ivoryos 1.3.0a0__tar.gz → 1.3.2__tar.gz

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.0a0
+Version: 1.3.2
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/__init__.py

@@ -2,12 +2,13 @@ from ivoryos.server import run
 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
 
 __all__ = [
     "block",
     "BUILDING_BLOCKS",
     "OPTIMIZER_REGISTRY",
     "run",
+    "app",
     "ivoryos_version",
 ]

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/app.py

@@ -20,6 +20,16 @@ from ivoryos.version import __version__ as ivoryos_version
 from sqlalchemy import inspect, text
 from flask import current_app
 
+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=f'{url_prefix}/{auth.name}')
+app.register_blueprint(library, url_prefix=f'{url_prefix}/{library.name}')
+app.register_blueprint(control, url_prefix=f'{url_prefix}/instruments')
+app.register_blueprint(design, url_prefix=f'{url_prefix}')
+app.register_blueprint(execute, url_prefix=f'{url_prefix}')
+app.register_blueprint(data, url_prefix=f'{url_prefix}')
+app.register_blueprint(api, url_prefix=f'{url_prefix}/{api.name}')
 
 def reset_old_schema(engine, db_dir):
     inspector = inspect(engine)
@@ -28,7 +38,7 @@ def reset_old_schema(engine, db_dir):
 
     # Check if old tables exist (no workflow_phases table)
     has_workflow_phase = 'workflow_phases' in tables
-    old_workflow_run = 'old_workflow_run' in tables
+    old_workflow_run = 'workflow_runs' in tables
     old_workflow_step = 'workflow_steps' in tables
 
     if not has_workflow_phase:
@@ -59,18 +69,6 @@ def create_app(config_class=None):
     create app, init database
     """
 
-    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=f'{url_prefix}/{auth.name}')
-    app.register_blueprint(library, url_prefix=f'{url_prefix}/{library.name}')
-    app.register_blueprint(control, url_prefix=f'{url_prefix}/instruments')
-    app.register_blueprint(design, url_prefix=f'{url_prefix}')
-    app.register_blueprint(execute, url_prefix=f'{url_prefix}')
-    app.register_blueprint(data, url_prefix=f'{url_prefix}')
-    app.register_blueprint(api, url_prefix=f'{url_prefix}/{api.name}')
-
-
     app.config.from_object(config_class or 'config.get_config()')
     os.makedirs(app.config["OUTPUT_FOLDER"], exist_ok=True)
     # Initialize extensions

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/auth/auth.py

@@ -15,16 +15,16 @@ def login():
     """
     .. :quickref: User; login user
 
-    .. http:get:: /login
+    .. http:get:: /auth/login
 
     load user login form.
 
-    .. http:post:: /login
+    .. http:post:: /auth/login
 
     :form username: username
     :form password: password
     :status 302: and then redirects to homepage
-    :status 401: incorrect password, redirects to :http:get:`/ivoryos/login`
+    :status 401: incorrect password, redirects to :http:get:`/ivoryos/auth/login`
     """
     if request.method == 'POST':
         username = request.form.get('username')
@@ -57,16 +57,16 @@ def signup():
     """
     .. :quickref: User; signup for a new account
 
-    .. http:get:: /signup
+    .. http:get:: /auth/signup
 
     load user sighup
 
-    .. http:post:: /signup
+    .. http:post:: /auth/signup
 
     :form username: username
     :form password: password
-    :status 302: and then redirects to :http:get:`/ivoryos/login`
-    :status 409: when user already exists, redirects to :http:get:`/ivoryos/signup`
+    :status 302: and then redirects to :http:get:`/ivoryos/auth/login`
+    :status 409: when user already exists, redirects to :http:get:`/ivoryos/auth/signup`
     """
     if request.method == 'POST':
         username = request.form.get('username')
@@ -92,6 +92,8 @@ def logout():
     """
     .. :quickref: User; logout the user
 
+    .. http:get:: /auth/logout
+
     logout the current user, clear session info, and redirect to the login page.
     """
     logout_user()

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/control/control.py

@@ -1,3 +1,5 @@
+import copy
+
 from flask import Blueprint, redirect, flash, request, render_template, session, current_app, jsonify
 from flask_login import login_required
 
@@ -95,8 +97,10 @@ def deck_controllers(instrument: str = None):
 
     # GET request → render web form or return snapshot for API
     if request.is_json or request.accept_mimetypes.best_match(['application/json', 'text/html']) == 'application/json':
-
-        snapshot = global_config.deck_snapshot.copy()
+        # 1.3.2 fix snapshot copy, add building blocks to snapshots
+        snapshot = copy.deepcopy(global_config.deck_snapshot)
+        building_blocks = copy.deepcopy(global_config.building_blocks)
+        snapshot.update(building_blocks)
         for instrument_key, instrument_data in snapshot.items():
             for function_key, function_data in instrument_data.items():
                 function_data["signature"] = str(function_data["signature"])

