refactor: tests for structure.template (#309)

* refactor: tests for structure.template

lock in the behavior seen in #306

* run linter

* missing some __init__.py files - otherwise it's ambigous to pytest

* more comprehensive tests

* remove crappy comments

* remove test_template_featurization.py

* e2e test: template save single-sequence prediction

* review comments from Jennifer

Author: jandom

openfold3/tests/core/data/pipelines/preprocessing/__init__.py

@@ -0,0 +1,111 @@
+# Copyright 2026 AlQuraishi Laboratory
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import dataclasses
+from pathlib import Path
+
+import numpy as np
+import pytest
+
+from openfold3.core.data.primitives.structure.template import sample_templates
+from openfold3.tests.utils.template_helpers import (
+    TEMPLATE_ID,
+    make_cache_entry,
+    template_structure_array_path,
+    write_cache_npz,
+)
+
+
+def _cache_entry():
+    """The single template both written to the cache and expected back out."""
+    return make_cache_entry([[1, 1], [2, 2]])
+
+
+def _write_cache_npz(path: Path) -> Path:
+    return write_cache_npz(path, {TEMPLATE_ID: _cache_entry()})
+
+
+def _assembly_data(cache_npz: Path) -> dict:
+    return {
+        "A": {
+            "template_ids": [TEMPLATE_ID],
+            "cache_entry_file_path": cache_npz,
+        }
+    }
+
+
+def _cache_none(tmp_path: Path) -> None:
+    return None
+
+
+def _cache_tmp_path(tmp_path: Path) -> Path:
+    return tmp_path
+
+
+def _structure_arrays_none(tmp_path: Path) -> None:
+    """No preparsed structure arrays -> the existence filter is skipped."""
+    return None
+
+
+def _structure_arrays_dummy(tmp_path: Path) -> Path:
+    """A dummy structure erray (empty inside)"""
+    array_dir = tmp_path / "arrays"
+    struct_path = template_structure_array_path(array_dir)
+    struct_path.parent.mkdir(parents=True, exist_ok=True)
+    struct_path.touch()
+    return array_dir
+
+
+@pytest.mark.parametrize(
+    "make_cache_directory, make_structure_array_directory, expected",
+    [
+        pytest.param(
+            _cache_none, _structure_arrays_none, {}, id="no_cache__no_arrays__drops"
+        ),
+        pytest.param(
+            _cache_none, _structure_arrays_dummy, {}, id="no_cache__with_arrays__drops"
+        ),
+        pytest.param(
+            _cache_tmp_path,
+            _structure_arrays_none,
+            {TEMPLATE_ID: _cache_entry()},
+            id="cache__no_arrays__loads",
+        ),
+        pytest.param(
+            _cache_tmp_path,
+            _structure_arrays_dummy,
+            {TEMPLATE_ID: _cache_entry()},
+            id="cache__with_arrays__loads",
+        ),
+    ],
+)
+def test_sample_templates_cache_directory_gate(
+    tmp_path, make_cache_directory, make_structure_array_directory, expected
+):
+    cache_npz = _write_cache_npz(tmp_path / "chainA.npz")
+
+    actual = sample_templates(
+        assembly_data=_assembly_data(cache_npz),
+        template_cache_directory=make_cache_directory(tmp_path),
+        n_templates=4,
+        take_top_k=True,  # deterministic: k = min(len(ids), n_templates)
+        chain_id="A",
+        template_structure_array_directory=make_structure_array_directory(tmp_path),
+        template_file_format="npz",
+    )
+
+    np.testing.assert_equal(
+        {k: dataclasses.asdict(v) for k, v in actual.items()},
+        {k: dataclasses.asdict(v) for k, v in expected.items()},
+    )