From 9a6148cb7c9dc01a8e22218723b834b4a218a9ac Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Mon, 9 Sep 2024 16:57:19 -0700
Subject: [PATCH] Update to use latest template with gh actions

---
 .github/workflows/check_external_links.yml |  32 ++++
 .github/workflows/codespell.yml            |  11 +-
 .github/workflows/ruff.yml                 |  14 ++
 .github/workflows/run_all_tests.yml        | 180 +++++++++++++++++++++
 .github/workflows/run_coverage.yml         |  57 +++++++
 .github/workflows/validate_schema.yml      |  22 +++
 .pre-commit-config.yaml                    |   8 +-
 LICENSE.txt                                |   2 +-
 NEXTSTEPS.md                               | 129 ++++++++++-----
 docs/make.bat                              |  70 ++++----
 docs/source/_static/theme_overrides.css    |  13 ++
 docs/source/conf.py                        | 108 +++++--------
 pyproject.toml                             |  44 ++---
 requirements-dev.txt                       |  23 ++-
 requirements-min.txt                       |   5 +-
 spec/ndx-events.extensions.yaml            |  10 +-
 src/pynwb/ndx_events/__init__.py           |   5 +-
 src/spec/create_extension_spec.py          |   2 +-
 18 files changed, 534 insertions(+), 201 deletions(-)
 create mode 100644 .github/workflows/check_external_links.yml
 create mode 100644 .github/workflows/ruff.yml
 create mode 100644 .github/workflows/run_all_tests.yml
 create mode 100644 .github/workflows/run_coverage.yml
 create mode 100644 .github/workflows/validate_schema.yml
 create mode 100644 docs/source/_static/theme_overrides.css

diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
new file mode 100644
index 0000000..9dd1a84
--- /dev/null
+++ b/.github/workflows/check_external_links.yml
@@ -0,0 +1,32 @@
+name: Check Sphinx external links
+on:
+  push:
+  schedule:
+    - cron: '0 5 * * 0'  # once every Sunday at midnight ET
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    name: Check for broken Sphinx external links
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # tags are required to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install Sphinx dependencies and package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Check Sphinx external links
+        run: |
+          cd docs  # run_doc_autogen assumes spec is found in ../spec/
+          sphinx-build -b linkcheck ./source ./test_build
diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
index 243ba8c..314b085 100644
--- a/.github/workflows/codespell.yml
+++ b/.github/workflows/codespell.yml
@@ -1,19 +1,14 @@
----
 name: Codespell
-
 on:
   push:
-    branches: [main]
-  pull_request:
-    branches: [main]
+  workflow_dispatch:
 
