From 2d484e064ae80c1b7207becad99708a8090cdc5a Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Tue, 7 Nov 2023 17:00:43 -0800
Subject: [PATCH] Migrated the remaining generics from biocgenerics.

---
 src/biocutils/__init__.py             |  3 +++
 src/biocutils/extract_column_names.py | 30 +++++++++++++++++++++++++++
 src/biocutils/extract_row_names.py    | 30 +++++++++++++++++++++++++++
 src/biocutils/show_as_cell.py         | 26 +++++++++++++++++++++++
 tests/test_extract_column_names.py    |  8 +++++++
 tests/test_extract_row_names.py       | 10 +++++++++
 tests/test_show_as_cell.py            |  6 ++++++
 7 files changed, 113 insertions(+)
 create mode 100644 src/biocutils/extract_column_names.py
 create mode 100644 src/biocutils/extract_row_names.py
 create mode 100644 src/biocutils/show_as_cell.py
 create mode 100644 tests/test_extract_column_names.py
 create mode 100644 tests/test_extract_row_names.py
 create mode 100644 tests/test_show_as_cell.py

diff --git a/src/biocutils/__init__.py b/src/biocutils/__init__.py
index 783b530..d6531ef 100644
--- a/src/biocutils/__init__.py
+++ b/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
diff --git a/src/biocutils/extract_column_names.py b/src/biocutils/extract_column_names.py
new file mode 100644
index 0000000..04d0104
--- /dev/null
+++ b/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)
diff --git a/src/biocutils/extract_row_names.py b/src/biocutils/extract_row_names.py
new file mode 100644
index 0000000..e9f06ce
--- /dev/null
+++ b/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)
diff --git a/src/biocutils/show_as_cell.py b/src/biocutils/show_as_cell.py
new file mode 100644
index 0000000..83f1d30
--- /dev/null
+++ b/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
diff --git a/tests/test_extract_column_names.py b/tests/test_extract_column_names.py
new file mode 100644
index 0000000..63be726
--- /dev/null
+++ b/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()
diff --git a/tests/test_extract_row_names.py b/tests/test_extract_row_names.py
new file mode 100644
index 0000000..92e681d
--- /dev/null
+++ b/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()
diff --git a/tests/test_show_as_cell.py b/tests/test_show_as_cell.py
new file mode 100644
index 0000000..3a5bed6
--- /dev/null
+++ b/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"]