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Comma sep display numbers
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@benjeffery
benjeffery committed Oct 11, 2024
1 parent dca04b3 commit fa1a9a4
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Showing 7 changed files with 86 additions and 88 deletions.
4 changes: 3 additions & 1 deletion python/CHANGELOG.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -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
--------------------
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50 changes: 23 additions & 27 deletions python/tests/test_highlevel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@
import random
import re
import tempfile
import textwrap
import unittest
import uuid as _uuid
import warnings
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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_()
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2 changes: 1 addition & 1 deletion python/tests/test_tables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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):
Expand Down
16 changes: 8 additions & 8 deletions python/tskit/genotypes.py
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Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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
]
Expand Down
34 changes: 18 additions & 16 deletions python/tskit/tables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand All @@ -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

Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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(
Expand Down
34 changes: 16 additions & 18 deletions python/tskit/trees.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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")

Expand Down Expand Up @@ -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(
Expand Down
34 changes: 17 additions & 17 deletions python/tskit/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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
]
Expand Down

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