cnotebook 1.0.1__py3-none-any.whl → 1.2.0__py3-none-any.whl

cnotebook/__init__.py

@@ -1,16 +1,14 @@
 import logging
 from .pandas_ext import render_dataframe
 from .context import cnotebook_context
-from .ipython_ext import (
-    register_ipython_formatters as _register_ipython_formatters,
-    render_molecule_grid
-)
+from .ipython_ext import register_ipython_formatters as _register_ipython_formatters
+from .render import render_molecule_grid
 
 # Only import formatter registration from the Pandas module, otherwise have users import functionality from there
 # to avoid confusion
 from cnotebook.pandas_ext import register_pandas_formatters as _register_pandas_formatters
 
-__version__ = '1.0.1'
+__version__ = '1.2.0'
 
 ###########################################
 

cnotebook/ipython_ext.py

@@ -1,16 +1,13 @@
 import logging
-from typing import Literal
-from math import floor, ceil
 from openeye import oechem, oedepict
-from collections.abc import Iterable, Sequence
 from .render import (
     CNotebookContext,
     pass_cnotebook_context,
     oemol_to_html,
     oedisp_to_html,
-    oeimage_to_html
+    oeimage_to_html,
+    render_molecule_grid  # Re-export for backward compatibility
 )
-from .helpers import create_structure_highlighter
 
 # Only register iPython formatters if that is present
 try:
@@ -23,199 +20,6 @@ except ModuleNotFoundError:
 log = logging.getLogger("cnotebook")
 
