diff --git a/core/nwb.ecephys.yaml b/core/nwb.ecephys.yaml index 5e5ee521..e4578d3f 100644 --- a/core/nwb.ecephys.yaml +++ b/core/nwb.ecephys.yaml @@ -69,9 +69,8 @@ groups: neurodata_type_inc: ElectricalSeries doc: "Stores snapshots/snippets of recorded spike events (i.e., threshold crossings). This may also be raw data, as reported by ephys hardware. If so, the TimeSeries::description - field should describe how events were detected. All SpikeEventSeries should - reside in a module (under EventWaveform interface) even if the spikes were reported - and stored by hardware. All events span the same recording channels and store + field should describe how events were detected. All events span the same recording + channels and store snapshots of equal duration. TimeSeries::data array structure: [num events] [num channels] [num samples] (or [num events] [num samples] for single electrode)." datasets: @@ -191,7 +190,7 @@ groups: - neurodata_type_def: EventWaveform neurodata_type_inc: NWBDataInterface default_name: EventWaveform - doc: Represents either the waveforms of detected events, as extracted from a raw + doc: DEPRECATED. Represents either the waveforms of detected events, as extracted from a raw data trace in /acquisition, or the event waveforms that were stored during experiment acquisition. groups: diff --git a/core/nwb.file.yaml b/core/nwb.file.yaml index 416c74aa..6b75da4f 100644 --- a/core/nwb.file.yaml +++ b/core/nwb.file.yaml @@ -7,7 +7,7 @@ groups: attributes: - name: nwb_version dtype: text - value: "2.7.0" + value: "2.8.0-alpha" doc: File version string. Use semantic versioning, e.g. 1.2.1. This will be the name of the format with trailing major, minor and patch numbers. datasets: @@ -241,6 +241,18 @@ groups: - name: file_name dtype: text doc: Name of script file. + - name: was_generated_by + dtype: text + doc: Name and version of software package(s) used to generate data contained in + this NWB File. For each software package or library, include the name of the + software as the first value and the version as the second value. + dims: + - num_sources + - name, version + shape: + - null + - 2 + quantity: '?' - name: stimulus dtype: text doc: Notes about stimuli, such as how and where they were presented. diff --git a/core/nwb.image.yaml b/core/nwb.image.yaml index 11c36fb5..3f782a63 100644 --- a/core/nwb.image.yaml +++ b/core/nwb.image.yaml @@ -118,7 +118,7 @@ groups: - neurodata_type_def: ImageMaskSeries neurodata_type_inc: ImageSeries - doc: An alpha mask that is applied to a presented visual stimulus. The 'data' array + doc: DEPRECATED. An alpha mask that is applied to a presented visual stimulus. The 'data' array contains an array of mask values that are applied to the displayed image. Mask values are stored as RGBA. Mask can vary with time. The timestamps array indicates the starting time of a mask, and that mask pattern continues until it's explicitly diff --git a/docs/format/source/format_release_notes.rst b/docs/format/source/format_release_notes.rst index b5b837e0..f573ffdd 100644 --- a/docs/format/source/format_release_notes.rst +++ b/docs/format/source/format_release_notes.rst @@ -5,6 +5,7 @@ Release Notes 2.8.0 (Upcoming) ------------------------ + Minor changes ^^^^^^^^^^^^^ - Added support to set boundary metadata for ``SpatialSeries``. (#524) @@ -12,7 +13,10 @@ Minor changes ``waveform_sd`` columns ragged. This allows for a different number of waveform means/SDs per unit which is useful when each unit is associated with a different number of electrodes and there is a waveform mean/SD for each electrode and unit. (#576) +- Added optional ``was_generated_by`` attribute to ``NWBFile`` to store provenance information (#578) +- Deprecated ``EventWaveform`` neurodata type. (#584) +- Deprecated ``ImageMaskSeries`` neurodata type. (#583) 2.7.0 (February 7, 2024) ------------------------ diff --git a/docs/format/source/software_process.rst b/docs/format/source/software_process.rst index 49996cd5..3640be28 100644 --- a/docs/format/source/software_process.rst +++ b/docs/format/source/software_process.rst @@ -130,5 +130,5 @@ released version of nwb-schema. Starting with nwb-schema version 2.2.0, the dev and MatNWB include only publicly released versions of nwb-schema. For more details, see the [PyNWB software process documentation](https://pynwb.readthedocs.io/en/stable/software_process.html). -The [NWB Extensions Versioning Guidelines](https://nwb-extensions.github.io/versioning_guidelines) are used to guide +The [NWB Extensions Versioning Guidelines](https://www.nwb.org/versioning-guidelines) are used to guide versioning of the NWB core schema, as well as extensions to NWB. diff --git a/docs/storage/.readthedocs.yaml b/docs/storage/.readthedocs.yaml new file mode 100644 index 00000000..78614ac1 --- /dev/null +++ b/docs/storage/.readthedocs.yaml @@ -0,0 +1,27 @@ +# Read the Docs configuration file for https://nwb-storage.readthedocs.io/en/latest/ + # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + + # Required + version: 2 + + build: + os: ubuntu-22.04 + tools: + python: "3.12" + + # Build documentation in the docs/ directory with Sphinx + sphinx: + configuration: docs/storage/source/conf.py + + # Optionally build your docs in additional formats such as PDF and ePub + formats: all + + # Optionally set the version of Python and requirements required to build your docs + python: + install: + - requirements: requirements-doc.txt + + # Optionally include all submodules + submodules: + include: all + recursive: true diff --git a/docs/storage/source/conf.py b/docs/storage/source/conf.py index 2f4a3219..409d167b 100644 --- a/docs/storage/source/conf.py +++ b/docs/storage/source/conf.py @@ -105,7 +105,7 @@ html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] def setup(app): - app.add_stylesheet("theme_overrides.css") # overrides for wide tables in RTD theme + app.add_css_file("theme_overrides.css") # overrides for wide tables in RTD theme # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the