Merge branch 'dev' into tmc

NeurodataWithoutBorders · May 20, 2024 · ba7e851 · ba7e851
2 parents 2dcc091 + 7a0d8b4
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diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
@@ -36,8 +36,8 @@ jobs:
           - { name: windows-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: windows-latest }
           - { name: windows-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: windows-latest }
           - { name: windows-python3.12-prerelease, test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.11", os: windows-latest }
-          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: macos-latest }
-          - { name: macos-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum    , python-ver: "3.8" , os: macos-13 }
+          - { name: macos-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-13 }
           - { name: macos-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: macos-latest }
           - { name: macos-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: macos-latest }
           - { name: macos-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: macos-latest }
@@ -95,7 +95,7 @@ jobs:
           - { name: windows-gallery-python3.8-minimum    , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: windows-latest }
           - { name: windows-gallery-python3.12-upgraded  , test-tox-env: gallery-py312-upgraded  , python-ver: "3.12", os: windows-latest }
           - { name: windows-gallery-python3.12-prerelease, test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: windows-latest }
-          - { name: macos-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-gallery-python3.8-minimum      , test-tox-env: gallery-py38-minimum    , python-ver: "3.8" , os: macos-13 }
           - { name: macos-gallery-python3.12-upgraded    , test-tox-env: gallery-py312-upgraded  , python-ver: "3.12", os: macos-latest }
           - { name: macos-gallery-python3.12-prerelease  , test-tox-env: gallery-py312-prerelease, python-ver: "3.12", os: macos-latest }
     steps:
@@ -198,7 +198,7 @@ jobs:
         include:
           - { name: conda-linux-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
           - { name: conda-windows-python3.12-ros3, python-ver: "3.12", os: windows-latest }
-          - { name: conda-macos-python3.12-ros3  , python-ver: "3.12", os: macos-latest }
+          - { name: conda-macos-python3.12-ros3  , python-ver: "3.12", os: macos-13 } # This is due to DANDI not supporting osx-arm64. Will support macos-latest when this changes. 
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -224,7 +224,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install -r requirements-dev.txt
-          pip install -e .
+          pip install .
           conda info
           conda list
           pip list
@@ -245,7 +245,7 @@ jobs:
         include:
           - { name: conda-linux-gallery-python3.12-ros3  , python-ver: "3.12", os: ubuntu-latest }
           - { name: conda-windows-gallery-python3.12-ros3, python-ver: "3.12", os: windows-latest }
-          - { name: conda-macos-gallery-python3.12-ros3  , python-ver: "3.12", os: macos-latest }
+          - { name: conda-macos-gallery-python3.12-ros3  , python-ver: "3.12", os: macos-13 } # This is due to DANDI not supporting osx-arm64. Will support macos-latest when this changes. 
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -271,7 +271,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install matplotlib
-          pip install -e .
+          pip install .
           pip list
 
       - name: Conda reporting

diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
@@ -53,20 +53,20 @@ jobs:
 
       - name: Install package
         run: |
-          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip install .
           python -m pip list
 
       - name: Run unit tests and generate coverage report
         run: |
           python -m coverage run test.py --pynwb
           python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          python -m coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
           flags: unit
-          files: coverage.xml
+          file: coverage.xml
           fail_ci_if_error: true
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
@@ -77,13 +77,13 @@ jobs:
           # validation CLI tests generate separate .coverage files that need to be merged
           python -m coverage combine
           python -m coverage xml  # codecov uploader requires xml format
-          python -m coverage report -m
+          python -m coverage report
 
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
           flags: integration
-          files: coverage.xml
+          file: coverage.xml
           fail_ci_if_error: true
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/run_dandi_read_tests.yml b/.github/workflows/run_dandi_read_tests.yml
@@ -31,7 +31,7 @@ jobs:
         run: |
           python -m pip install dandi fsspec requests aiohttp pytest
           python -m pip uninstall -y pynwb  # uninstall pynwb
-          python -m pip install -e .
+          python -m pip install .
           python -m pip list
 
       - name: Conda reporting

diff --git a/.github/workflows/run_inspector_tests.yml b/.github/workflows/run_inspector_tests.yml
@@ -34,8 +34,7 @@ jobs:
           git clone https://github.com/NeurodataWithoutBorders/nwbinspector.git
           cd nwbinspector
           python -m pip install -r requirements.txt pytest
-          # must install in editable mode for coverage to find sources
-          python -m pip install -e .  # this might install a pinned version of pynwb instead of the current one
+          python -m pip install .  # this might install a pinned version of pynwb instead of the current one
           cd ..
           python -m pip uninstall -y pynwb  # uninstall the pinned version of pynwb
           python -m pip install .  # reinstall current branch of pynwb

