diff --git a/.github/PULL_REQUEST_TEMPLATE/release.md b/.github/PULL_REQUEST_TEMPLATE/release.md
index e49d144d..ad8663af 100644
--- a/.github/PULL_REQUEST_TEMPLATE/release.md
+++ b/.github/PULL_REQUEST_TEMPLATE/release.md
@@ -2,10 +2,8 @@ Prepare for release of HDMF-Zarr [version]
 
 ### Before merging:
 - [ ] Make sure all PRs to be included in this release have been merged to `dev`.
-- [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`,
-  `requirements-doc.txt`, and `requirements-opt.txt` to the latest versions,
-  and update dependency ranges in `pyproject.toml` and minimums in `requirements-min.txt` as needed.
-  Run `pip install pur && pur -r requirements-dev.txt -r requirements.txt -r requirements-opt.txt`.
+- [ ] Major and minor releases: Update dependency ranges in `pyproject.toml` and minimums in 
+  `requirements-min.txt` as needed.
 - [ ] Check legal file dates and information in `Legal.txt`, `license.txt`, `README.rst`, `docs/source/conf.py`,
   and any other locations as needed
 - [ ] Update `pyproject.toml` as needed
@@ -27,5 +25,5 @@ Prepare for release of HDMF-Zarr [version]
 4. Either monitor [conda-forge/hdmf_zarr-feedstock](https://github.com/conda-forge/hdmf_zarr-feedstock) for the
    regro-cf-autotick-bot bot to create a PR updating the version of HDMF to the latest PyPI release, usually within
    24 hours of release, or manually create a PR updating `recipe/meta.yaml` with the latest version number
-   and SHA256 retrieved from PyPI > HDMF-Zarr > Download Files > View hashes for the `.tar.gz` file. Re-render and update
-   dependencies as needed.
+   and SHA256 retrieved from PyPI > HDMF-Zarr > Download Files > View hashes for the `.tar.gz` file. Re-render and 
+   update the dependencies as needed.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
new file mode 100644
index 00000000..24615639
--- /dev/null
+++ b/.github/dependabot.yml
@@ -0,0 +1,18 @@
+version: 2
+updates:
+  # disable checking python requirements files because there are too
+  # many updates and dependabot will not ignore requirements-min.txt
+  # until https://github.com/dependabot/dependabot-core/issues/2883 is resolved
+  # workaround is to continue updating these files manually
+
+  # - package-ecosystem: "pip"
+  #   directory: "/"
+  #   schedule:
+  #     # Check for updates to requirements files and pyproject.toml every week
+  #     interval: "weekly"
+
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
diff --git a/.github/workflows/HDMF_dev.yaml b/.github/workflows/HDMF_dev.yaml
index b493b079..4500b792 100644
--- a/.github/workflows/HDMF_dev.yaml
+++ b/.github/workflows/HDMF_dev.yaml
@@ -5,28 +5,23 @@ on: [pull_request, workflow_dispatch]
 jobs:
   check_compatibility:
     runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-          
-      - uses: actions/checkout@v4
-        with:
-            fetch-depth: 0  # tags are required for versioneer to determine the version
+      - name: Checkout repo
+        uses: actions/checkout@v4
       
-      - name: Set up Python 3.13
+      - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: "3.13"
 
       - name: Install HDMF_Zarr Requirements
         run: |
-          python -m pip install -r requirements-dev.txt -r requirements.txt
-          pip install .
+          python -m pip install ".[test]"
           
-      - name: Clone HDMF Dev Branch
+      - name: Clone and Install HDMF Dev Branch
         run: |
           git clone https://github.com/hdmf-dev/hdmf.git --recurse-submodules
           cd hdmf
@@ -36,7 +31,6 @@ jobs:
 
       - name: Run HDMF_Zarr Tests
         run:
+          # specify the tests directory so that we don't run the hdmf tests which are nested
+          # under the same base directory
           pytest -v tests
-          
-      
-          
diff --git a/.github/workflows/check_external_links.yml b/.github/workflows/check_external_links.yml
index 2fadbb80..1d2e2b65 100644
--- a/.github/workflows/check_external_links.yml
+++ b/.github/workflows/check_external_links.yml
@@ -8,16 +8,12 @@ on:
 jobs:
   check-external-links:
     runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -27,7 +23,7 @@ jobs:
       - name: Install Sphinx dependencies and package
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-doc.txt -r requirements.txt -r requirements-opt.txt
-          python -m pip install .
+          python -m pip install ".[test,docs,full]"
+
       - name: Check Sphinx external links
-        run: sphinx-build -b linkcheck ./docs/source ./test_build
+        run: sphinx-build -W -b linkcheck ./docs/source ./test_build
diff --git a/.github/workflows/deploy_release.yml b/.github/workflows/deploy_release.yml
index d8c4566c..bffde629 100644
--- a/.github/workflows/deploy_release.yml
+++ b/.github/workflows/deploy_release.yml
@@ -9,16 +9,13 @@ jobs:
     name: Deploy release from tag
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout repo with submodules
+      - name: Checkout repo
         uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install build dependencies
         run: |
@@ -28,11 +25,11 @@ jobs:
 
       - name: Run tox tests
         run: |
-          tox -e py312-upgraded
+          tox -e py313
 
       - name: Build wheel and source distribution
         run: |
-          tox -e build-py312-upgraded
+          tox -e build
           ls -1 dist
 
