bindmc 0.1.2__tar.gz → 0.1.3__tar.gz

{bindmc-0.1.2 → bindmc-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bindmc
-Version: 0.1.2
+Version: 0.1.3
 Keywords: chemistry,analytical chemistry,binding constants,supramolecular
 Author: Martin Peeks
 Author-email: Martin Peeks <martinp23@googlemail.com>, m.peeks@unsw.edu.au
@@ -12,7 +12,7 @@ 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>=0.1.0
+Requires-Dist: bindtools>=0.1.2
 Requires-Dist: corner==2.2.3
 Requires-Dist: emcee==3.1.6
 Requires-Dist: h5py==3.13.0
@@ -38,8 +38,8 @@ Description-Content-Type: text/markdown
 
 # bindmc
 
-[![PyPI version](https://badge.fury.io/py/bindtools.svg)](https://badge.fury.io/py/bindtools)
-[![Python Version](https://img.shields.io/pypi/pyversions/bindtools.svg)](https://pypi.org/project/bindtools/)
+[![PyPI version](https://badge.fury.io/py/bindmc.svg)](https://badge.fury.io/py/bindmc)
+[![Python Version](https://img.shields.io/pypi/pyversions/bindmc.svg)](https://pypi.org/project/bindmc/)
 
 `bindmc` is a tool for calculating binding constants, built on top of [bindtools](https://github.com/martinp23/bindtools).
 
@@ -60,4 +60,4 @@ If using the pre-built binary, run the downloaded executable.
 If installed via pip, run:
 ```bash
 python -m bindmc
-```
+```

{bindmc-0.1.2 → bindmc-0.1.3}/README.md

@@ -1,7 +1,7 @@
 # bindmc
 
-[![PyPI version](https://badge.fury.io/py/bindtools.svg)](https://badge.fury.io/py/bindtools)
-[![Python Version](https://img.shields.io/pypi/pyversions/bindtools.svg)](https://pypi.org/project/bindtools/)
+[![PyPI version](https://badge.fury.io/py/bindmc.svg)](https://badge.fury.io/py/bindmc)
+[![Python Version](https://img.shields.io/pypi/pyversions/bindmc.svg)](https://pypi.org/project/bindmc/)
 
 `bindmc` is a tool for calculating binding constants, built on top of [bindtools](https://github.com/martinp23/bindtools).
 
@@ -22,4 +22,4 @@ If using the pre-built binary, run the downloaded executable.
 If installed via pip, run:
 ```bash
 python -m bindmc
-```
+```

{bindmc-0.1.2 → bindmc-0.1.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "bindmc"
-version = "0.1.2"
+version = "0.1.3"
 readme = "README.md"
 keywords = ["chemistry", "analytical chemistry", "binding constants", "supramolecular"]
 classifiers = [
@@ -28,7 +28,7 @@ classifiers = [
 requires-python = ">=3.12"
 dependencies = [
     "arviz==0.21.0",
-    "bindtools>=0.1.0",
+    "bindtools>=0.1.2",
     "corner==2.2.3",
     "emcee==3.1.6",
     "h5py==3.13.0",

bindmc-0.1.3/src/bindmc/__main__.py

@@ -0,0 +1,4 @@
+"""Entry point for python -m bindmc."""
+
+if __name__ in {"__main__"}:
+    import bindmc.main

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/main.py

@@ -13,6 +13,7 @@ import matplotlib
 
 matplotlib.use("module://matplotlib.backends.backend_svg")
 import sys
+import webview
 from nicegui import native, ui, app
 from bindmc.webgui.app import BindMCServer
 import logging
@@ -24,6 +25,32 @@ from importlib.metadata import version
 
