bindmc 0.1.3__tar.gz → 0.1.5__tar.gz

{bindmc-0.1.3 → bindmc-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bindmc
-Version: 0.1.3
+Version: 0.1.5
 Keywords: chemistry,analytical chemistry,binding constants,supramolecular
 Author: Martin Peeks
 Author-email: Martin Peeks <martinp23@googlemail.com>, m.peeks@unsw.edu.au
@@ -12,10 +12,10 @@ Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Dist: arviz==0.21.0
-Requires-Dist: bindtools>=0.1.2
+Requires-Dist: bindtools>=0.1.3
 Requires-Dist: corner==2.2.3
 Requires-Dist: emcee==3.1.6
-Requires-Dist: h5py==3.13.0
+Requires-Dist: h5py>=3.14.0
 Requires-Dist: latex2mathml>=3.0.0
 Requires-Dist: lmfit==1.3.3
 Requires-Dist: matplotlib==3.10.7

{bindmc-0.1.3 → bindmc-0.1.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bindmc"
-version = "0.1.3"
+version = "0.1.5"
 readme = "README.md"
 keywords = ["chemistry", "analytical chemistry", "binding constants", "supramolecular"]
 classifiers = [
@@ -28,10 +28,10 @@ classifiers = [
 requires-python = ">=3.12"
 dependencies = [
     "arviz==0.21.0",
-    "bindtools>=0.1.2",
+    "bindtools>=0.1.3",
     "corner==2.2.3",
     "emcee==3.1.6",
-    "h5py==3.13.0",
+    "h5py>=3.14.0",
     "latex2mathml>=3.0.0",
     "lmfit==1.3.3",
     "matplotlib==3.10.7",

{bindmc-0.1.3 → bindmc-0.1.5}/src/bindmc/__main__.py

@@ -1,4 +1,4 @@
 """Entry point for python -m bindmc."""
 
-if __name__ in {"__main__"}:
+if __name__ in {"__main__", "__mp_main__"}:
     import bindmc.main

{bindmc-0.1.3 → bindmc-0.1.5}/src/bindmc/main.py

@@ -107,7 +107,7 @@ storage_path.mkdir(parents=True, exist_ok=True)
 # Redirect native window persistence data away from default paths
 app.native.start_args["storage_path"] = str(storage_path)
 
-
-ui.run(title="BindMC", reload=reload, native=native_mode, port=native.find_open_port(), storage_secret="bindmc_secret")
+if __name__ in {"__main__", "__mp_main__"}:
+    ui.run(title="BindMC", reload=reload, native=native_mode, port=native.find_open_port(), storage_secret="bindmc_secret")
 
 

{bindmc-0.1.3 → bindmc-0.1.5}/src/bindmc/webgui/components/bayes.py

@@ -245,7 +245,7 @@ class BayesPanel(BaseComponent):
             return
 
         if active_fit.bd_model is None:
-            print("No bindtools model selected for fitting, generating one.")
+            logger.info("No bindtools model selected for fitting, generating one.")
             ui.notify("Running an initial fit using least_sq")
             m1 = self.sm.generate_binding_model_for_fit(active_fit)
             m1 = await run.cpu_bound(
@@ -262,6 +262,7 @@ class BayesPanel(BaseComponent):
         nwalkers = int(self.nwalkers_input.value)
         obslist = self.sm.active_expt_data.get_obs_list(self.sm._expt_dtypes)
 
+        logger.info("Setting up for MCMC run")
         # Create MCMC simulation (not yet registered in state)
         self.mcmc = MCMCSim(
             model=self.sm.active_model,
@@ -281,12 +282,13 @@ class BayesPanel(BaseComponent):
                 type="info",
                 timeout=60000,
             )
+            logger.info("Running a trial run")
             try:
                 trial_elapsed = await run.cpu_bound(partial(_run_mcmc_trial, self.mcmc.mc, _TRIAL_STEPS))
                 it_s = _TRIAL_STEPS / trial_elapsed
                 full_seconds = nsteps_target * trial_elapsed / _TRIAL_STEPS
                 full_time_str = _format_duration(full_seconds)
-
+                logger.info("Trial run finished; took {trial_elapsed:.1f} s ({it_s:.2f} it/s).")
                 with ui.dialog() as timing_dialog, ui.card().classes("w-[min(560px,92vw)]"):
                     ui.label("Runtime estimate").classes("text-lg font-bold")
                     ui.label(f"{_TRIAL_STEPS:,} steps took {trial_elapsed:.1f} s ({it_s:.2f} it/s).").classes(
@@ -296,6 +298,8 @@ class BayesPanel(BaseComponent):
                         f"The full run ({nsteps_target:,} steps, {nwalkers} walkers) "
                         f"will take approximately {full_time_str}."
                     ).classes("mt-2")
+                    logger.info(f"The full run ({nsteps_target:,} steps, {nwalkers} walkers) "
+                        f"will take approximately {full_time_str}.")
                     ui.label("Do you want to continue?").classes("mt-1 font-medium")
                     with ui.row().classes("w-full justify-end gap-2 mt-3"):
                         ui.button("Cancel", on_click=lambda: timing_dialog.submit(False))
@@ -320,6 +324,7 @@ class BayesPanel(BaseComponent):
         self.run_button.set_enabled(False)
         self.stop_button.set_enabled(True)
         self.progress_bar.value = 0
+        logger.info("Starting MCMC analysis")
         self.progress_label.text = "Starting MCMC analysis..."
         self._log_status("Starting MCMC analysis...")
         self._start_run_timers()