       - name: Test installation from a wheel
diff --git a/.github/workflows/run_all_tests.yml b/.github/workflows/run_all_tests.yml
index 9c59b97a..13a38d2b 100644
--- a/.github/workflows/run_all_tests.yml
+++ b/.github/workflows/run_all_tests.yml
@@ -18,45 +18,37 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , 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-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }
-          - { name: linux-python3.13             , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }
-          - { name: linux-python3.13-optional    , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: ubuntu-latest }
-          - { name: linux-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
-          - { name: linux-python3.13-prerelease  , test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
-          - { name: windows-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , 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-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: windows-latest } 
-          - { name: windows-python3.13           , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: windows-latest } 
-          - { name: windows-python3.13-optional  , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: windows-latest }
-          - { name: windows-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: windows-latest }
-          - { name: windows-python3.13-prerelease, test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: windows-latest }
-          - { name: macos-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , 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-python3.12             , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: macos-latest }
-          - { name: macos-python3.13             , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: macos-latest }
-          - { name: macos-python3.13-optional    , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: macos-latest }
-          - { name: macos-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: macos-latest }
-          - { name: macos-python3.13-prerelease  , test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: macos-latest }
+          - { name: linux-python3.9-minimum      , test-tox-env: py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: linux-python3.10             , test-tox-env: py310           , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.11             , test-tox-env: py311           , python-ver: "3.11", os: ubuntu-latest }
+          - { name: linux-python3.12             , test-tox-env: py312           , python-ver: "3.12", os: ubuntu-latest }
+          - { name: linux-python3.13             , test-tox-env: py313           , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-optional    , test-tox-env: py313-optional  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.13-prerelease  , test-tox-env: py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-python3.9-minimum    , test-tox-env: py39-minimum    , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.10           , test-tox-env: py310           , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.11           , test-tox-env: py311           , python-ver: "3.11", os: windows-latest }
+          - { name: windows-python3.12           , test-tox-env: py312           , python-ver: "3.12", os: windows-latest } 
+          - { name: windows-python3.13           , test-tox-env: py313           , python-ver: "3.13", os: windows-latest } 
+          - { name: windows-python3.13-optional  , test-tox-env: py313-optional  , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-prerelease, test-tox-env: py313-prerelease, python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum      , test-tox-env: py39-minimum    , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.10             , test-tox-env: py310           , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.11             , test-tox-env: py311           , python-ver: "3.11", os: macos-latest }
+          - { name: macos-python3.12             , test-tox-env: py312           , python-ver: "3.12", os: macos-latest }
+          - { name: macos-python3.13             , test-tox-env: py313           , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-optional    , test-tox-env: py313-optional  , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-prerelease  , test-tox-env: py313-prerelease, python-ver: "3.13", os: macos-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -68,46 +60,49 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install tox
           python -m pip list
+
       - name: Run tox tests
         run: |
           tox -e ${{ matrix.test-tox-env }}
+
       - name: Build wheel and source distribution
         run: |
-          tox -e ${{ matrix.build-tox-env }}
+          tox -e build
           ls -1 dist
+
       - name: Test installation from a wheel
         run: |
           tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+
+      - name: Test installation from a source distribution
+        run: |
+          tox -e wheelinstall --recreate --installpkg dist/*.tar.gz
+        
   run-all-gallery-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-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-gallery-python3.13-optional    , test-tox-env: gallery-py313-optional  , python-ver: "3.13", os: ubuntu-latest }
           - { name: linux-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
           - { name: windows-gallery-python3.9-minimum    , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: windows-latest }
-          - { name: windows-gallery-python3.13-upgraded  , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: windows-latest }
+          - { name: windows-gallery-python3.13-optional  , test-tox-env: gallery-py313-optional  , python-ver: "3.13", os: windows-latest }
           - { name: windows-gallery-python3.13-prerelease, test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: windows-latest }
           - { name: macos-gallery-python3.9-minimum      , test-tox-env: gallery-py39-minimum    , python-ver: "3.9" , os: macos-latest }
-          - { name: macos-gallery-python3.13-upgraded    , test-tox-env: gallery-py313-upgraded  , python-ver: "3.13", os: macos-latest }
+          - { name: macos-gallery-python3.13-optional    , test-tox-env: gallery-py313-optional  , python-ver: "3.13", os: macos-latest }
           - { name: macos-gallery-python3.13-prerelease  , test-tox-env: gallery-py313-prerelease, python-ver: "3.13", os: macos-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -119,44 +114,41 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install tox
           python -m pip list
+
       - name: Run tox tests
         run: |
           tox -e ${{ matrix.test-tox-env }}
+
   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-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: conda-linux-python3.10           , test-tox-env: py310           , build-tox-env: build-py310           , python-ver: "3.10", os: ubuntu-latest }
-          - { name: conda-linux-python3.11           , test-tox-env: py311           , build-tox-env: build-py311           , python-ver: "3.11", os: ubuntu-latest }
-          - { name: conda-linux-python3.12           , test-tox-env: py312           , build-tox-env: build-py312           , python-ver: "3.12", os: ubuntu-latest }  
-          - { name: conda-linux-python3.13           , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }          
-          - { name: conda-linux-python3.13-optional  , test-tox-env: py313-optional  , build-tox-env: build-py313-optional  , python-ver: "3.13", os: ubuntu-latest }
-          - { name: conda-linux-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
-          - { name: conda-linux-python3.13-prerelease, test-tox-env: py313-prerelease, build-tox-env: build-py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.9-minimum    , test-tox-env: py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.10           , test-tox-env: py310           , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.11           , test-tox-env: py311           , python-ver: "3.11", os: ubuntu-latest }
+          - { name: conda-linux-python3.12           , test-tox-env: py312           , python-ver: "3.12", os: ubuntu-latest }  
+          - { name: conda-linux-python3.13           , test-tox-env: py313           , python-ver: "3.13", os: ubuntu-latest }          
+          - { name: conda-linux-python3.13-optional  , test-tox-env: py313-optional  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-prerelease, test-tox-env: py313-prerelease, python-ver: "3.13", os: ubuntu-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-ver }}
+          channels: conda-forge
 
