ivoryos 0.1.19__tar.gz → 0.1.20__tar.gz

{ivoryos-0.1.19/ivoryos.egg-info → ivoryos-0.1.20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.19
+Version: 0.1.20
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -13,6 +13,9 @@ License-File: LICENSE
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)
 [![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)
+
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
 # ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
@@ -24,6 +27,7 @@ License-File: LICENSE
 - [Installation](#installation)
 - [Instructions for use](#instructions-for-use)
 - [Demo](#demo)
+- [Roadmap](#roadmap)
 - [License](#license)
 
 ## Description
@@ -152,15 +156,10 @@ When you run the application for the first time, it will automatically create th
 - **`ivoryos.db`**: Database file that stores application data locally.
 
 
-### Demo video
-Intro + Tutorial + Demo with PurPOSE platform
-https://youtu.be/dFfJv9I2-1g 
-
-
 ## Roadmap
 
 - [x] Allow plugin pages ✅  
-- [ ] pause, resume, abort current and pending workflows
+- [x] pause, resume, abort current and pending workflows ✅ 
 - [ ] snapshot version control
 - [ ] dropdown input
 - [ ] show line number option

{ivoryos-0.1.19 → ivoryos-0.1.20}/README.md

@@ -1,6 +1,9 @@
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)
 [![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)
+
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
 # ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
@@ -12,6 +15,7 @@
 - [Installation](#installation)
 - [Instructions for use](#instructions-for-use)
 - [Demo](#demo)
+- [Roadmap](#roadmap)
 - [License](#license)
 
 ## Description
@@ -140,15 +144,10 @@ When you run the application for the first time, it will automatically create th
 - **`ivoryos.db`**: Database file that stores application data locally.
 
 
-### Demo video
-Intro + Tutorial + Demo with PurPOSE platform
-https://youtu.be/dFfJv9I2-1g 
-
-
 ## Roadmap
 
 - [x] Allow plugin pages ✅  
-- [ ] pause, resume, abort current and pending workflows
+- [x] pause, resume, abort current and pending workflows ✅ 
 - [ ] snapshot version control
 - [ ] dropdown input
 - [ ] show line number option

{ivoryos-0.1.19 → ivoryos-0.1.20}/ivoryos/routes/design/design.py

@@ -280,6 +280,7 @@ def experiment_run():
     try:
         for key, func_str in exec_string.items():
             exec(func_str)
+        line_collection = script.convert_to_lines(exec_string)
     except Exception:
         flash(f"Please check {key} syntax!!")
         return redirect(url_for("design.experiment_builder"))
@@ -323,7 +324,8 @@ def experiment_run():
                 flash(f"WARNING: Duplicate in config entries.")
         except Exception as e:
             flash(e)
-    return render_template('experiment_run.html', script=script.script_dict, filename=filename, dot_py=exec_string,
+    return render_template('experiment_run.html', script=script.script_dict, filename=filename,
+                           dot_py=exec_string, line_collection=line_collection,
                            return_list=return_list, config_list=config_list, config_file_list=config_file_list,
                            config_preview=config_preview, data_list=data_list, config_type_list=config_type_list,
                            no_deck_warning=no_deck_warning, dismiss=dismiss, design_buttons=design_buttons,

{ivoryos-0.1.19 → ivoryos-0.1.20}/ivoryos/routes/design/templates/design/experiment_run.html

@@ -28,7 +28,7 @@
                 <div class="accordion-body">
                     {% if script['script'] or script['prep'] or script['cleanup'] %}
                         <div class="row">
-                            <div class="col-lg-6 col-sm-12">
+                            <div class="col-lg-6 col-sm-12" id="run-panel">
                                 <ul class="nav nav-tabs" id="myTabs" role="tablist">
                                     <li class="nav-item" role="presentation">
                                         <a class="nav-link {{ 'disabled' if config_list else '' }} {{ 'active' if not config_list else '' }}" id="tab1-tab" data-bs-toggle="tab" href="#tab1" role="tab" aria-controls="tab1" aria-selected="false">Repeat</a>
@@ -217,6 +217,16 @@
                                     </div>
                                 </div>
                             </div>
+                            <div class="col-lg-6 col-sm-12" id="code-panel" style="display: none;">
+                                <p>
+                                    <h5>Progress：</h5>
+                                    {% for stype, script in line_collection.items() %}
+                                        {% for code in script %}
+                                            <pre style="margin: 0; padding: 0; line-height: 1;"><code class="python" id="{{ stype }}-{{ loop.index0 }}" >{{code}}</code></pre>
+                                        {% endfor %}
+                                    {% endfor %}
+                                </p>
+                            </div>
                             <div class="col-lg-6 col-sm-12 logging-panel">
                                 <p>
                                     <div class="p d-flex justify-content-between align-items-center">
@@ -237,7 +247,6 @@
                                         <small><strong>Note:</strong> The current step cannot be paused or stopped until it completes. </small>
                                     </div>
 
-                                </p>
                                 <div class="progress" role="progressbar" aria-label="Animated striped example" aria-valuenow="10" aria-valuemin="0" aria-valuemax="100">
                                     <div id="progress-bar-inner" class="progress-bar progress-bar-striped progress-bar-animated"></div>
                                 </div>
@@ -338,4 +347,22 @@
             }
         });
     </script>
+
+    <script>
+    var socket = io.connect(window.location.origin);
+
+    socket.on('execution', function(data) {
+        // Remove highlighting from all lines
+        document.querySelectorAll('pre code').forEach(el => el.style.backgroundColor = '');
+
+        // Get the currently executing line and highlight it
+        let executingLine = document.getElementById(data.section);
+        if (executingLine) {
+            executingLine.style.backgroundColor = '#cce5ff'; // Highlight
+            executingLine.style.transition = 'background-color 0.3s ease-in-out';
+
+        }
+    });
+</script>
+
 {% endblock %}

{ivoryos-0.1.19 → ivoryos-0.1.20}/ivoryos/static/js/socket_handler.js

@@ -10,11 +10,21 @@ document.addEventListener("DOMContentLoaded", function() {
         var progressBar = document.getElementById('progress-bar-inner');
         progressBar.style.width = progress + '%';
         progressBar.setAttribute('aria-valuenow', progress);
+        if (progress === 1) {
+                    document.getElementById("run-panel").style.display = "none";
+        document.getElementById("code-panel").style.display = "block";
 
+        // Optional: Scroll to the code panel
+        document.getElementById("code-panel").scrollIntoView({ behavior: "smooth" });
+        }
         if (progress === 100) {
             // Remove animation and set green color when 100% is reached
             progressBar.classList.remove('progress-bar-animated');
             progressBar.classList.add('bg-success'); // Bootstrap class for green color
+            setTimeout(() => {
+            document.getElementById("code-panel").style.display = "none";
+            document.getElementById("run-panel").style.display = "block";
+        }, 1000);  // Small delay to let users see the completion
         }
     });
     socket.on('log', function(data) {

{ivoryos-0.1.19 → ivoryos-0.1.20}/ivoryos/utils/db_models.py

@@ -390,6 +390,23 @@ class Script(db.Model):
             string += "\t"
         return string
 
+    def convert_to_lines(self, exec_str_collection: dict):
+        """
+        Parse a dictionary of script functions and extract function body lines.
+
+        :param exec_str_collection: Dictionary containing script types and corresponding function strings.
+        :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():
+            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])
+        return line_collection
+
     def compile(self, script_path=None):
         """
         Compile the current script to a Python file.
@@ -401,8 +418,9 @@ class Script(db.Model):
         exec_str_collection = {}
 
         for i in self.stypes:
-            func_str = self._generate_function_header(run_name, i) + self._generate_function_body(i)
-            exec_str_collection[i] = func_str
+            if self.script_dict[i]:
+                func_str = self._generate_function_header(run_name, i) + 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)
 
@@ -434,7 +452,7 @@ class Script(db.Model):
             function_header += ", ".join(configure)
 
         function_header += "):"
-        function_header += self.indent(1) + f"global {run_name}_{stype}"
+        # function_header += self.indent(1) + f"global {run_name}_{stype}"
         return function_header
 
     def _generate_function_body(self, stype):

{ivoryos-0.1.19 → ivoryos-0.1.20}/ivoryos/utils/script_runner.py

@@ -35,10 +35,12 @@ class ScriptRunner:
             return "Resumed"
 
     def reset_stop_event(self):
+        """Resets the stop event"""
         self.stop_pending_event.clear()
         self.stop_current_event.clear()
 
     def abort_pending(self):
+        """Abort the pending iteration after the current is finished"""
         self.stop_pending_event.set()
         # print("Stop pending tasks")
 
@@ -66,7 +68,7 @@ class ScriptRunner:
         thread.start()
         return thread
 
-    def execute_function_line_by_line(self, script, section_name, logger, **kwargs):
+    def execute_function_line_by_line(self, lines:list, section_name, logger, socketio, **kwargs):
         """
         Executes a function defined in a string line by line.
 
@@ -79,11 +81,7 @@ class ScriptRunner:
             deck = global_config.deck
         # func_str = script.compile()
         # Parse function body from string
-        module = ast.parse(script)
-        func_def = next(node for node in module.body if isinstance(node, ast.FunctionDef))
 
-        # Extract function body as source lines
-        lines = [ast.unparse(node) for node in func_def.body if not isinstance(node, ast.Return)]
         # Prepare execution environment
         exec_globals = {"deck": deck}  # Add required global objects
         exec_locals = {}  # Local execution scope
@@ -92,35 +90,41 @@ class ScriptRunner:
         exec_locals.update(kwargs)
 
         # Execute each line dynamically
-        for line in lines:
+        for index, line in enumerate(lines):
             if self.stop_current_event.is_set():
                 logger.info(f'Stopping execution during {section_name}')
                 break
             logger.info(f"Executing: {line}")  # Debugging output
+            socketio.emit('execution', {'section': f"{section_name}-{index}"})
+            # self._emit_progress(socketio, 100)
             exec(line, exec_globals, exec_locals)
             self.pause_event.wait()
 
         return exec_locals  # Return the 'results' variable
 
-    def _run_with_stop_check(self, script: Script, repeat_count, run_name, logger, socketio, config, bo_args,
+    def _run_with_stop_check(self, script: Script, repeat_count: int, run_name: str, logger, socketio, config, bo_args,
                              output_path):
         time.sleep(1)
         func_str = script.compile()
+        func_str_lines = script.convert_to_lines(func_str)
         self._emit_progress(socketio, 1)
         try:
             # Run "prep" section once
             script_dict = script.script_dict
-            self._run_actions(script_dict.get("prep", []), func_str.get("prep", ''), section_name="prep", logger=logger)
+            self._run_actions(script_dict.get("prep", []), func_str_lines.get("prep", []), section_name="prep", logger=logger, socketio=socketio)
             output_list = []
             _, arg_type = script.config("script")
             _, return_list = script.config_return()
             # Run "script" section multiple times
             if repeat_count:
-                self._run_repeat_section(repeat_count, arg_type, bo_args, output_list,  func_str.get("script", ''), run_name, return_list, logger, socketio)
+                self._run_repeat_section(repeat_count, arg_type, bo_args, output_list, func_str_lines.get("script", []),
+                                         run_name, return_list, logger, socketio)
             elif config:
-                self._run_config_section(config, arg_type, output_list, func_str.get("script", ''), run_name, logger, socketio)
+                self._run_config_section(config, arg_type, output_list, func_str_lines.get("script", []), run_name, logger,
+                                         socketio)
             # Run "cleanup" section once
-            self._run_actions(script_dict.get("cleanup", []), func_str.get("cleanup", ''), section_name="cleanup", logger=logger)
+            self._run_actions(script_dict.get("cleanup", []), func_str.get("cleanup", []), section_name="cleanup",
+                              logger=logger, socketio=socketio)
             # Save results if necessary
             if output_list:
                 self._save_results(run_name, arg_type, return_list, output_list, logger, output_path)
@@ -131,12 +135,12 @@ class ScriptRunner:
                 self.is_running = False  # Reset the running flag when done
             self._emit_progress(socketio, 100)
 