{bindmc-0.1.3 → bindmc-0.1.5}/src/bindmc/webgui/components/data_import.py

@@ -126,6 +126,7 @@ class DataImportPanel(BaseComponent):
                 rd = active_raw
                 new_expt_data = ExptData(name=rd.filename, init_raw_data=rd, init_model=self.sm.active_model)
                 self.sm.add_expt_data(new_expt_data)
+            self.sm.notify_listeners("data_imported")  # Trigger table and graph update
         else:
             ui.notify("No raw data selected to prepare data model from.", type="negative")
 

{bindmc-0.1.3 → bindmc-0.1.5}/src/bindmc/webgui/components/data_model.py

@@ -65,6 +65,10 @@ class DataModelPanel(BaseComponent):
 
         nmr_fast_ex = False
         nmr_slow_ex = False
+        
+        # make all visible to allow changes in the next code block before we hide them again if not needed
+        self.dataModel_specInteg_block.visible = True
+        self.dataModel_specFastExchange_block.visible = True
 
         # work out what we need
         if self.sm.active_expt_data_or_none is not None:
@@ -76,7 +80,7 @@ class DataModelPanel(BaseComponent):
                     if getattr(dtype, "meas", None) == "nmr_ppm" and f.get("depindep") == "dep":
                         nmr_fast_ex = True
                         self._gen_spec_fast_exchange_block()
-                    elif getattr(dtype, "meas", None) == "nmr_conc" and f.get("depindep") == "dep":
+                    elif getattr(dtype, "meas", None) == "nmr_integ" and f.get("depindep") == "dep":
                         nmr_slow_ex = True
                         self._gen_spec_integ_block()
 
@@ -142,7 +146,7 @@ class DataModelPanel(BaseComponent):
                     self.spec_integ_inps[spec] = ui.input().classes("flex-1").props("clearable")
 
                     self.spec_integ_inps[spec].on("blur", lambda c=self.spec_integ_inps[spec]: self.set_focus(c))
-                    b = ui.checkbox("Enabled", value=True)
+                    b = ui.checkbox("Enabled", value=True).props(f"testid=spec-enabled-{spec}")
                     self.spec_integ_inps[spec].bind_enabled_from(b, "value")
                     if (
                         hasattr(active_expt, "integ_to_spec")

{bindmc-0.1.3 → bindmc-0.1.5}/src/bindmc/webgui/components/fitting.py

@@ -108,7 +108,7 @@ def _infer_analytical_fast_exchange_config(model, expt_data, expt_dtypes: dict)
             has_nmr = True
         elif meas in ("uvvis", "fluorescence"):
             has_linear = True
-        else:
+        else: 
             return None  # Unknown or unsupported observable type for analytical path
 
     if has_nmr and has_linear:
@@ -442,6 +442,9 @@ class FittingPanel(BaseComponent):
             self.sm.active_expt_data,
             self.sm._expt_dtypes,
         )
+
+
+
         self.m1 = self.sm.generate_binding_model_for_fit(analytical_cfg=analytical_cfg)
         if analytical_cfg is not None:
             ui.notify(
@@ -492,7 +495,7 @@ class FittingPanel(BaseComponent):
                 init_model=self.sm.active_model,
                 bd_model=self.m1,
                 analytical_fast_exchange=analytical_cfg is not None,
-                analytical_topology=(str(analytical_cfg["topology"]) if analytical_cfg is not None else None),
+                analytical_topology=self.m1.analytical_topology,
                 analytical_obs_columns=(
                     [str(x) for x in cast(list[str], analytical_cfg["obs_columns"])]
                     if analytical_cfg is not None
@@ -503,11 +506,7 @@ class FittingPanel(BaseComponent):
                     if analytical_cfg is not None
                     else []
                 ),
-                analytical_complex_indices=(
-                    [int(x) for x in cast(list[int], analytical_cfg["complex_indices"])]
-                    if analytical_cfg is not None
-                    else []
-                ),
+                analytical_complex_indices=self.m1.analytical_complex_indices,
             )
             self.sm.add_fit(new_fit)
 
@@ -536,7 +535,7 @@ class FittingPanel(BaseComponent):
 
     def _update_fit_graphs(self, e=None) -> None:
         """Update the fit results display."""
-        print("Updating fit results...")
+        logger.info("Updating fit results...")
         self.fit_graph.clear_graph(update=False)
         if len(self.sm.fits) > 0:
             self.speciation_graph.clear_graph(update=False)

{bindmc-0.1.3 → bindmc-0.1.5}/src/bindmc/webgui/state/statemanager.py

@@ -1777,6 +1777,16 @@ bd.makeFitResidPlot(fit,plotMask=(0,1),ylabel='Chemical shift (ppm)')"""
                 model.analytical_linear_obs_columns = lin_cols
                 model.analytical_linear_obs_param_map = linear_obs_param_map
 
+        # Always infer topology to allow analytical concentrations in slow exchange
+        from bindmc.webgui.utils import _infer_simple_fast_exchange_topology
+        topology_res = _infer_simple_fast_exchange_topology(
+            self.active_model.eq_mat, len(self.active_model.component_names)
+        )
+        if topology_res is not None:
+            topo_name, complex_indices = topology_res
+            model.analytical_topology = topo_name
+            model.analytical_complex_indices = complex_indices
+
         model.prepModel()
 
         for k in self.active_model.binding_constants: