ivoryos 0.1.22__tar.gz → 0.1.24__tar.gz

{ivoryos-0.1.22/ivoryos.egg-info → ivoryos-0.1.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.22
+Version: 0.1.24
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/__init__.py

@@ -2,7 +2,7 @@ import os
 import sys
 from typing import Union
 
-from flask import Flask, redirect, url_for, g
+from flask import Flask, redirect, url_for, g, Blueprint
 
 from ivoryos.config import Config, get_config
 from ivoryos.routes.auth.auth import auth, login_manager
@@ -81,7 +81,8 @@ 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
+        enable_design=True,
+        blueprint_plugins=None,
         ):
     """
     Start ivoryOS app server.
@@ -99,7 +100,11 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     """
     app = create_app(config_class=config or get_config())  # Create app instance using factory function
 
-    plugins = load_plugins(app, socketio)
+    # plugins = load_installed_plugins(app, socketio)
+    plugins = {}
+    if blueprint_plugins:
+        config_plugins = load_plugins(blueprint_plugins, app, socketio)
+        plugins.extend(config_plugins)
 
     def inject_nav_config():
         """Make NAV_CONFIG available globally to all templates."""
@@ -143,7 +148,7 @@ def run(module=None, host="0.0.0.0", port=None, debug=None, llm_server=None, mod
     # return app
 
 
-def load_plugins(app, socketio):
+def load_installed_plugins(app, socketio):
     """
     Dynamically load installed plugins and attach Flask-SocketIO.
     """
@@ -160,4 +165,17 @@ def load_plugins(app, socketio):
 
     return plugin_names
 
-
+def load_plugins(blueprints:list[Blueprint], app, socketio):
+    """
+    Dynamically load installed plugins and attach Flask-SocketIO.
+    """
+    plugin_names = []
+    if not isinstance(blueprints, list):
+        blueprints = [blueprints]
+    for blueprint in blueprints:
+        # If the plugin has an `init_socketio()` function, pass socketio
+        if hasattr(blueprint, 'init_socketio'):
+            blueprint.init_socketio(socketio)
+        plugin_names.append(blueprint.name)
+        app.register_blueprint(blueprint, url_prefix=f"{url_prefix}/{blueprint.name}")
+    return plugin_names

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/routes/database/database.py

@@ -203,11 +203,27 @@ def list_workflows():
     return render_template('workflow_run_database.html', workflows=workflows)
 
 
-@database.route('/workflow_steps/<int:workflow_id>')
+@database.route("/workflow_steps/<int:workflow_id>")
 def get_workflow_steps(workflow_id):
-    steps = WorkflowStep.query.filter_by(workflow_id=workflow_id).all()
-    steps_data = [step.as_dict() for step in steps]
-    return jsonify({'steps': steps_data})
+    workflow = WorkflowRun.query.get_or_404(workflow_id)
+    steps = WorkflowStep.query.filter_by(workflow_id=workflow_id).order_by(WorkflowStep.start_time).all()
+
+    # Organize steps by phase + repeat_index
+    grouped = {
+        "prep": [],
+        "script": {},
+        "cleanup": [],
+    }
+
+    for step in steps:
+        if step.phase == "prep":
+            grouped["prep"].append(step)
+        elif step.phase == "script":
+            grouped["script"].setdefault(step.repeat_index, []).append(step)
+        elif step.phase == "cleanup" or step.method_name == "stop":
+            grouped["cleanup"].append(step)
+
+    return render_template("experiment_step_view.html", workflow=workflow, grouped=grouped)
 
 
 @database.route("/delete_workflow_data/<workflow_id>")

ivoryos-0.1.24/ivoryos/routes/database/templates/database/experiment_step_view.html