 jobs:
   codespell:
     name: Check for spelling errors
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Codespell
-        uses: codespell-project/actions-codespell@v1
+        uses: codespell-project/actions-codespell@v2
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
new file mode 100644
index 0000000..9b4f05d
--- /dev/null
+++ b/.github/workflows/ruff.yml
@@ -0,0 +1,14 @@
+name: Ruff
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    name: Check for style errors and common problems
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Ruff
+        uses: chartboost/ruff-action@v1
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
new file mode 100644
index 0000000..f2600fd
--- /dev/null
+++ b/.github/workflows/run_all_tests.yml
@@ -0,0 +1,180 @@
+name: Run all tests
+on:
+  push:
+  schedule:
+    - cron: '0 5 * * 0'  # once every Sunday at midnight ET
+  workflow_dispatch:
+
+jobs:
+  run-all-tests:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.8-minimum      , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.8              , requirements: pinned     , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: linux-python3.9              , requirements: pinned     , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.10             , requirements: pinned     , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.11             , requirements: pinned     , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.12             , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: ubuntu-latest }
+          - { name: windows-python3.8-minimum    , requirements: minimum    , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.8            , requirements: pinned     , python-ver: "3.8" , os: windows-latest }
+          - { name: windows-python3.9            , requirements: pinned     , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.10           , requirements: pinned     , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.11           , requirements: pinned     , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.12           , requirements: pinned     , python-ver: "3.12", os: windows-latest }
+          - { name: windows-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", os: windows-latest }
+          - { name: macos-python3.8-minimum      , requirements: minimum    , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.8              , requirements: pinned     , python-ver: "3.8" , os: macos-latest }
+          - { name: macos-python3.9              , requirements: pinned     , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.10             , requirements: pinned     , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.11             , requirements: pinned     , python-ver: "3.11", os: macos-latest }
+          - { name: macos-python3.12             , requirements: pinned     , python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.12-upgraded    , requirements: upgraded   , python-ver: "3.12", os: macos-latest }
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # tags are required to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip list
+          python -m pip check
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        if: ${{ matrix.os != 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_events"
+
+      - name: Test installation from a wheel (windows)
+        if: ${{ matrix.os == 'windows-latest' }}
+        run: |
+          python -m venv test-wheel-env
+          test-wheel-env/Scripts/activate.bat
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_events"
+
+  run-all-tests-on-conda:
+    name: ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    defaults:
+     run:
+       shell: bash -l {0}  # needed for conda environment to work
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: conda-linux-python3.8-minimum    , requirements: minimum    , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.8            , requirements: pinned     , python-ver: "3.8" , os: ubuntu-latest }
+          - { name: conda-linux-python3.9            , requirements: pinned     , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.10           , requirements: pinned     , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.11           , requirements: pinned     , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-python3.12           , requirements: pinned     , python-ver: "3.12", os: ubuntu-latest }
+          - { name: conda-linux-python3.12-upgraded  , requirements: upgraded   , python-ver: "3.12", os: ubuntu-latest }
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # tags are required to determine the version
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          auto-activate-base: true
+          activate-environment: true
+          python-version: ${{ matrix.python-ver }}
+
+      - name: Install build dependencies
+        run: |
+          conda config --set always_yes yes --set changeps1 no
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
+
+      - name: Install run requirements (minimum)
+        if: ${{ matrix.requirements == 'minimum' }}
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Install run requirements (pinned)
+        if: ${{ matrix.requirements == 'pinned' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          python -m pip install .
+
+      - name: Install run requirements (upgraded)
+        if: ${{ matrix.requirements == 'upgraded' }}
+        run: |
+          python -m pip install -r requirements-dev.txt
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
+
+      - name: Run tests
+        run: |
+          pytest -v
+
+      - name: Build wheel and source distribution
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+          ls -1 dist
+
+      - name: Test installation from a wheel (POSIX)
+        run: |
+          python -m venv test-wheel-env
+          source test-wheel-env/bin/activate
+          python -m pip install dist/*-none-any.whl
+          python -c "import ndx_events"
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
new file mode 100644
index 0000000..5aa6f9e
--- /dev/null
+++ b/.github/workflows/run_coverage.yml
@@ -0,0 +1,57 @@
+name: Run code coverage
+on:
+  push:
+  workflow_dispatch:
+
+jobs:
+  run-coverage:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    # TODO handle forks
+    # run pipeline on either a push event or a PR event on a fork
+    # if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    defaults:
+      run:
+        shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}
+      cancel-in-progress: true
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    env:  # used by codecov-action
+      OS: ${{ matrix.os }}
+      PYTHON: '3.12'
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # tags are required to determine the version
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt
+
+      - name: Install package
+        run: |
+          python -m pip install .
+          python -m pip list
+
+      - name: Run tests and generate coverage report
+        run: |
+          pytest --cov --cov-report=xml --cov-report=term  # codecov uploader requires xml format
+
+      # TODO uncomment after setting up repo on codecov.io and adding token
+      # - name: Upload coverage to Codecov
+      #   uses: codecov/codecov-action@v4
+      #   with:
+      #     fail_ci_if_error: true
+      #     file: ./coverage.xml
+      #   env:
+      #     CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/validate_schema.yml b/.github/workflows/validate_schema.yml
new file mode 100644
index 0000000..33e805f
--- /dev/null
+++ b/.github/workflows/validate_schema.yml
@@ -0,0 +1,22 @@
+name: Validate schema
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.12"
+    - name: Install HDMF
+      run: |
+        pip install hdmf
+    - name: Download latest nwb schema language specification
+      run: |
+        curl -L https://raw.githubusercontent.com/NeurodataWithoutBorders/nwb-schema/dev/nwb.schema.json -o nwb.schema.json
+    - name: Validate schema specification
+      run: |
+        validate_hdmf_spec spec -m nwb.schema.json
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 902b3b2..827eeb6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 # NOTE: run `pre-commit autoupdate` to update hooks to latest version
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
@@ -13,15 +13,15 @@ repos:
         args: [--pytest-test-first]
     -   id: check-docstring-first
 -   repo: https://github.com/psf/black
-    rev: 23.12.0
+    rev: 24.4.2
     hooks:
     -   id: black
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.8
+    rev: v0.4.10
     hooks:
     -   id: ruff
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
     -   id: codespell
         additional_dependencies:
diff --git a/LICENSE.txt b/LICENSE.txt
index 8850436..f803560 100644
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2023, Ryan Ly
+Copyright (c) 2024, Ryan Ly
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
diff --git a/NEXTSTEPS.md b/NEXTSTEPS.md
index 454ad7e..0377ffa 100644
--- a/NEXTSTEPS.md
+++ b/NEXTSTEPS.md
@@ -1,32 +1,67 @@
-# Next Steps for ndx-events Extension for NWB:N
 
