Merge pull request #149 from Hekstra-Lab/append

Remove `DataSet.append()` due to upcoming deprecation in Pandas

reciprocalspaceship/concat.py

@@ -27,10 +27,6 @@ def concat(*args, check_isomorphous=True, **kwargs):
     rs.DataSet or rs.DataSeries
         Returns rs.DataSeries when concatenating rs.DataSeries along the
         index (axis=0). Returns rs.DataSet in all other cases.
-
-    See Also
-    --------
-    DataSet.append : Concatenate DataSets
     """
     objs = kwargs.get("objs", args[0])
     objs, objs_tee = tee(objs)

reciprocalspaceship/dataset.py

@@ -3,7 +3,7 @@
 import pandas as pd
 from pandas.api.types import is_complex_dtype
 
-from reciprocalspaceship import dtypes
+from reciprocalspaceship import concat, dtypes
 from reciprocalspaceship.dataseries import DataSeries
 from reciprocalspaceship.decorators import (
     cellify,
@@ -404,50 +404,6 @@ def from_structurefactor(self, sf_key):
         """
         return from_structurefactor(self[sf_key])
 
-    def append(self, *args, check_isomorphous=True, **kwargs):
-        """
-        Append rows of `other` to the end of calling DataSet, returning
-        a new DataSet object. Any columns in `other` that are not present
-        in the calling DataSet are added as new columns.
-
-        For additional documentation on accepted arguments, see the
-        `Pandas DataFrame.append() API <https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.append.html>`_.
-
-        Parameters
-        ----------
-        check_isomorphous : bool
-            If True, the spacegroup and cell attributes of DataSets in `other`
-            will be compared to those of the calling DataSet to ensure
-            they are isomorphous.
-
-        Returns
-        -------
-        rs.DataSet
-
-        See Also
-        --------
-        concat : Concatenate ``rs`` objects
-        """
-        other = kwargs.get("other", args[0])
-        if check_isomorphous:
-            if isinstance(other, (list, tuple)):
-                for o in other:
-                    if isinstance(o, DataSet) and not self.is_isomorphous(o):
-                        raise ValueError("DataSet in `other` is not isomorphous")
-            else:
-                if isinstance(other, DataSet) and not self.is_isomorphous(other):
-                    raise ValueError("`other` DataSet is not isomorphous")
-        result = super().append(*args, **kwargs)
-
-        # If `ignore_index=True`, the _index_dtypes attribute should
-        # be reset.
-        if isinstance(result.index, pd.RangeIndex) and self._index_dtypes != {}:
-            result.__finalize__(self)
-            result._index_dtypes = {}
-            return result
-
-        return result.__finalize__(self)
-
     def merge(self, *args, check_isomorphous=True, **kwargs):
         """
         Merge DataSet or named DataSeries using a database-style join on
@@ -912,7 +868,7 @@ def stack_anomalous(
         column_mapping_minus = dict(zip(minus_labels, new_labels))
         dataset_plus.rename(columns=column_mapping_plus, inplace=True)
         dataset_minus.rename(columns=column_mapping_minus, inplace=True)
-        F = dataset_plus.append(dataset_minus)
+        F = concat([dataset_plus, dataset_minus])
         for label in new_labels:
             F[label] = F[label].from_friedel_dtype()
 
@@ -1216,7 +1172,7 @@ def expand_to_p1(self):
             ds = self.copy()
             ds["M/ISYM"] = isym
             ds["M/ISYM"] = ds["M/ISYM"].astype("M/ISYM")
-            p1 = p1.append(ds.hkl_to_observed(m_isym="M/ISYM"))
+            p1 = concat([p1, ds.hkl_to_observed(m_isym="M/ISYM")])
             p1.drop_duplicates(subset=["H", "K", "L"], inplace=True)
 
         # Restrict to p1 ASU
@@ -1236,7 +1192,7 @@ def expand_anomalous(self):
         DataSet
         """
         friedel = self.apply_symop("-x,-y,-z")
-        return self.append(friedel)
+        return concat([self, friedel])
 
     @inplace
     def canonicalize_phases(self, inplace=False):

reciprocalspaceship/utils/stats.py

@@ -77,7 +77,7 @@ def compute_redundancy(
             spacegroup=spacegroup,
         ).set_index(["H", "K", "L"])
         ASU = ASU.loc[ASU.index.difference(mult.index)]
-        mult = mult.append(ASU)
+        mult = rs.concat([mult, ASU])
 
     mult = mult.sort_index()
     return mult.get_hkls(), mult["Count"].to_numpy(np.int32)

tests/test_dataset_preserve_attributes.py

@@ -37,65 +37,6 @@ def test_concat(data_fmodel, check_isomorphous, sg, ignore_index):
             assert result.__getattr__(attr) == data_fmodel.__getattr__(attr)
 
 
-@pytest.mark.parametrize("check_isomorphous", [True, False])
-@pytest.mark.parametrize("sg", [gemmi.SpaceGroup(19), gemmi.SpaceGroup(96)])
-@pytest.mark.parametrize("ignore_index", [True, False])
-def test_append(data_fmodel, check_isomorphous, sg, ignore_index):
-    """
-    Test whether attributes of DataSet are preserved through calls to
-    DataSet.append()
-    """
-    other = data_fmodel.copy(deep=True)
-    other.spacegroup = sg
-    if check_isomorphous and sg.number == 19:
-        with pytest.raises(ValueError):
-            result = data_fmodel.append(
-                other, ignore_index, check_isomorphous=check_isomorphous
-            )
-    else:
-        result = data_fmodel.append(
-            other, ignore_index, check_isomorphous=check_isomorphous
-        )
-        assert isinstance(result, rs.DataSet)
-        assert len(result) == len(data_fmodel) * 2
-        if ignore_index:
-            assert result._index_dtypes == {}
-        for attr in data_fmodel._metadata:
-            if attr == "_index_dtypes":
-                continue
-            assert result.__getattr__(attr) == data_fmodel.__getattr__(attr)
-
-
-@pytest.mark.parametrize("check_isomorphous", [True, False])
-@pytest.mark.parametrize("sg", [gemmi.SpaceGroup(19), gemmi.SpaceGroup(96)])
-@pytest.mark.parametrize("ignore_index", [True, False])
-def test_append_list(data_fmodel, check_isomorphous, sg, ignore_index):
-    """
-    Test whether attributes of DataSet are preserved through calls to
-    DataSet.append() using a list for `other` argument
-    """
-    other = data_fmodel.copy(deep=True)
-    other.spacegroup = sg
-    other = [other] * 3
-    if check_isomorphous and sg.number == 19:
-        with pytest.raises(ValueError):
-            result = data_fmodel.append(
-                other, ignore_index, check_isomorphous=check_isomorphous
-            )
-    else:
-        result = data_fmodel.append(
-            other, ignore_index, check_isomorphous=check_isomorphous
-        )
-        assert isinstance(result, rs.DataSet)
-        assert len(result) == len(data_fmodel) * 4
-        if ignore_index:
-            assert result._index_dtypes == {}
-        for attr in data_fmodel._metadata:
-            if attr == "_index_dtypes":
-                continue
-            assert result.__getattr__(attr) == data_fmodel.__getattr__(attr)
-
-
 @pytest.mark.parametrize("check_isomorphous", [True, False])
 @pytest.mark.parametrize("sg", [gemmi.SpaceGroup(19), gemmi.SpaceGroup(96)])
 def test_merge(data_fmodel, check_isomorphous, sg):