From 2df7fc484406450aebb9a048ffb6558a045ba72e Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Tue, 13 Sep 2022 23:12:36 -0700
Subject: [PATCH 01/21] First pass

---
 hooks/post_gen_project.py                     |  11 +-
 .../workflows/check_external_links.yml        |  34 +++
 .../.github/workflows/run_all_tests.yml       | 200 ++++++++++++++++++
 .../.github/workflows/run_coverage.yml        |  58 +++++
 .../.github/workflows/run_flake8.yml          |  30 +++
 .../requirements-min.txt                      |   3 +
 .../requirements-opt.txt                      |   3 +
 7 files changed, 337 insertions(+), 2 deletions(-)
 create mode 100644 {{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
 create mode 100644 {{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
 create mode 100644 {{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml
 create mode 100644 {{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml
 create mode 100644 {{ cookiecutter.namespace }}/requirements-min.txt
 create mode 100644 {{ cookiecutter.namespace }}/requirements-opt.txt

diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
index a11e311..750d8bf 100644
--- a/hooks/post_gen_project.py
+++ b/hooks/post_gen_project.py
@@ -2,7 +2,7 @@
 import textwrap
 
 from hdmf_docutils.init_sphinx_extension_doc import main as init_sphinx_extension_doc
-from subprocess import check_call
+from subprocess import CalledProcessError, check_call
 
 
 def _generate_doc():
@@ -30,7 +30,14 @@ def _initialize_git():
     check_call(["git", "init"])
     check_call(["git", "add", "-A"])
     check_call(["git", "commit", "-m", "Initial commit"])
-    check_call(["git", "branch", "-m", "master", "main"])
+    try:
+        # check if the installed version of git created a master branch by default
+        # and if so, rename the branch to "main"
+        check_call(["git", "show-ref", "--verify", "--quiet", "refs/heads/master"])
+        check_call(["git", "branch", "-m", "master", "main"])
+    except CalledProcessError:
+        pass
+
 
 
 def main():
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
new file mode 100644
index 0000000..2a19133
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
@@ -0,0 +1,34 @@
+name: Check Sphinx external links
+on:
+  pull_request:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  workflow_dispatch:
+
+jobs:
+  check-external-links:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/cancel-workflow-action@0.9.1
+        with:
+          all_but_latest: true
+          access_token: ${{ "{{" }} github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+
+      - name: Install Sphinx dependencies and package
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt -r requirements.txt
+          python -m pip install .
+
+      - name: Check Sphinx external links
+        run: sphinx-build -b linkcheck ./docs/source ./test_build
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
new file mode 100644
index 0000000..3b93428
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -0,0 +1,200 @@
+name: Run all tests
+on:
+  schedule:
+    - cron: '0 5 * * *'  # once per day at midnight ET
+  pull_request:
+  push:
+  workflow_dispatch:
+
+jobs:
+  run-all-tests:
+    # the only differences between this job and "run_tests.yml" is the "strategy.matrix.include" and the upload
+    # distributions step.
+    # GitHub Actions does not yet support YAML anchors, easily reusable components, or easy dynamic matrix
+    # configurations based on the github event, so this job is duplicated for the most part
+    name: ${{ "{{" }} matrix.name }}
+    runs-on: ${{ "{{" }} matrix.os }}
+    defaults:
+      run:
+        shell: bash
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: linux-python3.7-minimum      , requirements: minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: linux-python3.7              , requirements: pinned     , python-ver: "3.7" , 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-python3.10-optional    , requirements: optional   , python-ver: "3.10", os: ubuntu-latest }
+          - { name: linux-python3.10-upgraded    , requirements: upgraded   , python-ver: "3.10", os: ubuntu-latest }
+          - { name: windows-python3.7-minimum    , requirements: minimum    , python-ver: "3.7" , os: windows-latest }
+          - { name: windows-python3.7            , requirements: pinned     , python-ver: "3.7" , 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-python3.10-optional  , requirements: optional   , python-ver: "3.10", os: windows-latest }
+          - { name: windows-python3.10-upgraded  , requirements: upgraded   , python-ver: "3.10", os: windows-latest }
+          - { name: macos-python3.7-minimum      , requirements: pinned     , python-ver: "3.7" , os: macos-latest }
+          - { name: macos-python3.7              , requirements: pinned     , python-ver: "3.7" , 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-python3.10-optional    , requirements: optional   , python-ver: "3.10", os: macos-latest }
+          - { name: macos-python3.10-upgraded    , requirements: upgraded   , python-ver: "3.10", os: macos-latest }
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        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 (minimal)
+        if: ${{ "{{" }} matrix.requirements }} == "minimum"
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ "{{" }} matrix.requirements }} == "pinned"
+        run: |
+          python -m pip install -r requirements.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned, optional)
+        if: ${{ "{{" }} matrix.requirements }} == "optional"
+        run: |
+          python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded, optional)
+        if: ${{ "{{" }} matrix.requirements }} == "upgraded"
+        run: |
+          python -m pip install -r requirements-opt.txt -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - 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 hdmf"
+
+      - 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 hdmf"
+
+  run-all-tests-on-conda:
+    name: ${{ "{{" }} matrix.name }}
+    runs-on: ubuntu-latest
+    defaults:
+     run:
+       shell: bash -l {0}  # needed for conda environment to work
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { name: conda-linux-python3.7-minimum    , requirements: minimum    , python-ver: "3.7" , os: ubuntu-latest }
+          - { name: conda-linux-python3.7            , requirements: pinned     , python-ver: "3.7" , 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-python3.10-optional  , requirements: optional   , python-ver: "3.10", os: ubuntu-latest }
+          - { name: conda-linux-python3.10-upgraded  , requirements: upgraded   , python-ver: "3.10", os: ubuntu-latest }
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/cancel-workflow-action@0.9.1
+        with:
+          access_token: ${{ "{{" }} github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Conda
+        uses: conda-incubator/setup-miniconda@v2
+        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 list
+
+      - name: Install run requirements (minimal)
+        if: ${{ "{{" }} matrix.requirements }} == "minimum"
+        run: |
+          python -m pip install -r requirements-min.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned)
+        if: ${{ "{{" }} matrix.requirements }} == "pinned"
+        run: |
+          python -m pip install -r requirements.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (pinned, optional)
+        if: ${{ "{{" }} matrix.requirements }} == "optional"
+        run: |
+          python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
+          python -m pip install -e .
+
+      - name: Install run requirements (upgraded, optional)
+        if: ${{ "{{" }} matrix.requirements }} == "upgraded"
+        run: |
+          python -m pip install -r requirements-opt.txt -r requirements-dev.txt
+          python -m pip install -U -e .
+
+      - 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 hdmf"
+
+      - 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 hdmf"
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml
new file mode 100644
index 0000000..bf149e0
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml	
@@ -0,0 +1,58 @@
+name: Run code coverage
+on:
+  push:
+  pull_request:
+  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
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+    env:  # used by codecov-action
+      OS: ${{ "{{" }} matrix.os }}
+      PYTHON: '3.10'
+    steps:
+      - name: Cancel any previous incomplete runs
+        uses: styfle/cancel-workflow-action@0.9.1
+        with:
+          all_but_latest: true
+          access_token: ${{ "{{" }} github.token }}
+
+      - uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
+
+      - name: Set up Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements-dev.txt -r requirements.txt
+
+      - name: Install package
+        run: |
+          python -m pip install -e .  # must install in editable mode for coverage to find sources
+          python -m pip list
+
+      - name: Run tests and generate coverage report
+        run: |
+          pytest --cov
+          python -m coverage xml  # codecov uploader requires xml format
+          python -m coverage report -m
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml
new file mode 100644
index 0000000..8cc2fe1
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml	
@@ -0,0 +1,30 @@
+name: Run style check
+on: pull_request
+
+jobs:
+  run-flake8:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Cancel any previous incomplete runs
+      uses: styfle/cancel-workflow-action@0.9.1
+      with:
+        all_but_latest: true
+        access_token: ${{ "{{" }} github.token }}
+
+    - uses: actions/checkout@v3
+      with:
+        submodules: 'recursive'
+
+    - name: Set up Python
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.10'
+
+    - name: Install flake8
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8
+        python -m pip list
+
+    - name: Run flake8
+      run: flake8
diff --git a/{{ cookiecutter.namespace }}/requirements-min.txt b/{{ cookiecutter.namespace }}/requirements-min.txt
new file mode 100644
index 0000000..ebff77f
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/requirements-min.txt	
@@ -0,0 +1,3 @@
+# minimum versions of package dependencies for installation
+pynwb==1.5.0
+hdmf==2.5.6
\ No newline at end of file
diff --git a/{{ cookiecutter.namespace }}/requirements-opt.txt b/{{ cookiecutter.namespace }}/requirements-opt.txt
new file mode 100644
index 0000000..ebff77f
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/requirements-opt.txt	
@@ -0,0 +1,3 @@
+# minimum versions of package dependencies for installation
+pynwb==1.5.0
+hdmf==2.5.6
\ No newline at end of file

