    Create forms for each method or signature
+    :param method: dict(docstring, signature)
+    :param autofill:bool if autofill is enabled
+    :param script:Script object
+    :param design: if design is enabled
+    """
+
     class DynamicForm(FlaskForm):
         pass
 
@@ -233,32 +234,60 @@ def create_form_for_method(method, method_name, autofill, script=None, design=Tr
     return DynamicForm
 
 
-# Create forms for each method in DummySDLDeck
-def create_add_form(attr, attr_name, autofill, script=None, design=True):
-    dynamic_form = create_form_for_method(attr, attr_name, autofill, script, design)
+def create_add_form(attr, attr_name, autofill: bool, script=None, design: bool = True):
+    """
+    Create forms for each method or signature
+    :param attr: dict(docstring, signature)
+    :param attr_name: method name
+    :param autofill:bool if autofill is enabled
+    :param script:Script object
+    :param design: if design is enabled. Design allows string input for parameter names ("#param") for all fields
+    """
+    signature = attr.get('signature', {})
+    docstring = attr.get('docstring', "")
+    dynamic_form = create_form_for_method(signature, autofill, script, design)
     if design:
         return_value = StringField(label='Save value as', render_kw={"placeholder": "Optional"})
         setattr(dynamic_form, 'return', return_value)
-    hidden_method_name = HiddenField(name=f'hidden_name', render_kw={"value": f'{attr_name}'})
+    hidden_method_name = HiddenField(name=f'hidden_name', description=docstring, render_kw={"value": f'{attr_name}'})
     setattr(dynamic_form, 'hidden_name', hidden_method_name)
     return dynamic_form
 
 
-def create_form_from_module(sdl_module, autofill: bool, script=None, design=True):
-    # sdl_deck = DummySDLDeck(DummyPump("COM1"), DummyBalance("COM2"))
+def create_form_from_module(sdl_module, autofill: bool = False, script=None, design: bool = False):
+    """
+    Create forms for each method, used for control routes
+    :param sdl_module: method module
+    :param autofill:bool if autofill is enabled
+    :param script:Script object
+    :param design: if design is enabled
+    """
     method_forms = {}
     for attr_name in dir(sdl_module):
-        attr = getattr(sdl_module, attr_name)
-        if inspect.ismethod(attr) and not attr_name.startswith('_'):
+        method = getattr(sdl_module, attr_name)
+        if inspect.ismethod(method) and not attr_name.startswith('_'):
+            signature = inspect.signature(method)
+            docstring = inspect.getdoc(method)
+            attr = dict(signature=signature, docstring=docstring)
             form_class = create_add_form(attr, attr_name, autofill, script, design)
             method_forms[attr_name] = form_class()
     return method_forms
 
 
 def create_form_from_pseudo(pseudo: dict, autofill: bool, script=None, design=True):
-    '''{'dose_liquid': < Signature(amount_in_ml: float, rate_ml_per_minute: float) >}'''
+    """
+    Create forms for pseudo method, used for design routes
+    :param pseudo:{'dose_liquid': {
+                        "docstring": "some docstring",
+                        "signature": Signature(amount_in_ml: float, rate_ml_per_minute: float) }
+                    }
+    :param autofill:bool if autofill is enabled
+    :param script:Script object
+    :param design: if design is enabled
+    """
     method_forms = {}
     for attr_name, signature in pseudo.items():
+        # signature = info.get('signature', {})
         form_class = create_add_form(signature, attr_name, autofill, script, design)
         method_forms[attr_name] = form_class()
     return method_forms
@@ -266,15 +295,18 @@ def create_form_from_pseudo(pseudo: dict, autofill: bool, script=None, design=Tr
 
 def create_form_from_action(action: dict, script=None, design=True):
     '''
-    {'action': 'dose_solid', 'arg_types': {'amount_in_mg': 'float', 'bring_in': 'bool'}, 'args': {'amount_in_mg':
-    5.0, 'bring_in': False}, 'id': 9, 'instrument': 'deck.sdl', 'return': '', 'uuid': 266929188668995}
+    Create forms for single action, used for design routes
+    :param action: {'action': 'dose_solid', 'arg_types': {'amount_in_mg': 'float', 'bring_in': 'bool'},
+                    'args': {'amount_in_mg': 5.0, 'bring_in': False}, 'id': 9,
+                    'instrument': 'deck.sdl', 'return': '', 'uuid': 266929188668995}
+    :param script:Script object
+    :param design: if design is enabled
+
     '''
-    # print(action)
 
     arg_types = action.get("arg_types", {})
     args = action.get("args", {})
     save_as = action.get("return")
-    action = action.get("action")
 
     class DynamicForm(FlaskForm):
         pass
@@ -314,7 +346,10 @@ def create_form_from_action(action: dict, script=None, design=True):
     return DynamicForm()
 
 
-def create_builtin_form(logic_type, autofill, script):
+def create_builtin_form(logic_type, script):
+    """
+    Create a builtin form {if, while, variable, repeat, wait}
+    """
     class BuiltinFunctionForm(FlaskForm):
         pass
 
