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Upgrade validation methods #1911

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dbadbd5
reconcile io path validator differences
stephprince Apr 17, 2024
fe81ad3
make io and path output the same
stephprince Apr 18, 2024
18826f8
update tests for io validation
stephprince Apr 18, 2024
923c1d3
add test that io and path output is same
stephprince Apr 18, 2024
41d9b9d
update tests for io output with status
stephprince May 29, 2024
8c921a3
add validate helper function and fix status tracking
stephprince May 29, 2024
95556a8
update arguments and status checks
stephprince May 29, 2024
87b1f1e
fix test comparing io and path outputs
stephprince May 29, 2024
6a748a5
update error message for io inputs
stephprince May 29, 2024
250513e
add tests to compare all io and path outputs
stephprince May 29, 2024
76a4f0f
remove script for testing
stephprince May 29, 2024
593c330
Merge branch 'dev' into upgrade-validator
stephprince Nov 12, 2024
25fc892
add initial json export option
stephprince Nov 13, 2024
6caa46b
update validator inputs and outputs, remove hdf5io references
stephprince Nov 13, 2024
4c48c67
update tests for non status output
stephprince Nov 13, 2024
216315a
add tests for json validator output
stephprince Nov 13, 2024
7c5f20f
move pynwb.validate into validation module
stephprince Nov 13, 2024
d791f6f
update json report
stephprince Nov 13, 2024
096013e
add validation entry point
stephprince Nov 13, 2024
ea4af1e
separate cli and validation function files
stephprince Nov 13, 2024
c14931a
update validation tutorial
stephprince Nov 21, 2024
c2a9522
move get_backend to pynwb init
stephprince Nov 21, 2024
2224b45
update example validation for new io behavior
stephprince Nov 23, 2024
f0912f3
update ruff ignores
stephprince Nov 23, 2024
8263b77
fix test comments
stephprince Nov 23, 2024
aa7b4ee
Merge branch 'dev' into upgrade-validator
stephprince Nov 23, 2024
8e5aa62
update CHANGELOG
stephprince Nov 27, 2024
72779d5
add tests for _get_backend
stephprince Nov 27, 2024
be666b6
update backend imports for optional zarr
stephprince Nov 27, 2024
0745bd2
Merge branch 'dev' into upgrade-validator
stephprince Nov 27, 2024
f319e88
fix test name
stephprince Nov 27, 2024
12bc84c
update test filename
stephprince Nov 27, 2024
35181ed
close io after validation
stephprince Dec 16, 2024
d2f7561
fix test assertion
stephprince Dec 16, 2024
11cc232
add condition for ros3 validation
stephprince Dec 16, 2024
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update CHANGELOG
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stephprince committed Nov 27, 2024
commit 8e5aa62efea21874eaa773b598265d12d5d5c86a
13 changes: 13 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
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# PyNWB Changelog

## PyNWB 3.0.0 (Upcoming)

### Breaking changes
- The validation methods have been updated with multiple breaking changes. @stephprince [#1911](https://github.com/NeurodataWithoutBorders/pynwb/pull/1911)
- The behavior of `pynwb.validate(io=...)` now matches the behavior of `pynwb.validate(path=...)`. In previous pynwb versions, `pynwb.validate(io=...)` did not use the cached namespaces during validation. To obtain the same behavior as in previous versions, you can update the function call to `pynwb.validate(io=..., used_cached_namespaces=False)`
- The validate module has been renamed to `validation.py`. The validate method can be
imported using `import pynwb; pynwb.validate` or `from pynwb.validation import validate`

### Enhancements and minor changes
- Added enhancements to the validation CLI. @stephprince [#1911](https://github.com/NeurodataWithoutBorders/pynwb/pull/1911)
- Added an entry point for the validation module. You can now use `pynwb-validate "file.nwb"` .
- Added the `--json-file-path` CLI argument to output validation results in a machine readable format.

## PyNWB 2.8.3 (November 19, 2024)

### Enhancements and minor changes