From 3fb4150c03e9902fb7ce4b34d58ee83ddbf73510 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Tue, 13 Sep 2022 23:22:24 -0700
Subject: [PATCH 02/21] Fixes

---
 cookiecutter.json                             |  2 +-
 .../.github/workflows/run_all_tests.yml       | 24 +++++++++----------
 .../requirements-dev.txt                      |  1 +
 .../requirements-opt.txt                      |  4 +---
 4 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/cookiecutter.json b/cookiecutter.json
index 1123796..1bb221f 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -4,7 +4,7 @@
   "author": "My Name",
   "email": "my_email@example.com",
   "github_username": "myname",
-  "copyright": "2021, {{ cookiecutter.author }}",
+  "copyright": "2022, {{ cookiecutter.author }}",
   "version": "0.1.0",
   "release": "alpha",
   "license": ["BSD-3", "MIT", "Apache Software License 2.0", "Other"],
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
index 3b93428..0383d08 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -59,25 +59,25 @@ jobs:
           python -m pip check
 
       - name: Install run requirements (minimal)
-        if: ${{ "{{" }} matrix.requirements }} == "minimum"
+        if: ${{ "{{" }} matrix.requirements == "minimum" }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned)
-        if: ${{ "{{" }} matrix.requirements }} == "pinned"
+        if: ${{ "{{" }} matrix.requirements }} == "pinned" }}
         run: |
           python -m pip install -r requirements.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned, optional)
-        if: ${{ "{{" }} matrix.requirements }} == "optional"
+        if: ${{ "{{" }} matrix.requirements == "optional" }}
         run: |
           python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (upgraded, optional)
-        if: ${{ "{{" }} matrix.requirements }} == "upgraded"
+        if: ${{ "{{" }} matrix.requirements == "upgraded" }}
         run: |
           python -m pip install -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -U -e .
@@ -93,7 +93,7 @@ jobs:
           ls -1 dist
 
       - name: Test installation from a wheel (POSIX)
-        if: ${{ "{{" }} matrix.os }} != "windows-latest"
+        if: ${{ "{{" }} matrix.os != "windows-latest" }}
         run: |
           python -m venv test-wheel-env
           source test-wheel-env/bin/activate
@@ -101,7 +101,7 @@ jobs:
           python -c "import hdmf"
 
       - name: Test installation from a wheel (windows)
-        if: ${{ "{{" }} matrix.os }} == "windows-latest"
+        if: ${{ "{{" }} matrix.os == "windows-latest" }}
         run: |
           python -m venv test-wheel-env
           test-wheel-env/Scripts/activate.bat
@@ -150,25 +150,25 @@ jobs:
           conda list
 
       - name: Install run requirements (minimal)
-        if: ${{ "{{" }} matrix.requirements }} == "minimum"
+        if: ${{ "{{" }} matrix.requirements == "minimum" }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned)
-        if: ${{ "{{" }} matrix.requirements }} == "pinned"
+        if: ${{ "{{" }} matrix.requirements == "pinned" }}
         run: |
           python -m pip install -r requirements.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned, optional)
-        if: ${{ "{{" }} matrix.requirements }} == "optional"
+        if: ${{ "{{" }} matrix.requirements == "optional" }}
         run: |
           python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (upgraded, optional)
-        if: ${{ "{{" }} matrix.requirements }} == "upgraded"
+        if: ${{ "{{" }} matrix.requirements == "upgraded" }}
         run: |
           python -m pip install -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -U -e .
@@ -184,7 +184,7 @@ jobs:
           ls -1 dist
 