       - name: Install build dependencies
         run: |
@@ -170,15 +162,20 @@ jobs:
           conda config --show-sources
           conda list --show-channel-urls
 
+      # NOTE tox installs packages from PyPI not conda-forge...
       - name: Run tox tests
         run: |
           tox -e ${{ matrix.test-tox-env }}
 
       - name: Build wheel and source distribution
         run: |
-          tox -e ${{ matrix.build-tox-env }}
+          tox -e build
           ls -1 dist
 
       - name: Test installation from a wheel
         run: |
           tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+      
+      - name: Test installation from a source distribution
+        run: |
+          tox -e wheelinstall --recreate --installpkg dist/*.tar.gz
diff --git a/.github/workflows/run_coverage.yml b/.github/workflows/run_coverage.yml
index 21150fc5..20011920 100644
--- a/.github/workflows/run_coverage.yml
+++ b/.github/workflows/run_coverage.yml
@@ -19,6 +19,9 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}-${{ matrix.opt_req }}
+      cancel-in-progress: true
     strategy:
       matrix:
         include:
@@ -26,48 +29,42 @@ jobs:
           - { os: ubuntu-latest , opt_req: false }
           - { os: windows-latest, opt_req: false }
           - { os: macos-latest  , opt_req: false }
-    env:
+    env:  # used by codecov-action
       OS: ${{ matrix.os }}
       PYTHON: '3.13'
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PYTHON }}
 
-      - name: Install dependencies
+      - name: Upgrade pip
         run: |
           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 package
+        if: ! ${{ matrix.opt_req }}
         run: |
-          python -m pip install .
-          python -m pip list
+          python -m pip install ".[test]"
+
+      - name: Install package with optional dependencies
+        if: ${{ matrix.opt_req }}
+        run: python -m pip install ".[test,full]"
 
       - name: Run tests and generate coverage report
         run: |
           # coverage is configured in pyproject.toml
-          pytest --cov --cov-report=xml --cov-report=term  # codecov uploader requires xml format
+          # codecov uploader requires xml format
+          python -m pip list
+          pytest --cov --cov-report=xml --cov-report=term
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
         with:
           fail_ci_if_error: true
-          file: ./coverage.xml
+          files: ./coverage.xml
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index 827606c0..521995c1 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -15,29 +15,26 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: linux-python3.13             , test-tox-env: py313           , build-tox-env: build-py313           , python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-python3.9-minimum  , test-tox-env: py39-minimum  , python-ver: "3.9" , os: ubuntu-latest }
           # NOTE config below with "upload-wheels: true" specifies that wheels should be uploaded as an artifact
-          - { name: linux-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest , upload-wheels: true }
-          - { name: windows-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: windows-latest }
-          - { name: windows-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: windows-latest }
-          - { name: macos-python3.9-minimum      , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: macos-latest }
-          - { name: macos-python3.13-upgraded    , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: macos-latest }
+          - { name: linux-python3.13         , test-tox-env: py313         , python-ver: "3.13", os: ubuntu-latest , upload-wheels: true }
+          - { name: linux-python3.13-optional, test-tox-env: py313-optional, python-ver: "3.13", os: ubuntu-latest }
+          - { name: windows-python3.9-minimum, test-tox-env: py39-minimum  , python-ver: "3.9" , os: windows-latest }
+          - { name: windows-python3.13       , test-tox-env: py313         , python-ver: "3.13", os: windows-latest }
+          - { name: windows-python3.13-optional, test-tox-env: py313-optional, python-ver: "3.13", os: windows-latest }
+          - { name: macos-python3.9-minimum  , test-tox-env: py39-minimum  , python-ver: "3.9" , os: macos-latest }
+          - { name: macos-python3.13         , test-tox-env: py313         , python-ver: "3.13", os: macos-latest }
+          - { name: macos-python3.13-optional, test-tox-env: py313-optional, python-ver: "3.13", os: macos-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -49,16 +46,24 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install tox
           python -m pip list
+
       - name: Run tox tests
         run: |
           tox -e ${{ matrix.test-tox-env }}
+
       - name: Build wheel and source distribution
         run: |
-          tox -e ${{ matrix.build-tox-env }}
+          tox -e build
           ls -1 dist
+
       - name: Test installation from a wheel
         run: |
           tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+
+      - name: Test installation from a source distribution
+        run: |
+          tox -e wheelinstall --recreate --installpkg dist/*.tar.gz
+
       - name: Upload distribution as a workspace artifact
         if: ${{ matrix.upload-wheels }}
         uses: actions/upload-artifact@v4
@@ -72,24 +77,20 @@ jobs:
     defaults:
       run:
         shell: bash
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
         include:
           - { name: linux-gallery-python3.9-minimum    , test-tox-env: gallery-py39-minimum  , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: linux-gallery-python3.13-upgraded  , test-tox-env: gallery-py313-upgraded, python-ver: "3.13", os: ubuntu-latest }
+          - { name: linux-gallery-python3.13-optional  , test-tox-env: gallery-py313-optional, python-ver: "3.13", os: ubuntu-latest }
           - { name: windows-gallery-python3.9-minimum  , test-tox-env: gallery-py39-minimum  , python-ver: "3.9" , os: windows-latest }
-          - { name: windows-gallery-python3.13-upgraded, test-tox-env: gallery-py313-upgraded, python-ver: "3.13", os: windows-latest }
+          - { name: windows-gallery-python3.13-optional, test-tox-env: gallery-py313-optional, python-ver: "3.13", os: windows-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -101,73 +102,79 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install tox
           python -m pip list
+
       - name: Run tox tests
         run: |
           tox -e ${{ matrix.test-tox-env }}
+
   run-tests-on-conda:
     name: ${{ matrix.name }}
     runs-on: ubuntu-latest
     defaults:
      run:
        shell: bash -l {0}
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.name }}
+      cancel-in-progress: true
     strategy:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.9-minimum    , test-tox-env: py39-minimum    , build-tox-env: build-py39-minimum    , python-ver: "3.9" , os: ubuntu-latest }
-          - { name: conda-linux-python3.13-upgraded  , test-tox-env: py313-upgraded  , build-tox-env: build-py313-upgraded  , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.9-minimum  , test-tox-env: py39-minimum  , python-ver: "3.9" , os: ubuntu-latest }
+          - { name: conda-linux-python3.13         , test-tox-env: py313         , python-ver: "3.13", os: ubuntu-latest }
+          - { name: conda-linux-python3.13-optional, test-tox-env: py313-optional, python-ver: "3.13", os: ubuntu-latest }
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
-          fetch-depth: 0  # tags are required for versioneer to determine the version
+      - name: Checkout repo
+        uses: actions/checkout@v4
 
