implementing Variant.__repr__

added tests for contents

edit changelog

fix changelog entry

Author: chriscrsmith

python/CHANGELOG.rst

@@ -1,3 +1,13 @@
+--------------------
+[0.5.5] - 2023-01-XX
+--------------------
+
+**Features**
+
+- Add ``__repr__`` for variants to return a string representation of the raw data
+  without spewing megabytes of text (:user:`chriscrsmith`, :pr:`2695`, :issue:`2694`)
+
+  
 --------------------
 [0.5.4] - 2023-01-13
 --------------------

python/tests/test_genotypes.py

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2019-2022 Tskit Developers
+# Copyright (c) 2019-2023 Tskit Developers
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -2215,3 +2215,17 @@ def test_variant_html_repr_no_site(self):
         html = v._repr_html_()
         ElementTree.fromstring(html)
         assert len(html) > 1600
+
+    def test_variant_repr(self, ts_fixture):
+        v = next(ts_fixture.variants())
+        str_rep = repr(v)
+        assert len(str_rep) > 0 and len(str_rep) < 10000
+        assert re.search(r"\AVariant", str_rep)
+        assert re.search(rf"\'site\': Site\(id={v.site.id}", str_rep)
+        assert re.search(rf"position={v.position}", str_rep)
+        alleles = re.escape("'alleles': " + str(v.alleles))
+        assert re.search(rf"{alleles}", str_rep)
+        assert re.search(r"\'genotypes\': array\(\[", str_rep)
+        assert re.search(rf"position={v.position}", str_rep)
+        assert re.search(rf"\'has_missing_data\': {v.has_missing_data}", str_rep)
+        assert re.search(rf"\'isolated_as_missing\': {v.isolated_as_missing}", str_rep)

python/tskit/genotypes.py

@@ -1,7 +1,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2018-2022 Tskit Developers
+# Copyright (c) 2018-2023 Tskit Developers
 # Copyright (c) 2015-2018 University of Oxford
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -340,6 +340,17 @@ def _repr_html_(self) -> str:
         """
         return util.variant_html(self)
 
+    def __repr__(self):
+        d = {
+            "site": self.site,
+            "samples": self.samples,
+            "alleles": self.alleles,
+            "genotypes": self.genotypes,
+            "has_missing_data": self.has_missing_data,
+            "isolated_as_missing": self.isolated_as_missing,
+        }
+        return f"Variant({repr(d)})"
+
 
 #
 # Miscellaneous auxiliary methods.