       - name: Test installation from a wheel (POSIX)
-        if: ${{ "{{" }} matrix.os }} != "windows-latest"
+        if: ${{ "{{" }} matrix.os != "windows-latest" }}
         run: |
           python -m venv test-wheel-env
           source test-wheel-env/bin/activate
@@ -192,7 +192,7 @@ jobs:
           python -c "import hdmf"
 
       - name: Test installation from a wheel (windows)
-        if: ${{ "{{" }} matrix.os }} == "windows-latest"
+        if: ${{ "{{" }} matrix.os == "windows-latest" }}
         run: |
           python -m venv test-wheel-env
           test-wheel-env/Scripts/activate.bat
diff --git a/{{ cookiecutter.namespace }}/requirements-dev.txt b/{{ cookiecutter.namespace }}/requirements-dev.txt
index 1482a06..41ddfdb 100644
--- a/{{ cookiecutter.namespace }}/requirements-dev.txt	
+++ b/{{ cookiecutter.namespace }}/requirements-dev.txt	
@@ -1,5 +1,6 @@
 # pinned dependencies to reproduce an entire development environment to run tests and check code style
 flake8==4.0.1
 pytest==6.2.5
+pytest-cov==3.0.0
 pytest-subtests==0.6.0
 hdmf-docutils==0.4.4
diff --git a/{{ cookiecutter.namespace }}/requirements-opt.txt b/{{ cookiecutter.namespace }}/requirements-opt.txt
index ebff77f..6322050 100644
--- a/{{ cookiecutter.namespace }}/requirements-opt.txt	
+++ b/{{ cookiecutter.namespace }}/requirements-opt.txt	
@@ -1,3 +1 @@
-# minimum versions of package dependencies for installation
-pynwb==1.5.0
-hdmf==2.5.6
\ No newline at end of file
+# pinned optional package dependencies for installation

From 1a28b1020139373d9c5994a9436443c2d7028c39 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Tue, 13 Sep 2022 23:24:22 -0700
Subject: [PATCH 03/21] Fixes

---
 .../.github/workflows/check_external_links.yml                | 1 +
 .../.github/workflows/run_all_tests.yml                       | 4 ++--
 {{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml | 4 +++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
index 2a19133..75b3103 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
@@ -1,5 +1,6 @@
 name: Check Sphinx external links
 on:
+  push:
   pull_request:
   schedule:
     - cron: '0 5 * * *'  # once per day at midnight ET
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
index 0383d08..84073bc 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -1,9 +1,9 @@
 name: Run all tests
 on:
+  push:
+  pull_request:
   schedule:
     - cron: '0 5 * * *'  # once per day at midnight ET
-  pull_request:
-  push:
   workflow_dispatch:
 
 jobs:
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml
index 8cc2fe1..025e472 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml	
@@ -1,5 +1,7 @@
 name: Run style check
-on: pull_request
+on:
+  push:
+  pull_request:
 
 jobs:
   run-flake8:

From baf61ec5f2221ed0243148dca3da009ea8032148 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Tue, 13 Sep 2022 23:29:55 -0700
Subject: [PATCH 04/21] Fix

---
 .../.github/workflows/run_all_tests.yml       | 24 +++++++++----------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
index 84073bc..fabc300 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -59,25 +59,25 @@ jobs:
           python -m pip check
 
       - name: Install run requirements (minimal)
-        if: ${{ "{{" }} matrix.requirements == "minimum" }}
+        if: ${{ "{{" }} matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned)
-        if: ${{ "{{" }} matrix.requirements }} == "pinned" }}
+        if: ${{ "{{" }} matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned, optional)
-        if: ${{ "{{" }} matrix.requirements == "optional" }}
+        if: ${{ "{{" }} matrix.requirements == 'optional' }}
         run: |
           python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (upgraded, optional)
-        if: ${{ "{{" }} matrix.requirements == "upgraded" }}
+        if: ${{ "{{" }} matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -U -e .
@@ -93,7 +93,7 @@ jobs:
           ls -1 dist
 
       - name: Test installation from a wheel (POSIX)
-        if: ${{ "{{" }} matrix.os != "windows-latest" }}
+        if: ${{ "{{" }} matrix.os != 'windows-latest' }}
         run: |
           python -m venv test-wheel-env
           source test-wheel-env/bin/activate
@@ -101,7 +101,7 @@ jobs:
           python -c "import hdmf"
 
       - name: Test installation from a wheel (windows)
-        if: ${{ "{{" }} matrix.os == "windows-latest" }}
+        if: ${{ "{{" }} matrix.os == 'windows-latest' }}
         run: |
           python -m venv test-wheel-env
           test-wheel-env/Scripts/activate.bat
@@ -150,25 +150,25 @@ jobs:
           conda list
 
       - name: Install run requirements (minimal)
-        if: ${{ "{{" }} matrix.requirements == "minimum" }}
+        if: ${{ "{{" }} matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned)
-        if: ${{ "{{" }} matrix.requirements == "pinned" }}
+        if: ${{ "{{" }} matrix.requirements == 'pinned' }}
         run: |
           python -m pip install -r requirements.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (pinned, optional)
-        if: ${{ "{{" }} matrix.requirements == "optional" }}
+        if: ${{ "{{" }} matrix.requirements == 'optional' }}
         run: |
           python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (upgraded, optional)
-        if: ${{ "{{" }} matrix.requirements == "upgraded" }}
+        if: ${{ "{{" }} matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -U -e .
@@ -184,7 +184,7 @@ jobs:
           ls -1 dist
 
       - name: Test installation from a wheel (POSIX)
-        if: ${{ "{{" }} matrix.os != "windows-latest" }}
+        if: ${{ "{{" }} matrix.os != 'windows-latest' }}
         run: |
           python -m venv test-wheel-env
           source test-wheel-env/bin/activate
@@ -192,7 +192,7 @@ jobs:
           python -c "import hdmf"
 
       - name: Test installation from a wheel (windows)
-        if: ${{ "{{" }} matrix.os == "windows-latest" }}
+        if: ${{ "{{" }} matrix.os == 'windows-latest' }}
         run: |
           python -m venv test-wheel-env
           test-wheel-env/Scripts/activate.bat

From dc63d989c1f5829f6949ab91b526152f979e745f Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Tue, 13 Sep 2022 23:32:39 -0700
Subject: [PATCH 05/21] Fix wheel check