 
-@pass_cnotebook_context
-def render_molecule_grid(
-        mols: Sequence[oechem.OEMolBase],
-        nrows: int | None = None,
-        ncols: int | None = None,
-        max_width: int = 1280,
-        max_columns: int = 100,
-        min_width: int | None = None,
-        min_height: int | None = None,
-        align: oechem.OEMolBase | Literal["first"] | None = None,
-        smarts: str | Iterable[str] | oechem.OESubSearch | Iterable[oechem.OESubSearch] | None = None,
-        color: oechem.OEColor = oechem.OEColor(oechem.OELightBlue),
-        style: int = oedepict.OEHighlightStyle_Stick,
-        scale: float = 1.0,
-        *,
-        ctx: CNotebookContext
-) -> oedepict.OEImage:
-    """
-    Convenience function to render a molecule grid
-    :param ctx: Current OpenEye rendering context
-    :param mols: Iterable of OpenEye molecules
-    :param nrows: Number of rows to display in the grid
-    :param ncols: Number of columns to display in the grid
-    :param max_width: Maximum width of the image
-    :param max_columns: Maximum number of columns (if ncols is being automatically calculated)
-    :param min_width: Minimum image width (prevents tiny images)
-    :param min_height: Minimum image height (prevents tiny images)
-    :param align: Alignment to the first molecule, or to a reference molecule
-    :param smarts: SMARTS substructure highlighting
-    :param color: SMARTS highlighting color
-    :param style: SMARTS highlighting style
-    :param scale: Image scale in the 2D grid
-    :return: Image of the molecule grid
-    """
-    # Re-scale the images
-    ctx.display_options.SetScale(ctx.display_options.GetScale() * scale)
-
-    # ---------------------------------------------------------------
-    # Input validation
-    # ---------------------------------------------------------------
-
-    # Handle single molecules
-    if isinstance(mols, oechem.OEMolBase):
-        mols = [mols]
-
-    # Make a copy of the molecules (so we do not modify them)
-    # We can use OEGraphMol here because we don't care about conformers
-    # Filter out None values first
-    mols = [oechem.OEGraphMol(mol) for mol in mols if mol is not None]
-
-    if len(mols) == 0:
-        log.warning("No molecules or display objects to render into a grid")
-        # Return a minimal 1x1 image instead of 0x0 to avoid OpenEye bug
-        return oedepict.OEImage(1, 1)
-
-    # Get the subset of molecules that will actually be displayed
-    valid = []
-
-    for idx, mol in enumerate(mols):
-        if mol is not None:
-            if isinstance(mol, oechem.OEMolBase):
-                if mol.IsValid():
-                    valid.append(mol)
-                else:
-                    log.warning(f'Molecule at index {idx} is not valid')
-
-            else:
-                log.warning(f'Object at index is not a molecule but type {type(mol).__name__}')
-
-    if len(valid) == 0:
-        log.warning("No valid molecules or display objects to render into a grid")
-        # Return a minimal 1x1 image instead of 0x0 to avoid OpenEye bug
-        return oedepict.OEImage(1, 1)
-
-    # ---------------------------------------------------------------
-    # For highlighting SMARTS
-    # ---------------------------------------------------------------
-
-    highlighers = None
-
-    if smarts is not None:
-        highlighers = []
-        # Case: Single pattern
-        if isinstance(smarts, (str, oechem.OESubSearch)):
-            highlighers.append(
-                create_structure_highlighter(
-                    smarts,
-                    color=color,
-                    style=style
-                )
-            )
-
-        else:
-            for pattern in smarts:
-                highlighers.append(
-                    create_structure_highlighter(
-                        pattern,
-                        color=color,
-                        style=style
-                    )
-                )
-
-    # ---------------------------------------------------------------
-    # For substructure alignment
