Merge pull request #365 from ChristopherBradley/continuation_table

Issues #352 and #363

doc/examples/handling_tabular_data.rst

@@ -1070,9 +1070,9 @@ We can likewise specify a writer, using a custom field formatter and provide thi
 
 .. doctest::
 
-    >>> from cogent3.format.table import FormatFields, SeparatorFormatWriter
-    >>> formatter = FormatFields([(0,'"%s"'), (1,'"%s"')])
-    >>> writer = SeparatorFormatWriter(formatter=formatter, sep=" | ")
+    >>> from cogent3.format.table import format_fields, separator_formatter
+    >>> formatter = format_fields([(0,'"%s"'), (1,'"%s"')])
+    >>> writer = separator_formatter(formatter=formatter, sep=" | ")
     >>> for formatted in writer(comma_sep, has_header=True):
     ...      print(formatted)
     edge.name | edge.parent | length | x | y | z

src/cogent3/format/table.py

@@ -519,7 +519,7 @@ def separator_format(header, formatted_table, title=None, legend=None, sep=None)
     return table
 
 
-def FormatFields(formats):
+def format_fields(formats):
     """Formats row fields by index.
 
     Parameters
@@ -543,7 +543,7 @@ def callable(line, index_format=index_format):
     return callable
 
 
-def SeparatorFormatWriter(formatter=None, ignore=None, sep=","):
+def separator_formatter(formatter=None, ignore=None, sep=","):
     """Returns a writer for a delimited tabular file. The writer has a
     has_header argument which ignores the formatter for a header line. Default
     format is string. Does not currently handle Titles or Legends.
@@ -562,7 +562,7 @@ def SeparatorFormatWriter(formatter=None, ignore=None, sep=","):
 
     def callable(lines, formatter=formatter, has_header=False):
         if not formatter:
-            formatter = FormatFields([(i, "%s") for i in range(len(lines[0]))])
+            formatter = format_fields([(i, "%s") for i in range(len(lines[0]))])
         header_done = None
         for line in lines:
             if has_header and not header_done:

src/cogent3/maths/stats/test.py

@@ -1971,4 +1971,3 @@ def get_ltm_cells(cells):
     # remove duplicates
     new_cells = sorted(set(new_cells))
     return new_cells
-

tests/test_util/test_table.py

@@ -13,7 +13,7 @@
 
 __author__ = "Thomas La"
 __copyright__ = "Copyright 2007-2019, The Cogent Project"
-__credits__ = ["Gavin Huttley", "Thomas La"]
+__credits__ = ["Gavin Huttley", "Thomas La", "Christopher Bradley"]
 __license__ = "BSD-3"
 __version__ = "2019.10.24a"
 __maintainer__ = "Gavin Huttley"
@@ -67,6 +67,10 @@ class TableTests(TestCase):
     t5_header = ["a", "b", "c", "d"]
     t5_rows = [[1, 1, 1, 1], [2, 0, 1, 1], [1, 3, 2, 2]]
 
+    # test table 6
+    t6_header = ["id", "foo", "bar"]
+    t6_rows = [["60", " | ", "666"], ["70", "bca", "777"]]
+
     def test_appended(self):
         """test the table appended method"""
         t2 = Table(header=self.t2_header, rows=self.t2_rows)
@@ -159,17 +163,18 @@ def test_grid_table_format(self):
         """test the table grid_table_format method"""
         from cogent3.format.table import grid_table_format
 
-        t6_header = ["id", "foo", "bar"]
-        t6_rows = [["60", " | ", "666"], ["70", "bca", "777"]]
         formatted_grid = grid_table_format(
-            t6_header, t6_rows, title="Test", legend="Units"
+            self.t6_header, self.t6_rows, title="Test", legend="Units"
         )
-        self.assertEqual(len(formatted_grid.split("\n")), len(t6_rows) * 2 + 7)
+        self.assertEqual(len(formatted_grid.split("\n")), len(self.t6_rows) * 2 + 7)
 
         formatted_grid = grid_table_format(
-            t6_header, t6_rows, title="Really Long Title", legend="Extra Long Legend"
+            self.t6_header,
+            self.t6_rows,
+            title="Really Long Title",
+            legend="Extra Long Legend",
         )
-        self.assertEqual(len(formatted_grid.split("\n")), len(t6_rows) * 2 + 7 + 2)
+        self.assertEqual(len(formatted_grid.split("\n")), len(self.t6_rows) * 2 + 7 + 2)
 
     def test_joined(self):
         """test the table joined method"""
@@ -197,16 +202,14 @@ def test_markdown(self):
         """Exercising the table markdown method"""
         from cogent3.format.table import markdown
 
-        t6_header = ["id", "foo", "bar"]
-        t6_rows = [["60", " | ", "666"], ["70", "bca", "777"]]
-        markdown_table = markdown(t6_header, t6_rows, justify="crl")
+        markdown_table = markdown(self.t6_header, self.t6_rows, justify="crl")
         markdown_list = markdown_table.split("\n")
         self.assertEqual(markdown_list[2].count(r"|"), 5)
         # the pipe symbol should have been escaped
         self.assertEqual(markdown_list[2].count(r"\|"), 1)
 
         with self.assertRaises(ValueError):
-            _ = markdown(t6_header, t6_rows, justify="cr1")
+            _ = markdown(self.t6_header, self.t6_rows, justify="cr1")
 
     def test_normalized(self):
         """test the table normalized method"""
@@ -326,22 +329,20 @@ def test_separator_format(self):
         """testing separator_format with title and legend, and contents that match the separator"""
         from cogent3.format.table import separator_format
 
-        t6_header = ["id", "foo", "bar"]
-        t6_rows = [["60", " | ", "666"], ["70", "bca", "777"]]
         with self.assertRaises(RuntimeError):
-            _ = separator_format(t6_header, t6_rows)
+            _ = separator_format(self.t6_header, self.t6_rows)
         separated_table = separator_format(
-            t6_header, t6_rows, sep=" | ", title="Test", legend="Units"
+            self.t6_header, self.t6_rows, sep=" | ", title="Test", legend="Units"
         )
-        self.assertEqual(len(separated_table.split("\n")), len(t6_rows) + 3)
+        self.assertEqual(len(separated_table.split("\n")), len(self.t6_rows) + 3)
 
     def test_separator_format_writer(self):
         """exercising separator_format_writer"""
-        from cogent3.format.table import SeparatorFormatWriter
+        from cogent3.format.table import separator_formatter
 
         t3 = Table(self.t3_header, rows=self.t3_rows)
         comma_sep = t3.to_string(sep=",").splitlines()
-        writer = SeparatorFormatWriter(sep=" | ")
+        writer = separator_formatter(sep=" | ")
         formatted = [
             f for f in writer([l.split(",") for l in comma_sep], has_header=True)
         ]