---
 .../.github/workflows/run_all_tests.yml                   | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
index fabc300..d0667fa 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -98,7 +98,7 @@ jobs:
           python -m venv test-wheel-env
           source test-wheel-env/bin/activate
           python -m pip install dist/*-none-any.whl
-          python -c "import hdmf"
+          python -c "import {{ cookiecutter.py_pkg_name }}"
 
       - name: Test installation from a wheel (windows)
         if: ${{ "{{" }} matrix.os == 'windows-latest' }}
@@ -106,7 +106,7 @@ jobs:
           python -m venv test-wheel-env
           test-wheel-env/Scripts/activate.bat
           python -m pip install dist/*-none-any.whl
-          python -c "import hdmf"
+          python -c "import {{ cookiecutter.py_pkg_name }}"
 
   run-all-tests-on-conda:
     name: ${{ "{{" }} matrix.name }}
@@ -189,7 +189,7 @@ jobs:
           python -m venv test-wheel-env
           source test-wheel-env/bin/activate
           python -m pip install dist/*-none-any.whl
-          python -c "import hdmf"
+          python -c "import {{ cookiecutter.py_pkg_name }}"
 
       - name: Test installation from a wheel (windows)
         if: ${{ "{{" }} matrix.os == 'windows-latest' }}
@@ -197,4 +197,4 @@ jobs:
           python -m venv test-wheel-env
           test-wheel-env/Scripts/activate.bat
           python -m pip install dist/*-none-any.whl
-          python -c "import hdmf"
+          python -c "import {{ cookiecutter.py_pkg_name }}"

From 0425b28de4a8fe61b6fe266d8041505b97d6e21e Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Wed, 14 Sep 2022 18:22:20 -0700
Subject: [PATCH 06/21] Fix tests

---
 .../.github/workflows/check_external_links.yml    |  4 +++-
 {{ cookiecutter.namespace }}/requirements.txt     |  4 ++--
 {{ cookiecutter.namespace }}/setup.py             |  2 +-
 .../src/pynwb/tests/test_tetrodeseries.py         | 15 +++------------
 4 files changed, 9 insertions(+), 16 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
index 75b3103..dccac48 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
@@ -32,4 +32,6 @@ jobs:
           python -m pip install .
 
       - name: Check Sphinx external links
-        run: sphinx-build -b linkcheck ./docs/source ./test_build
+        run: |
+          cd docs  # run_doc_autogen assumes spec is found in ../spec/
+          sphinx-build -b linkcheck ./source ./test_build
diff --git a/{{ cookiecutter.namespace }}/requirements.txt b/{{ cookiecutter.namespace }}/requirements.txt
index 1709b58..43db395 100644
--- a/{{ cookiecutter.namespace }}/requirements.txt	
+++ b/{{ cookiecutter.namespace }}/requirements.txt	
@@ -1,3 +1,3 @@
 # pinned dependencies to reproduce a working development environment
-hdmf==3.1.1
-pynwb==2.0.0
+hdmf==3.4.3
+pynwb==2.1.0
diff --git a/{{ cookiecutter.namespace }}/setup.py b/{{ cookiecutter.namespace }}/setup.py
index 771c1ff..507c211 100644
--- a/{{ cookiecutter.namespace }}/setup.py	
+++ b/{{ cookiecutter.namespace }}/setup.py	
@@ -31,7 +31,7 @@
     'url': '',
     'license': '{{ cookiecutter.license }}',
     'install_requires': [
-        'pynwb>=1.5.0,<3',
+        'pynwb>=2.1.0,<3',
         'hdmf>=2.5.6,<4',
     ],
     'packages': find_packages('src/pynwb', exclude=["tests", "tests.*"]),
diff --git a/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py b/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py
index b058e5a..79d4e86 100644
--- a/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py	
+++ b/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py	
@@ -31,10 +31,6 @@ def set_up_nwbfile():
 
     for i in np.arange(10.):
         nwbfile.add_electrode(
-            x=i,
-            y=i,
-            z=i,
-            imp=np.nan,
             location='location',
             filtering='filtering',
             group=electrode_group
@@ -56,7 +52,7 @@ def test_constructor(self):
             description='all the electrodes'
         )
 
-        data = np.random.rand(100, 3)
+        data = np.random.rand(100, 10)
         tetrode_series = TetrodeSeries(
             name='name',
             description='description',
@@ -95,7 +91,7 @@ def test_roundtrip(self):
             description='all the electrodes'
         )
 
-        data = np.random.rand(100, 3)
+        data = np.random.rand(100, 10)
         tetrode_series = TetrodeSeries(
             name='TetrodeSeries',
             description='description',
@@ -134,14 +130,9 @@ def setUpContainer(self):
         self.table = get_electrode_table()  # manually create a table of electrodes
         for i in np.arange(10.):
             self.table.add_row(
-                x=i,
-                y=i,
-                z=i,
-                imp=np.nan,
                 location='location',
                 filtering='filtering',
                 group=self.group,
-                group_name='electrode_group'
             )
 
         all_electrodes = DynamicTableRegion(
@@ -151,7 +142,7 @@ def setUpContainer(self):
             table=self.table
         )
 
-        data = np.random.rand(100, 3)
+        data = np.random.rand(100, 10)
         tetrode_series = TetrodeSeries(
             name='name',
             description='description',

From 6538265dd8fed1cee86b483f49e024698911a3d8 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Wed, 14 Sep 2022 18:23:20 -0700
Subject: [PATCH 07/21] Update min reqs

---
 {{ cookiecutter.namespace }}/requirements-min.txt | 5 +++--
 {{ cookiecutter.namespace }}/setup.py             | 2 +-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/requirements-min.txt b/{{ cookiecutter.namespace }}/requirements-min.txt
index ebff77f..da86d23 100644
--- a/{{ cookiecutter.namespace }}/requirements-min.txt	
+++ b/{{ cookiecutter.namespace }}/requirements-min.txt	
@@ -1,3 +1,4 @@
 # minimum versions of package dependencies for installation
-pynwb==1.5.0
-hdmf==2.5.6
\ No newline at end of file
+# NOTE: it may be possible to relax these minimum requirements
+pynwb==2.1.0
+hdmf==3.4.3
\ No newline at end of file
diff --git a/{{ cookiecutter.namespace }}/setup.py b/{{ cookiecutter.namespace }}/setup.py
index 507c211..1a403b7 100644
--- a/{{ cookiecutter.namespace }}/setup.py	
+++ b/{{ cookiecutter.namespace }}/setup.py	
@@ -32,7 +32,7 @@
     'license': '{{ cookiecutter.license }}',
     'install_requires': [
         'pynwb>=2.1.0,<3',
-        'hdmf>=2.5.6,<4',
+        'hdmf>=3.4.3,<4',
     ],
     'packages': find_packages('src/pynwb', exclude=["tests", "tests.*"]),
     'package_dir': {'': 'src/pynwb'},

