Fix bundled "upgraded" workflow to actually update dependencies (#89)

{{ cookiecutter.namespace }}/.github/workflows/run_all_tests.yml

@@ -73,7 +73,8 @@ jobs:
         if: ${{ "{{" }} matrix.requirements == 'upgraded' }}
         run: |
           python -m pip install -r requirements-dev.txt
-          python -m pip install -U .
+          # force upgrade of all dependencies to latest versions within allowed range
+          python -m pip install -U --upgrade-strategy eager .
 
       - name: Run tests
         run: |

{{ cookiecutter.namespace }}/pyproject.toml

@@ -38,8 +38,8 @@ keywords = [
     'ndx-extension',
 ]
 dependencies = [
-    "pynwb>=2.6.0",
-    "hdmf>=3.13.0",
+    "pynwb>=2.8.0",
+    "hdmf>=3.14.1",
 ]
 
 # TODO: add URLs before release

{{ cookiecutter.namespace }}/requirements-dev.txt

@@ -1,16 +1,15 @@
 # pinned dependencies to reproduce an entire development environment to
 # run tests, check code style, and generate documentation
-black==24.3.0
-codespell==2.2.6
-coverage==7.4.4
-hdmf==3.13.0
+black==24.4.2
+codespell==2.3.0
+coverage==7.5.4
+hdmf==3.14.1
 hdmf-docutils==0.4.7
 nwbwidgets==0.11.3
-pre-commit==3.5.0
-pynwb==2.6.0
-pytest==8.1.1
+pre-commit==3.5.0  # latest pre-commit does not support py3.8
+pynwb==2.8.0
+pytest==8.2.2
 pytest-cov==5.0.0
 pytest-subtests==0.12.1
 python-dateutil==2.8.2
-ruff==0.3.4
-tox==4.14.2
+ruff==0.4.10