ivoryos 1.4.0__py3-none-any.whl → 1.4.1__py3-none-any.whl

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/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/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/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/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/routes/execute/templates/components/logging_panel.html

@@ -1,31 +1,56 @@
 {# 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 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 class="text-muted mt-2">
-            <small><strong>Note:</strong> The current step cannot be paused or stopped until it completes. </small>
+    </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 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> 
+
+</div>
+<script>
+    function showPlot() {
+        const img = document.getElementById('optimizerPlot');
+        img.src = "{{ url_for('execute.get_optimizer_plot') }}";
+        img.style.display = 'block';
+    }
+</script>

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/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/version.py

@@ -1 +1 @@
-__version__ = "1.4.0"
+__version__ = "1.4.1"

{ivoryos-1.4.0.dist-info → ivoryos-1.4.1.dist-info}/METADATA

@@ -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.dist-info → ivoryos-1.4.1.dist-info}/RECORD

@@ -3,11 +3,11 @@ ivoryos/app.py,sha256=G6kzEOVzCduj7Fc2r1rMbMFHgDzZQV0lC20Oxps7RSM,4839
 ivoryos/config.py,sha256=y3RxNjiIola9tK7jg-mHM8EzLMwiLwOzoisXkDvj0gA,2174
 ivoryos/server.py,sha256=Idr41Boa8rPsh3bVJ8xy2Flwfxa1Xu6f2T0oMp4qBEk,7121
 ivoryos/socket_handlers.py,sha256=KSh8TxbLFTcmaa-lEb5rKJvOYjKgnGTtaKZST8Wh3b8,1326
-ivoryos/version.py,sha256=8UhoYEXHs1Oai7BW_ExBmuwWnRI-yMG_u1fQAXMizHQ,22
-ivoryos/optimizer/ax_optimizer.py,sha256=jdsMej_p-R0Ec3UdTYg0pCs9hlDScYRTfM3hyz38uVc,8253
-ivoryos/optimizer/base_optimizer.py,sha256=QtF4NVqasKBbcUHuUV1vKnPuBU8b0TYufOOwIp2ZqLY,2582
-ivoryos/optimizer/baybe_optimizer.py,sha256=aSB0FL_u_QucuslImGfYxIAAf9QAv3Pno_czjIfDzpk,8445
-ivoryos/optimizer/nimo_optimizer.py,sha256=00gDjhPyTvappYrKnzoBvuo0F6CD3sefJobHS2kny30,6868
+ivoryos/version.py,sha256=BqOI5y46o1G1RWC9bF1DPL-YM68lGYPmZt1pn6FZFZs,22
+ivoryos/optimizer/ax_optimizer.py,sha256=sLS6wyc_MfrPz_BfDlhFiuoOt5HhvB8X9tzNQqfYcKk,8310
+ivoryos/optimizer/base_optimizer.py,sha256=m_wXan_xPueUWNQi3-561Pe_060tsKuUcCTOOu0qu8s,2652
+ivoryos/optimizer/baybe_optimizer.py,sha256=grXmePNuTQsCgRDhJGsAWQuSvvt0hqjhvzpyrZKYjD0,8502
+ivoryos/optimizer/nimo_optimizer.py,sha256=ZevLJUhJKpwatyiOSmPEz3JAUZTdZNKEc_J7z1fAvVQ,7303
 ivoryos/optimizer/registry.py,sha256=dLMo5cszcwa06hfBxdINQIGpkHtRe5-J3J7t76Jq6X0,306
 ivoryos/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 ivoryos/routes/api/api.py,sha256=97Y7pqTwOaWgZgI5ovEPxEBm6Asrt0Iy0VhBkVp2xqA,2304
@@ -52,11 +52,11 @@ ivoryos/routes/design/templates/components/modals/new_script_modal.html,sha256=p
 ivoryos/routes/design/templates/components/modals/rename_modal.html,sha256=40rLNF9JprdXekB3mv_S3OdqVuQYOe-BZSCgOnIkxJQ,1202
 ivoryos/routes/design/templates/components/modals/saveas_modal.html,sha256=N5PEqUuK3qxDFbtDKFnzHwhLarQLPHiX-XQAdQPL1AU,1555
