ivoryos 1.4.0__tar.gz → 1.4.1__tar.gz

{ivoryos-1.4.0 → ivoryos-1.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.4.0
+Version: 1.4.1
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -25,9 +25,10 @@ Provides-Extra: optimizer-baybe
 Requires-Dist: baybe; extra == "optimizer-baybe"
 Provides-Extra: optimizer-nimo
 Requires-Dist: nimo; extra == "optimizer-nimo"
-Provides-Extra: optimizer
-Requires-Dist: ax-platform>=1.1.2; extra == "optimizer"
-Requires-Dist: baybe>=0.14.0; extra == "optimizer"
+Provides-Extra: optimizers
+Requires-Dist: ax-platform>=1.1.2; extra == "optimizers"
+Requires-Dist: baybe>=0.14.0; extra == "optimizers"
+Requires-Dist: nimo; extra == "optimizers"
 Provides-Extra: doc
 Requires-Dist: sphinx; extra == "doc"
 Requires-Dist: sphinx-rtd-theme; extra == "doc"

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos/optimizer/ax_optimizer.py

@@ -126,6 +126,9 @@ class AxOptimizer(OptimizerBase):
                 raw_data=obj_only_result
             )
 
+    def get_plots(self, plot_type):
+        return None
+
     @staticmethod
     def get_schema():
         return {

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos/optimizer/base_optimizer.py

@@ -48,6 +48,10 @@ class OptimizerBase(ABC):
     def append_existing_data(self, existing_data):
         pass
 
+    @abstractmethod
+    def get_plots(self, plot_type):
+        pass
+
     @staticmethod
     def _create_discrete_search_space(range_with_step=None, value_type ="float"):
         if range_with_step is None:

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos/optimizer/baybe_optimizer.py

@@ -153,6 +153,9 @@ class BaybeOptimizer(OptimizerBase):
             recommender=step_2_recommender
         )
 
+    def get_plots(self, plot_type):
+        return None
+
     @staticmethod
     def get_schema():
         """

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos/optimizer/nimo_optimizer.py

@@ -1,4 +1,5 @@
 ### ivoryos/optimizers/nimo_optimizer.py
+import glob
 import itertools
 import os
 
@@ -122,6 +123,14 @@ class NIMOOptimizer(OptimizerBase):
         # TODO, history is part of the candidate file, we probably won't need this
         pass
 
+    def get_plots(self, plot_type):
+        import nimo
+        nimo.visualization.plot_phase_diagram.plot(input_file=self.candidates,
+                                                   fig_folder=os.path.join(self.datapath, "nimo_data"))
+        files = sorted(glob.glob(os.path.join(os.path.join(self.datapath, "nimo_data"), "phase_diagram_*.png")))
+        if not files:
+            return None
+        return files[-1]
 
     @staticmethod
     def get_schema():

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos/routes/execute/execute.py

@@ -3,7 +3,7 @@ import os
 import time
 
 from flask import Blueprint, redirect, url_for, flash, jsonify, request, render_template, session, \
-    current_app, g
+    current_app, g, send_file
 from flask_login import login_required
 
