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DynamicEnums and Schemasheets integration #923

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first
mavaylon1 Jul 27, 2023
1664400
schemamaker
mavaylon1 Jul 27, 2023
c9f90e4
schemasheets support integration
sujaypatil96 Jul 27, 2023
c3aeac2
schemasheets files for term set test
sujaypatil96 Jul 27, 2023
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unit test for schemasheets integration
sujaypatil96 Jul 27, 2023
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test
mavaylon1 Jul 27, 2023
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add oaklib to termset
sujaypatil96 Jul 28, 2023
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Merge branch 'dev' into enums
mavaylon1 Jul 28, 2023
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 28, 2023
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dynamic
mavaylon1 Jul 28, 2023
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conflict
mavaylon1 Jul 28, 2023
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dynamic
mavaylon1 Jul 28, 2023
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example for dyanmic term set unit test
sujaypatil96 Jul 28, 2023
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Merge branch 'enums' of https://github.com/hdmf-dev/hdmf into enums
sujaypatil96 Jul 28, 2023
187dfef
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 28, 2023
b30f656
leverage oaklib to expand enums dyanmically
sujaypatil96 Jul 28, 2023
f615064
merge conflict in example dynamic term set
sujaypatil96 Jul 28, 2023
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 28, 2023
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unit test for enum expansion method
sujaypatil96 Jul 28, 2023
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Merge branch 'enums' of https://github.com/hdmf-dev/hdmf into enums
sujaypatil96 Jul 28, 2023
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dynamic
mavaylon1 Jul 28, 2023
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dynamic
mavaylon1 Jul 28, 2023
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join error
mavaylon1 Jul 28, 2023
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 28, 2023
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test
mavaylon1 Jul 28, 2023
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Merge branch 'enums' of https://github.com/hdmf-dev/hdmf into enums
mavaylon1 Jul 28, 2023
ede2e7a
correct prefix for cell ontology
sujaypatil96 Jul 28, 2023
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test skips/pyproject
mavaylon1 Jul 28, 2023
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ruff
mavaylon1 Jul 28, 2023
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pyproject
mavaylon1 Jul 28, 2023
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fix test for enum expander
sujaypatil96 Jul 28, 2023
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fix test for enum expander
sujaypatil96 Jul 28, 2023
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 28, 2023
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pyproject
mavaylon1 Jul 28, 2023
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pyproject
mavaylon1 Jul 28, 2023
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Update requirements-opt.txt
mavaylon1 Jul 28, 2023
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ruff
mavaylon1 Jul 28, 2023
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Merge branch 'enums' of https://github.com/hdmf-dev/hdmf into enums
mavaylon1 Jul 28, 2023
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Update pyproject.toml
mavaylon1 Jul 28, 2023
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Update requirements-opt.txt
mavaylon1 Jul 28, 2023
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mavaylon1 Jul 28, 2023
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Update requirements-doc.txt
mavaylon1 Jul 28, 2023
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gallery
mavaylon1 Jul 28, 2023
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Merge branch 'enums' of https://github.com/hdmf-dev/hdmf into enums
mavaylon1 Jul 28, 2023
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yaml
mavaylon1 Jul 28, 2023
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Update pyproject.toml
mavaylon1 Jul 28, 2023
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value error
mavaylon1 Jul 28, 2023
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quote
mavaylon1 Jul 28, 2023
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Update requirements-min.txt
mavaylon1 Jul 28, 2023
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Update requirements-opt.txt
mavaylon1 Jul 28, 2023
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Update requirements-doc.txt
mavaylon1 Jul 28, 2023
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except
mavaylon1 Jul 28, 2023
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gallery
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mavaylon1 Jul 28, 2023
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tests
mavaylon1 Jul 28, 2023
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tests
mavaylon1 Jul 28, 2023
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windows path resolution in termset
sujaypatil96 Jul 29, 2023
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fix linting errors in test_term_set
sujaypatil96 Jul 29, 2023
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normalize paths for cross OS tests fix
sujaypatil96 Jul 29, 2023
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normalize paths in missed test_enum_expander()
sujaypatil96 Jul 29, 2023
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notebook
mavaylon1 Aug 3, 2023
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notebook
mavaylon1 Aug 3, 2023
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name convention
mavaylon1 Aug 3, 2023
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name convention
mavaylon1 Aug 3, 2023
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Update CHANGELOG.md
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Update plot_term_set.py
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mavaylon1 Aug 3, 2023
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Merge branch 'dev' into enums
mavaylon1 Aug 12, 2023
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Update CHANGELOG.md
mavaylon1 Aug 12, 2023
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test reqs
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test reqs
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mavaylon1 Aug 13, 2023
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Update docs/gallery/plot_term_set.py
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Update src/hdmf/term_set.py
oruebel Aug 13, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -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)

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42 changes: 42 additions & 0 deletions docs/gallery/example_dynamic_term_set.yaml
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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
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