@@ -0,0 +1,130 @@
+{% extends 'base.html' %}
+
+{% block title %}IvoryOS | Experiment Results{% endblock %}
+
+{% block body %}
+<style>
+  .vis-time-axis .vis-text.vis-minor,
+  .vis-time-axis .vis-text.vis-major {
+    color: #666;
+  }
+  .vis-item.stop {
+    background-color: red;
+    color: white;
+    border: none;
+    font-weight: bold;
+  }
+</style>
+
+<div id="timeline"></div>
+
+<script src="https://unpkg.com/vis-timeline@latest/standalone/umd/vis-timeline-graph2d.min.js"></script>
+<link href="https://unpkg.com/vis-timeline@latest/styles/vis-timeline-graph2d.min.css" rel="stylesheet"/>
+
+<h1>Experiment Step View</h1>
+
+<div id="visualization"></div>
+
+<script type="text/javascript">
+  var container = document.getElementById('visualization');
+
+  const items = [
+    {% if grouped.prep %}
+      {
+        id: 'prep',
+        content: 'Prep Phase',
+        start: '{{ grouped.prep[0].start_time }}',
+        end: '{{ grouped.prep[-1].end_time }}',
+        className: 'prep',
+        group: 'prep'
+      },
+    {% endif %}
+
+    {% for repeat_index, step_list in grouped.script.items()|sort %}
+      {
+        id: 'iter{{ repeat_index }}',
+        content: 'Iteration {{ repeat_index }}',
+        start: '{{ step_list[0].start_time }}',
+        end: '{{ step_list[-1].end_time }}',
+        className: 'script',
+        group: 'iter{{ repeat_index }}'
+      },
+      {% for step in step_list %}
+        {% if step.method_name == "stop" %}
+          {
+            id: 'stop-{{ step.id }}',
+            content: '🛑 Stop',
+            start: '{{ step.start_time }}',
+            type: 'point',
+            className: 'stop',
+            group: 'iter{{ repeat_index }}'
+          },
+        {% endif %}
+      {% endfor %}
+    {% endfor %}
+
+    {% if grouped.cleanup %}
+      {
+        id: 'cleanup',
+        content: 'Cleanup Phase',
+        start: '{{ grouped.cleanup[0].start_time }}',
+        end: '{{ grouped.cleanup[-1].end_time }}',
+        className: 'cleanup',
+        group: 'cleanup'
+
+      },
+    {% endif %}
+  ];
+
+  const groups = [
+      {% if grouped.prep %}{ id: 'prep', content: 'Prep' },{% endif %}
+      {% for repeat_index in grouped.script.keys()|sort %}{ id: 'iter{{ repeat_index }}', content: 'Iteration {{ repeat_index }}' },{% endfor %}
+      {% if grouped.cleanup %}{ id: 'cleanup', content: 'Cleanup' },{% endif %}
+  ];
+
+  var options = {
+      clickToUse: true,
+      stack: false,  // important to keep point within group row
+      horizontalScroll: true,
+      zoomKey: 'ctrlKey'
+  };
+
+  // Initialize your timeline with the sorted groups
+  const timeline = new vis.Timeline(container, items, groups, options);
+
+  timeline.on('select', function (props) {
+    const id = props.items[0];
+    if (id && id.startsWith('iter')) {
+      const card = document.getElementById('card-' + id);
+      if (card) {
+        const yOffset = -80;
+        const y = card.getBoundingClientRect().top + window.pageYOffset + yOffset;
+        window.scrollTo({ top: y, behavior: 'smooth' });
+      }
+    }
+  });
+</script>
+
+<h2>Workflow: {{ workflow.name }}</h2>
+
+{% if grouped.prep %}
+  <h4 class="mt-4">Prep Phase</h4>
+  {% for step in grouped.prep %}
+    {% include "step_card.html" %}
+  {% endfor %}
+{% endif %}
+
+{% for repeat_index, step_list in grouped.script.items()|sort %}
+  <h4 class="mt-4" id="card-iter{{ repeat_index }}">Iteration {{ repeat_index }}</h4>
+  {% for step in step_list %}
+    {% include "step_card.html" %}
+  {% endfor %}
+{% endfor %}
+
+{% if grouped.cleanup %}
+  <h4 class="mt-4">Cleanup Phase</h4>
+  {% for step in grouped.cleanup %}
+    {% include "step_card.html" %}
+  {% endfor %}
+{% endif %}
+{% endblock %}

ivoryos-0.1.24/ivoryos/routes/database/templates/database/step_card.html

@@ -0,0 +1,7 @@
+<div class="card mb-2 {{ 'border-danger text-danger bg-light' if step.run_error else 'border-secondary' }}">
+  <div class="card-body p-2">
+    <strong>{{ step.method_name }}</strong>
+    <small>Start: {{ step.start_time }}</small>
+    <small>End: {{ step.end_time }}</small>
+  </div>
+</div>

