Comma sep display numbers

python/CHANGELOG.rst

@@ -85,9 +85,11 @@
   ``pack_untracked_polytomies`` allows large polytomies involving untracked samples to
   be summarised as a dotted line (:user:`hyanwong`, :issue:`3011` :pr:`3010`, :pr:`3012`)
 
-
 - Added a ``title`` parameter to ``.draw_svg()`` methods (:user:`hyanwong`, :pr:`3015`)
 
+- Add comma separation to all display numbers. (:user:`benjeffery`, :issue:`3017`, :pr:`3018`)
+
+
 --------------------
 [0.5.8] - 2024-06-27
 --------------------

python/tests/test_highlevel.py

@@ -39,7 +39,6 @@
 import random
 import re
 import tempfile
-import textwrap
 import unittest
 import uuid as _uuid
 import warnings
@@ -2191,7 +2190,7 @@ def test_html_repr(self, ts):
         # Parse to check valid
         ElementTree.fromstring(html)
         assert len(html) > 5000
-        assert f"<tr><td>Trees</td><td>{ts.num_trees}</td></tr>" in html
+        assert f"<tr><td>Trees</td><td>{ts.num_trees:,}</td></tr>" in html
         assert f"<tr><td>Time Units</td><td>{ts.time_units}</td></tr>" in html
         for table in ts.tables.table_name_map:
             assert f"<td>{table.capitalize()}</td>" in html
@@ -3759,32 +3758,29 @@ def test_complex_mutations(self):
     def test_str(self, ts_fixture):
         t = ts_fixture.first()
         assert isinstance(str(t), str)
-        assert re.match(
-            textwrap.dedent(
-                r"""
-            ╔═════════════════════════════╗
-            ║Tree                         ║
-            ╠═══════════════════╤═════════╣
-            ║Index              │        0║
-            ╟───────────────────┼─────────╢
-            ║Interval           │  0-1 \(1\)║
-            ╟───────────────────┼─────────╢
-            ║Roots              │[0-9 ]*║
-            ╟───────────────────┼─────────╢
-            ║Nodes              │[0-9 ]*║
-            ╟───────────────────┼─────────╢
-            ║Sites              │[0-9 ]*║
-            ╟───────────────────┼─────────╢
-            ║Mutations          │[0-9 ]*║
-            ╟───────────────────┼─────────╢
-            ║Total Branch Length│[0-9\. ]*║
-            ╚═══════════════════╧═════════╝
-        """[
-                    1:
-                ]
-            ),
-            str(t),
+        pattern = re.compile(
+            r"""
+            ╔═+╗\s*
+            ║Tree.*?║\s*
+            ╠═+╤═+╣\s*
+            ║Index.*?│\s*\d+║\s*
+            ╟─+┼─+╢\s*
+            ║Interval.*?│\s*\d+-\d+\s*\(\d+\)║\s*
+            ╟─+┼─+╢\s*
+            ║Roots.*?│\s*\d+║\s*
+            ╟─+┼─+╢\s*
+            ║Nodes.*?│\s*\d+║\s*
+            ╟─+┼─+╢\s*
+            ║Sites.*?│\s*\d+║\s*
+            ╟─+┼─+╢\s*
+            ║Mutations.*?│\s*\d+║\s*
+            ╟─+┼─+╢\s*
+            ║Total\s*Branch\s*Length.*?│\s*[\d,]+\.\d+║\s*
+            ╚═+╧═+╝\s*
+            """,
+            re.VERBOSE | re.DOTALL,
         )
+        assert pattern.search(str(t))
 
     def test_html_repr(self, ts_fixture):
         html = ts_fixture.first()._repr_html_()

python/tests/test_tables.py

@@ -697,7 +697,7 @@ def test_str_pos_time_integer(self):
                 table.set_columns(**input_data)
                 _, rows = table._text_header_and_rows()
                 for row in rows:
-                    assert f"{identifiable_integers[0]}" in row
+                    assert f"{identifiable_integers[0]:,}" in row
                     assert f"{identifiable_floats[0]:.8f}" not in row
 
