Merge branch 'dev' into fix/electrodegroup_position

.github/PULL_REQUEST_TEMPLATE.md

@@ -12,6 +12,6 @@ Show how to reproduce the new behavior (can be a bug fix or a new feature)
 - [ ] Did you update CHANGELOG.md with your changes?
 - [ ] Have you checked our [Contributing](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst) document?
 - [ ] Have you ensured the PR clearly describes the problem and the solution?
-- [ ] Is your contribution compliant with our coding style? This can be checked running `flake8` from the source directory.
+- [ ] Is your contribution compliant with our coding style? This can be checked running `ruff check . && codespell` from the source directory.
 - [ ] Have you checked to ensure that there aren't other open [Pull Requests](https://github.com/NeurodataWithoutBorders/pynwb/pulls) for the same change?
 - [ ] Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

.github/workflows/check_sphinx_links.yml

@@ -28,7 +28,7 @@ jobs:
       - name: Install Sphinx dependencies and package
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-doc.txt
+          python -m pip install -r requirements-doc.txt -r requirements-opt.txt
           python -m pip install .
 
       - name: Check Sphinx internal and external links

.github/workflows/run_all_tests.yml

@@ -26,20 +26,24 @@ jobs:
           - { name: linux-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: ubuntu-latest }
           - { name: linux-python3.10             , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
           - { name: linux-python3.11             , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.11-opt         , test-tox-env: py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
           - { name: linux-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
           - { name: linux-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: ubuntu-latest }
           - { name: linux-python3.12-prerelease  , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: ubuntu-latest }
           - { 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-python3.9            , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: windows-latest }
           - { name: windows-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: windows-latest }
           - { name: windows-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.11-opt       , test-tox-env: py311-optional  , build-tox-env: build-py311           , python-ver: "3.11", os: windows-latest }
           - { 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 }
+          # minimum versions of dependencies do not have wheels or cannot be built on macos-arm64
           - { 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-python3.9              , test-tox-env: py39            , build-tox-env: build-py39            , python-ver: "3.9" , os: macos-latest }
           - { 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-python3.11-opt         , test-tox-env: py311-optional  , 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 }
           - { name: macos-python3.12-upgraded    , test-tox-env: py312-upgraded  , build-tox-env: build-py312-upgraded  , python-ver: "3.12", os: macos-latest }
           - { name: macos-python3.12-prerelease  , test-tox-env: py312-prerelease, build-tox-env: build-py312-prerelease, python-ver: "3.12", os: macos-latest }
@@ -95,6 +99,7 @@ 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 }
+          # minimum versions of dependencies do not have wheels or cannot be built on macos-arm64
           - { 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 }
@@ -198,7 +203,7 @@ 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-13 } # This is due to DANDI not supporting osx-arm64. Will support macos-latest when this changes. 
+          - { name: conda-macos-python3.12-ros3  , python-ver: "3.12", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -245,7 +250,7 @@ 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-13 } # This is due to DANDI not supporting osx-arm64. Will support macos-latest when this changes. 
+          - { name: conda-macos-gallery-python3.12-ros3  , python-ver: "3.12", os: macos-latest }
     steps:
       - name: Cancel non-latest runs
         uses: styfle/[email protected]
@@ -270,7 +275,6 @@ jobs:
 
       - name: Install run dependencies
         run: |
-          pip install matplotlib
           pip install .
           pip list
 

.github/workflows/run_coverage.yml

@@ -11,7 +11,7 @@ on:
 
 jobs:
   run-coverage:
-    name: ${{ matrix.os }}
+    name: ${{ matrix.os }}, opt reqs ${{ matrix.opt_req }}
     runs-on: ${{ matrix.os }}
     # TODO handle forks
     # run pipeline on either a push event or a PR event on a fork
@@ -21,7 +21,11 @@ jobs:
         shell: bash
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        include:
+          - { os: ubuntu-latest , opt_req: true }
+          - { os: ubuntu-latest , opt_req: false }
+          - { os: windows-latest, opt_req: false }
+          - { os: macos-latest  , opt_req: false }
     env:
       OS: ${{ matrix.os }}
       PYTHON: '3.12'
@@ -47,9 +51,9 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -r requirements-dev.txt -r requirements.txt
 
-      # - name: Install optional dependencies
-      #   if: ${{ matrix.opt_req }}
-      #   run: python -m pip install -r requirements-opt.txt
+      - name: Install optional dependencies
+        if: ${{ matrix.opt_req }}
+        run: python -m pip install -r requirements-opt.txt
 
       - name: Install package
         run: |

.github/workflows/run_tests.yml

@@ -24,6 +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 }
+          # minimum versions of dependencies do not have wheels or cannot be built on macos-arm64
           - { 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

.readthedocs.yaml

@@ -25,6 +25,7 @@ formats: all
 python:
   install:
     - requirements: requirements-doc.txt
+    - requirements: requirements-opt.txt
     - requirements: requirements.txt
 