From cfb1d4b371d2c37a88a7b2d1efe97dfc53c5a088 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Wed, 14 Sep 2022 18:26:25 -0700
Subject: [PATCH 08/21] Fix test

---
 .../src/pynwb/tests/test_tetrodeseries.py                      | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py b/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py
index 79d4e86..59df39d 100644
--- a/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py	
+++ b/{{ cookiecutter.namespace }}/src/pynwb/tests/test_tetrodeseries.py	
@@ -32,7 +32,6 @@ def set_up_nwbfile():
     for i in np.arange(10.):
         nwbfile.add_electrode(
             location='location',
-            filtering='filtering',
             group=electrode_group
         )
 
@@ -131,8 +130,8 @@ def setUpContainer(self):
         for i in np.arange(10.):
             self.table.add_row(
                 location='location',
-                filtering='filtering',
                 group=self.group,
+                group_name='electrode_group'  # necessary when using add_row instead of NWBFile.add_electrode
             )
 
         all_electrodes = DynamicTableRegion(

From 86df7a340b7e067c73a84b669db8fcde42f1c71a Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Wed, 14 Sep 2022 22:52:57 -0700
Subject: [PATCH 09/21] Fix deprecations

---
 {{ cookiecutter.namespace }}/setup.cfg | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/setup.cfg b/{{ cookiecutter.namespace }}/setup.cfg
index f6c4008..f059e12 100644
--- a/{{ cookiecutter.namespace }}/setup.cfg	
+++ b/{{ cookiecutter.namespace }}/setup.cfg	
@@ -1,4 +1,4 @@
-[wheel]
+[bdist_wheel]
 universal = 1
 
 [flake8]
@@ -14,4 +14,4 @@ exclude =
   versioneer.py
 
 [metadata]
-description-file = README.md
+description_file = README.md

From 93e67daa38f9e9fbf11247731afae2a4ccb9e6c8 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 21 Oct 2023 14:37:12 -0700
Subject: [PATCH 10/21] Update check_external_links.yml

---
 .../.github/workflows/check_external_links.yml            | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
index dccac48..4e5ed11 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+        uses: styfle/cancel-workflow-action@0.12.0
         with:
           all_but_latest: true
           access_token: ${{ "{{" }} github.token }}
@@ -21,14 +21,14 @@ jobs:
           submodules: 'recursive'
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install Sphinx dependencies and package
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-dev.txt -r requirements.txt
+          python -m pip install -r requirements-dev.txt
           python -m pip install .
 
       - name: Check Sphinx external links

From d3e97687f41c2d9f866a78d71c620e383f969e67 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 21 Oct 2023 14:37:41 -0700
Subject: [PATCH 11/21] Update check_external_links.yml

---
 .../.github/workflows/check_external_links.yml                   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
index 4e5ed11..e48986c 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
@@ -19,6 +19,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # tags are required for versioneer to determine the version
 
       - name: Set up Python
         uses: actions/setup-python@v4

From f48972941c68adf89033814b23ac5fb6711c16d9 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 21 Oct 2023 14:38:34 -0700
Subject: [PATCH 12/21] Update check_external_links.yml

---
 .../.github/workflows/check_external_links.yml                  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
index e48986c..e00f682 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
@@ -29,7 +29,7 @@ jobs:
       - 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 -r requirements-dev.txt -r requirements-opt.txt
           python -m pip install .
 
       - name: Check Sphinx external links

From b0879de9e7d8df94f11c58ffa34e498baf921b00 Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 21 Oct 2023 14:41:05 -0700
Subject: [PATCH 13/21] Update requirements-min.txt

---
 {{ cookiecutter.namespace }}/requirements-min.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/requirements-min.txt b/{{ cookiecutter.namespace }}/requirements-min.txt
index da86d23..b13eb8f 100644
--- a/{{ cookiecutter.namespace }}/requirements-min.txt	
+++ b/{{ cookiecutter.namespace }}/requirements-min.txt	
@@ -1,4 +1,4 @@
 # minimum versions of package dependencies for installation
 # NOTE: it may be possible to relax these minimum requirements
-pynwb==2.1.0
-hdmf==3.4.3
\ No newline at end of file
+pynwb==2.5.0
+hdmf==3.11.0

From 671c0808f3f426c79fccd73fe2e6b7b0be7399ca Mon Sep 17 00:00:00 2001
From: Ryan Ly <rly@lbl.gov>
Date: Sat, 21 Oct 2023 14:41:38 -0700
Subject: [PATCH 14/21] Update pyproject.toml

---
 {{ cookiecutter.namespace }}/pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/{{ cookiecutter.namespace }}/pyproject.toml b/{{ cookiecutter.namespace }}/pyproject.toml
index 1cbec14..d0e2060 100644
--- a/{{ cookiecutter.namespace }}/pyproject.toml	
+++ b/{{ cookiecutter.namespace }}/pyproject.toml	
@@ -38,7 +38,8 @@ keywords = [
     'ndx-extension',
 ]
 dependencies = [
-    "pynwb>=2",
+    "pynwb>=2.5.0",
+    "hdmf>=3.11.0",
 ]
 
 # TODO: add URLs before release

From b9f40af1fb8989fb265c51c2c1d0b5806f1e7541 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sun, 22 Oct 2023 08:43:53 -0700
Subject: [PATCH 15/21] Update CI