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -24,7 +24,7 @@ jobs:
           - { name: linux-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: ubuntu-latest , upload-wheels: true }
           - { name: windows-python3.8-minimum    , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum   , python-ver: "3.8" , os: windows-latest }
           - { name: windows-python3.12-upgraded  , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded , python-ver: "3.12", os: windows-latest }
-          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum   , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.8-minimum      , test-tox-env: py38-minimum    , build-tox-env: build-py38-minimum   , python-ver: "3.8" , os: macos-13 }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -200,7 +200,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install -r requirements-dev.txt
-          pip install -e .
+          pip install .
           conda info
           conda list
           pip list
@@ -245,7 +245,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install matplotlib
-          pip install -e .
+          pip install .
           pip list
 
       - name: Conda reporting

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,19 +1,29 @@
 # PyNWB Changelog
 
-## PyNWB 2.7.0 (Upcoming)
+## PyNWB 2.8.0 (Upcoming)
 
 ### Enhancements and minor changes
+- Set rate default value inside `mock_ElectricalSeries` to avoid having to set `rate=None` explicitly when passing timestamps. @h-mayorquin [#1894](https://github.com/NeurodataWithoutBorders/pynwb/pull/1894)
+
+## PyNWB 2.7.0 (May 2, 2024)
+
+### Enhancements and minor changes
+- Added `bounds` field to `SpatialSeries` to set optional boundary range (min, max) for each dimension of data. @mavaylon1 [#1869](https://github.com/NeurodataWithoutBorders/pynwb/pull/1869/files)
 - Added support for NWB schema 2.7.0. See [2.7.0 release notes](https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html) for details
-  - Deprecated `ImagingRetinotopy` neurodata type. @rly [#1813](https://github.com/NeurodataWithoutBorders/pynwb/pull/1813)
-  - Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. @rly [#1812](https://github.com/NeurodataWithoutBorders/pynwb/pull/1812)
-  - Support `stimulus_template` as optional predefined column in `IntracellularStimuliTable`. @stephprince [#1815](https://github.com/NeurodataWithoutBorders/pynwb/pull/1815)
-  - Support `NWBDataInterface` and `DynamicTable` in `NWBFile.stimulus`. @rly [#1842](https://github.com/NeurodataWithoutBorders/pynwb/pull/1842)
+- Deprecated `ImagingRetinotopy` neurodata type. @rly [#1813](https://github.com/NeurodataWithoutBorders/pynwb/pull/1813)
+- Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. @rly [#1812](https://github.com/NeurodataWithoutBorders/pynwb/pull/1812)
+- Support `stimulus_template` as optional predefined column in `IntracellularStimuliTable`. @stephprince [#1815](https://github.com/NeurodataWithoutBorders/pynwb/pull/1815)
+- Support `NWBDataInterface` and `DynamicTable` in `NWBFile.stimulus`. @rly [#1842](https://github.com/NeurodataWithoutBorders/pynwb/pull/1842)
 - Added support for python 3.12 and upgraded dependency versions. This also includes infrastructure updates for developers. @mavaylon1 [#1853](https://github.com/NeurodataWithoutBorders/pynwb/pull/1853)
-- Added `mock_Units` for generating Units tables.  @h-mayorquin [#1875](https://github.com/NeurodataWithoutBorders/pynwb/pull/1875)
+- Added `grid_spacing`, `grid_spacing_unit`, `origin_coords`, `origin_coords_unit` to `ImagingPlane` fields. @h-mayorquin [#1892](https://github.com/NeurodataWithoutBorders/pynwb/pull/1892)
+- Added `mock_Units` for generating Units tables. @h-mayorquin [#1875](https://github.com/NeurodataWithoutBorders/pynwb/pull/1875) and [#1883](https://github.com/NeurodataWithoutBorders/pynwb/pull/1883)
+- Allow datetimes without a timezone and without a time. @rly [#1886](https://github.com/NeurodataWithoutBorders/pynwb/pull/1886)
+- No longer automatically set the timezone to the local timezone when not provided. [#1886](https://github.com/NeurodataWithoutBorders/pynwb/pull/1886)
+- Updated testing to not install in editable mode and not run `coverage` by default. [#1897](https://github.com/NeurodataWithoutBorders/pynwb/pull/1897)
 
 ### Bug fixes
 - Fix bug with reading file with linked `TimeSeriesReferenceVectorData` @rly [#1865](https://github.com/NeurodataWithoutBorders/pynwb/pull/1865)
-- Fix bug where extra keyword arguments could not be passed to `NWBFile.add_{x}_column`` for use in custom `VectorData`` classes. @rly [#1861](https://github.com/NeurodataWithoutBorders/pynwb/pull/1861)
+- Fix bug where extra keyword arguments could not be passed to `NWBFile.add_{x}_column` for use in custom `VectorData` classes. @rly [#1861](https://github.com/NeurodataWithoutBorders/pynwb/pull/1861)
 