     def test_repr_html(self):

python/tskit/genotypes.py

@@ -1,7 +1,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2018-2023 Tskit Developers
+# Copyright (c) 2018-2024 Tskit Developers
 # Copyright (c) 2015-2018 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -311,16 +311,16 @@ def __str__(self) -> str:
             freqs = self.frequencies()
             rows = (
                 [
-                    ["Site id", str(site_id)],
-                    ["Site position", str(site_position)],
-                    ["Number of samples", str(len(self.samples))],
-                    ["Number of alleles", str(self.num_alleles)],
+                    ["Site id", f"{site_id:,}"],
+                    ["Site position", f"{site_position:,}"],
+                    ["Number of samples", f"{len(self.samples):,}"],
+                    ["Number of alleles", f"{self.num_alleles:,}"],
                 ]
                 + [
                     [
-                        f"""Samples with allele {'missing' if k is None
-                            else "'" + k + "'"}""",
-                        f"{counts[k]} ({freqs[k] * 100:.2g}%)",
+                        f"Samples with allele "
+                        f"""{'missing' if k is None else "'" + k + "'"}""",
+                        f"{counts[k]:,} ({freqs[k] * 100:.2g}%)",
                     ]
                     for k in self.alleles
                 ]

python/tskit/tables.py

@@ -864,13 +864,13 @@ def _text_header_and_rows(self, limit=None):
         row_indexes = util.truncate_rows(self.num_rows, limit)
         for j in row_indexes:
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 row = self[j]
                 location_str = ", ".join(map(str, row.location))
-                parents_str = ", ".join(map(str, row.parents))
+                parents_str = ", ".join([f"{p:,}" for p in row.parents])
                 rows.append(
-                    "{}\t{}\t{}\t{}\t{}".format(
+                    "{:,}\t{}\t{}\t{}\t{}".format(
                         j,
                         row.flags,
                         location_str,
@@ -1139,10 +1139,10 @@ def _text_header_and_rows(self, limit=None):
         for j in row_indexes:
             row = self[j]
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 rows.append(
-                    "{}\t{}\t{}\t{}\t{:.{dp}f}\t{}".format(
+                    "{:,}\t{}\t{:,}\t{:,}\t{:,.{dp}f}\t{}".format(
                         j,
                         row.flags,
                         row.population,
@@ -1332,11 +1332,11 @@ def _text_header_and_rows(self, limit=None):
         decimal_places = 0 if self._columns_all_integer("left", "right") else 8
         for j in row_indexes:
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 row = self[j]
                 rows.append(
-                    "{}\t{:.{dp}f}\t{:.{dp}f}\t{}\t{}\t{}".format(
+                    "{:,}\t{:,.{dp}f}\t{:,.{dp}f}\t{:,}\t{:,}\t{}".format(
                         j,
                         row.left,
                         row.right,
@@ -1548,11 +1548,11 @@ def _text_header_and_rows(self, limit=None):
         decimal_places_times = 0 if self._columns_all_integer("time") else 8
         for j in row_indexes:
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 row = self[j]
                 rows.append(
-                    "{}\t{:.{dp_c}f}\t{:.{dp_c}f}\t{}\t{}\t{}\t{:.{dp_t}f}\t{}".format(
+                    "{:,}\t{:,.{dp_c}f}\t{:,.{dp_c}f}\t{:,}\t{:,}\t{:,}\t{:,.{dp_t}f}\t{}".format(
                         j,
                         row.left,
                         row.right,
@@ -1563,7 +1563,9 @@ def _text_header_and_rows(self, limit=None):
                         util.render_metadata(row.metadata),
                         dp_c=decimal_places_coords,
                         dp_t=decimal_places_times,
-                    ).split("\t")
+                    ).split(
+                        "\t"
+                    )
                 )
         return headers, rows
 
