Merge pull request #2015 from NeurodataWithoutBorders/release-3.0.0

Prepare release 3.0

Author: stephprince

.github/workflows/run_all_tests.yml

@@ -167,7 +167,7 @@ jobs:
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          conda install -c conda-forge tox
+          conda install -c conda-forge "tox>=4.0"
 
       - name: Conda reporting
         run: |

CHANGELOG.md

@@ -1,10 +1,40 @@
 # PyNWB Changelog
 
-## PyNWB 3.0.0 (Upcoming)
+## PyNWB 3.0.0 (February 26, 2025)
+
+### 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=..., use_cached_namespaces=False)`
+   - `pynwb.validate` will return only a list of validation errors instead of a tuple: (list of validation_errors, status code)
+   - the `pynwb.validate(path=...)` argument has been added as a replacement for `pynwb.validate(paths=[...])`, which will be deprecated in a future major release [#2024](https://github.com/NeurodataWithoutBorders/pynwb/pull/2024)
+   - The validate module has been renamed to `validation.py`. The validate method can be 
+   imported using `import pynwb; pynwb.validate` or `from pynwb import validate`
+
+### Deprecations
+- The following deprecated classes will now raise errors when creating new instances of these classes: ``ClusteringWaveforms``, ``Clustering``, ``SweepTable``. Reading files using these data types will continue to be supported.
+- The following methods and arguments have been deprecated:
+  - ``ProcessingModule.add_container`` and ``ProcessingModule.add_data_interface`` are replaced by  ``ProcessingModule.add``
+  - ``ProcessingModule.get_container`` and ``ProcessingModule.get_data_interface`` are replaced by ``ProcessingModule.get``
+  - ``ScratchData.notes`` is deprecated. Use ``ScratchData.description`` instead.
+  - ``NWBFile.ic_electrodes`` is deprecated. Use ``NWBFile.icephys_electrodes`` instead.
+  - ``NWBFile.ec_electrodes`` is deprecated. Use ``NWBFile.electrodes`` instead.
+  - ``NWBFile.icephys_filtering`` is deprecated. Use ``IntracellularElectrode.filtering`` instead.
+  - ``NWBFile.modules`` is deprecated. Use ``NWBFile.processing`` instead.
+  - ``ImageSeries.format`` is fixed to 'external' if an external file is provided.
+  - ``ImageSeries.bits_per_pixel`` is deprecated.
+  - ``ImagingPlane.manifold``, ``ImagingPlane.conversion`` and ``ImagingPlane.unit`` are deprecated. Use ``ImagingPlane.origin_coords`` and ``ImagingPlane.grid_spacing`` instead.
+  - ``IndexSeries.unit`` is fixed to "N\A". 
+  - ``IndexSeries.indexed_timeseries`` is deprecated. Use ``IndexSeries.indexed_images`` instead.
+- The following deprecated methods have been removed:
+  - ``NWBFile.add_ic_electrode`` is removed. Use ``NWBFile.add_icephys_electrode`` instead.
+  - ``NWBFile.create_ic_electrode`` is removed. Use ``NWBFile.create_icephys_electrode`` instead.
+  - ``NWBFile.get_ic_electrode`` is removed. Use ``NWBFile.get_icephys_electrode`` instead.
+  - ``pynwb._get_resources`` is removed.
 
 ### Enhancements and minor changes
 - Added `__all__` to modules. @bendichter [#2021](https://github.com/NeurodataWithoutBorders/pynwb/pull/2021)
 - Added `pynwb.read_nwb` convenience method to simplify reading an NWBFile written with any backend @h-mayorquin [#1994](https://github.com/NeurodataWithoutBorders/pynwb/pull/1994)
+- Constrained `hdmf<5` to prevent future compatibility issues. [#2040](https://github.com/NeurodataWithoutBorders/pynwb/pull/2040)   
 
 ### Bug fixes
 - Made distance, orientation, and field_of_view optional in OpticalSeries to match schema @bendichter [#2023](https://github.com/NeurodataWithoutBorders/pynwb/pull/2023)
@@ -14,7 +44,11 @@
   - Added support for `model_number`, `model_name`, and `serial_number` fields to `Device`. @stephprince [#1997](https://github.com/NeurodataWithoutBorders/pynwb/pull/1997)
   - Deprecated `EventWaveform` neurodata type. @rly [#1940](https://github.com/NeurodataWithoutBorders/pynwb/pull/1940)
   - Deprecated `ImageMaskSeries` neurodata type. @rly [#1941](https://github.com/NeurodataWithoutBorders/pynwb/pull/1941)
+- 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-outpath-path` CLI argument to output validation results in a machine readable format.
 - Removed python 3.8 support, added python 3.13 support. @stephprince [#2007](https://github.com/NeurodataWithoutBorders/pynwb/pull/2007)
+- Added warnings when using positional arguments in `Container` constructor methods. Positional arguments will raise errors in the next major release. @stephprince [#1972](https://github.com/NeurodataWithoutBorders/pynwb/pull/1972)
 - `mock_ElectricalSeries`. Make number of electrodes between data and electrode region agree when explicitly passing data @h-mayorquin [#2019](https://github.com/NeurodataWithoutBorders/pynwb/pull/2019)
 
 ### Documentation and tutorial enhancements

Legal.txt

@@ -1,4 +1,4 @@
-“pynwb” Copyright (c) 2017-2024, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+“pynwb” Copyright (c) 2017-2025, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 
 If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Innovation & Partnerships Office at [email protected].
 

README.rst

@@ -94,7 +94,7 @@ Citing NWB
 LICENSE
 =======
 
-"pynwb" Copyright (c) 2017-2024, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+"pynwb" Copyright (c) 2017-2025, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
 (1) Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
@@ -110,7 +110,7 @@ You are under no obligation whatsoever to provide any bug fixes, patches, or upg
 COPYRIGHT
 =========
 
-"pynwb" Copyright (c) 2017-2024, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
+"pynwb" Copyright (c) 2017-2025, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy).  All rights reserved.
 If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Innovation & Partnerships Office at [email protected].
 
 NOTICE.  This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit other to do so.

docs/gallery/domain/icephys.py

@@ -37,8 +37,7 @@
 ns_builder = NWBNamespaceBuilder(
     "Extension for use in my Lab", "mylab", version="0.1.0"
 )
-
-ns_builder.include_type("ElectricalSeries", namespace="core")
+ns_builder.include_namespace("core")
 
 ext = NWBGroupSpec(
     "A custom ElectricalSeries for my lab",
@@ -264,7 +263,7 @@ def __init__(self, **kwargs):
 ext_source = name + ".extensions.yaml"
 
 ns_builder = NWBNamespaceBuilder(name + " extensions", name, version="0.1.0")
-ns_builder.include_type("NWBDataInterface", namespace="core")
+ns_builder.include_namespace("core")
 
 potato = NWBGroupSpec(
     neurodata_type_def="Potato",

docs/gallery/general/extensions.py

@@ -145,7 +145,7 @@
 # Now lets do an analysis for which we do not have a specification, but we would like to store
 # the results for.
 
-filt_ts = nwb_scratch.modules["filtering_module"]["filtered_timeseries"]
+filt_ts = nwb_scratch.processing["filtering_module"]["filtered_timeseries"]
 
 fft = np.fft.fft(filt_ts.data)
 

docs/gallery/general/scratch.py

@@ -191,7 +191,7 @@ def __call__(self, filename):
 
 # General information about the project.
 project = u'PyNWB'
-copyright = u'2017-2024, Neurodata Without Borders'
+copyright = u'2017-2025, Neurodata Without Borders'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the