Improve string and html output

Author: benjeffery

python/CHANGELOG.rst

@@ -4,22 +4,24 @@
 
 **Breaking changes**
 
-- `Mutation.position` and `Mutation.index` which were deprecated in 0.2.2 (Sep '19) have
+- ``Mutation.position`` and ``Mutation.index`` which were deprecated in 0.2.2 (Sep '19) have
   been removed.
 
 **Features**
 
-- Add `Table.append` method for adding rows from classes such as `SiteTableRow` and
-  `Site` (:user:`benjeffery`, :issue:`1111`, :pr:`1254`).
+- Add ``Table.append`` method for adding rows from classes such as ``SiteTableRow`` and
+  ``Site`` (:user:`benjeffery`, :issue:`1111`, :pr:`1254`).
 
 - SVG visualization of a single tree allows all mutations on an edge to be plotted
   via the ``all_edge_mutations`` param (:user:`hyanwong`,:issue:`1253`, :pr:`1258`).
 
-- Entity classes such as `Mutation`, `Node` are now python dataclasses
+- Entity classes such as ``Mutation``, ``Node`` are now python dataclasses
   (:user:`benjeffery`, :pr:`1261`).
 
 - Metadata decoding for table row access is now lazy (:user:`benjeffery`, :pr:`1261`).
 
+- Improve display of tables when ``print``ed, limiting lines to ``tskit.MAX_LINES``
+  (:user:`benjeffery`,:issue:`1270`, :pr:`1300`)
 
 **Fixes**
 

python/tests/test_tables.py

@@ -540,7 +540,16 @@ def test_str(self):
             table = self.table_class()
             table.set_columns(**input_data)
             s = str(table)
-            assert len(s.splitlines()) == num_rows + 1
+            assert len(s.splitlines()) == num_rows + 4
+        input_data = self.make_input_data(41)
+        table = self.table_class()
+        table.set_columns(**input_data)
+        print(table)
+        assert "1 rows skipped" in str(table)
+        tskit.set_print_options(max_lines=None)
+        assert "1 rows skipped" not in str(table)
+        tskit.set_print_options(max_lines=40)
+        tskit.MAX_LINES = 40
 
     def test_repr_html(self):
         for num_rows in [0, 10, 40, 50]:
@@ -555,8 +564,8 @@ def test_repr_html(self):
             if num_rows == 50:
                 assert len(html.splitlines()) == num_rows + 11
                 assert (
-                    html.split("</tr>")[21]
-                    == "\n<tr><td><em>... skipped 10 rows ...</em></td>"
+                    html.split("</tr>")[21] == "\n<tr><td><em>10 rows skipped "
+                    "(tskit.set_print_options)</em></td>"
                 )
             else:
                 assert len(html.splitlines()) == num_rows + 20

python/tests/test_util.py

@@ -26,12 +26,14 @@
 import itertools
 import math
 import pickle
+import textwrap
 
 import numpy as np
 import pytest
 from numpy.testing import assert_array_equal
 
 import tests.tsutil as tsutil
+import tskit
 import tskit.util as util
 from tskit import UNKNOWN_TIME
 
@@ -407,35 +409,83 @@ def test_obj_to_collapsed_html(obj, expected):
     )
 
 
+def test_truncate_string_end():
+    assert util.truncate_string_end("testing") == "testing"
+    assert util.truncate_string_end("testing", 7) == "testing"
+    assert util.truncate_string_end("testing", 5) == "te..."
+
+
 def test_unicode_table():
     assert (
         util.unicode_table(
             [["5", "6", "7", "8"], ["90", "10", "11", "12"]],
             header=["1", "2", "3", "4"],
         )
-        == """╔══╤══╤══╤══╗
-║1 │2 │3 │4 ║
-╠══╪══╪══╪══╣
-║5 │ 6│ 7│ 8║
-╟──┼──┼──┼──╢
-║90│10│11│12║
-╚══╧══╧══╧══╝
-"""
+        == textwrap.dedent(
+            """
+           ╔══╤══╤══╤══╗
+           ║1 │2 │3 │4 ║
+           ╠══╪══╪══╪══╣
+           ║5 │ 6│ 7│ 8║
+           ╟──┼──┼──┼──╢
+           ║90│10│11│12║
+           ╚══╧══╧══╧══╝
+        """
+        )[1:]
+    )
+
+    assert (
+        util.unicode_table(
+            [
+                ["1", "2", "3", "4"],
+                ["5", "6", "7", "8"],
+                "__skipped__",
+                ["90", "10", "11", "12"],
+            ],
+            title="TITLE",
+        )
+        == textwrap.dedent(
+            """
+           ╔═══════════╗
+           ║TITLE      ║
+           ╠══╤══╤══╤══╣
+           ║1 │ 2│ 3│ 4║
+           ╟──┼──┼──┼──╢
+           ║5 │ 6│ 7│ 8║
+           ╟──┴──┴──┴──╢
+           ║ rows skipp║
+           ╟──┬──┬──┬──╢
+           ║90│10│11│12║
+           ╚══╧══╧══╧══╝
+        """
+        )[1:]
     )
 
     assert (
         util.unicode_table(
             [["1", "2", "3", "4"], ["5", "6", "7", "8"], ["90", "10", "11", "12"]],
             title="TITLE",
+            row_separator=False,
         )
-        == """╔═══════════╗
-║TITLE      ║
-╠══╤══╤══╤══╣
-║1 │ 2│ 3│ 4║
-╟──┼──┼──┼──╢
-║5 │ 6│ 7│ 8║
-╟──┼──┼──┼──╢
-║90│10│11│12║
-╚══╧══╧══╧══╝
-"""
+        == textwrap.dedent(
+            """
+           ╔═══════════╗
+           ║TITLE      ║
+           ╠══╤══╤══╤══╣
+           ║1 │ 2│ 3│ 4║
+           ║5 │ 6│ 7│ 8║
+           ║90│10│11│12║
+           ╚══╧══╧══╧══╝
+        """
+        )[1:]
     )
+
+
+def test_set_printoptions():
+    assert tskit._print_options == {"max_lines": 40}
+    util.set_print_options(max_lines=None)
+    assert tskit._print_options == {"max_lines": None}
+    util.set_print_options(max_lines=40)
+    assert tskit._print_options == {"max_lines": 40}
+    with pytest.raises(TypeError):
+        util.set_print_options(40)

python/tskit/__init__.py

@@ -47,11 +47,11 @@
 ALLELES_ACGT = ("A", "C", "G", "T")
 
 #: Special NAN value used to indicate unknown mutation times
-"""
-Say what
-"""
 UNKNOWN_TIME = _tskit.UNKNOWN_TIME
 
+#: Options for printing to strings and HTML, modify with tskit.set_print_options.
+_print_options = {"max_lines": 40}
+
 from tskit.provenance import __version__  # NOQA
 from tskit.provenance import validate_provenance  # NOQA
 from tskit.formats import *  # NOQA