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/data/data.py

@@ -44,7 +44,7 @@ def workflow_logs(workflow_id:int):
 
     get workflow data logs by workflow id
 
-    .. http:get:: /executions/<int:workflow_id>
+    .. http:get:: /executions/records/<int:workflow_id>
 
     :param workflow_id: workflow id
     :type workflow_id: int
@@ -109,6 +109,15 @@ def workflow_logs(workflow_id:int):
 
 @data.get("/executions/data/<int:workflow_id>")
 def workflow_phase_data(workflow_id: int):
+    """
+    .. :quickref: Workflow Data Database; get workflow data for plotting
+
+    get workflow data for plotting by workflow id
+
+    .. http:get:: /executions/data/<int: workflow_id>
+
+    :param workflow_id: workflow id
+    """
     workflow = db.session.get(WorkflowRun, workflow_id)
     if not workflow:
         return jsonify({})
@@ -140,7 +149,7 @@ def delete_workflow_record(workflow_id: int):
 
     delete a workflow execution record by workflow id
 
-    .. http:delete:: /executions/records/<int:workflow_id>
+    .. http:delete:: /executions/records/<int: workflow_id>
 
     :param workflow_id: workflow id
     :type workflow_id: int
@@ -163,7 +172,7 @@ def download_results(filename:str):
     :param filename: workflow data filename
     :type filename: str
 
-    # :status 302: load pseudo deck and then redirects to :http:get:`/ivoryos/executions`
+    # :status 302: load pseudo deck and then redirects to :http:get:`/ivoryos/executions/records`
     """
 
     filepath = os.path.join(current_app.config["DATA_FOLDER"], filename)

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/design/design.py

@@ -257,7 +257,7 @@ def submit_script():
     """
     .. :quickref: Workflow Design; convert Python to workflow script
 
-    .. http:post:: /design/submit_python
+    .. http:post:: /draft/submit_python
 
     Convert a Python script to a workflow script and save it in the database.
 
@@ -393,7 +393,7 @@ def get_operation_sidebar(instrument: str = ''):
     """
     .. :quickref: Workflow Design; handle methods of a specific instrument
 
-    .. http:get:: /design/instruments/<string:instrument>
+    .. http:get:: /draft/instruments/<string:instrument>
 
     :param instrument: The name of the instrument to handle methods for.
     :type instrument: str

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/design/design_file.py

@@ -17,7 +17,7 @@ def load_json():
     .. http:post:: /files/script-json
 
     :form file: workflow design JSON file
-    :status 302: load script json and then redirects to :http:get:`/ivoryos/design/draft`
+    :status 302: load script json and then redirects to :http:get:`/ivoryos/draft`
     """
 
     if request.method == "POST":
@@ -38,7 +38,7 @@ def download_python():
 
     .. http:post:: /files/script-python
 
-    :status 302: redirects to :http:get:`/ivoryos/design/script/`
+    :status 302: redirects to :http:get:`/ivoryos/draft`
     """
     script = utils.get_script_file()
     run_name = script.name if script.name else "untitled"
@@ -53,7 +53,7 @@ def download_json():
 
     .. http:post:: /files/script-json
 
-    :status 302: redirects to :http:get:`/ivoryos/design/script/`
+    :status 302: redirects to :http:get:`/ivoryos/draft`
     """
     script = utils.get_script_file()
     run_name = script.name if script.name else "untitled"

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/design/design_step.py

@@ -12,7 +12,7 @@ def get_step(uuid: int):
     """
     .. :quickref: Workflow Design Steps; get an action step editing form
 
-    .. http:get:: /steps/<int:uuid>
+    .. http:get:: /draft/steps/<int:uuid>
 
     get the editing form for an action step
 
@@ -36,7 +36,7 @@ def save_step(uuid: int):
     """
     .. :quickref: Workflow Design Steps; save an action step on canvas
 
-    .. http:post:: /steps/<int:uuid>
+    .. http:post:: /draft/steps/<int:uuid>
 
         save the changes of an action step
 
@@ -69,7 +69,7 @@ def delete_step(uuid: int):
     """
     .. :quickref: Workflow Design Steps; delete an action step on canvas
 
-    .. http:delete:: /steps/<int:uuid>
+    .. http:delete:: /draft/steps/<int:uuid>
 
         delete an action step
 

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/execute/execute.py

@@ -9,7 +9,7 @@ from flask_login import login_required
 from ivoryos.routes.execute.execute_file import files
 from ivoryos.utils import utils
 from ivoryos.utils.bo_campaign import parse_optimization_form
-from ivoryos.utils.db_models import SingleStep, WorkflowRun, WorkflowStep
+from ivoryos.utils.db_models import SingleStep, WorkflowRun, WorkflowStep, WorkflowPhase
 from ivoryos.utils.global_config import GlobalConfig
 from ivoryos.utils.form import create_action_button
 
@@ -157,6 +157,7 @@ def experiment_run():
 def run_bo():
     """
     .. :quickref: Workflow Execution; run Bayesian Optimization
+
     Run Bayesian Optimization with the given parameters and objectives.
 
