DynamicEnums and Schemasheets integration (#923)

* first

* schemamaker

* schemasheets support integration

* schemasheets files for term set test

* unit test for schemasheets integration

* test

* add oaklib to termset

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* dynamic

* dynamic

* example for dyanmic term set unit test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* leverage oaklib to expand enums dyanmically

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* unit test for enum expansion method

* dynamic

* join error

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* test

* correct prefix for cell ontology

* test skips/pyproject

* ruff

* pyproject

* fix test for enum expander

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* pyproject

* Update pyproject.toml

* Update requirements-opt.txt

* ruff

* Update pyproject.toml

* Update requirements-opt.txt

* Update requirements-min.txt

* Update requirements-doc.txt

* gallery

* yaml

* Update pyproject.toml

* value error

* quote

* Update requirements-min.txt

* Update requirements-opt.txt

* Update requirements-doc.txt

* except

* gallery

* gallery

* gallery

* ruff

* tests

* tests

* windows path resolution in termset

* fix linting errors in test_term_set

* normalize paths for cross OS tests fix

* normalize paths in missed test_enum_expander()

* notebook

* notebook

* name convention

* name convention

* Update CHANGELOG.md

* Update plot_term_set.py

* Update plot_term_set.py

* Update CHANGELOG.md

* test reqs

* test reqs

* pyproject

* gallery

* gallery

* gallery

* gallery

* gallery

* gallery

* gallery

* revert

* dynamic document clarify

* Update docs/gallery/plot_term_set.py

Co-authored-by: Oliver Ruebel <[email protected]>

* Update src/hdmf/term_set.py

Co-authored-by: Oliver Ruebel <[email protected]>

* Update src/hdmf/term_set.py

Co-authored-by: Oliver Ruebel <[email protected]>

* Update src/hdmf/term_set.py

Co-authored-by: Oliver Ruebel <[email protected]>

* fixes from review

* Update src/hdmf/term_set.py

---------

Co-authored-by: Sujay Patil <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Oliver Ruebel <[email protected]>

Author: 4 people

CHANGELOG.md

@@ -1,11 +1,13 @@
 # HDMF Changelog
 
+
 ## HDMF 3.9.0 (Upcoming)
 
 ### New features and minor improvements
 - Increase raw data chunk cache size for reading HDF5 files from 1 MiB to 32 MiB. @bendichter, @rly [#925](https://github.com/hdmf-dev/hdmf/pull/925)
 - Increase default chunk size for `GenericDataChunkIterator` from 1 MB to 10 MB. @bendichter, @rly [#925](https://github.com/hdmf-dev/hdmf/pull/925)
 - Added the magic `__reduce__` method as well as two private semi-abstract helper methods to enable pickling of the `GenericDataChunkIterator`. @codycbakerphd [#924](https://github.com/hdmf-dev/hdmf/pull/924)
+- Added Dynamic Enumerations and Schemasheets support to `TermSet`. @mavaylon1 [#923](https://github.com/hdmf-dev/hdmf/pull/923)
 
 ## HDMF 3.8.1 (July 25, 2023)
 

docs/gallery/example_dynamic_term_set.yaml

@@ -0,0 +1,42 @@
+id: https://w3id.org/linkml/examples/nwb_dynamic_enums
+title: dynamic enums example
+name: nwb_dynamic_enums
+description: this schema demonstrates the use of dynamic enums
+
+prefixes:
+  linkml: https://w3id.org/linkml/
+  CL: http://purl.obolibrary.org/obo/CL_
+
+imports:
+  - linkml:types
+
+default_range: string
+
+# ======================== #
+#         CLASSES          #
+# ======================== #
+classes:
+  BrainSample:
+    slots:
+      - cell_type
+
+# ======================== #
+#          SLOTS           #
+# ======================== #
+slots:
+  cell_type:
+    required: true
+    range: NeuronTypeEnum
+
+# ======================== #
+#          ENUMS           #
+# ======================== #
+enums:
+  NeuronTypeEnum:
+    reachable_from:
+      source_ontology: obo:cl
+      source_nodes:
+        - CL:0000540  ## neuron
+      include_self: false
+      relationship_types:
+        - rdfs:subClassOf