-    # ---------------------------------------------------------------
-
-    align_mcss = None
-
-    if align is not None:
-
-        # If we are doing an alignment
-        if isinstance(align, bool) and align:
-            align_ref = mols[0]
-
-        elif isinstance(align, oechem.OEMolBase):
-            align_ref = align
-
-        else:
-            raise TypeError(f'Cannot initialize MCSS alignment reference from type {type(align).__name__}')
-
-        # Set up the MCSS
-        align_mcss = oechem.OEMCSSearch(oechem.OEMCSType_Approximate)
-        align_mcss.Init(align_ref, oechem.OEExprOpts_DefaultAtoms, oechem.OEExprOpts_DefaultBonds)
-
-    # ---------------------------------------------------------------
-    # Create the display objects for each molecule
-    # ---------------------------------------------------------------
-
-    displays = []
-    max_disp_width = float('-inf')
-    max_disp_height = float('-inf')
-
-    for mol in valid:
-        if align_mcss is not None:
-            oedepict.OEPrepareAlignedDepiction(mol, align_mcss)
-        else:
-            oedepict.OEPrepareDepiction(mol)
-
-        # Create the display object
-        disp = ctx.create_molecule_display(mol, min_width=min_width, min_height=min_height)
-        # disp = oedepict.OE2DMolDisplay(mol, ctx.display_options)
-
-        # Highlight SMARTS patterns
-        if highlighers is not None:
-            for highlight in highlighers:
-                highlight(disp)
-
-        displays.append(disp)
-
-        if disp.GetWidth() > max_disp_width:
-            max_disp_width = disp.GetWidth()
-
-        if disp.GetHeight() > max_disp_height:
-            max_disp_height = disp.GetHeight()
-
-    # ---------------------------------------------------------------
-    # Figure out the geometry of the full image
-    # ---------------------------------------------------------------
-    # Case: We have one molecule
-    if len(displays) == 1:
-        ncols = 1
-        nrows = 1
-
-    # Case: We are computing based on max_width
-    elif ncols is None and nrows is None:
-
-        # Number of columns we can fit into max_width
-        ncols = min(floor(max_width / max_disp_width), max_columns, len(displays))
-        nrows = ceil(len(displays) / ncols)
-
-    elif nrows is not None:
-        ncols = ceil(len(displays) / nrows)
-
-    elif ncols is not None:
-        nrows = ceil(len(displays) / ncols)
-
-    else:
-        raise RuntimeError("Cannot determine number of rows and columns in molecule grid")
-
-    # Image width and height
-    width = max_disp_width * ncols
-    height = max_disp_height * nrows
-
-    image = oedepict.OEImage(width, height)
-    grid = oedepict.OEImageGrid(image, nrows, ncols)
-
-    # Render the molecules
-    for disp, cell in zip(displays, grid.GetCells()):
-        oedepict.OERenderMolecule(cell, disp)
-
-    return image
-
-
 ########################################################################################################################
 # Register iPython formatters
 ########################################################################################################################

cnotebook/marimo_ext.py

@@ -1,12 +1,42 @@
+"""
+Marimo integration for CNotebook.
+
+This module provides MIME handlers for OpenEye objects and patches Marimo's
+internal table implementation to support molecule rendering with callbacks
+(highlighting, alignment, etc.) in Marimo's built-in DataFrame table component.
+"""
+import logging
 import pandas as pd
 from openeye import oechem, oedepict
-from .context import cnotebook_context
-from .render import oemol_to_html, oedisp_to_html, oeimage_to_html
+
+# Import oepandas for dtype checking
+try:
+    import oepandas as oepd
+    oepandas_available = True
+except ImportError:
+    oepandas_available = False
+
+from .context import cnotebook_context, get_series_context
+from .render import (
+    oemol_to_html,
+    oedisp_to_html,
+    oeimage_to_html,
+    oemol_to_disp,
+    render_empty_molecule,
+    render_invalid_molecule
+)
 from .pandas_ext import render_dataframe
 
