Merge branch 'dev' into electrode

NeurodataWithoutBorders · Aug 1, 2024 · 6caa774 · 6caa774
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.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.
diff --git a/.github/workflows/check_sphinx_links.yml b/.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

diff --git a/.github/workflows/run_all_tests.yml b/.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]
@@ -224,7 +229,7 @@ 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 +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]
@@ -270,8 +275,7 @@ 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
@@ -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'
@@ -47,26 +51,26 @@ 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: |
-          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 +81,13 @@ 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
@@ -24,6 +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
@@ -200,7 +201,7 @@ 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 +246,7 @@ jobs:
       - name: Install run dependencies
         run: |
           pip install matplotlib
-          pip install -e .
+          pip install .
           pip list
 
       - name: Conda reporting

diff --git a/.readthedocs.yaml b/.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

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,17 +1,49 @@
 # 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)
+
+### Bug fixes
+- Fixed `can_read` method to return False if no nwbfile version can be found @stephprince [#1934](https://github.com/NeurodataWithoutBorders/pynwb/pull/1934)
+- Changed `epoch_tags` to be a NWBFile property instead of constructor argument. @stephprince [#1935](https://github.com/NeurodataWithoutBorders/pynwb/pull/1935)
+
+## 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)
 - 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 `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)
@@ -317,7 +349,7 @@
 
 ### 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)

diff --git a/MANIFEST.in b/MANIFEST.in
diff --git a/README.rst b/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

diff --git a/docs/gallery/advanced_io/h5dataio.py b/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
 

diff --git a/docs/gallery/advanced_io/linking_data.py b/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"