 # Optionally include all submodules

CHANGELOG.md

@@ -1,6 +1,31 @@
 # PyNWB Changelog
 
-## PyNWB 2.7.0 (Upcoming)
+## PyNWB 2.8.2 (Upcoming)
+
+### Documentation and tutorial enhancements
+- Added pre-release pull request instructions to release process documentation @stephprince [#1928](https://github.com/NeurodataWithoutBorders/pynwb/pull/1928)
+
+## PyNWB 2.8.1 (July 3, 2024)
+
+### Documentation and tutorial enhancements
+- Simplified the introduction to NWB tutorial. @rly [#1914](https://github.com/NeurodataWithoutBorders/pynwb/pull/1914)
+- Simplified the ecephys and ophys tutorials. [#1915](https://github.com/NeurodataWithoutBorders/pynwb/pull/1915)
+- Add comments to `src/pynwb/io/file.py` to improve developer documentation. @rly [#1925](https://github.com/NeurodataWithoutBorders/pynwb/pull/1925)
+
+### Bug fixes
+- Fixed use of `channel_conversion` in `TimeSeries` `get_data_in_units`. @rohanshah [1923](https://github.com/NeurodataWithoutBorders/pynwb/pull/1923)
+
+## PyNWB 2.8.0 (May 28, 2024)
+
+### 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)
+- Integrate validation through the `TypeConfigurator`. @mavaylon1 [#1829](https://github.com/NeurodataWithoutBorders/pynwb/pull/1829)
+- Exposed `aws_region` to `NWBHDF5IO`. @rly [#1903](https://github.com/NeurodataWithoutBorders/pynwb/pull/1903)
+
+### Bug fixes
+- Revert changes in PyNWB 2.7.0 that allow datetimes without a timezone and without a time while issues with DANDI upload of NWB files missing timezone are resolved. @rly [#1908](https://github.com/NeurodataWithoutBorders/pynwb/pull/1908)
+
+## 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)
@@ -321,7 +346,7 @@
 
 ### Tutorial enhancements:
 - Added new tutorial for intracellular electrophysiology to describe the use of the new metadata tables
-  and declared the previous tutoral using ``SweepTable`` as deprecated.  @oruebel (#1349)
+  and declared the previous tutorial using ``SweepTable`` as deprecated.  @oruebel (#1349)
 - Added new tutorial for querying intracellular electrophysiology metadata
   (``docs/gallery/domain/plot_icephys_pandas.py``). @oruebel (#1349, #1383)
 - Added thumbnails for tutorials to improve presentation of online docs.  @oruebel (#1349)

README.rst

@@ -49,10 +49,10 @@ Overall Health
      :target: https://github.com/neurodatawithoutborders/pynwb/blob/dev/license.txt
      :alt: PyPI - License
 
-**Conda**
+**Conda Feedstock**
 
-.. image:: https://circleci.com/gh/conda-forge/pynwb-feedstock.svg?style=shield
-     :target: https://circleci.com/gh/conda-forge/pynwb-feedstock
+.. image:: https://dev.azure.com/conda-forge/feedstock-builds/_apis/build/status/pynwb-feedstock?branchName=main
+     :target: https://dev.azure.com/conda-forge/feedstock-builds/_build/latest?definitionId=5703&branchName=main
      :alt: Conda Feedstock Status
 
 NWB Format API

docs/gallery/advanced_io/h5dataio.py

@@ -19,16 +19,20 @@
 #
 
 from datetime import datetime
+
+from dateutil.tz import tzlocal
+
 from pynwb import NWBFile
 
-start_time = datetime(2017, 4, 3, hour=11, minute=0)
+start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
 
 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
 

docs/gallery/advanced_io/linking_data.py

@@ -51,12 +51,15 @@
 # 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, hour=11, minute=0)
+start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
 data = np.arange(1000).reshape((100, 10))
 timestamps = np.arange(100)
 filename1 = "external1_example.nwb"

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, hour=2, minute=30, second=3)
+#     start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))
 #     fname = "test_parallel_pynwb.nwb"
 #     rank = MPI.COMM_WORLD.rank  # The process ID (integer 0-3 for 4-process run)
 #

docs/gallery/advanced_io/plot_iterative_write.py

@@ -110,9 +110,13 @@
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnails_iterative_write.png'
 from datetime import datetime
-from pynwb import NWBHDF5IO, NWBFile, TimeSeries
 from uuid import uuid4
 
+from dateutil.tz import tzlocal
+
+from pynwb import NWBHDF5IO, NWBFile, TimeSeries
+
+
 def write_test_file(filename, data, close_io=True):
     """
 
@@ -125,7 +129,7 @@ def write_test_file(filename, data, close_io=True):
     """
 
     # Create a test NWBfile
-    start_time = datetime(2017, 4, 3, hour=11, minute=30)
+    start_time = datetime(2017, 4, 3, 11, tzinfo=tzlocal())
     nwbfile = NWBFile(
         session_description="demonstrate iterative write",
         identifier=str(uuid4()),