[MNT] Remove deprecated code and columns (#235)

* remove deprecated code and columns

* remove deprecated functions

* remove annotation

* 💄

Author: lmmentel

alembic/versions/e7191e2ea28b_drop__annotation.py

@@ -0,0 +1,24 @@
+"""drop _annotation
+
+Revision ID: e7191e2ea28b
+Revises: 285dd74e23de
+Create Date: 2025-03-22 18:56:26.410019
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = 'e7191e2ea28b'
+down_revision = '285dd74e23de'
+branch_labels = None
+depends_on = None
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+    with op.batch_alter_table("elements") as batch_op:
+        batch_op.drop_column("_annotation")
+
+def downgrade():
+    pass

docs/source/api/mendeleev.fetch.rst

@@ -8,12 +8,9 @@
 
    .. autosummary::
 
-      add_plot_columns
       fetch_electronegativities
       fetch_ionic_radii
       fetch_ionization_energies
       fetch_neutral_data
       fetch_table
-      get_app_data
-      get_zeff
 

mendeleev/elements.db

@@ -3,37 +3,16 @@
 from typing import List, Union
 
 import pandas as pd
-from deprecated import deprecated
 from sqlalchemy.dialects import sqlite
 from sqlalchemy import text
 
-from mendeleev import element, get_all_elements
-from mendeleev import __version__ as version
+from mendeleev import get_all_elements
 from mendeleev.electronegativity import allred_rochow, gordy, cottrell_sutton
 
 from .db import get_engine, get_session
 from .models import Element, IonizationEnergy
 
 
-@deprecated(
-    reason="This function is deprecated and will be removed in the future version."
-)
-def get_zeff(an, method: str = "slater") -> float:
-    """
-    A helper function to calculate the effective nuclear charge.
-
-    Args:
-        method: str
-            Method to use, one of "slater" or "clementi", default="slater"
-
-    Returns:
-        zeff: float
-            Effective nuclear charge
-    """
-    e = element(an)
-    return e.zeff(method=method)
-
-
 def fetch_table(table: str, **kwargs) -> pd.DataFrame:
     """
     Return a table from the database as :py:class:`pandas.DataFrame`
@@ -242,53 +221,3 @@ def fetch_ionic_radii(radius: str = "ionic_radius") -> pd.DataFrame:
     return ir.pivot_table(
         columns="coordination", values=radius, index=["atomic_number", "charge"]
     )
-
-
-@deprecated(
-    reason="This function is deprecated and will be removed in the future version."
-)
-def add_plot_columns(elements: pd.DataFrame) -> pd.DataFrame:
-    """
-    Add columns needed for the creating the plots
-
-    Args:
-        elements: pd.DataFrame
-    """
-    mask = elements["group_id"].notnull()
-
-    elements.loc[mask, "x"] = elements.loc[mask, "group_id"].astype(int)
-    elements.loc[:, "y"] = elements.loc[:, "period"].astype(int)
-
-    elements.loc[mask, "group_name"] = (
-        elements.loc[mask, "group_id"].astype(int).astype(str)
-    )
-    elements.loc[~mask, "group_name"] = "f block"
-
-    for period in [6, 7]:
-        mask = (elements["block"] == "f") & (elements["period"] == period)
-        elements.loc[mask, "x"] = (
-            elements.loc[mask, "atomic_number"]
-            - elements.loc[mask, "atomic_number"].min()
-            + 3
-        )
-        elements.loc[mask, "y"] = elements.loc[mask, "period"] + 2.5
-
-    # additional columns for positioning of the text
-
-    elements.loc[:, "y_symbol"] = elements["y"] - 0.05
-    elements.loc[:, "y_anumber"] = elements["y"] - 0.3
-    elements.loc[:, "y_name"] = elements["y"] + 0.18
-
-    return elements
-
-
-@deprecated(
-    reason="This function is deprecated and will be removed in the future version."
-)
-def get_app_data() -> None:
-    "write a file with the neutral data"
-    data = fetch_neutral_data()
-    data = add_plot_columns(data)
-    fname = "neutral_{0:s}.pkl".format(version)
-    data.to_pickle(fname)
-    print("wrote file: ", fname)

mendeleev/fetch.py

@@ -61,7 +61,6 @@ class Element(Base):
     Args:
         abundance_crust (float): Abundance in the earth's crust in mg/kg
         abundance_sea (float): Abundance in the seas in mg/L
-        annotation (str): Annotations regarding the data. Deprecated.
         atomic_number (int): Atomic number
         atomic_radius (float): Atomic radius in pm
         atomic_radius_rahm (float): Atomic radius by Rahm et al. in pm
@@ -159,8 +158,6 @@ class Element(Base):
 
     abundance_crust = Column(Float)
     abundance_sea = Column(Float)
-    # TODO: remove in a future version
-    _annotation = Column(String)
     atomic_number = Column(Integer, primary_key=True)
     atomic_radius = Column(Float)
     atomic_radius_rahm = Column(Float)
@@ -326,18 +323,6 @@ def isotope(self, mass_number: int) -> Isotope:
         else:
             return selected
 
-    @property
-    def annotation(self):
-        "Temporary property before before removing annotation"
-        # TODO: remove in a future version
-        warnings.warn(
-            "The 'annotation' attribute is deprecated and will be removed in a future version. "
-            "Use the 'annotations' attribute of the 'PropertyMetadata' class instead.",
-            DeprecationWarning,
-            stacklevel=2,
-        )
-        return self._annotation
-
     @property
     def boiling_point(self) -> float | None:
         """Proxy for boiling point from the ``PhaseTransition`` object.