@@ -1760,11 +1762,11 @@ def _text_header_and_rows(self, limit=None):
         decimal_places = 0 if self._columns_all_integer("position") else 8
         for j in row_indexes:
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 row = self[j]
                 rows.append(
-                    "{}\t{:.{dp}f}\t{}\t{}".format(
+                    "{:,}\t{:,.{dp}f}\t{}\t{}".format(
                         j,
                         row.position,
                         row.ancestral_state,
@@ -1977,11 +1979,11 @@ def _text_header_and_rows(self, limit=None):
         decimal_places_times = 0 if self._columns_all_integer("time") else 8
         for j in row_indexes:
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 row = self[j]
                 rows.append(
-                    "{}\t{}\t{}\t{:.{dp}f}\t{}\t{}\t{}".format(
+                    "{:,}\t{:,}\t{:,}\t{:,.{dp}f}\t{}\t{:,}\t{}".format(
                         j,
                         row.site,
                         row.node,
@@ -2256,7 +2258,7 @@ def _text_header_and_rows(self, limit=None):
         row_indexes = util.truncate_rows(self.num_rows, limit)
         for j in row_indexes:
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 rows.append((str(j), util.render_metadata(self[j].metadata, length=70)))
         return headers, rows
@@ -2507,7 +2509,7 @@ def _text_header_and_rows(self, limit=None):
         row_indexes = util.truncate_rows(self.num_rows, limit)
         for j in row_indexes:
             if j == -1:
-                rows.append(f"__skipped__{self.num_rows-limit}")
+                rows.append(f"__skipped__{self.num_rows - limit}")
             else:
                 row = self[j]
                 rows.append(

python/tskit/trees.py

@@ -2797,16 +2797,17 @@ def __str__(self):
         Return a plain text summary of a tree in a tree sequence
         """
         tree_rows = [
-            ["Index", str(self.index)],
+            ["Index", f"{self.index:,}"],
             [
                 "Interval",
-                f"{self.interval.left:.8g}-{self.interval.right:.8g} ({self.span:.8g})",
+                f"{self.interval.left:,.8g}-{self.interval.right:,.8g}"
+                f"({self.span:,.8g})",
             ],
-            ["Roots", str(self.num_roots)],
-            ["Nodes", str(len(self.preorder()))],
-            ["Sites", str(self.num_sites)],
-            ["Mutations", str(self.num_mutations)],
-            ["Total Branch Length", f"{self.total_branch_length:.8g}"],
+            ["Roots", f"{self.num_roots:,}"],
+            ["Nodes", f"{len(self.preorder()):,}"],
+            ["Sites", f"{self.num_sites:,}"],
+            ["Mutations", f"{self.num_mutations:,}"],
+            ["Total Branch Length", f"{self.total_branch_length:,.8g}"],
         ]
         return util.unicode_table(tree_rows, title="Tree")
 
@@ -4369,17 +4370,14 @@ def __str__(self):
         for name, table in self.tables.table_name_map.items():
             table_rows.append(
                 [
-                    str(s)
-                    for s in [
-                        name.capitalize(),
-                        table.num_rows,
-                        util.naturalsize(table.nbytes),
-                        (
-                            "Yes"
-                            if hasattr(table, "metadata") and len(table.metadata) > 0
-                            else "No"
-                        ),
-                    ]
+                    name.capitalize(),
+                    f"{table.num_rows:,}",
+                    util.naturalsize(table.nbytes),
+                    (
+                        "Yes"
+                        if hasattr(table, "metadata") and len(table.metadata) > 0
+                        else "No"
+                    ),
                 ]
             )
         return util.unicode_table(ts_rows, title="TreeSequence") + util.unicode_table(