 __version__ = version("bindmc")
 
+def is_webview_available() -> bool:
+    """Check if pywebview GUI libraries can be initialized in-process."""
+    try:
+        from webview.guilib import initialize
+        from webview.util import WebViewException
+        
+        # Temporarily suppress pywebview's internal logger to prevent 
+        # missing backend errors from spamming your console output.
+        logger = logging.getLogger('pywebview')
+        old_level = logger.level
+        logger.setLevel(logging.CRITICAL)
+        
+        try:
+            # Attempts to load the default system GUI engine (e.g. Edge, Cocoa, GTK, QT)
+            initialize()
+            return True
+        except (WebViewException, ImportError, Exception):
+            return False
+        finally:
+            logger.setLevel(old_level)
+            
+    except ImportError:
+        # pywebview itself isn't even installed
+        return False
+
+
 logger = logging.getLogger(__name__)
 
 try:
@@ -43,6 +70,8 @@ else:
         raise RuntimeError(f"NiceGUI >= 3 is required; found {nicegui.__version__}")
 
 
+
+
 app.native.settings["ALLOW_DOWNLOADS"] = True
 
 # logging.basicConfig(level=logging.INFO, filename='BindMC.log')
@@ -51,17 +80,26 @@ logging.basicConfig(level=logging.INFO, format="%(levelname)s:%(message)s")
 logger.info(f"Starting BindMC {__version__} NiceGUI server...")
 BindMCServer()
 
-# Set DEV based on whether running from PyInstaller bundle
-DEV = not getattr(sys, "frozen", False)
+# pyinstaller?
+is_frozen = getattr(sys, "frozen", False)
+
+is_module_run = bool(globals().get("__package__"))
+
+DEV = not (is_frozen or is_module_run)
 
+native_mode = False
 if DEV:
     native_mode = False
     reload = True
 else:
-    native_mode = True
+    native_mode = is_webview_available()
+    if native_mode is False:
+        logger.warning("Native mode is not available; running via browser.")
     reload = False
 
 
+
+
 # make a sensible storage path for native mode
 storage_path = Path(user_data_dir(appname="BindMC", appauthor=False))
 storage_path.mkdir(parents=True, exist_ok=True)
@@ -69,4 +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")
+
+

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/webgui/components/bayes.py

@@ -6,7 +6,7 @@ import zipfile
 import numpy as np
 import pandas as pd
 from ..classes import MCMCSim
-from ..utils import safe_filename
+from ..utils import safe_filename, custom_download
 from functools import partial
 import asyncio
 import re
@@ -568,13 +568,13 @@ class BayesPanel(BaseComponent):
         f.tight_layout()
         self.result_corner.update()
 
-    def _download_figure(self, fig, filename: str) -> None:
+    async def _download_figure(self, fig, filename: str) -> None:
         buf = io.BytesIO()
         fig.savefig(buf, format="png", dpi=_EXPORT_DPI, bbox_inches="tight")
         buf.seek(0)
-        ui.download.content(buf.getvalue(), filename=filename)
+        await custom_download(buf.getvalue(), filename=filename)
 
-    def download_chain_figure(self) -> None:
+    async def download_chain_figure(self) -> None:
         if not hasattr(self, "mcmc") or self.mcmc.mc is None or self.mcmc.mc.sampler is None:
             ui.notify("No chain figure available for download.", type="warning")
             return
@@ -588,10 +588,10 @@ class BayesPanel(BaseComponent):
         active_fit = self.sm.active_fit_or_none
         stem = active_fit.name if active_fit is not None else "mcmc"
         filename = f"{safe_filename(stem, fallback='mcmc')}_chains.png"
-        self._download_figure(fig, filename)
+        await self._download_figure(fig, filename)
         plt.close(fig)
 
-    def download_corner_figure(self) -> None:
+    async def download_corner_figure(self) -> None:
         if not hasattr(self, "mcmc") or self.mcmc.mc is None or self.mcmc.mc.sampler is None:
             ui.notify("No corner figure available for download.", type="warning")
             return
@@ -606,7 +606,7 @@ class BayesPanel(BaseComponent):
         active_fit = self.sm.active_fit_or_none
         stem = active_fit.name if active_fit is not None else "mcmc"
         filename = f"{safe_filename(stem, fallback='mcmc')}_corner.png"
-        self._download_figure(fig, filename)
+        await self._download_figure(fig, filename)
         plt.close(fig)
 
