Renaming module feature_table as table (scikit-bio#1997)

* renamed feature_table as table

* added table to documentation

* fixed docstring format

doc/source/index.rst

@@ -72,5 +72,6 @@ API Reference
    workflow
    diversity
    stats
+   table
    metadata
    util

doc/source/table.rst

@@ -0,0 +1 @@
+.. automodule:: skbio.table

skbio/__init__.py

@@ -18,7 +18,7 @@
 from skbio.tree import TreeNode, nj
 from skbio.io import read, write
 from skbio.stats.ordination import OrdinationResults
-from skbio.feature_table import Table
+from skbio.table import Table
 import skbio.diversity  # noqa
 import skbio.stats.evolve  # noqa
 
@@ -37,7 +37,7 @@
     "read",
     "write",
     "OrdinationResults",
-    "Table"
+    "Table",
 ]
 
 __credits__ = "https://github.com/scikit-bio/scikit-bio/graphs/contributors"

skbio/diversity/_util.py

@@ -161,13 +161,13 @@ def _check_taxa_alias(taxa, tree, otu_ids):
 
 
 def _table_to_numpy(table):
-    """Convert a skbio.feature_table.Table to a dense representation.
+    """Convert a skbio.table.Table to a dense representation.
 
     This is a stop-gap solution to allow current Table objects to interoperate
     with existing driver methods, until they transition to be "sparse" aware.
     """
     sample_ids = list(table.ids())
-    obs_ids = list(table.ids(axis='observation'))
+    obs_ids = list(table.ids(axis="observation"))
 
     if table.is_empty():
         counts = np.array([[]] * len(sample_ids))
@@ -185,11 +185,11 @@ def _validate_table(counts, ids, kwargs):
     if ids is not None:
         raise ValueError("Cannot provide a `Table` as `counts` and `ids`")
 
-    if 'taxa' in kwargs:
+    if "taxa" in kwargs:
         raise ValueError("Cannot provide a `Table` as `counts` and `taxa`")
 
     dense_counts, sample_ids, feature_ids = _table_to_numpy(counts)
-    if 'tree' in kwargs:
-        kwargs['taxa'] = feature_ids
+    if "tree" in kwargs:
+        kwargs["taxa"] = feature_ids
 
     return dense_counts, sample_ids

skbio/diversity/tests/test_driver.py

@@ -14,7 +14,7 @@
 import numpy.testing as npt
 
 from skbio import DistanceMatrix, TreeNode
-from skbio.feature_table import Table, example_table
+from skbio.table import Table, example_table
 from skbio.util._testing import assert_series_almost_equal
 from skbio.diversity import (alpha_diversity, beta_diversity,
                              partial_beta_diversity,

skbio/diversity/tests/test_util.py

@@ -14,7 +14,7 @@
 import numpy.testing as npt
 
 from skbio import TreeNode
-from skbio.feature_table import example_table
+from skbio.table import example_table
 from skbio.diversity._util import (_validate_counts_vector,
                                    _validate_counts_matrix,
                                    _validate_taxa_and_tree,

skbio/io/format/biom.py

@@ -18,11 +18,11 @@
 --------------
 **Has Sniffer: Yes**
 
-+------+------+---------------------------------------------------------------+
-|Reader|Writer|                          Object Class                         |
-+======+======+===============================================================+
-|Yes   |Yes   |:mod:`skbio.feature_table.Table`                               |
-+------+------+---------------------------------------------------------------+
++------+------+-------------------------------------------------------+
+|Reader|Writer|                      Object Class                     |
++======+======+=======================================================+
+|Yes   |Yes   |:mod:`skbio.table.Table`                               |
++------+------+-------------------------------------------------------+
 
 Format Specification
 --------------------
@@ -36,7 +36,7 @@
 
 >>> import io, skbio
 >>> f = io.BytesIO()
->>> skbio.feature_table.example_table.write(f)  # doctest: +ELLIPSIS
+>>> skbio.table.example_table.write(f)  # doctest: +ELLIPSIS
 <_io.BytesIO object at ...>
 >>> roundtrip = skbio.read(f, into=skbio.Table)
 >>> roundtrip
@@ -60,7 +60,7 @@
 
 import skbio
 from skbio.io import create_format
-from skbio.feature_table import Table
+from skbio.table import Table
 
 from .. import BIOMFormatError
 
@@ -102,29 +102,29 @@ def _biom_sniffer(fh):
 
