Merge branch 'dev' into compound

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -10,7 +10,7 @@ Prepare for release of HDMF [version]
   and any other locations as needed
 - [ ] Update `pyproject.toml` as needed
 - [ ] Update `README.rst` as needed
-- [ ] Update `src/hdmf/common/hdmf-common-schema` submodule as needed. Check the version number and commit SHA manually
+- [ ] Update `src/hdmf/common/hdmf-common-schema` submodule as needed. Check the version number and commit SHA manually. Make sure we are using the latest release and not the latest commit on the `main` branch.
 - [ ] Update changelog (set release date) in `CHANGELOG.md` and any other docs as needed
 - [ ] Run tests locally including gallery tests, and inspect all warnings and outputs
   (`pytest && python test_gallery.py`)

CHANGELOG.md

@@ -1,9 +1,10 @@
 # HDMF Changelog
 
-## HDMF 3.13.0 (Upcoming)
+## HDMF 3.13.0 (March 20, 2024)
 
 ### Enhancements
 - Updated `TermSetWrapper` to support validating a single field within a compound array. @mavaylon1 [#1061](https://github.com/hdmf-dev/hdmf/pull/1061)
+- Unwrap `TermSetWrapper` within the builder to support different backends more efficiently. @mavaylon1 [#1070](https://github.com/hdmf-dev/hdmf/pull/1070)
 - Added docs page that lists limitations of support for the HDMF specification language. @rly [#1069](https://github.com/hdmf-dev/hdmf/pull/1069)
 - Added warning when using `add_row` or `add_column` to add a ragged array to `DynamicTable` without an index parameter. @stephprince [#1066](https://github.com/hdmf-dev/hdmf/pull/1066)
 

pyproject.toml

@@ -21,6 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: BSD License",
     "Development Status :: 5 - Production/Stable",
     "Operating System :: OS Independent",

requirements-dev.txt

@@ -2,7 +2,7 @@
 # compute coverage, and create test environments. note that depending on the version of python installed, different
 # versions of requirements may be installed due to package incompatibilities.
 #
-black==23.10.1
+black==24.3.0
 codespell==2.2.6
 coverage==7.3.2
 pre-commit==3.5.0

requirements-opt.txt

@@ -1,8 +1,8 @@
 # pinned dependencies that are optional. used to reproduce an entire development environment to use HDMF
-tqdm==4.66.1
-zarr==2.16.1
-linkml-runtime==1.6.0; python_version >= "3.9"
-schemasheets==0.1.24; python_version >= "3.9"
-oaklib==0.5.20; python_version >= "3.9"
-pydantic==1.10.13  # linkml-runtime 1.6.0 and related packages require pydantic<2
+tqdm==4.66.2
+zarr==2.17.1
+linkml-runtime==1.7.3; python_version >= "3.9"
+schemasheets==0.2.1; python_version >= "3.9"
+oaklib==0.5.31; python_version >= "3.9"
+pydantic==2.6.4
 pyyaml==6.0.1; python_version >= "3.9"

src/hdmf/backends/hdf5/h5tools.py

@@ -17,7 +17,6 @@
 from ...build import (Builder, GroupBuilder, DatasetBuilder, LinkBuilder, BuildManager, RegionBuilder,
                       ReferenceBuilder, TypeMap, ObjectMapper)
 from ...container import Container
-from ...term_set import TermSetWrapper
 from ...data_utils import AbstractDataChunkIterator
 from ...spec import RefSpec, DtypeSpec, NamespaceCatalog
 from ...utils import docval, getargs, popargs, get_data_shape, get_docval, StrDataset
@@ -1103,10 +1102,6 @@ def write_dataset(self, **kwargs):  # noqa: C901
             data = data.data
         else:
             options['io_settings'] = {}
-        if isinstance(data, TermSetWrapper):
-            # This is for when the wrapped item is a dataset
-            # (refer to objectmapper.py for wrapped attributes)
-            data = data.value
         attributes = builder.attributes
         options['dtype'] = builder.dtype
         dset = None

src/hdmf/build/objectmapper.py

@@ -752,7 +752,11 @@ def build(self, **kwargs):
                                           % (container.__class__.__name__, container.name, repr(source)))
                         try:
                             # use spec_dtype from self.spec when spec_ext does not specify dtype
-                            bldr_data, dtype = self.convert_dtype(spec, container.data, spec_dtype=spec_dtype)
+                            if isinstance(container.data, TermSetWrapper):
+                                data = container.data.value
+                            else:
+                                data = container.data
+                            bldr_data, dtype = self.convert_dtype(spec, data, spec_dtype=spec_dtype)
                         except Exception as ex:
                             msg = 'could not resolve dtype for %s \'%s\'' % (type(container).__name__, container.name)
                             raise Exception(msg) from ex

tests/unit/build_tests/mapper_tests/test_build.py

@@ -1,7 +1,8 @@
 from abc import ABCMeta, abstractmethod
 
 import numpy as np
-from hdmf import Container, Data
+from hdmf import Container, Data, TermSet, TermSetWrapper
+from hdmf.common import VectorData, get_type_map
 from hdmf.build import ObjectMapper, BuildManager, TypeMap, GroupBuilder, DatasetBuilder
 from hdmf.build.warnings import DtypeConversionWarning
 from hdmf.spec import GroupSpec, AttributeSpec, DatasetSpec, SpecCatalog, SpecNamespace, NamespaceCatalog, Spec
@@ -10,6 +11,29 @@
 
 from tests.unit.helpers.utils import CORE_NAMESPACE
 
+try:
+    import linkml_runtime  # noqa: F401
+    LINKML_INSTALLED = True
+except ImportError:
+    LINKML_INSTALLED = False
+
+
+class TestUnwrapTermSetWrapperBuild(TestCase):
+    """
+    Test the unwrapping of TermSetWrapper on regular datasets within build.
+    """
+    def setUp(self):
+        if not LINKML_INSTALLED:
+            self.skipTest("optional LinkML module is not installed")
+
+    def test_unwrap(self):
+        manager = BuildManager(get_type_map())
+        terms = TermSet(term_schema_path='tests/unit/example_test_term_set.yaml')
+        build = manager.build(VectorData(name='test_data',
+                                         description='description',
+                                         data=TermSetWrapper(value=['Homo sapiens'], termset= terms)))
+
+        self.assertEqual(build.data, ['Homo sapiens'])
 
 # TODO: test build of extended group/dataset that modifies an attribute dtype (commented out below), shape, value, etc.
 # by restriction. also check that attributes cannot be deleted or scope expanded.