+log = logging.getLogger("cnotebook")
+
+
+########################################################################################################################
+# MIME handlers for individual OpenEye objects
+########################################################################################################################
+
 def _display_mol(self: oechem.OEMolBase):
     ctx = cnotebook_context.get().copy()
-    ctx.image_format = "png"
+    # Allow user's image_format preference (SVG or PNG)
     return "text/html", oemol_to_html(self, ctx=ctx)
 
 oechem.OEMolBase._mime_ = _display_mol
@@ -14,21 +44,162 @@ oechem.OEMolBase._mime_ = _display_mol
 
 def _display_display(self: oedepict.OE2DMolDisplay):
     ctx = cnotebook_context.get().copy()
-    ctx.image_format = "png"
+    # Allow user's image_format preference (SVG or PNG)
     return "text/html", oedisp_to_html(self, ctx=ctx)
 
-oedepict.OE2DMolDisplay.__mime__ = _display_display
+oedepict.OE2DMolDisplay._mime_ = _display_display
 
 
 def _display_image(self: oedepict.OEImage):
     ctx = cnotebook_context.get().copy()
-    ctx.image_format = "png"
+    # Allow user's image_format preference (SVG or PNG)
     return "text/html", oeimage_to_html(self, ctx=ctx)
 
-oedepict.OEImage.__mime__ = _display_image
+oedepict.OEImage._mime_ = _display_image
 
-def display_dataframe(self: pd.DataFrame):
-    ctx = cnotebook_context.get().copy()
-    return render_dataframe(df=self, formatters=None, col_space=None)
 