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/routes/design/design.py

@@ -40,6 +40,13 @@ def handle_abort_current():
 
 @socketio.on('pause')
 def handle_pause():
+    runner.retry = False
+    msg = runner.toggle_pause()
+    socketio.emit('log', {'message': msg})
+
+@socketio.on('retry')
+def handle_pause():
+    runner.retry = True
     msg = runner.toggle_pause()
     socketio.emit('log', {'message': msg})
 

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/routes/design/templates/design/experiment_builder.html

@@ -144,6 +144,16 @@
                                                                     {{ field(class="btn btn-dark") }}
                                                                 {% elif field.type == "BooleanField" %}
                                                                     {{ field(class="form-check-input") }}
+                                                                {% elif field.type == "FlexibleEnumField" %}
+                                                                   <input type="text" id="{{ field.id }}" name="{{ field.name }}" value="{{ field.data }}"
+                                                                      list="{{ field.id }}_options" placeholder="{{ field.render_kw.placeholder if field.render_kw and field.render_kw.placeholder }}"
+                                                                      class="form-control">
+                                                                   <datalist id="{{ field.id }}_options">
+                                                                      {% for key in field.choices %}
+                                                                         <option value="{{ key }}">{{ key }}</option>
+                                                                      {% endfor %}
+                                                                   </datalist>
+
                                                                 {% else %}
                                                                     {{ field(class="form-control") }}
                                                                 {% endif %}
@@ -219,7 +229,7 @@
 
         {# canvas #}
         <div class="col-md-9 scroll-column">
-            <div>
+            <div class="d-flex align-items-center ">
 {#                file dropdown menu    #}
                 <ul class="nav nav-tabs">
                     <li class="nav-item dropdown">
@@ -242,6 +252,12 @@
                     <li class="nav-item"><a class="{{'nav-link active' if script.editing_type=='script' else 'nav-link'}}" aria-current="page" href="{{url_for('design.toggle_script_type', stype='script') }}">Experiment</a></li>
                     <li class="nav-item"><a class="{{'nav-link active' if script.editing_type=='cleanup' else 'nav-link'}}" aria-current="page" href="{{url_for('design.toggle_script_type', stype='cleanup') }}">Clean up</a></li>
                 </ul>
+
+                <div class="form-check form-switch ms-auto">
+                    <input class="form-check-input" type="checkbox" id="toggleLineNumbers" onchange="toggleLineNumbers()">
+                    <label class="form-check-label" for="toggleLineNumbers">Show Line Numbers</label>
+                </div>
+
             </div>
 
             <div class="canvas" droppable="true">
@@ -279,6 +295,7 @@
                     <ul class="reorder">
                     {% for button in buttons %}
                         <li id="{{ button['id'] }}" style="list-style-type: none;">
+                            <span class="line-number d-none">{{ button['id'] }}.</span>
                             <a href="{{ url_for('design.edit_action', uuid=button['uuid']) }}" type="button" class="btn btn-light" style="{{ button['style'] }}">{{ button['label'] }}</a>
                             {% if not button["instrument"] in ["if","while","repeat"] %}
                                 <a href="{{ url_for('design.duplicate_action', id=button['id']) }}" type="button" class="btn btn-light"><span class="bi bi-copy"></span></a>
@@ -406,14 +423,44 @@
 </div>
 
 
-    {% if instrument and use_llm %}
-        <script>
-            const buttonIds = {{ ['generate'] | tojson }};
-        </script>
-        <script src="{{ url_for('static', filename='js/overlay.js') }}"></script>
-    {% endif %}
-     <script>
-        const updateListUrl = "{{ url_for('design.update_list') }}";
+{% if instrument and use_llm %}
+    <script>
+        const buttonIds = {{ ['generate'] | tojson }};
     </script>
-    <script src="{{ url_for('static', filename='js/sortable_design.js') }}"></script>
+    <script src="{{ url_for('static', filename='js/overlay.js') }}"></script>
+{% endif %}
+
+<script>
+    const updateListUrl = "{{ url_for('design.update_list') }}";
+
+    // Toggle visibility of line numbers
+    function toggleLineNumbers(save = true) {
+        const show = document.getElementById('toggleLineNumbers').checked;
+        document.querySelectorAll('.line-number').forEach(el => {
+            el.classList.toggle('d-none', !show);
+        });
+
+        if (save) {
+            localStorage.setItem('showLineNumbers', show ? 'true' : 'false');
+        }
+    }
+
+    // Restore state on page load
+    document.addEventListener('DOMContentLoaded', () => {
+        const savedState = localStorage.getItem('showLineNumbers');
+        const checkbox = document.getElementById('toggleLineNumbers');
+
+        if (savedState === 'true') {
+            checkbox.checked = true;
+        }
+
+        toggleLineNumbers(false);  // don't overwrite localStorage on load
+
+        checkbox.addEventListener('change', () => toggleLineNumbers());
+    });
+</script>
+
+
+<script src="{{ url_for('static', filename='js/sortable_design.js') }}"></script>
+
 {% endblock %}

