ivoryos 1.3.4__tar.gz → 1.3.5__tar.gz

{ivoryos-1.3.4 → ivoryos-1.3.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.4
+Version: 1.3.5
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -17,9 +17,19 @@ Requires-Dist: Flask-WTF
 Requires-Dist: SQLAlchemy-Utils
 Requires-Dist: python-dotenv
 Requires-Dist: astor; python_version < "3.9"
+Provides-Extra: optimizer-ax
+Requires-Dist: ax-platform; extra == "optimizer-ax"
+Provides-Extra: optimizer-baybe
+Requires-Dist: baybe; extra == "optimizer-baybe"
 Provides-Extra: optimizer
 Requires-Dist: ax-platform; extra == "optimizer"
 Requires-Dist: baybe; extra == "optimizer"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-rtd-theme; extra == "doc"
+Requires-Dist: sphinxcontrib-httpdomain; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/__init__.py

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

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/routes/control/control.py

@@ -23,7 +23,7 @@ control.register_blueprint(control_temp)
 @control.route("/", strict_slashes=False, methods=["GET", "POST"])
 @control.route("/<string:instrument>", strict_slashes=False, methods=["GET", "POST"])
 @login_required
-def deck_controllers(instrument: str = None):
+async def deck_controllers(instrument: str = None):
     """
     .. :quickref: Direct Control; device (instruments) and methods
 
@@ -82,7 +82,7 @@ def deck_controllers(instrument: str = None):
 
         wait = str(payload.get("hidden_wait", "true")).lower() == "true"
 
-        output = runner.run_single_step(
+        output = await runner.run_single_step(
             component=instrument, method=method_name, kwargs=kwargs, wait=wait,
             current_app=current_app._get_current_object()
         )

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/routes/design/design.py

@@ -87,8 +87,11 @@ def experiment_builder():
 
     # edit_action_info = session.get("edit_action")
 
-
-    exec_string = script.python_script if script.python_script else script.compile(current_app.config['SCRIPT_FOLDER'])
+    try:
+        exec_string = script.python_script if script.python_script else script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        flash(f"Error in Python script: {e}")
     session['python_code'] = exec_string
 
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
@@ -316,6 +319,7 @@ def methods_handler(instrument: str = ''):
     msg = ""
     request.form
     if "hidden_name" in request.form:
+        deck_snapshot = global_config.deck_snapshot
         method_name = request.form.get("hidden_name", None)
         form = forms.get(method_name) if forms else None
         insert_position = request.form.get("drop_target_id", None)
@@ -334,7 +338,9 @@ def methods_handler(instrument: str = ''):
                 action = {"instrument": instrument, "action": function_name,
                           "args": kwargs,
                           "return": save_data,
-                          'arg_types': primitive_arg_types}
+                          'arg_types': primitive_arg_types,
+                          "coroutine": deck_snapshot[instrument][function_name].get("coroutine", False) if deck_snapshot else False,
+                          }
                 script.add_action(action=action, insert_position=insert_position)
             else:
                 msg = [f"{field}: {', '.join(messages)}" for field, messages in form.errors.items()]

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/routes/design/design_step.py

@@ -47,6 +47,7 @@ def save_step(uuid: int):
     """
     script = utils.get_script_file()
     action = script.find_by_uuid(uuid)
+    warning = None
     if action is not None:
         forms = create_form_from_action(action, script=script)
         kwargs = {field.name: field.data for field in forms if field.name != 'csrf_token'}
@@ -55,14 +56,19 @@ def save_step(uuid: int):
             kwargs = script.validate_variables(kwargs)
             script.update_by_uuid(uuid=uuid, args=kwargs, output=save_as)
         else:
-            flash(forms.errors)
+            warning = f"Compilation failed: {str(forms.errors)}"
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
     return render_template("components/canvas_main.html",
-                               script=script,
-                               buttons_dict=design_buttons)
+                           script=script,
+                           buttons_dict=design_buttons,
+                           warning=warning)
 