 from ivoryos.routes.execute.execute_file import files
@@ -185,26 +185,39 @@ def run_bo():
     """
     script = utils.get_script_file()
     run_name = script.name if script.name else "untitled"
-    payload = request.form.to_dict()
-    repeat = payload.pop("repeat", None)
-    optimizer_type = payload.pop("optimizer_type", None)
-    existing_data = payload.pop("existing_data", None)
-    batch_mode = payload.pop("batch_mode", None)
-    batch_size = payload.pop("batch_size", 1)
-
-    # Get constraint expressions (new single-line input)
-    constraint_exprs = request.form.getlist("constraint_expr")
-    constraints = [expr.strip() for expr in constraint_exprs if expr.strip()]
-
-    # Remove constraint_expr entries from payload before parsing parameters
-    for key in list(payload.keys()):
-        if key.startswith("constraint_expr"):
-            payload.pop(key, None)
-
-    parameters, objectives, steps = parse_optimization_form(payload)
-    try:
+
+    if request.accept_mimetypes.best_match(['application/json', 'text/html']) == 'application/json':
+        payload_json = request.get_json()
+        objectives = payload_json.pop("objectives", None)
+        parameters = payload_json.pop("parameters", None)
+        steps = payload_json.pop("steps", None)
+        constraints = payload_json.pop("parameter_constraints", None)
+        repeat = payload_json.pop("repeat", None)
+        batch_size = payload_json.pop("batch_size", None)
+        optimizer_type = payload_json.pop("optimizer_type", None)
+        existing_data = payload_json.pop("existing_data", None)
+
+    else:
+        payload = request.form.to_dict()
+        repeat = payload.pop("repeat", None)
+        optimizer_type = payload.pop("optimizer_type", None)
+        existing_data = payload.pop("existing_data", None)
+        batch_mode = payload.pop("batch_mode", None)
+        batch_size = payload.pop("batch_size", 1)
+
+        # Get constraint expressions (new single-line input)
+        constraint_exprs = request.form.getlist("constraint_expr")
+        constraints = [expr.strip() for expr in constraint_exprs if expr.strip()]
+
+        # Remove constraint_expr entries from payload before parsing parameters
+        for key in list(payload.keys()):
+            if key.startswith("constraint_expr"):
+                payload.pop(key, None)
+
+        parameters, objectives, steps = parse_optimization_form(payload)
 
     # if True:
+    try:
         datapath = current_app.config["DATA_FOLDER"]
         run_name = script.validate_function_name(run_name)
         Optimizer = global_config.optimizers.get(optimizer_type, None)
@@ -213,10 +226,11 @@ def run_bo():
         optimizer = Optimizer(experiment_name=run_name, parameter_space=parameters, objective_config=objectives,
                               parameter_constraints = constraints,
                               optimizer_config=steps, datapath=datapath)
+        current_app.config["LAST_OPTIMIZER"] = optimizer
         runner.run_script(script=script, run_name=run_name, optimizer=optimizer,
                           logger=g.logger, socketio=g.socketio, repeat_count=repeat,
                           output_path=datapath, compiled=False, history=existing_data,
-                          current_app=current_app._get_current_object(), batch_mode=batch_mode, batch_size=int(batch_size),
+                          current_app=current_app._get_current_object(), batch_size=int(batch_size),
                           objectives=objectives
                           )
 
@@ -227,6 +241,21 @@ def run_bo():
             flash(e.__str__())
     return redirect(url_for("execute.experiment_run"))
 
+@execute.route("/executions/latest_plot")
+@login_required
+def get_optimizer_plot():
+
+    optimizer = current_app.config.get("LAST_OPTIMIZER")
+    if optimizer is not None:
+        # the placeholder is for showing different plots
+        latest_file = optimizer.get_plots('placeholder')
+        # print(latest_file)
+        if files:
+            return send_file(latest_file, mimetype="image/png")
+    # print("No plots found")
+    return jsonify({"error": "No plots found"}), 404
+
+
 
 
 @execute.route("/executions/status", methods=["GET"])