     # ------------------------------------------------------------------
@@ -646,19 +646,20 @@ class BayesPanel(BaseComponent):
                     "text-sm text-orange-600 mt-1"
                 )
 
+            async def export_and_close():
+                dialog.close()
+                await self._do_export_notebook(include_chains["value"])
+
             with ui.row().classes("mt-4 gap-2 justify-end w-full"):
                 ui.button("Cancel", on_click=dialog.close)
                 ui.button(
                     "Export",
-                    on_click=lambda: (
-                        dialog.close(),
-                        self._do_export_notebook(include_chains["value"]),
-                    ),
+                    on_click=export_and_close,
                 ).props("color=primary")
 
         dialog.open()
 
-    def _do_export_notebook(self, include_chains: bool) -> None:
+    async def _do_export_notebook(self, include_chains: bool) -> None:
         active_fit = self.sm.active_fit_or_none
         if active_fit is None:
             ui.notify("No active fit to export.", type="negative")
@@ -684,5 +685,5 @@ class BayesPanel(BaseComponent):
         buf.seek(0)
 
         zip_filename = f"{stem}_mcmc_notebook.zip"
-        ui.download.content(buf.read(), filename=zip_filename)
+        await custom_download(buf.read(), filename=zip_filename)
         ui.notify(f"Notebook exported as {zip_filename}.", type="positive")

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/webgui/components/data_gen.py

@@ -4,6 +4,7 @@ import numpy as np
 import pandas as pd
 from ..classes import Component
 from .graph import Graph
+from ..utils import custom_download
 
 from nicegui.events import UploadEventArguments
 from collections import Counter
@@ -127,9 +128,12 @@ class DataGenerationPanel(BaseComponent):
             template_text += "\nmM" + ",mM" * (len(self.sm.components) - 1)  # Header row with units
             template_text += "\n" + "0.001" + ",0" * (len(self.sm.components) - 1)  # Add a newline after the header
 
+            async def download_template():
+                await custom_download(template_text, "component_concentrations_template.csv")
+
             ui.button(
                 "Download template CSV",
-                on_click=lambda: ui.download.content(template_text, "component_concentrations_template.csv"),
+                on_click=download_template,
             )
 
             ui.label("""

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/webgui/components/fitting.py

@@ -12,7 +12,7 @@ import bindtools.binding as bd
 from .base import BaseComponent
 from .graph import Graph
 from ..classes import FitResult
-from ..utils import safe_filename, _infer_simple_fast_exchange_topology
+from ..utils import safe_filename, _infer_simple_fast_exchange_topology, custom_download
 from functools import partial
 from typing import cast
 
@@ -647,7 +647,7 @@ class FittingPanel(BaseComponent):
         self.sm.active_fit.name = self.fit_name_input.value
         self.sm.active_fit.description = self.fit_comment_input.value
 
-    def download_fit_data_csv(self) -> None:
+    async def download_fit_data_csv(self) -> None:
         if self.sm.active_fit_id is None:
             ui.notify("No active fit to download.", type="negative")
             return
@@ -685,10 +685,10 @@ class FittingPanel(BaseComponent):
         export_df = pd.concat(export_frames, axis=1)
         filename = f"fit_{safe_filename(fit.name, fallback='fit')}_data.csv"
         csv = export_df.to_csv(index=False, encoding="utf-8", float_format="{:.5e}".format)
-        ui.download.content(csv, filename=filename)
+        await custom_download(csv, filename=filename)
         ui.notify(f"Fit data downloaded as {filename}.", type="info")
 