---
 .../workflows/check_external_links.yml        |  3 +-
 .../.github/workflows/codespell.yml           | 15 ++++
 .../.github/workflows/ruff.yml                | 15 ++++
 .../.github/workflows/run_all_tests.yml       | 85 ++++++++-----------
 .../.github/workflows/run_coverage.yml        | 11 +--
 .../.github/workflows/run_flake8.yml          | 32 -------
 .../requirements-min.txt                      |  1 +
 .../requirements-opt.txt                      |  1 -
 8 files changed, 73 insertions(+), 90 deletions(-)
 create mode 100644 {{ cookiecutter.namespace }}/.github/workflows/codespell.yml
 create mode 100644 {{ cookiecutter.namespace }}/.github/workflows/ruff.yml
 delete mode 100644 {{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml
 delete mode 100644 {{ cookiecutter.namespace }}/requirements-opt.txt

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml
index e00f682..cfc9050 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/check_external_links.yml	
@@ -8,6 +8,7 @@ on:
 
 jobs:
   check-external-links:
+    name: Check for broken Sphinx external links
     runs-on: ubuntu-latest
     steps:
       - name: Cancel any previous incomplete runs
@@ -29,7 +30,7 @@ jobs:
       - name: Install Sphinx dependencies and package
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-dev.txt -r requirements-opt.txt
+          python -m pip install -r requirements-dev.txt
           python -m pip install .
 
       - name: Check Sphinx external links
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/codespell.yml b/{{ cookiecutter.namespace }}/.github/workflows/codespell.yml
new file mode 100644
index 0000000..71317d4
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/.github/workflows/codespell.yml	
@@ -0,0 +1,15 @@
+name: Codespell
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
\ No newline at end of file
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/ruff.yml b/{{ cookiecutter.namespace }}/.github/workflows/ruff.yml
new file mode 100644
index 0000000..4679ceb
--- /dev/null
+++ b/{{ cookiecutter.namespace }}/.github/workflows/ruff.yml	
@@ -0,0 +1,15 @@
+name: Ruff
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  ruff:
+    name: Check for style errors and common problems
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Ruff
+        uses: chartboost/ruff-action@v1
\ No newline at end of file
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
index d0667fa..365c373 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -8,10 +8,6 @@ on:
 
 jobs:
   run-all-tests:
-    # the only differences between this job and "run_tests.yml" is the "strategy.matrix.include" and the upload
-    # distributions step.
-    # GitHub Actions does not yet support YAML anchors, easily reusable components, or easy dynamic matrix
-    # configurations based on the github event, so this job is duplicated for the most part
     name: ${{ "{{" }} matrix.name }}
     runs-on: ${{ "{{" }} matrix.os }}
     defaults:
@@ -21,34 +17,41 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: linux-python3.7-minimum      , requirements: minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: linux-python3.7              , requirements: pinned     , python-ver: "3.7" , os: ubuntu-latest }
+          - { 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-python3.10-optional    , requirements: optional   , python-ver: "3.10", os: ubuntu-latest }
-          - { name: linux-python3.10-upgraded    , requirements: upgraded   , python-ver: "3.10", os: ubuntu-latest }
-          - { name: windows-python3.7-minimum    , requirements: minimum    , python-ver: "3.7" , os: windows-latest }
-          - { name: windows-python3.7            , requirements: pinned     , python-ver: "3.7" , os: windows-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-python3.10-optional  , requirements: optional   , python-ver: "3.10", os: windows-latest }
-          - { name: windows-python3.10-upgraded  , requirements: upgraded   , python-ver: "3.10", os: windows-latest }
-          - { name: macos-python3.7-minimum      , requirements: pinned     , python-ver: "3.7" , os: macos-latest }
-          - { name: macos-python3.7              , requirements: pinned     , python-ver: "3.7" , os: macos-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-python3.10-optional    , requirements: optional   , python-ver: "3.10", os: macos-latest }
-          - { name: macos-python3.10-upgraded    , requirements: upgraded   , 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: Cancel non-latest runs
+        uses: styfle/cancel-workflow-action@0.11.0
+        with:
+          all_but_latest: true
+          access_token: ${{ github.token }}
+
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ "{{" }} matrix.python-ver }}
 
@@ -58,7 +61,7 @@ jobs:
           python -m pip list
           python -m pip check
 
-      - name: Install run requirements (minimal)
+      - name: Install run requirements (minimum)
         if: ${{ "{{" }} matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
@@ -67,19 +70,12 @@ jobs:
       - name: Install run requirements (pinned)
         if: ${{ "{{" }} matrix.requirements == 'pinned' }}
         run: |
-          python -m pip install -r requirements.txt -r requirements-dev.txt
+          python -m pip install -r requirements-dev.txt
           python -m pip install -e .
 
-      - name: Install run requirements (pinned, optional)
-        if: ${{ "{{" }} matrix.requirements == 'optional' }}
-        run: |
-          python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
-          python -m pip install -e .
-
-      - name: Install run requirements (upgraded, optional)
+      - name: Install run requirements (upgraded)
         if: ${{ "{{" }} matrix.requirements == 'upgraded' }}
         run: |
-          python -m pip install -r requirements-opt.txt -r requirements-dev.txt
           python -m pip install -U -e .
 
       - name: Run tests
@@ -118,22 +114,23 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { name: conda-linux-python3.7-minimum    , requirements: minimum    , python-ver: "3.7" , os: ubuntu-latest }
-          - { name: conda-linux-python3.7            , requirements: pinned     , python-ver: "3.7" , os: ubuntu-latest }
+          - { 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-python3.10-optional  , requirements: optional   , python-ver: "3.10", os: ubuntu-latest }
-          - { name: conda-linux-python3.10-upgraded  , requirements: upgraded   , 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: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           access_token: ${{ "{{" }} github.token }}
 
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
 
       - name: Set up Conda
         uses: conda-incubator/setup-miniconda@v2
@@ -147,9 +144,10 @@ jobs:
         run: |
           conda config --set always_yes yes --set changeps1 no
           conda info
-          conda list
+          conda config --show-sources
+          conda list --show-channel-urls
 
-      - name: Install run requirements (minimal)
+      - name: Install run requirements (minimum)
         if: ${{ "{{" }} matrix.requirements == 'minimum' }}
         run: |
           python -m pip install -r requirements-min.txt -r requirements-dev.txt
@@ -161,16 +159,10 @@ jobs:
           python -m pip install -r requirements.txt -r requirements-dev.txt
           python -m pip install -e .
 
