ivoryos 0.1.24__tar.gz → 1.0.0__tar.gz

{ivoryos-0.1.24/ivoryos.egg-info → ivoryos-1.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.24
+Version: 1.0.0
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -14,7 +14,7 @@ License-File: LICENSE
 [![PyPI version](https://img.shields.io/pypi/v/ivoryos)](https://pypi.org/project/ivoryos/)
 ![License](https://img.shields.io/pypi/l/ivoryos)
 [![YouTube](https://img.shields.io/badge/YouTube-video-red?logo=youtube)](https://youtu.be/dFfJv9I2-1g)
-[![Research Square](https://img.shields.io/badge/Preprint-blue)](https://www.researchsquare.com/article/rs-5307798/v1)
+[![Published](https://img.shields.io/badge/Nature_Communications-paper-blue)](https://www.nature.com/articles/s41467-025-60514-w)
 
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
@@ -163,11 +163,10 @@ When you run the application for the first time, it will automatically create th
 ## Roadmap
 
 - [x] Allow plugin pages ✅  
-- [x] pause, resume, abort current and pending workflows ✅ 
+- [x] pause, resume, abort current and pending workflows ✅
+- [x] dropdown input ✅  
+- [x] show line number option ✅  
 - [ ] snapshot version control
-- [ ] dropdown input
-- [ ] show line number option
-
 
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao

{ivoryos-0.1.24 → ivoryos-1.0.0}/README.md

@@ -2,7 +2,7 @@
 [![PyPI version](https://img.shields.io/pypi/v/ivoryos)](https://pypi.org/project/ivoryos/)
 ![License](https://img.shields.io/pypi/l/ivoryos)
 [![YouTube](https://img.shields.io/badge/YouTube-video-red?logo=youtube)](https://youtu.be/dFfJv9I2-1g)
-[![Research Square](https://img.shields.io/badge/Preprint-blue)](https://www.researchsquare.com/article/rs-5307798/v1)
+[![Published](https://img.shields.io/badge/Nature_Communications-paper-blue)](https://www.nature.com/articles/s41467-025-60514-w)
 
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
@@ -151,11 +151,10 @@ When you run the application for the first time, it will automatically create th
 ## Roadmap
 
 - [x] Allow plugin pages ✅  
-- [x] pause, resume, abort current and pending workflows ✅ 
+- [x] pause, resume, abort current and pending workflows ✅
+- [x] dropdown input ✅  
+- [x] show line number option ✅  
 - [ ] snapshot version control
-- [ ] dropdown input
-- [ ] show line number option
-
 
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao

{ivoryos-0.1.24 → ivoryos-1.0.0}/ivoryos/__init__.py

@@ -17,11 +17,13 @@ from ivoryos.utils.global_config import GlobalConfig
 from ivoryos.utils.script_runner import ScriptRunner
 from ivoryos.version import __version__ as ivoryos_version
 from importlib.metadata import entry_points
+
 global_config = GlobalConfig()
 from sqlalchemy import event
 from sqlalchemy.engine import Engine
 import sqlite3
 
+
 @event.listens_for(Engine, "connect")
 def enforce_sqlite_foreign_keys(dbapi_connection, connection_record):
     if isinstance(dbapi_connection, sqlite3.Connection):
@@ -29,6 +31,7 @@ def enforce_sqlite_foreign_keys(dbapi_connection, connection_record):
         cursor.execute("PRAGMA foreign_keys=ON")
         cursor.close()
 
+
 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)
@@ -81,8 +84,9 @@ 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,
-        blueprint_plugins=None,
+        enable_design: bool = True,
+        blueprint_plugins: Union[list[Blueprint], Blueprint] = [],
+        exclude_names: list[str] = [],
         ):
     """
     Start ivoryOS app server.
@@ -97,11 +101,13 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     :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: enable design canvas, database and workflow execution
+    :param blueprint_plugins: custom Blueprint pages
+    :param exclude_names: module names to exclude from parsing
     """
     app = create_app(config_class=config or get_config())  # Create app instance using factory function
 
     # plugins = load_installed_plugins(app, socketio)
-    plugins = {}
+    plugins = []
     if blueprint_plugins:
         config_plugins = load_plugins(blueprint_plugins, app, socketio)
         plugins.extend(config_plugins)
@@ -126,7 +132,10 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
         app.config["OFF_LINE"] = False
         global_config.deck = sys.modules[module]
         global_config.deck_snapshot = utils.create_deck_snapshot(global_config.deck,
-                                                                 output_path=app.config["DUMMY_DECK"], save=True)
+                                                                 output_path=app.config["DUMMY_DECK"],
+                                                                 save=True,
+                                                                 exclude_names=exclude_names
+                                                                 )
     else:
         app.config["OFF_LINE"] = True
     if model:
@@ -165,7 +174,8 @@ def load_installed_plugins(app, socketio):
 
     return plugin_names
 
-def load_plugins(blueprints:list[Blueprint], app, socketio):
+
+def load_plugins(blueprints: Union[list[Blueprint], Blueprint], app, socketio):
     """
     Dynamically load installed plugins and attach Flask-SocketIO.
     """

{ivoryos-0.1.24 → ivoryos-1.0.0}/ivoryos/routes/design/design.py

@@ -627,3 +627,8 @@ def duplicate_action(id: int):
     script.duplicate_action(id)
     utils.post_script_file(script)
     return redirect(back)
+
+
+@design.route("/backend/status", methods=["GET"])
+def runner_status():
+    return jsonify(runner.get_status())

