Add __repr__ to Region and CacheMiss for better debugging (fixes #1219)

- Region.__repr__ returns a constructor-style string, e.g. Region('2L', 100000, 200000)
  so that Region objects display usefully inside lists, dicts, and REPL sessions,
  complementing the existing __str__ (e.g. '2L:100,000-200,000').

- CacheMiss gains a default message and __repr__:
  - CacheMiss()          → str 'Cache miss: requested item not found in cache.'
  - CacheMiss('key')     → str "Cache miss for key: 'key'"
  - repr(CacheMiss('k')) → "CacheMiss('k')"

- Added tests/test_util.py covering both classes.

Author: Yashsingh045

malariagen_data/util.py

@@ -570,6 +570,9 @@ def __eq__(self, other):
             and (self.end == other.end)
         )
 
+    def __repr__(self):
+        return f"Region({self._contig!r}, {self._start!r}, {self._end!r})"
+
     def __str__(self):
         out = self._contig
         if self._start is not None or self._end is not None:
@@ -904,7 +907,20 @@ def _jitter(a, fraction):
 
 
 class CacheMiss(Exception):
-    pass
+    """Raised when a requested item is not present in the cache."""
+
+    def __init__(self, key=None):
+        self.key = key
+        if key is not None:
+            message = f"Cache miss for key: {key!r}"
+        else:
+            message = "Cache miss: requested item not found in cache."
+        super().__init__(message)
+
+    def __repr__(self):
+        if self.key is not None:
+            return f"CacheMiss({self.key!r})"
+        return "CacheMiss()"
 
 
 class LoggingHelper:

tests/test_util.py

@@ -0,0 +1,80 @@
+"""Tests for Region.__repr__ and CacheMiss.__repr__ / default message."""
+import importlib.util as ilu
+import sys
+
+# Load malariagen_data/util.py directly, bypassing the package __init__.py
+# which has heavy transitive imports (bokeh, plotly, etc.).
+_spec = ilu.spec_from_file_location(
+    "malariagen_data.util",
+    "malariagen_data/util.py",
+)
+_util = ilu.module_from_spec(_spec)
+sys.modules["malariagen_data.util"] = _util
+
+try:
+    _spec.loader.exec_module(_util)
+except Exception:
+    # If util.py itself can't be loaded (missing deps), fall back to a
+    # normal import so the tests still work in a fully-installed env.
+    import malariagen_data.util as _util  # type: ignore[assignment]
+
+Region = _util.Region
+CacheMiss = _util.CacheMiss
+
+import pytest  # noqa: E402
+
+
+# ---------------------------------------------------------------------------
+# Region
+# ---------------------------------------------------------------------------
+
+def test_region_repr_contig_only():
+    r = Region("2L")
+    assert repr(r) == "Region('2L', None, None)"
+    assert str(r) == "2L"
+
+
+def test_region_repr_with_coords():
+    r = Region("2L", 100_000, 200_000)
+    assert repr(r) == "Region('2L', 100000, 200000)"
+    assert str(r) == "2L:100,000-200,000"
+
+
+def test_region_repr_in_list():
+    regions = [Region("2L", 10, 20), Region("3R", 30, 40)]
+    assert repr(regions) == "[Region('2L', 10, 20), Region('3R', 30, 40)]"
+
+
+def test_region_repr_start_only():
+    r = Region("X", start=500, end=None)
+    assert repr(r) == "Region('X', 500, None)"
+    assert str(r) == "X:500-"
+
+
+# ---------------------------------------------------------------------------
+# CacheMiss
+# ---------------------------------------------------------------------------
+
+def test_cache_miss_no_key():
+    cm = CacheMiss()
+    assert repr(cm) == "CacheMiss()"
+    assert "Cache miss" in str(cm)
+
+
+def test_cache_miss_string_key():
+    cm = CacheMiss("my_key")
+    assert repr(cm) == "CacheMiss('my_key')"
+    assert "my_key" in str(cm)
+
+
+def test_cache_miss_tuple_key():
+    cm = CacheMiss(("contig", 100))
+    assert repr(cm) == "CacheMiss(('contig', 100))"
+    assert "('contig', 100)" in str(cm)
+
+
+def test_cache_miss_is_exception():
+    with pytest.raises(CacheMiss) as exc_info:
+        raise CacheMiss("lookup_key")
+    assert "lookup_key" in str(exc_info.value)
+    assert repr(exc_info.value) == "CacheMiss('lookup_key')"