Merge branch 'dev' into electrodes_table

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:

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.

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

docs/format/source/format_release_notes.rst

@@ -5,14 +5,18 @@ Release Notes
 
 2.8.0 (Upcoming)
 ------------------------
+
 Minor changes
 ^^^^^^^^^^^^^
 - Added support to set boundary metadata for ``SpatialSeries``. (#524)
 - Added columns ``waveform_mean_index`` and ``waveform_sd_index`` to ``Units`` to make the ``waveform_mean`` and
   ``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)
 ------------------------

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.

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

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