 
 @biom.reader(Table)
-def _biom_to_feature_table_into(fh):
-    return _biom_to_feature_table(fh)
+def _biom_to_table_into(fh):
+    return _biom_to_table(fh)
 
 
 @biom.reader(None)
-def _biom_to_feature_table_default(fh):
+def _biom_to_table_default(fh):
     # skbio.read('foo.biom', format='biom')
     # will return a generator, that subsequently iterates the table.
     # returning a single item tuple yields expected behavior such that:
     # next(skbio.read('foo.biom', format='biom')) == Table
-    return (_biom_to_feature_table(fh),)
+    return (_biom_to_table(fh),)
 
 
-def _biom_to_feature_table(fh):
+def _biom_to_table(fh):
     h5grp = h5py.File(fh, "r")
     return Table.from_hdf5(h5grp)
 
 
 @biom.writer(Table)
 def _sktable_to_biom(obj, fh):
-    _feature_table_to_biom(obj, fh)
+    _table_to_biom(obj, fh)
 
 
-def _feature_table_to_biom(obj, fh):
+def _table_to_biom(obj, fh):
     h5grp = h5py.File(fh, "w")
     obj.to_hdf5(h5grp, f"Written by scikit-bio version {skbio.__version__}")

skbio/io/format/tests/test_biom.py

@@ -13,9 +13,9 @@
 
 import h5py
 
-from skbio.feature_table import Table, example_table
+from skbio.table import Table, example_table
 from skbio.io.format.biom import (
-    _biom_to_feature_table, _feature_table_to_biom, _biom_sniffer)
+    _biom_to_table, _table_to_biom, _biom_sniffer)
 
 
 class BIOMFormatTests(unittest.TestCase):
@@ -52,13 +52,13 @@ def test_sniffer(self):
         self.assertEqual(_biom_sniffer(self.nonbiom_hdf5_path), (False, {}))
         self.assertEqual(_biom_sniffer(self.difbiomver_path), (False, {}))
 
-    def test_biom_to_feature_table(self):
-        tab = _biom_to_feature_table(self.valid_biom_path)
+    def test_biom_to_table(self):
+        tab = _biom_to_table(self.valid_biom_path)
         self.assertEqual(tab, self.table)
 
-    def test_feature_table_to_biom(self):
-        _feature_table_to_biom(self.table, self.writable_biom_path)
-        roundtrip = _biom_to_feature_table(self.writable_biom_path)
+    def test_table_to_biom(self):
+        _table_to_biom(self.table, self.writable_biom_path)
+        roundtrip = _biom_to_table(self.writable_biom_path)
         self.assertEqual(roundtrip, self.table)
 
 

skbio/feature_table/__init__.py → skbio/table/__init__.py

@@ -1,7 +1,7 @@
-r"""Feature Table (:mod:`skbio.feature_table`)
-==========================
+r"""Feature Table (:mod:`skbio.table`)
+==================================
 
-.. currentmodule:: skbio.feature_table
+.. currentmodule:: skbio.table
 
 This module provides support for interaction with BIOM Tables.
 
@@ -14,6 +14,6 @@
 #
 # The full license is in the file LICENSE.txt, distributed with this software.
 # ----------------------------------------------------------------------------
-from skbio.feature_table._base import Table, example_table
+from skbio.table._base import Table, example_table
 
-__all__ = ['Table', 'example_table']
+__all__ = ["Table", "example_table"]

skbio/feature_table/_base.py → skbio/table/_base.py

@@ -8,4 +8,4 @@
 
 from biom import Table, example_table
 
-Table.default_write_format = 'biom'
+Table.default_write_format = "biom"

skbio/feature_table/tests/test_base.py → skbio/table/tests/test_base.py

@@ -7,12 +7,12 @@
 # ----------------------------------------------------------------------------
 
 from unittest import TestCase, main
-from skbio.feature_table import Table
+from skbio.table import Table
 import numpy as np
 
 
-class FeatureTable(TestCase):
-    def test_feature_table(self):
+class TableTests(TestCase):
+    def test_table(self):
         data = np.arange(40).reshape(10, 4)
         sample_ids = ['S%d' % i for i in range(4)]
         observ_ids = ['O%d' % i for i in range(10)]