Fix missing vias when more than two input files are used

piptools/resolver.py

@@ -502,7 +502,18 @@ def __init__(
         self.unsafe_constraints: set[InstallRequirement] = set()
 
         self.existing_constraints = existing_constraints
-        self._constraints_map = {key_from_ireq(ireq): ireq for ireq in constraints}
+
+        # Categorize InstallRequirements into sets by key
+        constraints_sets: DefaultDict[
+            str, set[InstallRequirement]
+        ] = collections.defaultdict(set)
+        for ireq in constraints:
+            constraints_sets[key_from_ireq(ireq)].add(ireq)
+        # Collapse each set of InstallRequirements using combine_install_requirements
+        self._constraints_map = {
+            ireq_key: combine_install_requirements(ireqs)
+            for ireq_key, ireqs in constraints_sets.items()
+        }
 
         # Make sure there is no enabled legacy resolver
         options.deprecated_features_enabled = omit_list_value(
@@ -759,9 +770,14 @@ def _get_install_requirement_from_candidate(
         ireq_key = key_from_ireq(ireq)
         pinned_ireq._required_by = reverse_dependencies.get(ireq_key, set())
 
-        # Save source for annotation
-        source_ireq = self._constraints_map.get(ireq_key)
-        if source_ireq is not None:
-            pinned_ireq._source_ireqs = [source_ireq]
+        # Save sources for annotation
+        constraint_ireq = self._constraints_map.get(ireq_key)
+        if constraint_ireq is not None:
+            if hasattr(constraint_ireq, "_source_ireqs"):
+                # If the constraint is combined (has _source_ireqs), use those
+                pinned_ireq._source_ireqs = constraint_ireq._source_ireqs
+            else:
+                # Otherwise (the constraint is not combined) it is the source
+                pinned_ireq._source_ireqs = [constraint_ireq]
 
         return pinned_ireq

tests/test_cli_compile.py

@@ -1909,6 +1909,42 @@ def test_upgrade_package_doesnt_remove_annotation(pip_conf, runner):
         )
 
 
+@pytest.mark.parametrize(("num_inputs"), (2, 3, 10))
+def test_many_inputs_includes_all_annotations(pip_conf, runner, tmp_path, num_inputs):
+    """
+    Tests that an entry required by multiple input files is attributed to all of them in the
+    annotation.
+    See: https://github.com/jazzband/pip-tools/issues/1853
+    """
+    req_ins = [tmp_path / f"requirements{n:02d}.in" for n in range(num_inputs)]
+    for req_in in req_ins:
+        req_in.write_text("small-fake-a==0.1\n")
+
+    out = runner.invoke(
+        cli,
+        [
+            "--output-file",
+            "-",
+            "--quiet",
+            "--no-header",
+            "--no-emit-find-links",
+        ]
+        + [str(r) for r in req_ins],
+    )
+    assert out.exit_code == 0, out.stderr
+    assert (
+        out.stdout
+        == "\n".join(
+            [
+                "small-fake-a==0.1",
+                "    # via",
+            ]
+            + [f"    #   -r {req_in}" for req_in in req_ins]
+        )
+        + "\n"
+    )
+
+
 @pytest.mark.parametrize(
     "options",
     (