-## Creating Your Extension
 
-1. In a terminal, change directory into the new ndx-events directory.
+# Next Steps for ndx-events Extension for NWB
+
+## Creating Your Extension
 
-2. Add any packages required by your extension to `requirements.txt` and `setup.py`.
+1. In a terminal, change directory into the new ndx-events directory: `cd ndx-events`
 
-3. Run `python -m pip install -r requirements.txt` to install the `pynwb` package
-and any other packages required by your extension.
+2. Add any packages required by your extension to the `dependencies` key in `pyproject.toml`.
 
-4. Modify `src/create_extension_spec.py` to define your extension.
+3. Run `python -m pip install -e .` to install your new extension Python package
+and any other packages required to develop, document, and run your extension.
 
-    - If you want to create any custom classes for interacting with the extension,
-      add them to the `src/pynwb`.
-      - If present, the `src/pynwb` folder MUST contain the following:
-        - `ndx-events` - Folder with the sources of the NWB extension
-        - `ndx-events/__init__.py` - Python file that may be empty
-      - If present, the `src/pynwb` folder MAY contain the following files/folders:
-        - `test` - Folder for unit tests for the extensions
-        - `jupyter_widgets` - Optional package with custom widgets for use with Jupyter
+4. Modify `src/spec/create_extension_spec.py` to define your extension.
 
 5. Run `python src/spec/create_extension_spec.py` to generate the
 `spec/ndx-events.namespace.yaml` and
 `spec/ndx-events.extensions.yaml` files.
 
-6. You may need to modify `setup.py` and re-run `python setup.py install` if you
+6. Define API classes for your new extension data types.
+
+    - As a starting point, `src/pynwb/ndx_events/__init__.py` includes an
+      example for how to use
+      the `pynwb.get_class` to generate a basic Python class for your new extension data
+      type. This class contains a constructor and properties for the new data type.
+    - Instead of using `pynwb.get_class`, you can define your own custom class for the
+      new type, which will allow you to customize the class methods, customize the
+      object mapping, and create convenience functions. See the
+      [Extending NWB tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/general/extensions.html)
+      for more details.
+
+7. Define tests for your new extension data types in
+`src/pynwb/ndx_events/tests` or `src/matnwb/tests`.
+A test for the example `TetrodeSeries` data type is provided as a reference and should be
+replaced or removed.
+
+     - Python tests should be runnable by executing [`pytest`](https://docs.pytest.org/en/latest/)
+     from the root of the extension directory. Use of PyNWB testing infrastructure from
+     `pynwb.testing` is encouraged (see
+     [documentation](https://pynwb.readthedocs.io/en/stable/pynwb.testing.html)).
+     - Creating both **unit tests** (e.g., testing initialization of new data type classes and
+     new functions) and **integration tests** (e.g., write the new data types to file, read
+     the file, and confirm the read data types are equal to the written data types) is
+     highly encouraged.
+     - By default, to aid with debugging, the project is configured NOT to run code coverage as
+     part of the tests.
+     Code coverage reporting is useful to help with creation of tests and report test coverage.
+     However, with this option enabled, breakpoints for debugging with pdb are being ignored.
+     To enable this option for code coverage reporting, uncomment out the following line in
+     your `pyproject.toml`: [line](https://github.com/nwb-extensions/ndx-template/blob/11ae225b3fd3934fa3c56e6e7b563081793b3b43/%7B%7B%20cookiecutter.namespace%20%7D%7D/pyproject.toml#L82-L83
+)
+
+7. (Optional) Define custom visualization widgets for your new extension data types in
+`src/pynwb/ndx_events/widgets` so that the visualizations can be displayed with
+[nwbwidgets](https://github.com/NeurodataWithoutBorders/nwbwidgets).
+You will also need to update the `vis_spec` dictionary in
+`src/pynwb/ndx_events/widgets/__init__.py` so that
+nwbwidgets can find your custom visualizations.
+
+8. You may need to modify `pyproject.toml` and re-run `python -m pip install -e .` if you
 use any dependencies.
 
