Merge from devel to master to create release 1.1.0

CHANGELOG

@@ -5,6 +5,26 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased]
 
+## [1.1.0] 2026-04-23
+
+### Changed
+
+* Previously unused function `get_wafer_content_by_lims_id` is renamed to
+  `get_records_by_wafer_lims_id` to reflect its functionality and leave room
+  for retrieval by other LIMS IDs in future. Since the wafers have their own
+  manufacturer-assigned IDs, it is important to emphasise that the argument
+  to this function is the ID assigned by LIMS.
+
+  In this function the type of the returned object is changed from `list` to
+  `Sequence` to be consistent with other code in this package.
+
+  To follow the existing pattern of naming files with unit tests,  tests for
+  the function are moved from `tests/test_schema.py` to `tests/test_wafer.py`.
+
+### Removed
+
+  `tests/test_schema.py`
+
 ## [1.0.1] 2026-04-16
 
 ### Changed

src/npgmlwarehouse/db/wafer.py

@@ -16,9 +16,11 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 """
-Functions for retrieving the barcoded moieties loaded into one wafer/flowcell/smrtcell
+Functions for retrieving the barcoded moieties loaded into one wafer.
 """
 
+from typing import Sequence
+
 from sqlalchemy import select
 from sqlalchemy.orm import Session
 
@@ -29,23 +31,25 @@
 )
 
 
-def get_wafer_content_by_lims_id(
+def get_records_by_wafer_lims_id(
     session: Session, id_wafer_lims: str
-) -> list[UseqWafer]:
+) -> Sequence[UseqWafer]:
     """
-    Get the LIMS entities that were assigned to a wafer for an Ultimagen run with sample and study metadata.
+    Get all LIMS entities that correspond to an Ultimagen wafer along with
+    their sample and study data.
 
     Args:
         session (sqlalchemy.orm.Session):
             Database session
-        id_wafer_lims (str): Unique ID for Ultimagen runs which consists of
-            <batch_for_opentrons>_<id_pool_id>_<runcount>
+        id_wafer_lims (str): Unique ID for an Ultimagen wafer which consists of
+            <batch_for_opentrons>_<pool_barcode>_<count>. The count is used to
+            disambiguate multiple wafers which were processed in the same batch
+            opentrons process for the same library pool.
 
     Returns:
-    -------
-        list[UseqWafer]: Collection of samples from wafer data
+        Sequence[UseqWafer]: Collection of wafer records
     """
     query = (select(UseqWafer).join(Sample).join(Study)).where(
         UseqWafer.id_wafer_lims == id_wafer_lims
     )
-    return list(session.scalars(query).all())
+    return session.scalars(query).all()

tests/test_wafer.py

@@ -0,0 +1,37 @@
+from pytest import mark as m
+
+from npgmlwarehouse.db.wafer import get_records_by_wafer_lims_id
+
+
+@m.describe("Test data retrieval for a wafer")
+class TestProduct(object):
+    @m.context("Wafer records are present in `useq_wafer` table")
+    @m.it("Retrieves correct records")
+    def test_get_wafer_records(self, testdb):
+        records = get_records_by_wafer_lims_id(testdb, "122_NT109338I_1")
+        assert len(records) == 2
+        assert records[0].id_wafer_lims == "122_NT109338I_1"
+        assert records[1].id_wafer_lims == "122_NT109338I_1"
+
+        metadata = [
+            (w.sample.uuid_sample_lims, w.id_library_lims, w.study.id_study_lims)
+            for w in records
+        ]
+        for md in [
+            ("1788c8d0-6a6c-11e4-8e19-68b59977951c", "SQPU-346269-E:A1", "619"),
+            ("178df8f0-6a6c-11e4-8e19-68b59977951c", "SQPU-346269-E:A2", "619"),
+        ]:
+            assert md in metadata
+
+        records = get_records_by_wafer_lims_id(testdb, "123_NT109345H_1")
+        assert len(records) == 1
+        assert records[0].id_wafer_lims == "123_NT109345H_1"
+        assert (
+            records[0].sample.uuid_sample_lims == "d41d4a40-a521-11e3-8055-3c4a9275d6c6"
+        )
+
+    @m.context("No records for a given ID in `useq_wafer` table")
+    @m.it("Returns an empty list")
+    def test_get_wafer_records_no_record(self, testdb):
+        records = get_records_by_wafer_lims_id(testdb, "122_NT109338I_2")
+        assert len(records) == 0