 ## PyNWB 2.6.0 (February 21, 2024)
 

diff --git a/docs/gallery/advanced_io/h5dataio.py b/docs/gallery/advanced_io/h5dataio.py
@@ -19,20 +19,16 @@
 #
 
 from datetime import datetime
-
-from dateutil.tz import tzlocal
-
 from pynwb import NWBFile
 
-start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
+start_time = datetime(2017, 4, 3, hour=11, minute=0)
 
 nwbfile = NWBFile(
     session_description="demonstrate advanced HDF5 I/O features",
     identifier="NWB123",
     session_start_time=start_time,
 )
 
-
 ####################
 # Normally if we create a :py:class:`~pynwb.base.TimeSeries` we would do
 

diff --git a/docs/gallery/advanced_io/linking_data.py b/docs/gallery/advanced_io/linking_data.py
@@ -51,15 +51,12 @@
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_linking_data.png'
 
 from datetime import datetime
-from uuid import uuid4
-
 import numpy as np
-from dateutil.tz import tzlocal
-
 from pynwb import NWBHDF5IO, NWBFile, TimeSeries
+from uuid import uuid4
 
 # Create the base data
-start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
+start_time = datetime(2017, 4, 3, hour=11, minute=0)
 data = np.arange(1000).reshape((100, 10))
 timestamps = np.arange(100)
 filename1 = "external1_example.nwb"

diff --git a/docs/gallery/advanced_io/parallelio.py b/docs/gallery/advanced_io/parallelio.py
@@ -32,7 +32,7 @@
 #     from datetime import datetime
 #     from hdmf.backends.hdf5.h5_utils import H5DataIO
 #
-#     start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))
+#     start_time = datetime(2018, 4, 25, hour=2, minute=30, second=3)
 #     fname = "test_parallel_pynwb.nwb"
 #     rank = MPI.COMM_WORLD.rank  # The process ID (integer 0-3 for 4-process run)
 #

diff --git a/docs/gallery/advanced_io/plot_iterative_write.py b/docs/gallery/advanced_io/plot_iterative_write.py
@@ -110,12 +110,8 @@
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_iterative_write.png'
 from datetime import datetime
-from uuid import uuid4
-
-from dateutil.tz import tzlocal
-
 from pynwb import NWBHDF5IO, NWBFile, TimeSeries
-
+from uuid import uuid4
 
 def write_test_file(filename, data, close_io=True):
     """
@@ -129,7 +125,7 @@ def write_test_file(filename, data, close_io=True):
     """
 
     # Create a test NWBfile
-    start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
+    start_time = datetime(2017, 4, 3, hour=11, minute=30)
     nwbfile = NWBFile(
         session_description="demonstrate iterative write",
         identifier=str(uuid4()),

diff --git a/docs/gallery/domain/images.py b/docs/gallery/domain/images.py
@@ -19,23 +19,18 @@
 The following examples will reference variables that may not be defined within the block they are used in. For
 clarity, we define them here:
 """
-# Define file paths used in the tutorial
-
-import os
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_image_data.png'
 from datetime import datetime
-from uuid import uuid4
-
 import numpy as np
-from dateutil import tz
-from dateutil.tz import tzlocal
+import os
 from PIL import Image
-
 from pynwb import NWBHDF5IO, NWBFile
 from pynwb.base import Images
 from pynwb.image import GrayscaleImage, ImageSeries, OpticalSeries, RGBAImage, RGBImage
+from uuid import uuid4
 
+# Define file paths used in the tutorial
 nwbfile_path = os.path.abspath("images_tutorial.nwb")
 moviefiles_path = [
     os.path.abspath("image/file_1.tiff"),
@@ -50,12 +45,12 @@
 # Create an :py:class:`~pynwb.file.NWBFile` object with the required fields
 # (``session_description``, ``identifier``, ``session_start_time``) and additional metadata.
 
-session_start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))
+session_start_time = datetime(2018, 4, 25, hour=2, minute=30)
 