+9. Update the `CHANGELOG.md` regularly to document changes to your extension.
+
 
 ## Documenting and Publishing Your Extension to the Community
 
@@ -48,16 +83,26 @@ your extension.
 
 7. Add a license file. Permissive licenses should be used if possible. **A [BSD license](https://opensource.org/licenses/BSD-3-Clause) is recommended.**
 
-8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.1.0, then this page should exist: https://github.com/rly/ndx-events/releases/tag/0.1.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
+8. Update the `CHANGELOG.md` to document changes to your extension.
 
-9. Publish your updated extension on PyPi.
-    - Follow these directions: https://packaging.python.org/tutorials/packaging-projects/
-    - You may need to modify `setup.py`
-    - If your extension version is 0.1.0, then this page should exist: https://pypi.org/project/ndx-events/0.1.0
+8. Push your repository to GitHub. A default set of GitHub Actions workflows is set up to
+test your code on Linux, Windows, Mac OS, and Linux using conda; upload code coverage
+stats to codecov.io; check for spelling errors; check for style errors; and check for broken
+links in the documentation. For the code coverage workflow to work, you will need to
+set up the repo on codecov.io and uncomment the "Upload coverage to Codecov" step
+in `.github/workflows/run_coverage.yml`.
 
-   Once your GitHub release and ``setup.py`` are ready, publishing on PyPi:
+8. Make a release for the extension on GitHub with the version number specified. e.g. if version is 0.3.0, then this page should exist: https://github.com/rly/ndx-events/releases/tag/0.3.0 . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).
+
+9. Publish your updated extension on [PyPI](https://pypi.org/).
+    - Follow these directions: https://packaging.python.org/en/latest/tutorials/packaging-projects/
+    - You may need to modify `pyproject.toml`
+    - If your extension version is 0.3.0, then this page should exist: https://pypi.org/project/ndx-events/0.3.0
+
+   Once your GitHub release and `pyproject.toml` are ready, publishing on PyPI:
     ```bash
-    python setup.py sdist bdist_wheel
+    python -m pip install --upgrade build twine
+    python -m build
     twine upload dist/*
     ```
 
@@ -81,28 +126,26 @@ with information on where to find your NWB extension.
       - src: URL for the main page of the public repository (e.g. on GitHub, BitBucket, GitLab) that contains the sources of the extension
       - pip: URL for the main page of the extension on PyPI
       - license: name of the license of the extension
-      - maintainers: list of GitHub
-      usernames of those who will reliably maintain the extension
-    -
-
-  You may copy and modify the following YAML that was auto-generated:
-```yaml
-name: ndx-events
-version: 0.1.0
-src: https://github.com/rly/ndx-events
-pip: https://pypi.org/project/ndx-events/
-license: BSD 3-Clause
-maintainers:
-  - rly
-```
+      - maintainers: list of GitHub usernames of those who will reliably maintain the extension
+    - You may copy and modify the following YAML that was auto-generated:
+
+      ```yaml
+      name: ndx-events
+      version: 0.3.0
+      src: https://github.com/rly/ndx-events
+      pip: https://pypi.org/project/ndx-events/
+      license: BSD-3
+      maintainers:
+        - rly
+      ```
 
 14. Edit `staged-extensions/ndx-events/README.md`
 to add information about your extension. You may copy it from
 `ndx-events/README.md`.
 