       - name: Set up Conda
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
-          auto-activate-base: true
-          activate-environment: true
           python-version: ${{ matrix.python-ver }}
+          channels: conda-forge
 
       - name: Install build dependencies
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
           conda install -c conda-forge tox
-          conda list
+
+      - name: Conda reporting
+        run: |
+          conda info
+          conda config --show-sources
+          conda list --show-channel-urls
+
+      # NOTE tox installs packages from PyPI not conda-forge...
       - name: Run tox tests
         run: |
           tox -e ${{ matrix.test-tox-env }}
+
       - name: Build wheel and source distribution
         run: |
-          tox -e ${{ matrix.build-tox-env }}
+          tox -e build
           ls -1 dist
+
       - name: Test installation from a wheel
         run: |
           tox -e wheelinstall --recreate --installpkg dist/*-none-any.whl
+
+      - name: Test installation from a source distribution
+        run: |
+          tox -e wheelinstall --recreate --installpkg dist/*.tar.gz
+
   deploy-dev:
     name: Deploy pre-release from dev
     needs: [run-tests, run-gallery-tests, run-tests-on-conda]
     if: ${{ github.event_name == 'push' }}
     runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
-      - name: Cancel non-latest runs
-        uses: styfle/cancel-workflow-action@0.11.0
-        with:
-          all_but_latest: true
-          access_token: ${{ github.token }}
-
-      - name: Checkout repo with submodules
+      - name: Checkout repo
         uses: actions/checkout@v4
-        with:
-          submodules: 'recursive'
 
       - name: Set up Python
         uses: actions/setup-python@v5
diff --git a/.gitignore b/.gitignore
index 65aa7ee8..91d64df9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -78,6 +78,7 @@ docs/build/
 docs/source/hdmf_zarr*.rst
 docs/source/gen_modules
 docs/source/tutorials
+docs/source/sg_execution_times.rst
 # example data generated by the tutorials
 docs/gallery/*.h5
 docs/gallery/*.zarr
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 8d6ffb00..a200e362 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -6,9 +6,9 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: '3.12'
+    python: '3.13'
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -24,10 +24,7 @@ formats: all
 # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: requirements-doc.txt
-    - requirements: requirements.txt
-    - requirements: requirements-opt.txt
-    - path: . # path to the package relative to the root
+    - path: .[docs,full] # path to the package relative to the root
 
 # Optionally include all submodules
 submodules:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ff767365..639958cf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # HDMF-ZARR Changelog
 
-## 1.0.0 (Upcoming)
+## 0.10.0 (Upcoming)
 
 ### Enhancements
 * Added initial refactor of export, supporting references and internal/external links from Zarr to Zarr. This will introduce breaking changes that could lead to existing exported files to be invalid. This update removes '.' as the object default file source. @mavaylon1 [#194](https://github.com/hdmf-dev/hdmf-zarr/pull/194)
@@ -8,27 +8,34 @@
 * Updated packages used for testing and readthedocs configuration. @mavaylon1, @rly [#214](https://github.com/hdmf-dev/hdmf-zarr/pull/214)
 * Add `force_overwite` parameter for `ZarrIO.__init__` to allow overwriting an existing file or directory. @oruebel [#229](https://github.com/hdmf-dev/hdmf-zarr/pull/229)
 * Remove allowance of `hdmf.Array` in `__init__` of `AbstractZarrTableDataset` and `ZarrDataset` to be compatible with HDMF 4.0. @rly [#236](https://github.com/hdmf-dev/hdmf-zarr/pull/236)
-* Remove support for python 3.8. @mavaylon1 [#240](https://github.com/hdmf-dev/hdmf-zarr/pull/240)
+* Remove support for python 3.8 and added testing for Python 3.13. @mavaylon1 [#240](https://github.com/hdmf-dev/hdmf-zarr/pull/240)
+* Added `NWBZarrIO.read_nwb` convenience method to simplify reading an NWB file. @oruebel [#226](https://github.com/hdmf-dev/hdmf-zarr/pull/226)
+* Updated optional dependency groups in `pyproject.toml` and GitHub Actions workflows. @rly, @mavaylon1 [#239](https://github.com/hdmf-dev/hdmf-zarr/pull/239)
 