-pd.DataFrame.__mime__ = display_dataframe
+########################################################################################################################
+# Formatter factories for mo.ui.table format_mapping
+########################################################################################################################
+
+def _create_molecule_formatter(ctx):
+    """
+    Create a formatter closure that renders molecules with callbacks applied.
+
+    :param ctx: CNotebookContext with callbacks (e.g., highlighting)
+    :return: Formatter function for use in mo.ui.table format_mapping
+    """
+    def formatter(mol):
+        if mol is None:
+            return ""
+
+        if not isinstance(mol, oechem.OEMolBase):
+            return str(mol)
+
+        # Handle invalid molecules
+        if not mol.IsValid():
+            return render_invalid_molecule(ctx=ctx)
+
+        # Handle empty molecules
+        if mol.NumAtoms() == 0:
+            return render_empty_molecule(ctx=ctx)
+
+        # Create display object
+        disp = oemol_to_disp(mol, ctx=ctx)
+
+        # Apply callbacks (highlighting, etc.)
+        if ctx.callbacks:
+            for callback in ctx.callbacks:
+                callback(disp)
+
+        # Return display object
+        return disp
+
+    return formatter
+
+
+def _create_display_formatter(ctx):
+    """
+    Create a formatter closure that renders OE2DMolDisplay objects.
+
+    :param ctx: CNotebookContext for rendering options
+    :return: Formatter function for use in mo.ui.table format_mapping
+    """
+    def formatter(disp):
+        if disp is None:
+            return ""
+
+        if not isinstance(disp, oedepict.OE2DMolDisplay):
+            return str(disp)
+
+        if not disp.IsValid():
+            return str(disp)
+
+        # Copy the display to avoid modifying the original
+        disp_copy = oedepict.OE2DMolDisplay(disp)
+
+        # Apply callbacks if any
+        if ctx.callbacks:
+            for callback in ctx.callbacks:
+                callback(disp_copy)
+
+        return disp_copy
+
+    return formatter
+
+
+########################################################################################################################
+# Marimo DataFrame formatter registration
+#
+# This registers a custom formatter with Marimo's OPINIONATED_FORMATTERS registry
+# to handle DataFrames containing molecule columns. The formatter:
+# - Detects MoleculeDtype and DisplayDtype columns
+# - Creates format_mapping entries that apply callbacks (highlighting, alignment, etc.)
+# - Returns OE2DMolDisplay objects which Marimo renders via their _mime_() method
+########################################################################################################################
+
+try:
+    import marimo as mo
+    # noinspection PyProtectedMember,PyUnusedImports
+    from marimo._output.formatting import OPINIONATED_FORMATTERS
+    # noinspection PyProtectedMember,PyUnusedImports
+    from marimo._plugins.ui._impl.table import table
+
+
+    # 1. Define the custom formatting logic
+    def marimo_pandas_formatter(df: pd.DataFrame):
+        """
+        Monkey patch the Marimo DataFrame formatter
+        """
+        format_mapping = {}
+
+        # Check for MoleculeDtype / DisplayDtype (OEPandas specific)
+        if oepandas_available:
+            for col in df.columns:
+                dtype = df[col].dtype
+
+                if isinstance(dtype, oepd.MoleculeDtype):
+                    arr = df[col].array
+                    ctx = get_series_context(arr.metadata).copy()
+                    format_mapping[col] = _create_molecule_formatter(ctx)
+
+                elif isinstance(dtype, oepd.DisplayDtype):
+                    arr = df[col].array
+                    ctx = get_series_context(arr.metadata).copy()
+                    format_mapping[col] = _create_display_formatter(ctx)
+
+        # Return a Marimo table with our custom mapping
+        # noinspection PyProtectedMember,PyTypeChecker
+        return table(df, selection=None, format_mapping=format_mapping, pagination=True)._mime_()
+
+    # 2. Inject into the Registry
+    def install_marimo_pandas_formatter():
+        # Check if we've already installed it to avoid duplicates
+        for typ, func in OPINIONATED_FORMATTERS.formatters.items():
+            if typ is pd.DataFrame and func.__name__ == "marimo_pandas_formatter":
+                return  # Already installed
+
+        OPINIONATED_FORMATTERS.formatters[pd.DataFrame] = marimo_pandas_formatter
+
+    # Do the installation
+    install_marimo_pandas_formatter()
+
+except (ImportError, AttributeError) as ex:
+    # Marimo not installed or API changed - skip formatter registration
+    log.debug(f'Marimo formatter registration skipped: {ex}')
+
+
+########################################################################################################################
+# Fallback DataFrame MIME handler for non-Marimo contexts
+########################################################################################################################
+
+def _display_dataframe(self: pd.DataFrame):
+    """
+    Fallback MIME hook for Pandas DataFrames in non-Marimo contexts.
+
+    In Marimo, the internal table patch handles DataFrame display.
+    This is used for static exports or other tools that check _mime_.
+    """
+    return "text/html", render_dataframe(df=self, formatters=None, col_space=None)
+
+pd.DataFrame._mime_ = _display_dataframe

cnotebook/pandas_ext.py

@@ -126,9 +126,17 @@ def render_dataframe(
     # Render columns with MoleculeDtype
     molecule_columns = set()
 
+    # Capture metadata from ORIGINAL DataFrame BEFORE copying
+    # (df.copy() may not preserve array metadata)
+    original_metadata_by_col = {}
+
     for col in df.columns:
         if isinstance(df.dtypes[col], oepd.MoleculeDtype):
             molecule_columns.add(col)
+            # Get metadata from the original array before any copying
+            arr = df[col].array
+            if hasattr(arr, 'metadata') and arr.metadata:
+                original_metadata_by_col[col] = arr.metadata.copy()
 
     # We need to copy both the DataFrame and the molecules, because we modify them in-place to render them
     df = df.copy()
@@ -137,7 +145,11 @@ def render_dataframe(
         # Direct assignment to help IDE understand this is a MoleculeArray
         arr = df[col].array
         assert isinstance(arr, oepd.MoleculeArray)
-        df[col] = pd.Series(arr.deepcopy(), index=df[col].index, dtype=oepd.MoleculeDtype())
+        # Use preserved metadata from original DataFrame (not the copy which may have lost it)
+        original_metadata = original_metadata_by_col.get(col, {})
+        new_arr = arr.deepcopy()
+        new_arr.metadata.update(original_metadata)
+        df[col] = pd.Series(new_arr, index=df[col].index, dtype=oepd.MoleculeDtype())
 