     .. http:post:: /executions/campaign
@@ -166,6 +167,7 @@ def run_bo():
     :form existing_data: existing data to use for optimization
     :form parameters: parameters for optimization
     :form objectives: objectives for optimization
+
     TODO: merge to experiment_run or not, add more details about the form fields and their expected values.
     """
     script = utils.get_script_file()
@@ -225,7 +227,9 @@ def runner_status():
         if task_type == "workflow":
             workflow = WorkflowRun.query.get(task_id)
             if workflow is not None:
-                latest_step = WorkflowStep.query.filter_by(workflow_id=workflow.id).order_by(
+                phases = WorkflowPhase.query.filter_by(run_id=workflow.id).order_by(WorkflowPhase.start_time).all()
+                current_phase = phases[-1]
+                latest_step = WorkflowStep.query.filter_by(phase_id=current_phase.id).order_by(
                     WorkflowStep.start_time.desc()).first()
                 if latest_step is not None:
                     current_step = latest_step.as_dict()

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/routes/library/library.py

@@ -13,25 +13,25 @@ library = Blueprint('library', __name__, template_folder='templates')
 def workflow_script(script_name:str):
     # todo: split this into two routes, one for GET and POST, another for DELETE
     """
-    .. :quickref: Workflow Script Database; get, post, delete workflow script
+    .. :quickref: Workflow Script Database; get, post, delete a workflow script
 
-    .. http:get:: /<string:script_name>
+    .. http:get:: /library/<string: script_name>
 
     :param script_name: script name
     :type script_name: str
-    :status 302: redirect to :http:get:`/ivoryos/design/script/`
+    :status 302: redirect to :http:get:`/ivoryos/draft`
 
-    .. http:post:: /<string:script_name>
+    .. http:post:: /library/<string: script_name>
 
     :param script_name: script name
     :type script_name: str
     :status 200: json response with success status
 
-    .. http:delete:: /<string:script_name>
+    .. http:delete:: /library/<string: script_name>
 
     :param script_name: script name
     :type script_name: str
-    :status 302: redirect to :http:get:`/ivoryos/design/script/`
+    :status 302: redirect to :http:get:`/ivoryos/draft`
 
     """
     row = Script.query.get(script_name)
@@ -89,10 +89,8 @@ def load_from_database():
 
     backend control through http requests
 
-    .. http:get:: /designs/get/<deck_name>
+    .. http:get:: /library
 
-    :param deck_name: filter for deck name
-    :type deck_name: str
 
     """
     session.pop('edit_action', None)  # reset cache
@@ -132,10 +130,10 @@ def save_as():
 
     save the current workflow script as
 
-    .. http:post:: /library/save_as
+    .. http:post:: /library
 
     : form run_name: new workflow name
-    :status 302: redirect to :http:get:`/ivoryos/design/script/`
+    :status 302: redirect to :http:get:`/ivoryos/draft`
 
     """
     if request.method == "POST":

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/utils/py_to_json.py

@@ -143,12 +143,38 @@ def convert_to_cards(source_code: str):
                 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"):
+            if not func_parts:
                 return
 
             instrument = ".".join(func_parts[:-1])
             action = func_parts[-1]
 
+
+            # --- special case for time.sleep ---
+            if instrument == "time" and action == "sleep":
+                wait_value = None
+                if node.args:
+                    arg_node = node.args[0]
+                    if isinstance(arg_node, ast.Constant):
+                        wait_value = arg_node.value
+                    elif isinstance(arg_node, ast.Name):
+                        wait_value = f"#{arg_node.id}"
+                    else:
+                        wait_value = ast.unparse(arg_node)
+
+                add_card({
+                    "action": "wait",
+                    "arg_types": {"statement": infer_type(wait_value)},
+                    "args": {"statement": wait_value},
+                    "id": new_id(),
+                    "instrument": "wait",
+                    "return": ret_var,
+                    "uuid": generate_uuid()
+                })
+                return
+            # -----------------------------------
+
+
             args = {}
             arg_types = {}
 

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos/utils/script_runner.py

@@ -170,7 +170,7 @@ class ScriptRunner:
             #     line = line.replace("registered_workflows.", "")
             try:
                 if line.startswith("time.sleep("): # add safe sleep for time.sleep lines
-                    duration_str = line[len("time.sleep("):-1]
+                    duration_str = line.strip()[len("time.sleep("):-1]
                     duration = float(duration_str)
                     self.safe_sleep(duration)
                 else:

ivoryos-1.3.2/ivoryos/version.py

@@ -0,0 +1 @@
+__version__ = "1.3.2"

{ivoryos-1.3.0a0 → ivoryos-1.3.2}/ivoryos.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.3.0a0
+Version: 1.3.2
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT

ivoryos-1.3.0a0/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "1.3.0a0"