ivoryos-1.4.1/ivoryos/routes/execute/templates/components/logging_panel.html

@@ -0,0 +1,56 @@
+{# Logging panel component for experiment run #}
+<div class="col-lg-6 col-sm-12 logging-panel">
+    <div class="d-flex justify-content-between align-items-center">
+        <h5>Progress：</h5>
+        <div class="d-flex gap-2 ms-auto">
+            <button id="pause-resume" class="btn btn-info text-white">
+            {% if pause_status %}
+            <i class="bi bi-play-circle"></i>
+            {% else %}
+            <i class="bi bi-pause-circle"></i>
+            {% endif %}
+            </button>
+            <button id="abort-current" class="btn btn-danger text-white">
+            <i class="bi bi-stop-circle"></i>
+            </button>
+            <button id="abort-pending" class="btn btn-warning text-white">
+            <i class="bi bi-hourglass-split"></i>
+            </button>
+        </div>
+    </div>
+    <small class="text-muted mt-2">
+    <strong>Note:</strong> The current step cannot be paused or stopped until it completes.
+    </small>
+    <div class="progress my-3">
+        <div id="progress-bar-inner" class="progress-bar progress-bar-striped progress-bar-animated"></div>
+    </div>
+    <!-- Tabs -->
+    <ul class="nav nav-tabs" id="logPlotTabs" role="tablist">
+        <li class="nav-item" role="presentation">
+            <button class="nav-link active" id="log-tab" data-bs-toggle="tab" data-bs-target="#log" type="button" role="tab">Log</button>
+        </li>
+        <li class="nav-item" role="presentation">
+            <button class="nav-link" id="plot-tab" data-bs-toggle="tab" data-bs-target="#plot" type="button" role="tab">Optimizer Plot</button>
+        </li>
+    </ul>
+    <div class="tab-content mt-3" id="logPlotTabsContent">
+        <div class="tab-pane fade show active" id="log" role="tabpanel">
+            <div id="logging-panel" class="border p-2 bg-light" style="max-height: 400px; overflow-y: auto;"></div>
+        </div>
+        <div class="tab-pane fade" id="plot" role="tabpanel">
+            <button class="btn btn-success mb-2" onclick="showPlot()">Refresh Plot</button>
+            <small class="text-muted d-block mt-1" id="plot-info">This function is only available for NIMO optimizers.</small>
+            <br>
+            <img id="optimizerPlot" src="" class="img-fluid rounded shadow-sm d-block mx-auto" style="max-width:100%; display:none;">
+        </div>
+
+    </div>
+
+</div>
+<script>
+    function showPlot() {
+        const img = document.getElementById('optimizerPlot');
+        img.src = "{{ url_for('execute.get_optimizer_plot') }}";
+        img.style.display = 'block';
+    }
+</script>

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos/utils/form.py

@@ -350,13 +350,16 @@ def create_form_from_module(sdl_module, autofill: bool = False, script=None, des
     """
     method_forms = {}
     for attr_name in dir(sdl_module):
-        method = getattr(sdl_module, attr_name)
-        if inspect.ismethod(method) and not attr_name.startswith('_'):
-            signature = inspect.signature(method)
-            docstring = inspect.getdoc(method)
-            attr = dict(signature=signature, docstring=docstring)
-            form_class = create_add_form(attr, attr_name, autofill, script, design)
-            method_forms[attr_name] = form_class()
+        try:
+            method = getattr(sdl_module, attr_name)
+            if inspect.ismethod(method) and not attr_name.startswith('_'):
+                signature = inspect.signature(method)
+                docstring = inspect.getdoc(method)
+                attr = dict(signature=signature, docstring=docstring)
+                form_class = create_add_form(attr, attr_name, autofill, script, design)
+                method_forms[attr_name] = form_class()
+        except Exception as e:
+            print(f"Error creating form for {attr_name}: {e}")
     return method_forms
 
 

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos/utils/script_runner.py

@@ -534,12 +534,12 @@ class ScriptRunner:
 
     async def _execute_repeat_batched(self, step: Dict, contexts: List[Dict[str, Any]], phase_id, step_index, section_name):
         """Execute repeat block for multiple samples."""
-        times = step["args"].get("times", 1)
+        times = step["args"].get("statement", 1)
 
         for i in range(times):
             # Add repeat index to all contexts
-            for context in contexts:
-                context["repeat_index"] = i
+            # for context in contexts:
+            #     context["repeat_index"] = i
 
             await self._execute_steps_batched(step["repeat_block"], contexts, phase_id=phase_id, step_index=step_index, section_name=section_name)
 
@@ -594,7 +594,8 @@ class ScriptRunner:
         db.session.add(step_db)
         db.session.flush()
         try:
-            self.socketio.emit('execution', {'section': f"{section_name}-{step_index}"})
+            # print(f"step {section_name}-{step_index}")
+            self.socketio.emit('execution', {'section': f"{section_name}-{step_index-1}"})
             if action == "wait":
                 duration = float(substituted_args["statement"])
                 self.safe_sleep(duration)

ivoryos-1.4.1/ivoryos/version.py

@@ -0,0 +1 @@
+__version__ = "1.4.1"