     # ---------------------------------------------------
     # Molecule columns
@@ -522,7 +534,7 @@ class SeriesRecalculateDepictionCoordinatesAccessor:
 
 
 @register_dataframe_accessor("reset_depictions")
-class SeriesResetDepictionsAccessor:
+class DataFrameResetDepictionsAccessor:
     def __init__(self, pandas_obj: pd.DataFrame):
         self._obj = pandas_obj
 

cnotebook/render.py

@@ -2,6 +2,9 @@ import logging
 import base64
 from .context import CNotebookContext, pass_cnotebook_context
 from openeye import oechem, oedepict
+from typing import Literal
+from math import floor, ceil
+from collections.abc import Iterable, Sequence
 
 log = logging.getLogger("cnotebook")
 
@@ -196,3 +199,197 @@ def oeimage_to_html(image: oedepict.OEImage, *, ctx: CNotebookContext) -> str:
         image_bytes=image_bytes,
         wrap_svg=ctx.structure_scale != oedepict.OEScale_AutoScale
     )
+
+
+@pass_cnotebook_context
+def render_molecule_grid(
+        mols: Sequence[oechem.OEMolBase],
+        nrows: int | None = None,
+        ncols: int | None = None,
+        max_width: int = 1280,
+        max_columns: int = 100,
+        min_width: int | None = None,
+        min_height: int | None = None,
+        align: oechem.OEMolBase | Literal["first"] | None = None,
+        smarts: str | Iterable[str] | oechem.OESubSearch | Iterable[oechem.OESubSearch] | None = None,
+        color: oechem.OEColor = oechem.OEColor(oechem.OELightBlue),
+        style: int = oedepict.OEHighlightStyle_Stick,
+        scale: float = 1.0,
+        *,
+        ctx: CNotebookContext
+) -> oedepict.OEImage:
+    """
+    Convenience function to render a molecule grid
+    :param ctx: Current OpenEye rendering context
+    :param mols: Iterable of OpenEye molecules
+    :param nrows: Number of rows to display in the grid
+    :param ncols: Number of columns to display in the grid
+    :param max_width: Maximum width of the image
+    :param max_columns: Maximum number of columns (if ncols is being automatically calculated)
+    :param min_width: Minimum image width (prevents tiny images)
+    :param min_height: Minimum image height (prevents tiny images)
+    :param align: Alignment to the first molecule, or to a reference molecule
+    :param smarts: SMARTS substructure highlighting
+    :param color: SMARTS highlighting color
+    :param style: SMARTS highlighting style
+    :param scale: Image scale in the 2D grid
+    :return: Image of the molecule grid
+    """
+    from .helpers import create_structure_highlighter
+
+    # Re-scale the images
+    ctx.display_options.SetScale(ctx.display_options.GetScale() * scale)
+
+    # ---------------------------------------------------------------
+    # Input validation
+    # ---------------------------------------------------------------
+
+    # Handle single molecules
+    if isinstance(mols, oechem.OEMolBase):
+        mols = [mols]
+
+    # Make a copy of the molecules (so we do not modify them)
+    # We can use OEGraphMol here because we don't care about conformers
+    # Filter out None values first
+    mols = [oechem.OEGraphMol(mol) for mol in mols if mol is not None]
+
+    if len(mols) == 0:
+        log.warning("No molecules or display objects to render into a grid")
+        # Return a minimal 1x1 image instead of 0x0 to avoid OpenEye bug
+        return oedepict.OEImage(1, 1)
+
+    # Get the subset of molecules that will actually be displayed
+    valid = []
+
+    for idx, mol in enumerate(mols):
+        if mol is not None:
+            if isinstance(mol, oechem.OEMolBase):
+                if mol.IsValid():
+                    valid.append(mol)
+                else:
+                    log.warning(f'Molecule at index {idx} is not valid')
+
+            else:
+                log.warning(f'Object at index is not a molecule but type {type(mol).__name__}')
+
+    if len(valid) == 0:
+        log.warning("No valid molecules or display objects to render into a grid")
+        # Return a minimal 1x1 image instead of 0x0 to avoid OpenEye bug
+        return oedepict.OEImage(1, 1)
+
+    # ---------------------------------------------------------------
+    # For highlighting SMARTS
+    # ---------------------------------------------------------------
+
+    highlighers = None
+
+    if smarts is not None:
+        highlighers = []
+        # Case: Single pattern
+        if isinstance(smarts, (str, oechem.OESubSearch)):
+            highlighers.append(
+                create_structure_highlighter(
+                    smarts,
+                    color=color,
+                    style=style
+                )
+            )
+
+        else:
+            for pattern in smarts:
+                highlighers.append(
+                    create_structure_highlighter(
+                        pattern,
+                        color=color,
+                        style=style
+                    )
+                )
+
+    # ---------------------------------------------------------------
+    # For substructure alignment
+    # ---------------------------------------------------------------
+
+    align_mcss = None
+
+    if align is not None:
+
+        # If we are doing an alignment
+        if isinstance(align, bool) and align:
+            align_ref = mols[0]
+
+        elif isinstance(align, oechem.OEMolBase):
+            align_ref = align
+
+        else:
+            raise TypeError(f'Cannot initialize MCSS alignment reference from type {type(align).__name__}')
+
+        # Set up the MCSS
+        align_mcss = oechem.OEMCSSearch(oechem.OEMCSType_Approximate)
+        align_mcss.Init(align_ref, oechem.OEExprOpts_DefaultAtoms, oechem.OEExprOpts_DefaultBonds)
+
+    # ---------------------------------------------------------------
+    # Create the display objects for each molecule
+    # ---------------------------------------------------------------
+
+    displays = []
+    max_disp_width = float('-inf')
+    max_disp_height = float('-inf')
+
+    for mol in valid:
+        if align_mcss is not None:
+            oedepict.OEPrepareAlignedDepiction(mol, align_mcss)
+        else:
+            oedepict.OEPrepareDepiction(mol)
+
+        # Create the display object
+        disp = ctx.create_molecule_display(mol, min_width=min_width, min_height=min_height)
+
+        # Highlight SMARTS patterns
+        if highlighers is not None:
+            for highlight in highlighers:
+                highlight(disp)
+
+        displays.append(disp)
+
+        if disp.GetWidth() > max_disp_width:
+            max_disp_width = disp.GetWidth()
+
+        if disp.GetHeight() > max_disp_height:
+            max_disp_height = disp.GetHeight()
+
+    # ---------------------------------------------------------------
+    # Figure out the geometry of the full image
+    # ---------------------------------------------------------------
+    # Case: We have one molecule
+    if len(displays) == 1:
+        ncols = 1
+        nrows = 1
+
+    # Case: We are computing based on max_width
+    elif ncols is None and nrows is None:
+
+        # Number of columns we can fit into max_width
+        ncols = min(floor(max_width / max_disp_width), max_columns, len(displays))
+        nrows = ceil(len(displays) / ncols)
+
+    elif nrows is not None:
+        ncols = ceil(len(displays) / nrows)
+
+    elif ncols is not None:
+        nrows = ceil(len(displays) / ncols)
+
+    else:
+        raise RuntimeError("Cannot determine number of rows and columns in molecule grid")
+
+    # Image width and height
+    width = max_disp_width * ncols
+    height = max_disp_height * nrows
+
+    image = oedepict.OEImage(width, height)
+    grid = oedepict.OEImageGrid(image, nrows, ncols)
+
+    # Render the molecules
+    for disp, cell in zip(displays, grid.GetCells()):
+        oedepict.OERenderMolecule(cell, disp)
+
+    return image