 ivoryos/routes/execute/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-ivoryos/routes/execute/execute.py,sha256=80m63cPxDhOVooKv56zTErcJekil7jm67XZfIWJs7Yg,13606
+ivoryos/routes/execute/execute.py,sha256=e08Yl7pcMFBE-6PSF3gSqVqRRr1_li92PsZe-UJFOec,14816
 ivoryos/routes/execute/execute_file.py,sha256=TelWYV295p4ZPhkUDJSVxfYROfVaKodEmDPTS2plQHI,2816
 ivoryos/routes/execute/templates/experiment_run.html,sha256=fvHRrG5ii1v5zPHL9N_ljDGHUo3t3amiproVPtnOFVE,944
 ivoryos/routes/execute/templates/components/error_modal.html,sha256=5Dmp9V0Ys6781Y-pKn_mc4N9J46c8EwIkjkHX22xCsw,1025
-ivoryos/routes/execute/templates/components/logging_panel.html,sha256=FllozlPd6o7uBd8eflGjRktPV435J3XgiEeLZugoUi0,1623
+ivoryos/routes/execute/templates/components/logging_panel.html,sha256=-elcawnE4CaumyivzxaHW3S5xSv5CgZtXt0OHljlits,2554
 ivoryos/routes/execute/templates/components/progress_panel.html,sha256=-nX76aFLxSOiYgI1xMjznC9rDYF-Vb92TmfjXYpBtps,1323
 ivoryos/routes/execute/templates/components/run_panel.html,sha256=CmK-LYJ4K6RonHn6l9eJkqRw0XQizThOugxiXZonSDs,373
 ivoryos/routes/execute/templates/components/run_tabs.html,sha256=HZUBQxJIigp9DgMvcxZOoR_pqz4ZW9kpxhbCjW6_dRg,2724
@@ -89,17 +89,17 @@ ivoryos/utils/bo_campaign.py,sha256=Z4WXJwbf1Hhg1dtlvhWHncBiq9Cuaf0BiqR60bWy36U,
 ivoryos/utils/client_proxy.py,sha256=74G3HAuq50iEHkSvlMZFmQaukm613FbRgOdzO_T3dMg,10191
 ivoryos/utils/db_models.py,sha256=C0iTN_SuM3ew6CajuPpeqAusZGjaNrf6eCzRMtVi3fw,36641
 ivoryos/utils/decorators.py,sha256=pcD8WijFjNfkNvr-wmJSWTHn_OqCOCpAO-7w_qg9_xM,1051
-ivoryos/utils/form.py,sha256=I4Bikx4wDDPuq5tSP5b36yeOkp9GpJbK0fTJETOd79Q,23334
+ivoryos/utils/form.py,sha256=MNIvmx4RhDukFACwyrXS-88tBeMKeNdxVba_KzOab_Y,23469
 ivoryos/utils/global_config.py,sha256=leYoEXvAS0AH4xQpYsqu4HI9CJ9-wiLM-pIh_bEG4Ak,3087
 ivoryos/utils/llm_agent.py,sha256=-lVCkjPlpLues9sNTmaT7bT4sdhWvV2DiojNwzB2Lcw,6422
 ivoryos/utils/nest_script.py,sha256=kc4V0cBca5TviqQuquMFBF8Q5IjqKqj2R6g-_N6gMak,10645
 ivoryos/utils/py_to_json.py,sha256=ZtejHgwdEAUCVVMYeVNR8G7ceLINue294q6WpiJ6jn0,9734
-ivoryos/utils/script_runner.py,sha256=wz1vT7vcaPVq30oYXRbUS_ZUG8Gmk0PomsuFHMBjP90,34584
+ivoryos/utils/script_runner.py,sha256=nFYyTeY1X0ZR2e3WOBQjQkjAji-C1ba872JTI1Df5oA,34651
 ivoryos/utils/serilize.py,sha256=lkBhkz8r2bLmz2_xOb0c4ptSSOqjIu6krj5YYK4Nvj8,6784
 ivoryos/utils/task_runner.py,sha256=xiMzK8gQ0mHsg0A1Ah8fmXe3azpaJh4hJiQJLHA11ZQ,3682
 ivoryos/utils/utils.py,sha256=QUAeZYLBUl7iLOcIS89PC5vH2nnXAVX-MLDwNVaNFDg,15181
-ivoryos-1.4.0.dist-info/licenses/LICENSE,sha256=p2c8S8i-8YqMpZCJnadLz1-ofxnRMILzz6NCMIypRag,1084
-ivoryos-1.4.0.dist-info/METADATA,sha256=hmI02h6MUh2vsW0Wj559BCJzchoCn14uKVy4uzEBnTk,8546
-ivoryos-1.4.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-ivoryos-1.4.0.dist-info/top_level.txt,sha256=FRIWWdiEvRKqw-XfF_UK3XV0CrnNb6EmVbEgjaVazRM,8
-ivoryos-1.4.0.dist-info/RECORD,,
+ivoryos-1.4.1.dist-info/licenses/LICENSE,sha256=p2c8S8i-8YqMpZCJnadLz1-ofxnRMILzz6NCMIypRag,1084
+ivoryos-1.4.1.dist-info/METADATA,sha256=nvAS0espk2mVj44H9m_wIMvLe5xa2YKfYzn9rCGL2xs,8592
+ivoryos-1.4.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+ivoryos-1.4.1.dist-info/top_level.txt,sha256=FRIWWdiEvRKqw-XfF_UK3XV0CrnNb6EmVbEgjaVazRM,8
+ivoryos-1.4.1.dist-info/RECORD,,