python/tskit/util.py

@@ -518,7 +518,7 @@ def tree_sequence_html(ts):
         f"""
             <tr>
                 <td>{name.capitalize()}</td>
-                <td>{table.num_rows}</td>
+                <td>{table.num_rows:,}</td>
                 <td>{naturalsize(table.nbytes)}</td>
                 <td style="text-align: center;">
                     {'✅' if hasattr(table, "metadata") and len(table.metadata) > 0
@@ -598,10 +598,10 @@ def tree_sequence_html(ts):
                             </tr>
                         </thead>
                         <tbody>
-                            <tr><td>Trees</td><td>{ts.num_trees}</td></tr>
-                            <tr><td>Sequence Length</td><td>{ts.sequence_length}</td></tr>
+                            <tr><td>Trees</td><td>{ts.num_trees:,}</td></tr>
+                            <tr><td>Sequence Length</td><td>{ts.sequence_length:,}</td></tr>
                             <tr><td>Time Units</td><td>{ts.time_units}</td></tr>
-                            <tr><td>Sample Nodes</td><td>{ts.num_samples}</td></tr>
+                            <tr><td>Sample Nodes</td><td>{ts.num_samples:,}</td></tr>
                             <tr><td>Total Size</td><td>{naturalsize(ts.nbytes)}</td></tr>
                             <tr>
                                 <td>Metadata</td><td style="text-align: left;">{md}</td>
@@ -670,13 +670,13 @@ def tree_html(tree):
                       </tr>
                     </thead>
                     <tbody>
-                      <tr><td>Index</td><td>{tree.index}</td></tr>
-                      <tr><td>Interval</td><td>{tree.interval.left:.8g}-{tree.interval.right:.8g} ({tree.span:.8g})</td></tr>
-                      <tr><td>Roots</td><td>{tree.num_roots}</td></tr>
-                      <tr><td>Nodes</td><td>{len(tree.preorder())}</td></tr>
-                      <tr><td>Sites</td><td>{tree.num_sites}</td></tr>
-                      <tr><td>Mutations</td><td>{tree.num_mutations}</td></tr>
-                      <tr><td>Total Branch Length</td><td>{tree.total_branch_length:.8g}</td></tr>
+                      <tr><td>Index</td><td>{tree.index:,}</td></tr>
+                      <tr><td>Interval</td><td>{tree.interval.left:,.8g}-{tree.interval.right:,.8g} ({tree.span:,.8g})</td></tr>
+                      <tr><td>Roots</td><td>{tree.num_roots:,}</td></tr>
+                      <tr><td>Nodes</td><td>{len(tree.preorder()):,}</td></tr>
+                      <tr><td>Sites</td><td>{tree.num_sites:,}</td></tr>
+                      <tr><td>Mutations</td><td>{tree.num_mutations:,}</td></tr>
+                      <tr><td>Total Branch Length</td><td>{tree.total_branch_length:,.8g}</td></tr>
                     </tbody>
                   </table>
                 </div>
@@ -745,18 +745,18 @@ def variant_html(variant):
         return (
             html_body_head
             + f"""
-                <tr><td>Site Id</td><td>{site_id}</td></tr>
-                <tr><td>Site Position</td><td>{site_position}</td></tr>
-                <tr><td>Number of Samples</td><td>{num_samples}</td></tr>
-                <tr><td>Number of Alleles</td><td>{num_alleles}</td></tr>
+                <tr><td>Site Id</td><td>{site_id:,}</td></tr>
+                <tr><td>Site Position</td><td>{site_position:,.8g}</td></tr>
+                <tr><td>Number of Samples</td><td>{num_samples:,}</td></tr>
+                <tr><td>Number of Alleles</td><td>{num_alleles:,}</td></tr>
             """
             + "\n".join(
                 [
                     f"""<tr><td>Samples with Allele {'missing' if k is None
                                                      else "'" + k + "'"}</td><td>"""
-                    + f"{counts[k]}"
+                    + f"{counts[k]:,}"
                     + " "
-                    + f"({freqs[k] * 100:.2g}%)"
+                    + f"({freqs[k] * 100:,.2g}%)"
                     + "</td></tr>"
                     for k in variant.alleles
                 ]