 @steps.delete("/draft/steps/<int:uuid>")
 def delete_step(uuid: int):
@@ -82,12 +88,17 @@ def delete_step(uuid: int):
     if request.method == 'DELETE':
         script.delete_action(uuid)
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    warning = None
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
     return render_template("components/canvas_main.html",
                                script=script,
-                               buttons_dict=design_buttons)
+                               buttons_dict=design_buttons, warning=warning)
 
 
 @steps.route("/draft/steps/<int:uuid>/duplicate", methods=["POST"], strict_slashes=False,)
@@ -107,13 +118,18 @@ def duplicate_action(uuid: int):
     script = utils.get_script_file()
     script.duplicate_action(uuid)
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    warning = None
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
 
     return render_template("components/canvas_main.html",
                          script=script,
-                         buttons_dict=design_buttons)
+                         buttons_dict=design_buttons, warning=warning)
 
 
 @steps.route("/draft/steps/order", methods=['POST'])
@@ -133,13 +149,18 @@ def update_list():
     script = utils.get_script_file()
     script.currently_editing_order = order.split(",", len(script.currently_editing_script))
     script.sort_actions()
+    warning = None
 
     utils.post_script_file(script)
-    exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    try:
+        exec_string = script.compile(current_app.config['SCRIPT_FOLDER'])
+    except Exception as e:
+        exec_string = {}
+        warning = f"Compilation failed: {str(e)}"
     session['python_code'] = exec_string
 
     # Return the updated canvas HTML instead of JSON
     design_buttons = {stype: create_action_button(script, stype) for stype in script.stypes}
     return render_template("components/canvas_main.html",
                            script=script,
-                           buttons_dict=design_buttons)
+                           buttons_dict=design_buttons, warning=warning)

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/routes/design/templates/components/canvas_main.html

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

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/static/js/action_handlers.js

@@ -103,6 +103,12 @@ function submitEditForm(event) {
                 document.getElementById('instrument-panel').innerHTML = previousHtmlState;
                 previousHtmlState = null;  // Clear the stored state
             }
+            const parser = new DOMParser();
+            const doc = parser.parseFromString(html, 'text/html');
+            const warningDiv = doc.querySelector('#warning');
+            if (warningDiv && warningDiv.textContent.trim()) {
+                alert(warningDiv.textContent.trim()); // or use a nicer toast
+            }
         }
     })
     .catch(error => {
@@ -149,6 +155,13 @@ function duplicateAction(uuid) {
     .then(response => response.text())
     .then(html => {
         updateActionCanvas(html);
+
+        const parser = new DOMParser();
+        const doc = parser.parseFromString(html, 'text/html');
+        const warningDiv = doc.querySelector('#warning');
+        if (warningDiv && warningDiv.textContent.trim()) {
+            alert(warningDiv.textContent.trim()); // or use a nicer toast
+        }
     })
     .catch(error => console.error('Error:', error));
 }
@@ -202,6 +215,13 @@ function deleteAction(uuid) {
     .then(html => {
         // Find the first list element's content and replace it
         updateActionCanvas(html);
+        // Optionally, check if a warning element exists
+        const parser = new DOMParser();
+        const doc = parser.parseFromString(html, 'text/html');
+        const warningDiv = doc.querySelector('#warning');
+        if (warningDiv && warningDiv.textContent.trim()) {
+            alert(warningDiv.textContent.trim()); // or use a nicer toast
+        }
     })
     .catch(error => console.error('Error:', error));
 }

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/utils/db_models.py

@@ -434,14 +434,21 @@ class Script(db.Model):
         :return: A dict containing script types as keys and lists of function body lines as values.
         """
         line_collection = {}
+
         for stype, func_str in exec_str_collection.items():
             if func_str:
                 module = ast.parse(func_str)
-                func_def = next(node for node in module.body if isinstance(node, ast.FunctionDef))
 