-    def download_fit_notebook(self) -> None:
+    async def download_fit_notebook(self) -> None:
         """Export the active fit as a zip containing a Jupyter notebook and a data CSV."""
         if self.sm.active_fit_id is None:
             ui.notify("No active fit to export.", type="negative")
@@ -712,7 +712,7 @@ class FittingPanel(BaseComponent):
         buf.seek(0)
 
         zip_filename = f"{stem}_notebook.zip"
-        ui.download.content(buf.read(), filename=zip_filename)
+        await custom_download(buf.read(), filename=zip_filename)
         ui.notify(f"Notebook exported as {zip_filename}.", type="positive")
 
 

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/webgui/components/graph.py

@@ -1,10 +1,10 @@
 import json
 
-from nicegui import ui
+from nicegui import ui, app
 
 from .base import BaseComponent
 from ..classes import Simulation, FitResult
-from ..utils import safe_filename
+from ..utils import safe_filename, custom_download
 import pandas as pd
 import uuid
 
@@ -399,7 +399,39 @@ class Graph(BaseComponent):
             ui.notify(f"No plotted data available for {filename}.", type="warning")
             return
 
-        js = f"""
+        is_native = False
+        try:
+            if getattr(app.native, "main_window", None) is not None:
+                is_native = True
+        except Exception:
+            pass
+
+        if is_native:
+            js = f"""
+const root = getElement({self.graph.id});
+const container = root?.$el ?? root;
+const plot = container?.querySelector('.js-plotly-plot') ?? container;
+if (!plot || typeof Plotly === 'undefined') {{
+    null;
+}} else {{
+    Plotly.toImage(plot, {{format: 'png', scale: 2}});
+}}
+"""
+            data_url = await ui.run_javascript(js)
+            if not data_url or not data_url.startswith("data:image/png;base64,"):
+                ui.notify(f"Unable to export {filename}.png", type="negative")
+                return
+
+            try:
+                import base64
+
+                header, encoded = data_url.split(",", 1)
+                image_bytes = base64.b64decode(encoded)
+                await custom_download(image_bytes, filename=f"{filename}.png")
+            except Exception as e:
+                ui.notify(f"Failed to export {filename}.png: {str(e)}", type="negative")
+        else:
+            js = f"""
 (() => {{
   const root = getElement({self.graph.id});
   const container = root?.$el ?? root;
@@ -409,9 +441,9 @@ class Graph(BaseComponent):
   return true;
 }})()
 """
-        ok = await ui.run_javascript(js)
-        if not ok:
-            ui.notify(f"Unable to export {filename}.png", type="negative")
+            ok = await ui.run_javascript(js)
+            if not ok:
+                ui.notify(f"Unable to export {filename}.png", type="negative")
 
     def update_plot_compfree(self, e):
         """Update the plot to show or hide component free concentrations."""

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/webgui/components/simulation.py

@@ -5,7 +5,7 @@ from nicegui import run, ui
 import bindtools.binding as bd
 
 from ..classes import Simulation
-from ..utils import safe_filename
+from ..utils import safe_filename, custom_download
 from .base import BaseComponent
 from .graph import Graph
 
@@ -50,7 +50,7 @@ class SimulationPanel(BaseComponent):
                     self.save_sim_details_button.set_enabled(False)
                     self.download_sim_button = ui.button(
                         "Download Simulation Data",
-                        on_click=lambda: self.download_sim_data(),
+                        on_click=self.download_sim_data,
                     ).classes("ml-4")
                     self.export_sim_notebook_button = ui.button(
                         "Export to Notebook",
@@ -325,7 +325,7 @@ class SimulationPanel(BaseComponent):
         """Delete a simulation and update the UI."""
         self.sm.delete_simulation(sim)
 
-    def download_sim_data(self):
+    async def download_sim_data(self):
         """Download the current simulation data as a CSV file."""
         active_sim = self.sm.active_sim_or_none
         if active_sim is None:
@@ -335,10 +335,10 @@ class SimulationPanel(BaseComponent):
         sim_data = active_sim.results
         csv = sim_data.to_csv(index=False, encoding="utf-8", float_format="{:.5e}".format)
         filename = f"simulation_{safe_filename(active_sim.name, fallback='simulation')}_data.csv"
-        ui.download.content(csv, filename=filename)
+        await custom_download(csv, filename=filename)
         ui.notify(f"Simulation data downloaded as {filename}.", type="info")
 