 ### Bug Fixes
 * Fix reading of cached specs and caching of specs during export. @rly [#232](https://github.com/hdmf-dev/hdmf-zarr/pull/232)
 * Fix hiding of pynwb compatibility errors. @rly [242](https://github.com/hdmf-dev/hdmf-zarr/pull/242)
 
+
 ## 0.9.0 (September 16, 2024)
+
 ### Enhancements
 * Added support for appending a dataset of references. @mavaylon1 [#203](https://github.com/hdmf-dev/hdmf-zarr/pull/203)
 * NWBZarrIO load_namespaces=True by default. @mavaylon1 [#204](https://github.com/hdmf-dev/hdmf-zarr/pull/204)
 * Added test for opening file with consolidated metadata from DANDI. @mavaylon1 [#206](https://github.com/hdmf-dev/hdmf-zarr/pull/206)
 * Add dimension labels compatible with xarray. @mavaylon1 [#207](https://github.com/hdmf-dev/hdmf-zarr/pull/207)
 * Added link_data --> clear_cache relationship to support repacking zarr nwbfiles: [#215](https://github.com/hdmf-dev/hdmf-zarr/pull/215)
-* Added `NWBZarrIO.read_nwb` convenience method to simplify reading an NWB file. @oruebel [#226](https://github.com/hdmf-dev/hdmf-zarr/pull/226)
+
 
 ## 0.8.0 (June 4, 2024)
+
 ### Bug Fixes
 * Fixed bug when opening a file in with `mode=r+`. The file will open without using the consolidated metadata. @mavaylon1 [#182](https://github.com/hdmf-dev/hdmf-zarr/issues/182)
 * Fixed bug on how we access scalar arrays. Added warning filter for Zarr deprecation of NestedDirectoryStore. Fixed bug on how we write a dataset of references. @mavaylon1 [#195](https://github.com/hdmf-dev/hdmf-zarr/pull/195)
 
+
 ## 0.7.0 (May 2, 2024)
+
 ### Enhancements
 * Added support for python 3.12. @mavaylon1 [#172](https://github.com/hdmf-dev/hdmf-zarr/pull/172)
 * Added support for forcing read of files without consolidated metadata using  `mode=r-` in `ZarrIO`. @oruebel [#183](https://github.com/hdmf-dev/hdmf-zarr/pull/183)
@@ -41,6 +48,7 @@
 * Fixed bug in `ZarrIO.__open_file_consolidated` that led to remote files being opened without consolidated metadata. @oruebel  [#184](https://github.com/hdmf-dev/hdmf-zarr/pull/184)
 * Fixed minor bug where `ZarrIO.__open_file_consolidated` used properties of `ZarrIO` instead of the provided input parameters. @oruebel [#183](https://github.com/hdmf-dev/hdmf-zarr/pull/183)
 
+
 ## 0.6.0 (February 21, 2024)
 
 ### Enhancements
diff --git a/docs/source/conf.py b/docs/source/conf.py
index d3bc2002..39669770 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -116,7 +116,6 @@
 # a list of builtin themes.
 #
 html_theme = "sphinx_rtd_theme"
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 html_theme_options = {
     'logo_only': False,  # Only show the hdmf-zarr logo without the documentation title
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 9656c3f7..f9910075 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -6,8 +6,8 @@
 Welcome to hdmf-zarr's documentation!
 =====================================
 
-**hdmf_zarr** implements a Zarr backend for `HDMF <https://hdmf.readthedocs.io>`_ as well as
-convenience classes for integration of Zarr with `PyNWB <https://pynwb.readthedocs.io>`_ to
+**hdmf_zarr** implements a Zarr backend for `HDMF <https://hdmf.readthedocs.io/en/stable/>`_ as well as
+convenience classes for integration of Zarr with `PyNWB <https://pynwb.readthedocs.io/en/stable/>`_ to
 support writing of NWB files to `Zarr <https://zarr.readthedocs.io/en/stable/>`_.
 
 **Status:** The Zarr backend is **under development** and may still change. See the
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
index fc55f947..e203f2d7 100644
--- a/docs/source/installation.rst
+++ b/docs/source/installation.rst
@@ -24,14 +24,15 @@ For Developers
 Install hdmf-zarr from GitHub
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The following illustrates how to install both ``hdmf`` and ``hdfm_zarr`` from GitHub
-in a Conda environment. Normally we don't need to install ``hdmf`` directly, but until
-``hdmf 3.4.0`` is released we need to use the ``dev`` version of ``hdmf``.
+The following illustrates how to install both ``hdmf`` and ``hdmf_zarr`` from GitHub
+in a Conda environment, with all of the optional, testing, and documentation dependencies
+for hdmf-zarr. Normally, we don't need to install ``hdmf`` directly, but it is
+often useful to use the ``dev`` branch of the ``hdmf`` GitHub repository.
 