-                # Extract function body as source lines
-                line_collection[stype] = [ast_unparse(node) for node in func_def.body if not isinstance(node, ast.Return)]
-                # print(line_collection[stype])
+                # Find the first function (regular or async)
+                func_def = next(
+                    node for node in module.body
+                    if isinstance(node, (ast.FunctionDef, ast.AsyncFunctionDef))
+                )
+
+                # Extract function body as source lines, skipping 'return' nodes
+                line_collection[stype] = [
+                    ast_unparse(node) for node in func_def.body if not isinstance(node, ast.Return)
+                ]
         return line_collection
 
     def compile(self, script_path=None):
@@ -459,7 +466,8 @@ class Script(db.Model):
 
         for i in self.stypes:
             if self.script_dict[i]:
-                func_str = self._generate_function_header(run_name, i) + self._generate_function_body(i)
+                is_async = any(a.get("coroutine", False) for a in self.script_dict[i])
+                func_str = self._generate_function_header(run_name, i, is_async) + self._generate_function_body(i)
                 exec_str_collection[i] = func_str
         if script_path:
             self._write_to_file(script_path, run_name, exec_str_collection)
@@ -477,7 +485,7 @@ class Script(db.Model):
             name += '_'
         return name
 
-    def _generate_function_header(self, run_name, stype):
+    def _generate_function_header(self, run_name, stype, is_async):
         """
         Generate the function header.
         """
@@ -487,7 +495,8 @@ class Script(db.Model):
                      config_type.items()]
 
         script_type = f"_{stype}" if stype != "script" else ""
-        function_header = f"def {run_name}{script_type}("
+        async_str = "async " if is_async else ""
+        function_header = f"{async_str}def {run_name}{script_type}("
 
         if stype == "script":
             function_header += ", ".join(configure)
@@ -540,7 +549,8 @@ class Script(db.Model):
         # elif instrument == 'registered_workflows':
         #     return inspect.getsource(my_function)
         else:
-            return self._process_instrument_action(indent_unit, instrument, action_name, args, save_data)
+            is_async = action.get("coroutine", False)
+            return self._process_instrument_action(indent_unit, instrument, action_name, args, save_data, is_async)
 
     def _process_args(self, args):
         """
@@ -600,10 +610,12 @@ class Script(db.Model):
             indent_unit -= 1
         return exec_string, indent_unit
 
-    def _process_instrument_action(self, indent_unit, instrument, action, args, save_data):
+    def _process_instrument_action(self, indent_unit, instrument, action, args, save_data, is_async=False):
         """
         Process actions related to instruments.
         """
+        async_str = "await " if is_async else ""
+
         function_call = f"{instrument}.{action}"
         if instrument.startswith("blocks"):
             self.blocks_included = True
@@ -611,11 +623,11 @@ class Script(db.Model):
 
         if isinstance(args, dict) and args != {}:
             args_str = self._process_dict_args(args)
-            single_line = f"{function_call}(**{args_str})"
+            single_line = f"{async_str}{function_call}(**{args_str})"
         elif isinstance(args, str):
             single_line = f"{function_call} = {args}"
         else:
-            single_line = f"{function_call}()"
+            single_line = f"{async_str}{function_call}()"
 
         if save_data:
             save_data += " = "

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/utils/py_to_json.py

@@ -55,6 +55,10 @@ def convert_to_cards(source_code: str):
         )
 
     class CardVisitor(ast.NodeVisitor):
+        def __init__(self):
+            self.defined_types = {}  # <-- always exists
+
+
         def visit_FunctionDef(self, node):
             self.defined_types = {
                 arg.arg: ast.unparse(arg.annotation) if arg.annotation else "float"
@@ -142,14 +146,20 @@ def convert_to_cards(source_code: str):
                     "return": "",
                     "uuid": generate_uuid()
                 })
+            elif isinstance(node.value, ast.Await):
+                self.handle_call(node.value.value, ret_var=node.targets[0].id, awaited=True)
+
             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):
+            if isinstance(node.value, ast.Await):
+                # node.value is ast.Await
+                self.handle_call(node.value.value, awaited=True)
+            elif isinstance(node.value, ast.Call):
                 self.handle_call(node.value)
 