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/routes/design/templates/design/experiment_run.html

@@ -423,8 +423,9 @@
             <p>Do you want to continue execution or stop?</p>
           </div>
           <div class="modal-footer">
-            <button type="button" class="btn btn-danger" id="stop-btn" data-bs-dismiss="modal">Stop Execution</button>
-            <button type="button" class="btn btn-success" id="continue-btn" data-bs-dismiss="modal">Continue</button>
+              <button type="button" class="btn btn-primary" id="retry-btn" data-bs-dismiss="modal">Rerun Current Step</button>
+              <button type="button" class="btn btn-success" id="continue-btn" data-bs-dismiss="modal">Continue</button>
+              <button type="button" class="btn btn-danger" id="stop-btn" data-bs-dismiss="modal">Stop Execution</button>
           </div>
         </div>
       </div>

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/static/js/socket_handler.js

@@ -68,6 +68,11 @@ document.addEventListener("DOMContentLoaded", function() {
         console.log("Execution resumed.");
     });
 
+    document.getElementById('retry-btn').addEventListener('click', function() {
+        socket.emit('retry');  // Resume execution
+        console.log("Execution resumed, retrying.");
+    });
+
     document.getElementById('stop-btn').addEventListener('click', function() {
         socket.emit('pause');  // Resume execution
         socket.emit('abort_current');  // Stop execution

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/utils/form.py

@@ -1,6 +1,8 @@
+from enum import Enum
+
 from wtforms.fields.choices import SelectField
 from wtforms.fields.core import Field
-from wtforms.validators import InputRequired
+from wtforms.validators import InputRequired, ValidationError
 from wtforms.widgets.core import TextInput
 
 from flask_wtf import FlaskForm
@@ -187,6 +189,30 @@ class VariableOrBoolField(BooleanField):
         return "y"
 
 
+class FlexibleEnumField(StringField):
+    def __init__(self, label=None, validators=None, choices=None, script=None, **kwargs):
+        super().__init__(label, validators, **kwargs)
+        self.script = script
+        self.enum_class = choices
+        self.choices = [e.name for e in self.enum_class]
+        # self.value_list = [e.name for e in self.enum_class]
+
+
+    def process_formdata(self, valuelist):
+        if valuelist:
+            key = valuelist[0]
+            if key in self.choices:
+                # Convert the string key to Enum instance
+                self.data = self.enum_class[key].value
+            elif self.data.startswith("#"):
+                if not self.script.editing_type == "script":
+                    raise ValueError(self.gettext("Variable is not supported in prep/cleanup"))
+                self.data = self.data
+            else:
+                raise ValidationError(
+                    f"Invalid choice: '{key}'. Must match one of {list(self.enum_class.__members__.keys())}")
+
+
 def format_name(name):
     """Converts 'example_name' to 'Example Name'."""
     name = name.split(".")[-1]
@@ -218,20 +244,39 @@ def create_form_for_method(method, autofill, script=None, design=True):
         if param.name == 'self':
             continue
         formatted_param_name = format_name(param.name)
+
+        default_value = None
+        if autofill:
+            default_value = f'#{param.name}'
+        else:
+            if param.default is not param.empty:
+                if isinstance(param.default, Enum):
+                    default_value = param.default.name
+                else:
+                    default_value = param.default
+
         field_kwargs = {
             "label": formatted_param_name,
-            "default": f'#{param.name}' if autofill else (param.default if param.default is not param.empty else None),
+            "default": default_value,
             "validators": [InputRequired()] if param.default is param.empty else None,
             **({"script": script} if (autofill or design) else {})
         }
-        field_class, placeholder_text = annotation_mapping.get(
-            param.annotation,
-            (VariableOrStringField if design else StringField, f'Enter {param.annotation} value')
-        )
+        if isinstance(param.annotation, type) and issubclass(param.annotation, Enum):
+            # enum_class = [(e.name, e.value) for e in param.annotation]
+            field_class = FlexibleEnumField
+            placeholder_text = f"Choose or type a value for {param.annotation.__name__} (start with # for custom)"
+            extra_kwargs = {"choices": param.annotation}
+        else:
+            field_class, placeholder_text = annotation_mapping.get(
+                param.annotation,
+                (VariableOrStringField if design else StringField, f'Enter {param.annotation} value')
+            )
+            extra_kwargs = {}
+
         render_kwargs = {"placeholder": placeholder_text}
 