{ivoryos-0.1.24 → ivoryos-1.0.0}/ivoryos/utils/script_runner.py

@@ -307,4 +307,14 @@ class ScriptRunner:
         while time.time() < end_time:
             if self.stop_current_event.is_set():
                 return  # Exit early if stop is requested
-            time.sleep(min(interval, end_time - time.time()))
+            time.sleep(min(interval, end_time - time.time()))
+
+    def get_status(self):
+        """Returns current status of the script runner."""
+        with self.lock:
+            return {
+                "is_running": self.is_running,
+                "paused": self.paused,
+                "stop_pending": self.stop_pending_event.is_set(),
+                "stop_current": self.stop_current_event.is_set(),
+            }

{ivoryos-0.1.24 → ivoryos-1.0.0}/ivoryos/utils/utils.py

@@ -8,6 +8,7 @@ import subprocess
 import sys
 from collections import Counter
 
+import flask
 from flask import session
 from flask_socketio import SocketIO
 
@@ -239,7 +240,7 @@ def start_logger(socketio: SocketIO, logger_name: str, log_filename: str = None)
     return logger
 
 
-def ax_wrapper(data: dict, arg_types:list):
+def ax_wrapper(data: dict, arg_types: list):
     """
     Ax platform wrapper function for creating optimization campaign parameters and objective from the web form input
     :param data: e.g.,
@@ -363,17 +364,62 @@ def web_config_entry_wrapper(data: dict, config_type: list):
     return filtered_rows
 
 
-def create_deck_snapshot(deck, save: bool = False, output_path: str = ''):
+def create_deck_snapshot(deck, save: bool = False, output_path: str = '', exclude_names: list[str] = []):
     """
     Create a deck snapshot of the given script
     :param deck: python module name to create the deck snapshot from e.g. __main__
     :param save: save the deck snapshot into pickle file
     :param output_path: path to save the pickle file
-    """
-    deck_snapshot = {f"deck.{name}": _inspect_class(val) for name, val in vars(deck).items()
-                     if not type(val).__module__ == 'builtins'
-                     and not name[0].isupper()
-                     and not name.startswith("_")}
+    :param exclude_names: module names to exclude from deck snapshot
+    """
+    exclude_classes = (flask.Blueprint, logging.Logger)
+
+    deck_snapshot = {}
+    included = {}
+    excluded = {}
+    failed = {}
+
+    for name, val in vars(deck).items():
+        qualified_name = f"deck.{name}"
+
+        # Exclusion checks
+        if (
+                type(val).__module__ == 'builtins'
+                or name[0].isupper()
+                or name.startswith("_")
+                or isinstance(val, exclude_classes)
+                or name in exclude_names
+        ):
+            excluded[qualified_name] = type(val).__name__
+            continue
+
+        try:
+            deck_snapshot[qualified_name] = _inspect_class(val)
+            included[qualified_name] = type(val).__name__
+        except Exception as e:
+            failed[qualified_name] = str(e)
+
+    # Final result
+    deck_summary = {
+        "included": included,
+        # "excluded": excluded,
+        "failed": failed
+    }
+
+    def print_deck_snapshot(deck_summary):
+        def print_section(title, items):
+            print(f"\n=== {title} ({len(items)}) ===")
+            if not items:
+                return
+            for name, class_type in items.items():
+                print(f"  {name}: {class_type}")
+
+        print_section("✅ INCLUDED", deck_summary["included"])
+        print_section("❌ FAILED", deck_summary["failed"])
+        print("\n")
+
+    print_deck_snapshot(deck_summary)
+
     if deck_snapshot and save:
         # pseudo_deck = parse_dict
         parse_dict = deck_snapshot.copy()
@@ -418,7 +464,6 @@ def get_method_from_workflow(function_string, func_name="workflow"):
     # Get the function name dynamically
     return namespace[func_name]
 
-
 # def load_workflows(script):
 #
 #     class RegisteredWorkflows:

ivoryos-1.0.0/ivoryos/version.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"

{ivoryos-0.1.24 → ivoryos-1.0.0/ivoryos.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.24
+Version: 1.0.0
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -14,7 +14,7 @@ License-File: LICENSE
 [![PyPI version](https://img.shields.io/pypi/v/ivoryos)](https://pypi.org/project/ivoryos/)
 ![License](https://img.shields.io/pypi/l/ivoryos)
 [![YouTube](https://img.shields.io/badge/YouTube-video-red?logo=youtube)](https://youtu.be/dFfJv9I2-1g)
-[![Research Square](https://img.shields.io/badge/Preprint-blue)](https://www.researchsquare.com/article/rs-5307798/v1)
+[![Published](https://img.shields.io/badge/Nature_Communications-paper-blue)](https://www.nature.com/articles/s41467-025-60514-w)
 
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
@@ -163,11 +163,10 @@ When you run the application for the first time, it will automatically create th
 ## Roadmap
 
 - [x] Allow plugin pages ✅  
-- [x] pause, resume, abort current and pending workflows ✅ 
+- [x] pause, resume, abort current and pending workflows ✅
+- [x] dropdown input ✅  
+- [x] show line number option ✅  
 - [ ] snapshot version control
-- [ ] dropdown input
-- [ ] show line number option
-
 
 ## Authors and Acknowledgement
 Ivory Zhang, Lucy Hao

ivoryos-0.1.24/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "0.1.24"