 nwbfile = NWBFile(
     session_description="my first synthetic recording",
     identifier=str(uuid4()),
-    session_start_time=datetime.now(tzlocal()),
+    session_start_time=session_start_time,
     experimenter=[
         "Baggins, Bilbo",
     ],
@@ -138,21 +133,21 @@
 # ^^^^^^^^^^^^^^
 #
 # External files (e.g. video files of the behaving animal) can be added to the :py:class:`~pynwb.file.NWBFile`
-# by creating an :py:class:`~pynwb.image.ImageSeries` object using the 
+# by creating an :py:class:`~pynwb.image.ImageSeries` object using the
 # :py:attr:`~pynwb.image.ImageSeries.external_file` attribute that specifies
 # the path to the external file(s) on disk.
 # The file(s) path must be relative to the path of the NWB file.
 # Either ``external_file`` or ``data`` must be specified, but not both.
 #
-# If the sampling rate is constant, use :py:attr:`~pynwb.base.TimeSeries.rate` and 
+# If the sampling rate is constant, use :py:attr:`~pynwb.base.TimeSeries.rate` and
 # :py:attr:`~pynwb.base.TimeSeries.starting_time` to specify time.
 # For irregularly sampled recordings, use :py:attr:`~pynwb.base.TimeSeries.timestamps` to specify time for each sample
 # image.
 #
 # Each external image may contain one or more consecutive frames of the full :py:class:`~pynwb.image.ImageSeries`.
 # The :py:attr:`~pynwb.image.ImageSeries.starting_frame` attribute serves as an index to indicate which frame
 # each file contains.
-# For example, if the ``external_file`` dataset has three paths to files and the first and the second file have 2 
+# For example, if the ``external_file`` dataset has three paths to files and the first and the second file have 2
 # frames, and the third file has 3 frames, then this attribute will have values `[0, 2, 4]`.
 
 external_file = [

diff --git a/docs/gallery/domain/plot_behavior.py b/docs/gallery/domain/plot_behavior.py
@@ -105,13 +105,17 @@
 #
 # For position data ``reference_frame`` indicates the zero-position, e.g.
 # the 0,0 point might be the bottom-left corner of an enclosure, as viewed from the tracking camera.
+# In :py:class:`~pynwb.behavior.SpatialSeries`, the ``bounds`` field allows the user to set
+# the boundary range, i.e.,  (min, max), for each dimension of ``data``. The units are the same as in ``data``.
+# This field does not enforce a boundary on the dataset itself.
 
 timestamps = np.linspace(0, 50) / 200
 
 position_spatial_series = SpatialSeries(
     name="SpatialSeries",
     description="Position (x, y) in an open field.",
     data=position_data,
+    bounds=[(0,50), (0,50)],
     timestamps=timestamps,
     reference_frame="(0,0) is bottom left corner",
 )

diff --git a/docs/gallery/general/add_remove_containers.py b/docs/gallery/general/add_remove_containers.py
@@ -33,7 +33,7 @@
 nwbfile = NWBFile(
     session_description="demonstrate adding to an NWB file",
     identifier="NWB123",
-    session_start_time=datetime.datetime.now(datetime.timezone.utc),
+    session_start_time=datetime.datetime.now(),
 )
 
 filename = "nwbfile.nwb"
@@ -91,7 +91,7 @@
 nwbfile = NWBFile(
     session_description="demonstrate export of an NWB file",
     identifier="NWB123",
-    session_start_time=datetime.datetime.now(datetime.timezone.utc),
+    session_start_time=datetime.datetime.now(),
 )
 data1 = list(range(100, 200, 10))
 timestamps1 = np.arange(10, dtype=float)

diff --git a/docs/gallery/general/extensions.py b/docs/gallery/general/extensions.py
@@ -164,16 +164,15 @@ def __init__(self, **kwargs):
 # To demonstrate this, first we will make some simulated data using our extensions.
 
 from datetime import datetime
-
-from dateutil.tz import tzlocal
-
 from pynwb import NWBFile
+from uuid import uuid4
 
-start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
-create_date = datetime(2017, 4, 15, 12, tzinfo=tzlocal())
+session_start_time = datetime(2017, 4, 3, hour=11, minute=0)
 
 nwbfile = NWBFile(
-    "demonstrate caching", "NWB456", start_time, file_create_date=create_date
+    session_description="demonstrate caching",
+    identifier=str(uuid4()),
+    session_start_time=session_start_time,
 )
 
 device = nwbfile.create_device(name="trodes_rig123")
@@ -333,18 +332,18 @@ class PotatoSack(MultiContainerInterface):
 # Then use the objects (again, this would often be done in a different file).
 
 from datetime import datetime
-
-from dateutil.tz import tzlocal
-
 from pynwb import NWBHDF5IO, NWBFile
 
 # You can add potatoes to a potato sack in different ways
 potato_sack = PotatoSack(potatos=Potato(name="potato1", age=2.3, weight=3.0))
 potato_sack.add_potato(Potato("potato2", 3.0, 4.0))
 potato_sack.create_potato("big_potato", 10.0, 20.0)
 
+session_start_time = datetime(2017, 4, 3, hour=12, minute=0)
 nwbfile = NWBFile(
-    "a file with metadata", "NB123A", datetime(2018, 6, 1, tzinfo=tzlocal())
+    session_description="a file with metadata",
+    identifier=str(uuid4()),
+    session_start_time = session_start_time,
 )
 
 pmod = nwbfile.create_processing_module("module_name", "desc")