 .. code-block::
 
-    conda create --name hdmf-zarr-test python=3.9
-    conda activate hdmf-zarr-test
+    conda create --name hdmf-zarr-dev python=3.13
+    conda activate hdmf-zarr-dev
 
     git clone --recurse-submodules https://github.com/hdmf-dev/hdmf.git
     cd hdmf
@@ -41,12 +42,11 @@ in a Conda environment. Normally we don't need to install ``hdmf`` directly, but
 
     git clone https://github.com/hdmf-dev/hdmf-zarr.git
     cd hdmf-zarr
-    pip install -r requirements.txt -r requirements-dev.txt -r requirements-doc.txt
-    pip install -e .
+    pip install -e ".[all]"
 
 .. note::
 
-   Depending on versions, it is possible that when installing ``hdmf-zarr`` that pip will
+   Depending on versions, it is possible that when installing ``hdmf-zarr``, that ``pip`` will
    install HDMF directly from PyPI instead of using the development version of HDMF
    that is already installed. In that case call ``pip uninstall hdmf`` and
    go to the ``hdmf`` directory and run ``pip install -e .`` again
diff --git a/pyproject.toml b/pyproject.toml
index 9b36cba3..25adfcce 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,19 +28,47 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Medical Science Apps."
 ]
 dependencies = [
-    'hdmf>=3.14.5',
-    'zarr>=2.18.0, <3.0', # pin below 3.0 until HDMF-zarr supports zarr 3.0
-    'numpy>=1.24',
-    'numcodecs>=0.10.0',
-    'pynwb>=2.8.3',
-    'threadpoolctl>=3.1.0',
+    "hdmf>=3.14.5",
+    "zarr>=2.18.0, <3.0",  # pin below 3.0 until HDMF-zarr supports zarr 3.0
+    "numpy>=1.24.0",
+    "numcodecs>=0.10.0",
+    "pynwb>=2.8.3",
+    "threadpoolctl>=3.1.0",
 ]
 dynamic = ["version"]
 
 [project.optional-dependencies]
-tqdm = ["tqdm>=4.41.0"]
-fsspec = ["fsspec"]
-s3fs = ["s3fs"]
+# all optional dependencies
+full = [
+    "tqdm>=4.41.0",
+    "fsspec",
+    "s3fs",
+]
+
+# development dependencies
+test = [
+    "codespell",
+    "hdf5plugin",  # hdf5plugin is used to test conversion of plugin filters
+    "pre-commit",
+    "pytest",
+    "pytest-cov",
+    "python-dateutil",
+    "ruff",
+    "tox",
+]
+
+# documentation dependencies
+docs = [
+    "matplotlib",
+    "sphinx>=4",  # improved support for docutils>=0.17
+    "sphinx_rtd_theme>=1",  # <1 does not work with docutils>=0.17
+    "sphinx-gallery",
+    "sphinx-copybutton",
+]
+
+# all possible dependencies
+all = ["hdmf-zarr[full,test,docs]"]
+
 
 [project.urls]
 "Homepage" = "https://github.com/hdmf-dev/hdmf-zarr"
diff --git a/requirements-dev.txt b/requirements-dev.txt
deleted file mode 100644
index 75e9ba1c..00000000
--- a/requirements-dev.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-# pinned dependencies to reproduce an entire development environment to use HDMF-Zarr,
-# run HDMF-Zarr tests, check code style,
-# compute coverage, and create test environments. note that depending on the version of python installed, different
-# versions of requirements may be installed due to package incompatibilities.
-#
-black==24.3.0
-codespell==2.2.6
-coverage==7.6.7
-hdf5plugin==4.3.0  # hdf5plugin is used to test conversion of plugin filters
-pre-commit==3.5.0
-pytest==8.3.3
-pytest-cov==6.0.0
-python-dateutil==2.8.2
-ruff==0.1.3
-tox==4.11.3
diff --git a/requirements-doc.txt b/requirements-doc.txt
deleted file mode 100644
index 4b921319..00000000
--- a/requirements-doc.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-# dependencies to generate the documentation for HDMF-Zarr
-matplotlib
-sphinx>=4  # improved support for docutils>=0.17
-sphinx_rtd_theme>=1  # <1 does not work with docutils>=0.17
-sphinx-gallery
-sphinx-copybutton
diff --git a/requirements-min.txt b/requirements-min.txt
index bc954b0a..72bbb64d 100644
--- a/requirements-min.txt
+++ b/requirements-min.txt
@@ -1,6 +1,8 @@
+# minimum versions of package dependencies for installing HDMF
+# NOTE: these should match the minimum bound for dependencies in pyproject.toml
 hdmf==3.14.5
-zarr==2.13.0
+zarr==2.18.0
+numpy==1.24.0
 numcodecs==0.10.0
 pynwb==2.8.3
-setuptools
 threadpoolctl==3.1.0
diff --git a/requirements-opt.txt b/requirements-opt.txt
deleted file mode 100644
index 6fc3bcb0..00000000
--- a/requirements-opt.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-tqdm==4.67.0
-fsspec==2024.10.0
-s3fs==2024.10.0
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 57647cf2..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-# pinned dependencies to reproduce an entire development environment to use HDMF-ZARR
-hdmf==3.14.5
-zarr==2.18.3; python_version >= "3.10"  # zarr 2.18.3 dropped support for python 3.9
-zarr==2.18.2; python_version < "3.10"
-pynwb==2.8.3
-numpy==2.1.3; python_version >= "3.10"  # numpy 2.1.0 dropped support for python 3.9
-numpy==2.0.2; python_version < "3.10"
-numcodecs==0.13.1
-threadpoolctl==3.5.0
diff --git a/tests/unit/test_zarrdataio.py b/tests/unit/test_zarrdataio.py
index d6070784..f52f2f5c 100644
--- a/tests/unit/test_zarrdataio.py
+++ b/tests/unit/test_zarrdataio.py
@@ -47,7 +47,7 @@ def test_hdf5_to_zarr_filters_scaleoffset(self):
         msg = "/test_dset HDF5 scaleoffset filter ignored in Zarr"
         with self.assertWarnsWith(UserWarning, msg):
             filters = ZarrDataIO.hdf5_to_zarr_filters(h5dset)
-            self.assertEqual(len(filters), 0)
+        self.assertEqual(len(filters), 0)
         # Close the HDF5 file
         h5file.close()
 