   ```bash
-cp ndx-events/README.md staged-extensions/ndx-events/README.md
-```
+  cp ndx-events/README.md staged-extensions/ndx-events/README.md
+  ```
 
 15. Add and commit your changes to Git and push your changes to GitHub.
 ```
@@ -117,7 +160,7 @@ Mac, and Linux. The technical team will review your extension shortly after
 and provide feedback and request changes, if any.
 
 17. When your pull request is merged, a new repository, called
-ndx-events-feedstock will be created in the nwb-extensions
+ndx-events-record will be created in the nwb-extensions
 GitHub organization and you will be added as a maintainer for that repository.
 
 
@@ -125,12 +168,12 @@ GitHub organization and you will be added as a maintainer for that repository.
 
 1. Update your ndx-events GitHub repository.
 
-2. Publish your updated extension on PyPi.
+2. Publish your updated extension on PyPI.
 
-3. Fork the ndx-events-feedstock repository on GitHub.
+3. Fork the ndx-events-record repository on GitHub.
 
 4. Open a pull request to test the changes automatically. The technical team
 will review your changes shortly after and provide feedback and request changes,
- if any.
+if any.
 
 5. Your updated extension is approved.
diff --git a/docs/make.bat b/docs/make.bat
index 9534b01..747ffb7 100644
--- a/docs/make.bat
+++ b/docs/make.bat
@@ -1,35 +1,35 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/docs/source/_static/theme_overrides.css b/docs/source/_static/theme_overrides.css
new file mode 100644
index 0000000..63ee6cc
--- /dev/null
+++ b/docs/source/_static/theme_overrides.css
@@ -0,0 +1,13 @@
+/* override table width restrictions */
+@media screen and (min-width: 767px) {
+
+   .wy-table-responsive table td {
+      /* !important prevents the common CSS stylesheets from overriding
+         this as on RTD they are loaded after this stylesheet */
+      white-space: normal !important;
+   }
+
+   .wy-table-responsive {
+      overflow: visible !important;
+   }
+}
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 80ce7a2..ac8c925 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -1,76 +1,46 @@
 # Configuration file for the Sphinx documentation builder.
 #
-# This file only contains a selection of the most common options. For a full
-# list see the documentation:
+# For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# -- Path setup --------------------------------------------------------------
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#
-# import os
-# import sys
-# sys.path.insert(0, os.path.abspath('.'))
-
-
 # -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-project = 'ndx-events'
-copyright = '2020, Ryan Ly'
-author = 'Ryan Ly'
-
-# The short X.Y version
-version = '0.2.0'
-
-# The full version, including alpha/beta/rc tags
-release = 'alpha'
+project = "ndx-events"
+copyright = "2024, Ryan Ly"
+author = "Ryan Ly"
 
+version = "0.3.0"
+release = "alpha"
 
 # -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
-# Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
 extensions = [
-              'sphinx.ext.ifconfig',
-              'sphinx.ext.autodoc',
-              'sphinx.ext.intersphinx',
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
 ]
 
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#
-# This is also used if you do content translation via gettext catalogs.
-# Usually you set "language" from the command line for these cases.
-language = 'English'
-
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-# This pattern also affects html_static_path and html_extra_path.
+templates_path = ["_templates"]
 exclude_patterns = []
 
+language = "en"
 
 # -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes.
-#
-html_theme = 'alabaster'
+html_theme = "alabaster"
+html_static_path = ["_static"]
 
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# -- Options for intersphinx extension ---------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#configuration
 
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+}
 
-# -- Extension configuration -------------------------------------------------
 
-# -- Options for intersphinx extension ---------------------------------------
 ############################################################################
 #  CUSTOM CONFIGURATIONS ADDED BY THE NWB TOOL FOR GENERATING FORMAT DOCS
 ###########################################################################
@@ -79,7 +49,12 @@
 import textwrap  # noqa: E402
 
 # -- Options for intersphinx  ---------------------------------------------
-intersphinx_mapping = {'core': ('https://nwb-schema.readthedocs.io/en/latest/', None)}
+intersphinx_mapping.update(
+    {
+        "core": ("https://nwb-schema.readthedocs.io/en/latest/", None),
+        "hdmf-common": ("https://hdmf-common-schema.readthedocs.io/en/latest/", None),
+    }
+)
 
 # -- Generate sources from YAML---------------------------------------------------
 # Always rebuild the source docs from YAML even if the folder with the source files already exists
@@ -90,26 +65,32 @@ def run_doc_autogen(_):
     # Execute the autogeneration of Sphinx format docs from the YAML sources
     import sys
     import os
+
     conf_file_dir = os.path.dirname(os.path.abspath(__file__))
     sys.path.append(conf_file_dir)  # Need so that generate format docs can find the conf_doc_autogen file
     from conf_doc_autogen import spec_output_dir
 
     if spec_doc_rebuild_always or not os.path.exists(spec_output_dir):
-        sys.path.append('./docs')  # needed to enable import of generate_format docs
+        sys.path.append("./docs")  # needed to enable import of generate_format docs
         from hdmf_docutils.generate_format_docs import main as generate_docs
+
         generate_docs()
 
 
 def setup(app):
-    app.connect('builder-inited', run_doc_autogen)
-    app.add_stylesheet("theme_overrides.css")  # overrides for wide tables in RTD theme
+    app.connect("builder-inited", run_doc_autogen)
+    # overrides for wide tables in RTD theme
+    try:
+        app.add_css_file("theme_overrides.css")  # Used by newer Sphinx versions
+    except AttributeError:
+        app.add_stylesheet("theme_overrides.css")  # Used by older version of Sphinx
 
 
 # -- Customize sphinx settings
 numfig = True
-autoclass_content = 'both'
+autoclass_content = "both"
 autodoc_docstring_signature = True
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 add_function_parentheses = False
 
 
@@ -120,17 +101,16 @@ def setup(app):
 # LaTeX Sphinx options
 latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
-    'papersize': 'letterpaper',
-
+    "papersize": "letterpaper",
     # The font size ('10pt', '11pt' or '12pt').
-    'pointsize': '10pt',
-
+    "pointsize": "10pt",
     # Additional stuff for the LaTeX preamble.
-    'preamble': textwrap.dedent(
-        '''
+    "preamble": textwrap.dedent(
+        """
         \\setcounter{tocdepth}{3}
         \\setcounter{secnumdepth}{6}
         \\usepackage{enumitem}
         \\setlistdepth{100}
-        '''),
+        """
+    ),
 }
diff --git a/pyproject.toml b/pyproject.toml
index 6ef711f..4d73325 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -44,43 +44,42 @@ dependencies = [
 "Discussions" = "https://github.com/rly/ndx-events/discussions"
 "Changelog" = "https://github.com/rly/ndx-events/CHANGELOG.md"
 
-[tool.hatch.build]
-include = [
-    "src/pynwb",
-    "spec/ndx-events.extensions.yaml",
-    "spec/ndx-events.namespace.yaml",
-]
-exclude = [
-    "src/pynwb/tests",
-]
-
+# Include only the source code under `src/pynwb/ndx_events` and the spec files under `spec`
+# in the wheel.
 [tool.hatch.build.targets.wheel]
 packages = [
     "src/pynwb/ndx_events",
     "spec"
 ]
 
+# Rewrite the path to the `spec` directory to `ndx_events/spec`.
+# `ndx_events/__init__.py` will look there first for the spec files.
+# The resulting directory structure within the wheel will be:
+# ndx_events/
+# ├── __init__.py
+# ├── spec
+# └── widgets
 [tool.hatch.build.targets.wheel.sources]
 "spec" = "ndx_events/spec"
 
+# The source distribution includes everything in the package except for the `src/matnwb` directory and
+# git and github-related files.
 [tool.hatch.build.targets.sdist]
-include = [
-    "src/pynwb",
-    "spec/ndx-events.extensions.yaml",
-    "spec/ndx-events.namespace.yaml",
-    "docs",
+exclude = [
+    ".git*",
+    "src/matnwb",
 ]
-exclude = []
 
 [tool.pytest.ini_options]
-addopts = "--cov --cov-report html"
+# uncomment below to run pytest always with code coverage reporting. NOTE: breakpoints may not work
+# addopts = "--cov --cov-report html"
 
 [tool.codespell]
 skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,hdmf-common-schema,./docs/_build/*,*.ipynb"
 
 [tool.coverage.run]
 branch = true
-source = ["src/pynwb"]
+source = ["ndx_events"]
 
 [tool.coverage.report]
 exclude_lines = [
@@ -94,19 +93,20 @@ preview = true
 exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb|docs/"
 
 [tool.ruff]