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ivoryos
-Version: 1.4.0
+Version: 1.4.1
 Summary: an open-source Python package enabling Self-Driving Labs (SDLs) interoperability
 Author-email: Ivory Zhang <ivoryzhang@chem.ubc.ca>
 License: MIT
@@ -25,9 +25,10 @@ Provides-Extra: optimizer-baybe
 Requires-Dist: baybe; extra == "optimizer-baybe"
 Provides-Extra: optimizer-nimo
 Requires-Dist: nimo; extra == "optimizer-nimo"
-Provides-Extra: optimizer
-Requires-Dist: ax-platform>=1.1.2; extra == "optimizer"
-Requires-Dist: baybe>=0.14.0; extra == "optimizer"
+Provides-Extra: optimizers
+Requires-Dist: ax-platform>=1.1.2; extra == "optimizers"
+Requires-Dist: baybe>=0.14.0; extra == "optimizers"
+Requires-Dist: nimo; extra == "optimizers"
 Provides-Extra: doc
 Requires-Dist: sphinx; extra == "doc"
 Requires-Dist: sphinx-rtd-theme; extra == "doc"

{ivoryos-1.4.0 → ivoryos-1.4.1}/ivoryos.egg-info/requires.txt

@@ -20,10 +20,6 @@ sphinx
 sphinx-rtd-theme
 sphinxcontrib-httpdomain
 
-[optimizer]
-ax-platform>=1.1.2
-baybe>=0.14.0
-
 [optimizer-ax]
 ax-platform
 
@@ -32,3 +28,8 @@ baybe
 
 [optimizer-nimo]
 nimo
+
+[optimizers]
+ax-platform>=1.1.2
+baybe>=0.14.0
+nimo

{ivoryos-1.4.0 → ivoryos-1.4.1}/pyproject.toml

@@ -30,9 +30,10 @@ dependencies = [
 optimizer-ax = ["ax-platform"]
 optimizer-baybe = ["baybe"]
 optimizer-nimo = ["nimo"]
-optimizer = [
+optimizers = [
     "ax-platform>=1.1.2",
-    "baybe>=0.14.0"
+    "baybe>=0.14.0",
+    "nimo"
 ]
 doc = [
     "sphinx",

ivoryos-1.4.0/ivoryos/routes/execute/templates/components/logging_panel.html

@@ -1,31 +0,0 @@
-{# Logging panel component for experiment run #}
-<div class="col-lg-6 col-sm-12 logging-panel">
-    <p>
-        <div class="p d-flex justify-content-between align-items-center">
-            <h5>Progress：</h5>
-            <div class="d-flex gap-2 ms-auto">
-                <button id="pause-resume" class="btn btn-info text-white" data-bs-toggle="tooltip" title="Pause execution">
-                    {% if pause_status %}
-                        <i class="bi bi-play-circle"></i>
-                    {% else %}
-                        <i class="bi bi-pause-circle"></i>
-                    {% endif %}
-                </button>
-                <button id="abort-current" class="btn btn-danger text-white" data-bs-toggle="tooltip" title="Stop execution after current step">
-                    <i class="bi bi-stop-circle"></i>
-                </button>
-                <button id="abort-pending" class="btn btn-warning text-white" data-bs-toggle="tooltip" title="Stop execution after current iteration">
-                    <i class="bi bi-hourglass-split"></i>
-                </button>
-            </div>
-        </div>
-        <div class="text-muted mt-2">
-            <small><strong>Note:</strong> The current step cannot be paused or stopped until it completes. </small>
-        </div>
-
-    <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>
-    <p><h5>Log：</h5></p>
-    <div id="logging-panel"></div>
-</div> 

ivoryos-1.4.0/ivoryos/version.py

@@ -1 +0,0 @@
-__version__ = "1.4.0"