-    def download_sim_notebook(self) -> None:
+    async def download_sim_notebook(self) -> None:
         """Export the active simulation as a Jupyter notebook (.ipynb) and download it."""
         active_sim = self.sm.active_sim_or_none
         if active_sim is None:
@@ -354,5 +354,5 @@ class SimulationPanel(BaseComponent):
         stem = safe_filename(active_sim.name, fallback="simulation")
         filename = f"{stem}.ipynb"
         content = json.dumps(notebook, indent=1)
-        ui.download.content(content, filename=filename)
+        await custom_download(content, filename=filename)
         ui.notify(f"Notebook exported as {filename}.", type="positive")

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/webgui/state/statemanager.py

@@ -27,7 +27,7 @@ from ..classes import (
     MCMCSim,
     UIBindings,
 )
-from ..utils import eq_mat_from_equation_str_infer_components
+from ..utils import eq_mat_from_equation_str_infer_components, custom_download
 from lmfit import Parameter as LMFitParameter
 import logging
 
@@ -1048,7 +1048,7 @@ class StateManager:
         # Ensure data is flushed and gzip stream is closed before reading
         buffer.seek(0)
         filename = f"bindtools_project_{timestamp}.json.gz"
-        ui.download.content(buffer.read(), filename=filename)
+        await custom_download(buffer.read(), filename=filename)
         ui.notify(f"Project saved as {filename}", type="info")
 
     def to_json(self):

{bindmc-0.1.2 → bindmc-0.1.3}/src/bindmc/webgui/utils.py

@@ -326,3 +326,55 @@ def _infer_simple_fast_exchange_topology(eq_mat: np.ndarray, n_comp: int) -> tup
     if len(bound_indices) == 2 and sigs == {(1, 1), (2, 1)}:
         return "2:1", [sig_to_idx[(1, 1)], sig_to_idx[(2, 1)]]
     return None
+
+
+async def custom_download(content: bytes | str, filename: str) -> None:
+    """Download content. If in native mode, open a save dialog; otherwise, use ui.download.content."""
+    from nicegui import ui, app
+
+    # Check if the content is a file-like object and read it
+    if hasattr(content, "read"):
+        content = content.read()
+    elif hasattr(content, "getvalue"):
+        content = content.getvalue()
+
+    # Check if we are running in native mode
+    is_native = False
+    try:
+        if getattr(app.native, "main_window", None) is not None:
+            is_native = True
+    except Exception:
+        pass
+
+    if is_native:
+        try:
+            import webview
+
+            save_dialog_type = getattr(webview, "SAVE_DIALOG", 30)
+            if hasattr(webview, "FileDialog") and hasattr(webview.FileDialog, "SAVE"):
+                save_dialog_type = webview.FileDialog.SAVE
+
+            # app.native.main_window is an async wrapper around pywebview window
+            selected = await app.native.main_window.create_file_dialog(
+                dialog_type=save_dialog_type, save_filename=filename
+            )
+            if selected:
+                filepath = selected[0] if isinstance(selected, (list, tuple)) else selected
+                if isinstance(content, str):
+                    with open(filepath, "w", encoding="utf-8") as f:
+                        f.write(content)
+                else:
+                    with open(filepath, "wb") as f:
+                        f.write(content)
+                ui.notify(f"File saved to {filepath}", type="positive")
+            else:
+                ui.notify("Save cancelled", type="warning")
+        except Exception as e:
+            ui.notify(f"Failed to save file: {str(e)}", type="negative")
+    else:
+        # Standard browser download
+        if isinstance(content, str):
+            content_bytes = content.encode("utf-8")
+        else:
+            content_bytes = content
+        ui.download.content(content_bytes, filename=filename)