         # Create the field with additional rendering kwargs for placeholder text
-        field = field_class(**field_kwargs, render_kw=render_kwargs)
+        field = field_class(**field_kwargs, render_kw=render_kwargs, **extra_kwargs)
         setattr(DynamicForm, param.name, field)
 
     # setattr(DynamicForm, f'add', fname)

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos/utils/script_runner.py

@@ -17,6 +17,7 @@ deck = None
 
 class ScriptRunner:
     def __init__(self, globals_dict=None):
+        self.retry = False
         if globals_dict is None:
             globals_dict = globals()
         self.globals_dict = globals_dict
@@ -143,7 +144,12 @@ class ScriptRunner:
             # if line.startswith("registered_workflows"):
             #     line = line.replace("registered_workflows.", "")
             try:
-                exec(line, exec_globals, exec_locals)
+                if line.startswith("time.sleep("): # add safe sleep for time.sleep lines
+                    duration_str = line[len("time.sleep("):-1]
+                    duration = float(duration_str)
+                    self.safe_sleep(duration)
+                else:
+                    exec(line, exec_globals, exec_locals)
                 step.run_error = False
             except Exception as e:
                 logger.error(f"Error during script execution: {e}")
@@ -152,14 +158,18 @@ class ScriptRunner:
                 step.run_error = True
                 self.toggle_pause()
             step.end_time = datetime.now()
+            db.session.add(step)
+            db.session.commit()
+
             self.pause_event.wait()
 
             # todo update script during the run
             # _func_str = script.compile()
             # step_list: list = script.convert_to_lines(_func_str).get(section_name, [])
-            db.session.add(step)
-            db.session.commit()
-            index += 1
+            if not step.run_error:
+                index += 1
+            elif not self.retry:
+                index += 1
         return exec_locals  # Return the 'results' variable
 
     def _run_with_stop_check(self, script: Script, repeat_count: int, run_name: str, logger, socketio, config, bo_args,
@@ -290,3 +300,11 @@ class ScriptRunner:
     @staticmethod
     def _emit_progress(socketio, progress):
         socketio.emit('progress', {'progress': progress})
+
+    def safe_sleep(self, duration: float):
+        interval = 1  # check every 1 second
+        end_time = time.time() + duration
+        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()))

ivoryos-0.1.24/ivoryos/version.py

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

{ivoryos-0.1.22 → ivoryos-0.1.24/ivoryos.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ivoryos
-Version: 0.1.22
+Version: 0.1.24
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Home-page: https://gitlab.com/heingroup/ivoryos
 Author: Ivory Zhang

{ivoryos-0.1.22 → ivoryos-0.1.24}/ivoryos.egg-info/SOURCES.txt

@@ -23,6 +23,8 @@ ivoryos/routes/control/templates/control/controllers_new.html
 ivoryos/routes/database/__init__.py
 ivoryos/routes/database/database.py
 ivoryos/routes/database/templates/database/experiment_database.html
+ivoryos/routes/database/templates/database/experiment_step_view.html
+ivoryos/routes/database/templates/database/step_card.html
 ivoryos/routes/database/templates/database/workflow_run_database.html
 ivoryos/routes/design/__init__.py
 ivoryos/routes/design/design.py

ivoryos-0.1.22/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "0.1.22"