-        def handle_call(self, node, ret_var=""):
+        def handle_call(self, node, ret_var="", awaited=False):
             func_parts = []
             f = node.func
             while isinstance(f, ast.Attribute):
@@ -229,7 +239,7 @@ def convert_to_cards(source_code: str):
                         else infer_type(value)
                     )
 
-            add_card({
+            card = {
                 "action": action,
                 "arg_types": arg_types,
                 "args": args,
@@ -237,7 +247,12 @@ def convert_to_cards(source_code: str):
                 "instrument": instrument,
                 "return": ret_var,
                 "uuid": generate_uuid()
-            })
+            }
+
+            if awaited:
+                card["coroutine"] = True  # mark as coroutine if awaited
+
+            add_card(card)
 
     CardVisitor().visit(tree)
     return cards

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/utils/script_runner.py

@@ -1,4 +1,5 @@
 import ast
+import asyncio
 import os
 import csv
 import threading
@@ -182,7 +183,26 @@ class ScriptRunner:
                     duration = float(duration_str)
                     self.safe_sleep(duration)
                 else:
-                    exec(line, exec_globals, exec_locals)
+                    if "await " in line:
+                        async_code = f"async def __async_exec_wrapper():\n"
+                        # indent all code lines by 4 spaces
+                        async_code += "\n".join("    " + line for line in line.splitlines())
+                        async_code += f"\n    return locals()"
+                        exec(async_code, exec_globals, exec_locals)
+                        func = exec_locals.get("__async_exec_wrapper") or exec_globals.get("__async_exec_wrapper")
+                        # Capture the return value from asyncio.run
+                        result_locals = asyncio.run(func())
+
+                        # Update exec_locals with the returned locals
+                        exec_locals.update(result_locals)
+
+
+                    else:
+                        print("just exec synchronously")
+                        exec(line, exec_globals, exec_locals)
+                        exec_globals.update(exec_locals)
+                        # return locals_dict
+                    # exec(line, exec_globals, exec_locals)
                 # step.run_error = False
 
             except HumanInterventionRequired as e:
@@ -198,6 +218,7 @@ class ScriptRunner:
 
                 step.run_error = True
                 self.toggle_pause()
+            exec_locals.pop("__async_exec_wrapper", None)
             step.end_time = datetime.now()
             step.output = exec_locals
             db.session.commit()
@@ -249,7 +270,7 @@ class ScriptRunner:
                 self._run_actions(script, section_name="cleanup", logger=logger, socketio=socketio,run_id=run_id)
                 # Reset the running flag when done
                 # Save results if necessary
-                if not script.python_script and output_list:
+                if not script.python_script and return_list:
                     filename = self._save_results(run_name, arg_type, return_list, output_list, logger, output_path)
                 self._emit_progress(socketio, 100)
 

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/utils/task_runner.py

@@ -1,3 +1,5 @@
+import inspect
+import asyncio
 import threading
 import time
 from datetime import datetime
@@ -19,8 +21,7 @@ class TaskRunner:
         self.globals_dict = globals_dict
         self.lock = global_config.runner_lock
 
-
-    def run_single_step(self, component, method, kwargs, wait=True, current_app=None):
+    async def run_single_step(self, component, method, kwargs, wait=True, current_app=None):
         global deck
         if deck is None:
             deck = global_config.deck
@@ -32,16 +33,15 @@ class TaskRunner:
             current_status["output"] = "busy"
             return current_status
 
-
         if wait:
-            output = self._run_single_step(component, method, kwargs, current_app)
+            output = await self._run_single_step(component, method, kwargs, current_app)
         else:
-            print("running with thread")
-            thread = threading.Thread(
-                target=self._run_single_step, args=(component, method, kwargs, current_app)
-            )
-            thread.start()
-            time.sleep(0.1)
+            # Create background task properly
+            async def background_runner():
+                await self._run_single_step(component, method, kwargs, current_app)
+
+            asyncio.create_task(background_runner())
+            await asyncio.sleep(0.1)  # Change time.sleep to await asyncio.sleep
             output = {"status": "task started", "task_id": global_config.runner_status.get("id")}
 
         return output
@@ -60,22 +60,32 @@ class TaskRunner:
             function_executable = getattr(instrument, method)
         return function_executable
 