{cnotebook-1.0.1.dist-info → cnotebook-1.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cnotebook
-Version: 1.0.1
+Version: 1.2.0
 Summary: Chemistry visualization in Jupyter Notebooks with the OpenEye Toolkits
 Author-email: Scott Arne Johnson <scott.arne.johnson@gmail.com>
 License-Expression: MIT
@@ -23,12 +23,12 @@ Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Operating System :: OS Independent
 Classifier: Framework :: Jupyter
 Classifier: Framework :: IPython
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: pandas<3.0.0,>=2.0.0
+Requires-Dist: pandas>=2.2.0
 Requires-Dist: oepandas>=2.0.0
-Requires-Dist: openeye-toolkits
+Requires-Dist: openeye-toolkits>=2025.2.1
 Provides-Extra: dev
 Requires-Dist: invoke; extra == "dev"
 Requires-Dist: build; extra == "dev"
@@ -38,7 +38,12 @@ Requires-Dist: pytest; extra == "test"
 Requires-Dist: pytest-cov; extra == "test"
 Dynamic: license-file
 
-# CNotebook - Chemistry Visualization for Jupyter & Marimo
+# CNotebook
+
+[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
+[![OpenEye Toolkits](https://img.shields.io/badge/OpenEye-2025.2.1+-green.svg)](https://www.eyesopen.com/toolkits)
+[![Pandas 2.2+](https://img.shields.io/badge/pandas-2.2+-orange.svg)](https://pandas.pydata.org/)
+
 
 **Author:** Scott Arne Johnson ([scott.arne.johnson@gmail.com](mailto:scott.arne.johnson@gmail.com))
 
@@ -70,33 +75,33 @@ mol
 
 That's it! CNotebook automatically registers formatters so that OpenEye molecule objects display as chemical structures instead of cryptic text representations.
 
-## 📚 Features
+## Features
 
-### ✨ Automatic Rendering
+### Automatic Rendering
 - **Zero Configuration**: Just import and go - molecules automatically render as structures
 - **Multiple Formats**: Supports both Jupyter Notebooks and Marimo environments
 - **Smart Detection**: Automatically detects your notebook environment
 
-### 🧪 Molecule Support
+### Molecule Support
 - **OEMol Objects**: Direct rendering of `oechem.OEMolBase` derived objects
 - **OE2DMolDisplay**: Advanced rendering with custom depiction options
 - **Pandas Integration**: Seamless rendering in DataFrames with oepandas
 
-### 🎨 Visualization Options
+### Visualization Options
 - **Multiple Formats**: PNG (default) or SVG output
 - **Customizable Sizing**: Configurable width, height, and scaling
 - **Grid Layouts**: Multi-molecule grid displays
 - **Substructure Highlighting**: SMARTS pattern highlighting
 - **Molecular Alignment**: Align molecules to reference structures
 
-### 📊 Pandas Integration
+### Pandas Integration
 - **DataFrame Rendering**: Automatic molecule column detection and rendering
 - **Column Highlighting**: Highlight different patterns per row
 - **Alignment Tools**: Align molecular depictions in DataFrames
 - **Fingerprint Similarity**: Visual similarity coloring
 - **Property Calculation**: Chemistry-aware DataFrame operations
 
-## 🛠️ Environment Support
+## Environment Support
 
 ### Jupyter Notebooks
 CNotebook automatically integrates with Jupyter when imported:
@@ -126,7 +131,7 @@ oechem.OESmilesToMol(mol, "c1ccccc1")
 mol  # Automatically renders as PNG for Marimo compatibility
 ```
 
-## 📖 Advanced Usage
+## Advanced Usage
 
 ### Rendering Configuration
 
@@ -204,7 +209,7 @@ df.fingerprint_similarity("Molecule", reference_mol, inplace=True)
 df  # Shows similarity coloring and Tanimoto coefficients
 ```
 
-## 📁 Demo Notebooks
+## Demo Notebooks
 
 Explore comprehensive examples in the `demos/` directory:
 
@@ -228,7 +233,7 @@ Explore comprehensive examples in the `demos/` directory:
 - High-quality crisp molecular graphics
 - SVG compatibility considerations
 
-## 🔧 Configuration Options
+## Configuration Options
 
 ### Global Context Settings
 
@@ -254,7 +259,7 @@ ctx.scale = 1.0          # Scaling factor
 - **Marimo**: Automatically uses PNG format for compatibility
 - **Console**: Falls back to string representations
 
-## 🤝 Contributing
+## Contributing
 
 We welcome contributions! Please ensure your code:
 - Follows existing code style and conventions
@@ -262,11 +267,11 @@ We welcome contributions! Please ensure your code:
 - Works with both Jupyter and Marimo environments
 - Maintains compatibility with OpenEye Toolkits
 
-## 📄 License
+## License
 
 This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.
 
-## 🐛 Issues & Support
+## Issues & Support
 
 For bug reports, feature requests, or general support, please open an issue on GitHub or contact the author at [scott.arne.johnson@gmail.com](mailto:scott.arne.johnson@gmail.com).
 

cnotebook-1.2.0.dist-info/RECORD

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cnotebook-1.0.1.dist-info/RECORD

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