-    def _run_actions(self, actions, func_str, section_name="", logger=None):
+    def _run_actions(self, actions, func_str, section_name="", logger=None, socketio=None):
         logger.info(f'Executing {section_name} steps') if actions else logger.info(f'No {section_name} steps')
         if self.stop_pending_event.is_set():
             logger.info(f"Stopping execution during {section_name} section.")
             return
-        self.execute_function_line_by_line(func_str, section_name, logger)
+        self.execute_function_line_by_line(func_str, section_name, logger, socketio)
 
     def _run_config_section(self, config, arg_type, output_list, func_str, run_name, logger, socketio):
         compiled = True
@@ -158,12 +162,13 @@ class ScriptRunner:
                 self._emit_progress(socketio, progress)
                 # fname = f"{run_name}_script"
                 # function = self.globals_dict[fname]
-                output = self.execute_function_line_by_line(func_str, "script", logger, **kwargs)
+                output = self.execute_function_line_by_line(func_str, "script", logger, socketio, **kwargs)
                 if output:
                     # kwargs.update(output)
                     output_list.append(output)
 
-    def _run_repeat_section(self, repeat_count, arg_types, bo_args, output_list,  func_str, run_name, return_list, logger, socketio):
+    def _run_repeat_section(self, repeat_count, arg_types, bo_args, output_list, func_str, run_name, return_list,
+                            logger, socketio):
         if bo_args:
             logger.info('Initializing optimizer...')
             ax_client = utils.ax_initiation(bo_args, arg_types)
@@ -180,7 +185,7 @@ class ScriptRunner:
                     logger.info(f'Output value: {parameters}')
                     # fname = f"{run_name}_script"
                     # function = self.globals_dict[fname]
-                    output = self.execute_function_line_by_line(func_str, "script", logger, **parameters)
+                    output = self.execute_function_line_by_line(func_str, "script", logger, socketio, **parameters)
 
                     _output = {key: value for key, value in output.items() if key in return_list}
                     ax_client.complete_trial(trial_index=trial_index, raw_data=_output)
@@ -191,7 +196,7 @@ class ScriptRunner:
             else:
                 # fname = f"{run_name}_script"
                 # function = self.globals_dict[fname]
-                output = self.execute_function_line_by_line(func_str, "script", logger)
+                output = self.execute_function_line_by_line(func_str, "script", logger, socketio)
 
             if output:
                 output_list.append(output)

ivoryos-0.1.20/ivoryos/version.py

@@ -0,0 +1 @@
+__version__ = "0.1.20"

{ivoryos-0.1.19 → ivoryos-0.1.20/ivoryos.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.19
+Version: 0.1.20
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang
@@ -13,6 +13,9 @@ License-File: LICENSE
 [![Documentation Status](https://readthedocs.org/projects/ivoryos/badge/?version=latest)](https://ivoryos.readthedocs.io/en/latest/?badge=latest)
 [![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)
+
 
 ![](https://gitlab.com/heingroup/ivoryos/raw/main/docs/source/_static/ivoryos.png)
 # ivoryOS: interoperable Web UI for self-driving laboratories (SDLs)
@@ -24,6 +27,7 @@ License-File: LICENSE
 - [Installation](#installation)
 - [Instructions for use](#instructions-for-use)
 - [Demo](#demo)
+- [Roadmap](#roadmap)
 - [License](#license)
 
 ## Description
@@ -152,15 +156,10 @@ When you run the application for the first time, it will automatically create th
 - **`ivoryos.db`**: Database file that stores application data locally.
 
 
-### Demo video
-Intro + Tutorial + Demo with PurPOSE platform
-https://youtu.be/dFfJv9I2-1g 
-
-
 ## Roadmap
 
 - [x] Allow plugin pages ✅  
-- [ ] pause, resume, abort current and pending workflows
+- [x] pause, resume, abort current and pending workflows ✅ 
 - [ ] snapshot version control
 - [ ] dropdown input
 - [ ] show line number option

ivoryos-0.1.19/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "0.1.19"