@@ -355,12 +390,22 @@ def create_builtin_form(logic_type, autofill, script):
 
 
 def create_action_button(script, stype=None):
+    """
+    Creates action buttons for design route (design canvas)
+    :param script: Script object
+    :param stype: script type (script, prep, cleanup)
+    """
     stype = stype or script.editing_type
     variables = script.get_variables()
     return [_action_button(i, variables) for i in script.get_script(stype)]
 
 
 def _action_button(action: dict, variables: dict):
+    """
+    Creates action button for one action
+    :param action: Action dict
+    :param variables: created variable dict
+    """
     style = {
         "repeat": "background-color: lightsteelblue",
         "if": "background-color: salmon",
@@ -368,7 +413,7 @@ def _action_button(action: dict, variables: dict):
     }.get(action['instrument'], "")
 
     if action['instrument'] in ['if', 'while', 'repeat']:
-        text = f"{action['action']} {action['args']}"
+        text = f"{action['action']} {action['args'].get('statement', '')}"
     elif action['instrument'] == 'variable':
         text = f"{action['action']} = {action['args'].get('statement')}"
     else:
@@ -382,18 +427,13 @@ def _action_button(action: dict, variables: dict):
                 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 ""
-
                     else:
                         value = v  # Keep the original value if not a dict
-
                     arg_list.append(f"{k} = {value}")  # Format the key-value pair
-
                 arg_string = "(" + ", ".join(arg_list) + ")"
             else:
                 arg_string = f"= {action['args']}"
-
         text = f"{prefix}{action_text}  {arg_string}"
-
     return dict(label=text, style=style, uuid=action["uuid"], id=action["id"], instrument=action['instrument'])

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos/utils/utils.py

@@ -7,7 +7,6 @@ import pickle
 import subprocess
 import sys
 from collections import Counter
-from typing import Optional, Dict, Tuple
 
 from flask import session
 from flask_socketio import SocketIO
@@ -102,20 +101,9 @@ def _inspect_class(class_object=None, debug=False):
         if not function.startswith(under_score) and not function.isupper():
             try:
                 annotation = inspect.signature(method)
-                # if doc_string:
                 docstring = inspect.getdoc(method)
                 functions[function] = dict(signature=annotation, docstring=docstring)
 
-                # handle getter setters todo
-                # if callable(att):
-                #     functions[function] = inspect.signature(att)
-                # else:
-                #     att = getattr(class_object.__class__, function)
-                #     if isinstance(att, property) and att.fset is not None:
-                #         setter = att.fset.__annotations__
-                #         setter.pop('return', None)
-                #         if setter:
-                #             functions[function] = setter
             except Exception:
                 pass
     return functions
@@ -146,23 +134,6 @@ def _get_type_from_parameters(arg, parameters):
             arg_type = annotation.__name__
     return arg_type
 
-# # moved to script
-# def find_variable_in_script(script: Script, args: Dict[str, str]) -> Optional[Tuple[Dict[str, str], Dict[str, str]]]:
-#     # TODO: need to search for if the variable exists
-#     added_variables: list[Dict[str, str]] = [action for action in script.currently_editing_script if
-#                                              action["instrument"] == "variable"]
-#
-#     possible_variable_arguments = {}
-#     possible_variable_types = {}
-#
-#     for arg_name, arg_val in args.items():
-#         for added_variable in added_variables:
-#             if added_variable["action"] == arg_val:
-#                 possible_variable_arguments[arg_name] = added_variable["action"]
-#                 possible_variable_types[arg_name] = "variable"
-#
-#     return possible_variable_arguments, possible_variable_types
-
 
 def _convert_by_str(args, arg_types):
     """
@@ -203,9 +174,6 @@ def convert_config_type(args, arg_types, is_class: bool = False):
     """
     Converts an argument from str to an arg type
     """
-    bool_dict = {"True": True, "False": False}
-    # print(args, arg_types)
-    # print(globals())
     if args:
         for arg in args:
             if arg not in arg_types.keys():
@@ -340,8 +308,10 @@ def ax_initiation(data, arg_types):
 
 
 def get_arg_type(args, parameters):
+    """get argument type from signature"""
     arg_types = {}
     # print(args, parameters)
+    parameters = parameters.get("signature")
     if args:
         for arg in args:
             arg_types[arg] = _get_type_from_parameters(arg, parameters)

{ivoryos-0.1.13 → ivoryos-0.1.15/ivoryos.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.13
+Version: 0.1.15
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang

{ivoryos-0.1.13 → ivoryos-0.1.15}/ivoryos.egg-info/SOURCES.txt

@@ -4,7 +4,6 @@ README.md
 setup.py
 ivoryos/__init__.py
 ivoryos/config.py
-ivoryos/version.py
 ivoryos.egg-info/PKG-INFO
 ivoryos.egg-info/SOURCES.txt
 ivoryos.egg-info/dependency_links.txt
@@ -31,6 +30,8 @@ ivoryos/routes/main/__init__.py
 ivoryos/routes/main/main.py
 ivoryos/routes/main/templates/main/help.html
 ivoryos/routes/main/templates/main/home.html
+ivoryos/routes/monitor/monitor.py
+ivoryos/routes/monitor/templates/monitor/monitor.html
 ivoryos/static/favicon.ico
 ivoryos/static/logo.webp
 ivoryos/static/style.css

{ivoryos-0.1.13 → ivoryos-0.1.15}/setup.py

@@ -1,5 +1,5 @@
 from setuptools import setup, find_packages
-from ivoryos.version import __version__ as ivoryos_version
+from version import __version__ as ivoryos_version
 
 setup(
     name='ivoryos',

ivoryos-0.1.13/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "0.1.13"