-    def _run_single_step(self, component, method, kwargs, current_app=None):
+    async def _run_single_step(self, component, method, kwargs, current_app=None):
         try:
             function_executable = self._get_executable(component, deck, method)
             method_name = f"{component}.{method}"
         except Exception as e:
             self.lock.release()
-            return {"status": "error", "msg": e.__str__()}
+            return {"status": "error", "msg": str(e)}
 
-        # with self.lock:
+        # Flask context is NOT async → just use normal "with"
         with current_app.app_context():
-            step = SingleStep(method_name=method_name, kwargs=kwargs, run_error=None, start_time=datetime.now())
+            step = SingleStep(
+                method_name=method_name,
+                kwargs=kwargs,
+                run_error=None,
+                start_time=datetime.now()
+            )
             db.session.add(step)
             db.session.flush()
-            global_config.runner_status = {"id":step.id, "type": "task"}
+            global_config.runner_status = {"id": step.id, "type": "task"}
+
             try:
-                output = function_executable(**kwargs)
+                if inspect.iscoroutinefunction(function_executable):
+                    output = await function_executable(**kwargs)
+                else:
+                    output = function_executable(**kwargs)
+
                 step.output = output
                 step.end_time = datetime.now()
                 success = True
@@ -87,4 +97,5 @@ class TaskRunner:
             finally:
                 db.session.commit()
                 self.lock.release()
-            return dict(success=success, output=output)
+
+            return dict(success=success, output=output)

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos/utils/utils.py

@@ -105,7 +105,8 @@ def _inspect_class(class_object=None, debug=False):
             try:
                 annotation = inspect.signature(method)
                 docstring = inspect.getdoc(method)
-                functions[function] = dict(signature=annotation, docstring=docstring)
+                coroutine = inspect.iscoroutinefunction(method)
+                functions[function] = dict(signature=annotation, docstring=docstring, coroutine=coroutine,)
 
             except Exception:
                 pass

ivoryos-1.3.5/ivoryos/version.py

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

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.4
+Version: 1.3.5
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -17,9 +17,19 @@ Requires-Dist: Flask-WTF
 Requires-Dist: SQLAlchemy-Utils
 Requires-Dist: python-dotenv
 Requires-Dist: astor; python_version < "3.9"
+Provides-Extra: optimizer-ax
+Requires-Dist: ax-platform; extra == "optimizer-ax"
+Provides-Extra: optimizer-baybe
+Requires-Dist: baybe; extra == "optimizer-baybe"
 Provides-Extra: optimizer
 Requires-Dist: ax-platform; extra == "optimizer"
 Requires-Dist: baybe; extra == "optimizer"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx-rtd-theme; extra == "doc"
+Requires-Dist: sphinxcontrib-httpdomain; extra == "doc"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
 Dynamic: license-file
 
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)

{ivoryos-1.3.4 → ivoryos-1.3.5}/ivoryos.egg-info/requires.txt

@@ -10,6 +10,20 @@ python-dotenv
 [:python_version < "3.9"]
 astor
 
+[dev]
+pytest
+
+[doc]
+sphinx
+sphinx-rtd-theme
+sphinxcontrib-httpdomain
+
 [optimizer]
 ax-platform
 baybe
+
+[optimizer-ax]
+ax-platform
+
+[optimizer-baybe]
+baybe

{ivoryos-1.3.4 → ivoryos-1.3.5}/pyproject.toml

@@ -25,7 +25,18 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-optimizer = ["ax-platform", "baybe"]
+optimizer-ax = ["ax-platform"]
+optimizer-baybe = ["baybe"]
+optimizer = [
+    "ax-platform",
+    "baybe"
+]
+doc = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "sphinxcontrib-httpdomain"
+]
+dev = ["pytest"]
 
 [project.urls]
 Homepage = "https://gitlab.com/heingroup/ivoryos"

ivoryos-1.3.4/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "1.3.4"