@@ -60,7 +60,7 @@ def test_hdf5_to_zarr_filters_lzf(self):
         msg = "/test_dset HDF5 szip or lzf compression ignored in Zarr"
         with self.assertWarnsWith(UserWarning, msg):
             filters = ZarrDataIO.hdf5_to_zarr_filters(h5dset)
-            self.assertEqual(len(filters), 0)
+        self.assertEqual(len(filters), 0)
         # Close the HDF5 file
         h5file.close()
 
@@ -76,7 +76,7 @@ def test_hdf5_to_zarr_filters_lz4(self):
         msg = "/test_dset HDF5 lz4 compression ignored in Zarr"
         with self.assertWarnsWith(UserWarning, msg):
             filters = ZarrDataIO.hdf5_to_zarr_filters(h5dset)
-            self.assertEqual(len(filters), 0)
+        self.assertEqual(len(filters), 0)
         # Close the HDF5 file
         h5file.close()
 
@@ -92,7 +92,7 @@ def test_hdf5_to_zarr_filters_bitshuffle(self):
         msg = "/test_dset HDF5 bitshuffle compression ignored in Zarr"
         with self.assertWarnsWith(UserWarning, msg):
             filters = ZarrDataIO.hdf5_to_zarr_filters(h5dset)
-            self.assertEqual(len(filters), 0)
+        self.assertEqual(len(filters), 0)
         # Close the HDF5 file
         h5file.close()
 
@@ -109,10 +109,10 @@ def test_hdf5_to_zarr_filters_other_unsupported(self):
             data=[1, 2, 3, 4, 5],
             **hdf5plugin.FciDecomp())
         # test that we warn due to the FciDecomp
-        msg = "/test_fcidecomp HDF5 filter id 32018 with properties None ignored in Zarr."
-        with self.assertWarnsWith(UserWarning, msg):
+        msg = r"/test_fcidecomp HDF5 filter id 32018 with properties .* ignored in Zarr."
+        with self.assertWarnsRegex(UserWarning, msg):
             filters = ZarrDataIO.hdf5_to_zarr_filters(h5dset_FciDecomp)
-            self.assertEqual(len(filters), 0)
+        self.assertEqual(len(filters), 0)
         # Close the HDF5 file
         h5file.close()
 
diff --git a/tox.ini b/tox.ini
index 96c145e5..22e02a64 100644
--- a/tox.ini
+++ b/tox.ini
@@ -2,201 +2,105 @@
 # in multiple virtualenvs. This configuration file will run the
 # test suite on all supported python versions. To use it, "python -m pip install tox"
 # and then run "tox" from this directory.
+# Tox is used by the GitHub Actions workflow to run tests on multiple environments.
 
 [tox]
+# NOTE: if the string "py39" is in the environment name, then the py39 interpreter is used,
+# so we can omit specifying the basepython version below.
 envlist = py39, py310, py311, py312, py313
-requires = pip >= 22.0
+requires = pip >= 24.3.1
 
 [testenv]
 download = True
 setenv =
   PYTHONDONTWRITEBYTECODE = 1
-  VIRTUALENV_python -m pip = 22.3.1
 install_command =
-    python -m pip install {opts} {packages}
-
-deps =
-    -rrequirements-dev.txt
-    -rrequirements.txt
-
+    python -m pip install -U {opts} {packages}
+extras = test
 commands =
-    python -m pip check  # Check for conflicting packages
+    python -m pip list
+    python -m pip check
     pytest -v
 
 # Env to create coverage report locally
 [testenv:localcoverage]
 basepython = python3.13
 commands =
+    python -m pip list
+    python -m pip check
     pytest --cov=hdmf_zarr
     coverage html -d tests/coverage/htmlcov
 
-# Test with python 3.13; pinned dev and optional reqs
-[testenv:py312-optional]
-basepython = python3.13
-install_command =
-    python -m pip install {opts} {packages}
-deps =
-    {[testenv]deps}
-    -rrequirements-opt.txt
+# Envs that run tests
+[testenv:py{39,310,311,312,313}]
 commands = {[testenv]commands}
 
-# Test with python 3.13; pinned dev and optional reqs; upgraded run reqs
-[testenv:py313-upgraded]
-basepython = python3.13
-install_command =
-    python -m pip install -U {opts} {packages}
-deps =
-    -rrequirements-dev.txt
-    -rrequirements-opt.txt
+# Test with python 3.13 and all optional dependencies
+[testenv:py313-optional]
+extras = {[testenv]extras}, full
 commands = {[testenv]commands}
 