-      - name: Install run requirements (pinned, optional)
-        if: ${{ "{{" }} matrix.requirements == 'optional' }}
-        run: |
-          python -m pip install -r requirements.txt -r requirements-opt.txt -r requirements-dev.txt
-          python -m pip install -e .
-
-      - name: Install run requirements (upgraded, optional)
+      - name: Install run requirements (upgraded)
         if: ${{ "{{" }} matrix.requirements == 'upgraded' }}
         run: |
-          python -m pip install -r requirements-opt.txt -r requirements-dev.txt
+          python -m pip install -r requirements-dev.txt
           python -m pip install -U -e .
 
       - name: Run tests
@@ -184,17 +176,8 @@ jobs:
           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 {{ cookiecutter.py_pkg_name }}"
-
-      - 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 {{ cookiecutter.py_pkg_name }}"
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml
index bf149e0..b3b9caf 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml	
@@ -19,10 +19,10 @@ jobs:
         os: [ubuntu-latest, windows-latest, macos-latest]
     env:  # used by codecov-action
       OS: ${{ "{{" }} matrix.os }}
-      PYTHON: '3.10'
+      PYTHON: '3.11'
     steps:
       - name: Cancel any previous incomplete runs
-        uses: styfle/cancel-workflow-action@0.9.1
+        uses: styfle/cancel-workflow-action@0.11.0
         with:
           all_but_latest: true
           access_token: ${{ "{{" }} github.token }}
@@ -30,16 +30,17 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: 'recursive'
+          fetch-depth: 0  # fetch tags
 
       - name: Set up Python
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: ${{ "{{" }} env.PYTHON }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install -r requirements-dev.txt -r requirements.txt
+          python -m pip install -r requirements-dev.txt
 
       - name: Install package
         run: |
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml
deleted file mode 100644
index 025e472..0000000
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_flake8.yml	
+++ /dev/null
@@ -1,32 +0,0 @@
-name: Run style check
-on:
-  push:
-  pull_request:
-
-jobs:
-  run-flake8:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Cancel any previous incomplete runs
-      uses: styfle/cancel-workflow-action@0.9.1
-      with:
-        all_but_latest: true
-        access_token: ${{ "{{" }} github.token }}
-
-    - uses: actions/checkout@v3
-      with:
-        submodules: 'recursive'
-
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.10'
-
-    - name: Install flake8
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install flake8
-        python -m pip list
-
-    - name: Run flake8
-      run: flake8
diff --git a/{{ cookiecutter.namespace }}/requirements-min.txt b/{{ cookiecutter.namespace }}/requirements-min.txt
index b13eb8f..5730ae4 100644
--- a/{{ cookiecutter.namespace }}/requirements-min.txt	
+++ b/{{ cookiecutter.namespace }}/requirements-min.txt	
@@ -1,4 +1,5 @@
 # minimum versions of package dependencies for installation
+# these should match the minimum versions specified in pyproject.toml
 # NOTE: it may be possible to relax these minimum requirements
 pynwb==2.5.0
 hdmf==3.11.0
diff --git a/{{ cookiecutter.namespace }}/requirements-opt.txt b/{{ cookiecutter.namespace }}/requirements-opt.txt
deleted file mode 100644
index 6322050..0000000
--- a/{{ cookiecutter.namespace }}/requirements-opt.txt	
+++ /dev/null
@@ -1 +0,0 @@
-# pinned optional package dependencies for installation

From 985f06c5e2a0cd6216fff74682e0c1ad2ac6f3d4 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sun, 22 Oct 2023 08:45:41 -0700
Subject: [PATCH 16/21] Fix

---
 .../.github/workflows/run_all_tests.yml                         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
index 365c373..2b7d6da 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -43,7 +43,7 @@ jobs:
         uses: styfle/cancel-workflow-action@0.11.0
         with:
           all_but_latest: true
-          access_token: ${{ github.token }}
+          access_token: ${{ "{{" }} github.token }}
 
       - uses: actions/checkout@v3
         with:

From e0755897b84798fc75be9ca5d2de5d062c34dd91 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sun, 22 Oct 2023 08:50:18 -0700
Subject: [PATCH 17/21] Fix

---
 {{ cookiecutter.namespace }}/pyproject.toml       | 2 +-
 {{ cookiecutter.namespace }}/requirements-min.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/pyproject.toml b/{{ cookiecutter.namespace }}/pyproject.toml
index d0e2060..15f9215 100644
--- a/{{ cookiecutter.namespace }}/pyproject.toml	
+++ b/{{ cookiecutter.namespace }}/pyproject.toml	
@@ -39,7 +39,7 @@ keywords = [
 ]
 dependencies = [
     "pynwb>=2.5.0",
-    "hdmf>=3.11.0",
+    "hdmf>=3.10.0",
 ]
 
 # TODO: add URLs before release
diff --git a/{{ cookiecutter.namespace }}/requirements-min.txt b/{{ cookiecutter.namespace }}/requirements-min.txt
index 5730ae4..695410a 100644
--- a/{{ cookiecutter.namespace }}/requirements-min.txt	
+++ b/{{ cookiecutter.namespace }}/requirements-min.txt	
@@ -2,4 +2,4 @@
 # these should match the minimum versions specified in pyproject.toml
 # NOTE: it may be possible to relax these minimum requirements
 pynwb==2.5.0
-hdmf==3.11.0
+hdmf==3.10.0

From c8337cb68795aaf47517328573a6b147925e6f03 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sun, 22 Oct 2023 09:00:17 -0700
Subject: [PATCH 18/21] Update CI

---
 .github/workflows/codespell.yml | 15 +++++++++++++++
 .github/workflows/run_tests.yml | 20 +++++++++++---------
 2 files changed, 26 insertions(+), 9 deletions(-)
 create mode 100644 .github/workflows/codespell.yml

diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml
new file mode 100644
index 0000000..71317d4
--- /dev/null
+++ b/.github/workflows/codespell.yml
@@ -0,0 +1,15 @@
+name: Codespell
+on:
+  push:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
\ No newline at end of file
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index c7d6764..fe15bd2 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -19,15 +19,17 @@ jobs:
       fail-fast: false
       matrix:
         include:
-        - { name: linux-python3.8   , os: ubuntu-latest , python-ver: "3.8"  }
-        - { name: linux-python3.12  , os: ubuntu-latest , python-ver: "3.12" }
-        - { name: windows-python3.8 , os: windows-latest, python-ver: "3.8"  }
-        - { name: windows-python3.9 , os: windows-latest, python-ver: "3.9"  }
-        - { name: windows-python3.10, os: windows-latest, python-ver: "3.10" }
-        - { name: windows-python3.11, os: windows-latest, python-ver: "3.11" }
-        - { name: windows-python3.12, os: windows-latest, python-ver: "3.12" }
-        - { name: macos-python3.8   , os: macos-latest  , python-ver: "3.8"  }
-        - { name: macos-python3.12  , os: macos-latest  , python-ver: "3.12" }
+        - { name: linux-python3.8    , os: ubuntu-latest  , python-ver: "3.8"  }
+        - { name: linux-python3.11   , os: ubuntu-latest  , python-ver: "3.11" }
+        - { name: linux-python3.12   , os: ubuntu-latest  , python-ver: "3.12" }
+        - { name: windows-python3.8  , os: windows-latest , python-ver: "3.8"  }
+        - { name: windows-python3.9  , os: windows-latest , python-ver: "3.9"  }
+        - { name: windows-python3.10 , os: windows-latest , python-ver: "3.10" }
+        - { name: windows-python3.11 , os: windows-latest , python-ver: "3.11" }
+        - { name: windows-python3.12 , os: windows-latest , python-ver: "3.12" }
+        - { name: macos-python3.8    , os: macos-latest   , python-ver: "3.8"  }
+        - { name: macos-python3.11   , os: macos-latest   , python-ver: "3.11" }
+        - { name: macos-python3.12   , os: macos-latest   , python-ver: "3.12" }
     steps:
     - name: Cancel non-latest runs
       uses: styfle/cancel-workflow-action@0.12.0

From 7a2b300278c3833dd91924288e8244b7942036d2 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sun, 22 Oct 2023 09:04:19 -0700
Subject: [PATCH 19/21] Update doc

---
 {{ cookiecutter.namespace }}/NEXTSTEPS.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/{{ cookiecutter.namespace }}/NEXTSTEPS.md b/{{ cookiecutter.namespace }}/NEXTSTEPS.md
index b92e465..8e23caf 100644
--- a/{{ cookiecutter.namespace }}/NEXTSTEPS.md	
+++ b/{{ cookiecutter.namespace }}/NEXTSTEPS.md	
@@ -69,6 +69,11 @@ your extension.
 
 8. Update the `CHANGELOG.md` to document changes to your extension.
 
+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; check for spelling errors; check for style errors; and check for broken
+links in the documentation.
+
 8. Make a release for the extension on GitHub with the version number specified. e.g. if version is {{ cookiecutter.version }}, then this page should exist: https://github.com/{{ github_username_list[0] }}/{{ cookiecutter.namespace }}/releases/tag/{{ cookiecutter.version }} . 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/).

From b6e6f63d287f3ab14f9eb159df9707fa8d61cbee Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sun, 22 Oct 2023 10:19:19 -0700
Subject: [PATCH 20/21] Update CI

---
 .../.github/workflows/run_all_tests.yml                  | 3 ++-
 .../.github/workflows/run_coverage.yml                   | 9 +++++----
 {{ cookiecutter.namespace }}/requirements-dev.txt        | 2 ++
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml
index 2b7d6da..177ac4b 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml	
@@ -76,6 +76,7 @@ jobs:
       - name: Install run requirements (upgraded)
         if: ${{ "{{" }} matrix.requirements == 'upgraded' }}
         run: |
+          python -m pip install -r requirements-dev.txt
           python -m pip install -U -e .
 
       - name: Run tests
@@ -156,7 +157,7 @@ jobs:
       - name: Install run requirements (pinned)
         if: ${{ "{{" }} matrix.requirements == 'pinned' }}
         run: |
-          python -m pip install -r requirements.txt -r requirements-dev.txt
+          python -m pip install -r requirements-dev.txt
           python -m pip install -e .
 
       - name: Install run requirements (upgraded)
diff --git a/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml b/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml
index b3b9caf..80483e1 100644
--- a/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml	
+++ b/{{ cookiecutter.namespace }}/.github/workflows/run_coverage.yml	
@@ -53,7 +53,8 @@ jobs:
           python -m coverage xml  # codecov uploader requires xml format
           python -m coverage report -m
 
-      - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v3
-        with:
-          fail_ci_if_error: true
+      # TODO uncomment after setting up repo on codecov.io
+      # - name: Upload coverage to Codecov
+      #   uses: codecov/codecov-action@v3
+      #   with:
+      #     fail_ci_if_error: true
diff --git a/{{ cookiecutter.namespace }}/requirements-dev.txt b/{{ cookiecutter.namespace }}/requirements-dev.txt
index 66463c2..7655a0a 100644
--- a/{{ cookiecutter.namespace }}/requirements-dev.txt	
+++ b/{{ cookiecutter.namespace }}/requirements-dev.txt	
@@ -3,8 +3,10 @@
 black==23.9.1
 codespell==2.2.6
 coverage==7.3.2
+hdmf==3.10.0
 hdmf-docutils==0.4.5
 pre-commit==3.4.0
+pynwb==2.5.0
 pytest==7.4.2
 pytest-cov==4.1.0
 python-dateutil==2.8.2

From 8a4853cafd464390f602ab8064ba6b3cec5c2c42 Mon Sep 17 00:00:00 2001
From: rly <rly@lbl.gov>
Date: Sun, 22 Oct 2023 10:41:08 -0700
Subject: [PATCH 21/21] Update doc

---
 {{ cookiecutter.namespace }}/NEXTSTEPS.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/{{ cookiecutter.namespace }}/NEXTSTEPS.md b/{{ cookiecutter.namespace }}/NEXTSTEPS.md
index 8e23caf..816110d 100644
--- a/{{ cookiecutter.namespace }}/NEXTSTEPS.md	
+++ b/{{ cookiecutter.namespace }}/NEXTSTEPS.md	
@@ -71,8 +71,10 @@ your extension.
 
 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; check for spelling errors; check for style errors; and check for broken
-links in the documentation.
+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`.
 
 8. Make a release for the extension on GitHub with the version number specified. e.g. if version is {{ cookiecutter.version }}, then this page should exist: https://github.com/{{ github_username_list[0] }}/{{ cookiecutter.namespace }}/releases/tag/{{ cookiecutter.version }} . For instructions on how to make a release on GitHub see [here](https://help.github.com/en/github/administering-a-repository/creating-releases).