-select = ["E", "F", "T100", "T201", "T203"]
+lint.select = ["E", "F", "T100", "T201", "T203"]
 exclude = [
   ".git",
   ".tox",
   "__pycache__",
   "build/",
   "dist/",
+  "docs/source/conf.py",
 ]
 line-length = 120
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
+"src/pynwb/ndx_events/__init__.py" = ["E402", "F401"]
 "src/spec/create_extension_spec.py" = ["T201"]
-"src/pynwb/tests/test_example_usage.py" = ["T201"]
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 max-complexity = 17
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 38eb48c..07e3a8b 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,15 +1,14 @@
 # pinned dependencies to reproduce an entire development environment to
 # run tests, check code style, and generate documentation
-black==23.9.1
-codespell==2.2.6
-coverage==7.3.2
-hdmf==3.11.0
-hdmf-docutils==0.4.6
-pre-commit==3.4.0
-pynwb==2.5.0
-pytest==7.4.2
-pytest-cov==4.1.0
+black==24.4.2
+codespell==2.3.0
+coverage==7.5.4
+hdmf==3.14.4
+hdmf-docutils==0.4.7
+pre-commit==3.5.0  # latest pre-commit does not support py3.8
+pynwb==2.8.2
+pytest==8.2.2
+pytest-cov==5.0.0
+pytest-subtests==0.12.1
 python-dateutil==2.8.2
-pytest-subtests==0.6.0
-ruff==0.0.292
-tox==4.11.3
+ruff==0.4.10
diff --git a/requirements-min.txt b/requirements-min.txt
index 12925ce..d8142c7 100644
--- a/requirements-min.txt
+++ b/requirements-min.txt
@@ -1,4 +1,5 @@
 # minimum versions of package dependencies for installation
 # these should match the minimum versions specified in pyproject.toml
-pynwb==2.5.0
-hdmf==3.11.0  # required for bug fixes for generating some classes
+# NOTE: it may be possible to relax these minimum requirements
+pynwb==2.8.0
+hdmf==3.14.1
diff --git a/spec/ndx-events.extensions.yaml b/spec/ndx-events.extensions.yaml
index d749773..34418c8 100644
--- a/spec/ndx-events.extensions.yaml
+++ b/spec/ndx-events.extensions.yaml
@@ -6,7 +6,7 @@ datasets:
   - num_times
   shape:
   - null
-  doc: A VectorData that stores timestamps in seconds.
+  doc: A 1-dimensional VectorData that stores timestamps in seconds.
   attributes:
   - name: unit
     dtype: text
@@ -24,7 +24,7 @@ datasets:
   - num_events
   shape:
   - null
-  doc: A VectorData that stores durations in seconds.
+  doc: A 1-dimensional VectorData that stores durations in seconds.
   attributes:
   - name: unit
     dtype: text
@@ -54,9 +54,9 @@ groups:
   neurodata_type_inc: DynamicTable
   default_name: EventsTable
   doc: A column-based table to store information about events (event instances), one
-    event per row. Each event must have an event_type, which is a row in the EventTypesTable.
-    Additional columns may be added to store metadata about each event, such as the
-    duration of the event, or a text value of the event.
+    event per row. Each event must have an event_type, which is a reference to a row
+    in the EventTypesTable. Additional columns may be added to store metadata about
+    each event, such as the duration of the event, or a text value of the event.
   datasets:
   - name: timestamp
     neurodata_type_inc: TimestampVectorData
diff --git a/src/pynwb/ndx_events/__init__.py b/src/pynwb/ndx_events/__init__.py
index 1a58541..7f462bc 100644
--- a/src/pynwb/ndx_events/__init__.py
+++ b/src/pynwb/ndx_events/__init__.py
@@ -18,10 +18,7 @@
 # Load the namespace
 load_namespaces(str(__spec_path))
 
-# TODO: Define your classes here to make them accessible at the package level.
-# Either have PyNWB generate a class from the spec using `get_class` as shown
-# below or write a custom class and register it using the class decorator
-# `@register_class("TetrodeSeries", "ndx-hed")`
+# Define the new classes
 Task = get_class("Task", "ndx-events")
 TimestampVectorData = get_class("TimestampVectorData", "ndx-events")
 DurationVectorData = get_class("DurationVectorData", "ndx-events")
diff --git a/src/spec/create_extension_spec.py b/src/spec/create_extension_spec.py
index 32a5f60..be63fe5 100644
--- a/src/spec/create_extension_spec.py
+++ b/src/spec/create_extension_spec.py
@@ -26,7 +26,7 @@ def main():
                 name="unit",
                 dtype="text",
                 doc="The unit of measurement for the timestamps, fixed to 'seconds'.",
-                value="xseconds",
+                value="seconds",
             ),
             # NOTE: this requires all timestamps to have the same resolution which may not be true
             # if they come from different acquisition systems or processing pipelines...