-# Test with python 3.13; pinned dev and optional reqs; upgraded, pre-release run reqs
+# Test with python 3.13 and all optional dependencies, using pre-release versions
 [testenv:py313-prerelease]
-basepython = python3.13
 install_command =
     python -m pip install -U --pre {opts} {packages}
-deps =
-    -rrequirements-dev.txt
-    -rrequirements-opt.txt
+extras = {[testenv]extras}, full
 commands = {[testenv]commands}
 
-# Test with python 3.9; pinned dev reqs; minimum run reqs
+# Test with python 3.9 and minimum dependencies
 [testenv:py39-minimum]
-basepython = python3.9
+install_command =
+    python -m pip install {opts} {packages}
 deps =
-    -rrequirements-dev.txt
-    -rrequirements-min.txt
+    -r requirements-min.txt
 commands = {[testenv]commands}
 
+
 # Envs that builds wheels and source distribution
 [testenv:build]
 commands =
-    python -m pip install --upgrade build
+    python -m pip install -U build
+    python -m pip list
+    python -m pip check
     python -m build
-
-[testenv:build-py39]
-basepython = python3.9
-commands = {[testenv:build]commands}
-
-[testenv:build-py310]
-basepython = python3.10
-commands = {[testenv:build]commands}
-
-[testenv:build-py311]
-basepython = python3.11
-commands = {[testenv:build]commands}
-
-[testenv:build-py312]
-basepython = python3.12
-commands = {[testenv:build]commands}
-
-[testenv:build-py313]
-basepython = python3.13
-commands = {[testenv:build]commands}
-
-[testenv:build-py313-optional]
-basepython = python3.13
-deps =
-    {[testenv]deps}
-    -rrequirements-opt.txt
-commands = {[testenv:build]commands}
-
-[testenv:build-py313-upgraded]
-basepython = python3.13
-install_command =
-    python -m pip install -U {opts} {packages}
-deps =
-    -rrequirements-dev.txt
-    -rrequirements-opt.txt
-commands = {[testenv:build]commands}
-
-[testenv:build-py313-prerelease]
-basepython = python3.13
-install_command =
-    python -m pip install -U --pre {opts} {packages}
-deps =
-    -rrequirements-dev.txt
-    -rrequirements-opt.txt
-commands = {[testenv:build]commands}
-
-[testenv:build-py39-minimum]
-basepython = python3.9
-deps =
-    -rrequirements-dev.txt
-    -rrequirements-min.txt
-commands = {[testenv:build]commands}
+    
 
 # Envs that will test installation from a wheel
 [testenv:wheelinstall]
-deps = null
-commands = python -c "import hdmf_zarr"
+extras = null
+commands =
+    python -m pip list
+    python -m pip check
+    python -c "import hdmf_zarr"
+
 
 # Envs that will execute gallery tests
 [testenv:gallery]
-install_command =
-    python -m pip install {opts} {packages}
-
-deps =
-    -rrequirements-dev.txt
-    -rrequirements.txt
-    -rrequirements-doc.txt
-
+# NOTE: the gallery tests do not require the "docs" extras
 commands =
+    python -m pip list
+    python -m pip check
     python test_gallery.py
 
-[testenv:gallery-py39]
-basepython = python3.9
-deps = {[testenv:gallery]deps}
-commands = {[testenv:gallery]commands}
-
-[testenv:gallery-py310]
-basepython = python3.10
-deps = {[testenv:gallery]deps}
+[testenv:gallery-{py39,py310,py311,py312,py313}]
 commands = {[testenv:gallery]commands}
 
-[testenv:gallery-py311]
-basepython = python3.11
-deps = {[testenv:gallery]deps}
+# Test with python 3.13 and all optional dependencies
+[testenv:gallery-py313-optional]
+extras = {[testenv:gallery]extras}, full
 commands = {[testenv:gallery]commands}
 
-[testenv:gallery-py312]
-basepython = python3.12
-deps = {[testenv:gallery]deps}
-commands = {[testenv:gallery]commands}
-
-[testenv:gallery-py313]
-basepython = python3.13
-deps = {[testenv:gallery]deps}
-commands = {[testenv:gallery]commands}
-
-# Test with python 3.12; pinned dev, doc, and optional reqs; upgraded run reqs
-[testenv:gallery-py313-upgraded]
-basepython = python3.13
-install_command =
-    python -m pip install -U {opts} {packages}
-deps =
-    -rrequirements-dev.txt
-    -rrequirements-doc.txt
-    -rrequirements-opt.txt
-commands = {[testenv:gallery]commands}
-
-# Test with python 3.13; pinned dev, doc, and optional reqs; pre-release run reqs
+# Test with python 3.13 and all optional dependencies, using pre-release versions
 [testenv:gallery-py313-prerelease]
-basepython = python3.13
 install_command =
     python -m pip install -U --pre {opts} {packages}
-deps =
-    -rrequirements-dev.txt
-    -rrequirements-doc.txt
-    -rrequirements-opt.txt
+extras = {[testenv:gallery]extras}, full
 commands = {[testenv:gallery]commands}
 
-# Test with python 3.9; pinned dev and doc reqs; minimum run reqs
+# Test with python 3.9 and minimum dependencies
 [testenv:gallery-py39-minimum]
-basepython = python3.9
+install_command =
+    python -m pip install {opts} {packages}
 deps =
-    -rrequirements-dev.txt
-    -rrequirements-min.txt
-    -rrequirements-doc.txt
-    -rrequirements-opt.txt
+    -r requirements-min.txt
 commands = {[testenv:gallery]commands}