Migrated the remaining generics from biocgenerics.

src/biocutils/__init__.py

@@ -33,4 +33,7 @@
 from .combine_columns import combine_columns
 from .combine_sequences import combine_sequences
 
+from .extract_row_names import extract_row_names
+from .extract_column_names import extract_column_names
+from .show_as_cell import show_as_cell
 from .convert_to_dense import convert_to_dense

src/biocutils/extract_column_names.py

@@ -0,0 +1,30 @@
+from functools import singledispatch
+from typing import Any
+import numpy
+
+from .package_utils import is_package_installed
+
+__author__ = "jkanche"
+__copyright__ = "jkanche"
+__license__ = "MIT"
+
+
+@singledispatch
+def extract_column_names(x: Any) -> numpy.ndarray:
+    """Access column names from 2-dimensional representations.
+
+    Args:
+        x: Any object.
+
+    Returns:
+        Array of strings containing column names.
+    """
+    raise NotImplementedError(f"`colnames` is not supported for class: '{type(x)}'.")
+
+
+if is_package_installed("pandas") is True:
+    from pandas import DataFrame
+
+    @extract_column_names.register(DataFrame)
+    def _colnames_dataframe(x: DataFrame) -> list:
+        return numpy.array(x.columns, dtype=str)

src/biocutils/extract_row_names.py

@@ -0,0 +1,30 @@
+from functools import singledispatch
+from typing import Any
+import numpy
+
+from .package_utils import is_package_installed
+
+__author__ = "jkanche"
+__copyright__ = "jkanche"
+__license__ = "MIT"
+
+
+@singledispatch
+def extract_row_names(x: Any) -> numpy.ndarray:
+    """Access row names from 2-dimensional representations.
+
+    Args:
+        x: Any object.
+
+    Returns:
+        Array of strings containing row names.
+    """
+    raise NotImplementedError(f"`rownames` do not exist for class: '{type(x)}'.")
+
+
+if is_package_installed("pandas") is True:
+    from pandas import DataFrame
+
+    @extract_row_names.register(DataFrame)
+    def _rownames_dataframe(x: DataFrame) -> list:
+        return numpy.array(x.index, dtype=str)

src/biocutils/show_as_cell.py

@@ -0,0 +1,26 @@
+from typing import Sequence, List, Any, Optional
+from functools import singledispatch
+
+
+@singledispatch
+def show_as_cell(x: Any, indices: Sequence[int]) -> List[str]:
+    """
+    Show the contents of ``x`` as a cell of a table, typically for use in the
+    ``__str__`` method of a class that contains ``x``.
+
+    Args:
+        x:
+            Any object. By default, we assume that it can be treated as
+            a sequence, with a valid ``__getitem__`` method for an index.
+
+        indices:
+            List of indices to be extracted.
+
+    Returns:
+        List of strings of length equal to ``indices``, containing a
+        string summary of each of the specified elements of ``x``.
+    """
+    output = []
+    for i in indices:
+        output.append(str(x[i]))
+    return output

tests/test_extract_column_names.py

@@ -0,0 +1,8 @@
+from biocutils import extract_column_names
+import pandas
+import numpy
+
+
+def test_pandas_column_names():
+    p = pandas.DataFrame({ "A": [1,2,3,4,5], "B": ["a", "b", "c", "d", "e" ]})
+    assert (extract_column_names(p) == numpy.array(["A", "B"])).all()

tests/test_extract_row_names.py

@@ -0,0 +1,10 @@
+from biocutils import extract_row_names
+import pandas
+import numpy
+
+
+def test_pandas_row_names():
+    p = pandas.DataFrame({ "A": [1,2,3,4,5] })
+    rn = ["a", "b", "c", "d", "e" ]
+    p.index = rn
+    assert (extract_row_names(p) == numpy.array(rn)).all()

tests/test_show_as_cell.py

@@ -0,0 +1,6 @@
+from biocutils import show_as_cell
+
+
+def test_show_as_cell():
+    assert show_as_cell([1, 2, 3, 4], range(4)) == ["1", "2", "3", "4"]
+    assert show_as_cell([1, 2, 3, 4], [1, 3]) == ["2", "4"]