Merge branch 'dev' into better_shape_error_message

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1 +1 @@
-src/hdmf/_version.py export-subst
+.git_archival.txt export-subst

.github/CODE_OF_CONDUCT.md

@@ -44,5 +44,3 @@ This Code of Conduct is adapted from the [Contributor Covenant][homepage], versi
 
 [homepage]: http://contributor-covenant.org
 [version]: http://contributor-covenant.org/version/1/4/
-
-

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -35,9 +35,7 @@ body:
         Please copy and paste the full traceback produced by the error.
 
         This section will be automatically formatted into code, so no need for backticks.
-      render: shell
-    validations:
-      required: true
+      render: pytb
   - type: dropdown
     id: os
     attributes:
@@ -62,10 +60,10 @@ body:
     attributes:
       label: Python Version
       options:
-        - "3.7"
         - "3.8"
         - "3.9"
         - "3.10"
+        - "3.11"
     validations:
       required: true
   - type: textarea

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -2,19 +2,19 @@ Prepare for release of HDMF [version]
 
 ### Before merging:
 - [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`,
-  `requirements-doc.txt`, `requirements-min.txt`, `requirements-opt.txt`, `setup.py` as needed
-  See https://requires.io/github/hdmf-dev/hdmf/requirements/?branch=dev
+  `requirements-doc.txt`, `requirements-opt.txt`, and `environment-ros3.yml` to the latest versions,
+  and 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 `setup.py` as needed
+- [ ] Update `pyproject.toml` as needed
 - [ ] Update `README.rst` as needed
 - [ ] Update `src/hdmf/common/hdmf-common-schema` submodule as needed. Check the version number and commit SHA manually
 - [ ] Update changelog (set release date) in `CHANGELOG.md` and any other docs as needed
 - [ ] Run tests locally including gallery tests, and inspect all warnings and outputs
   (`pytest && python test_gallery.py`)
 - [ ] Run PyNWB tests locally including gallery and validation tests, and inspect all warnings and outputs
   (`cd pynwb; python test.py -v > out.txt 2>&1`)
-- [ ] Test docs locally (`make clean`, `make html`)
+- [ ] Test docs locally and inspect all warnings and outputs `cd docs; make clean && make html`
 - [ ] Push changes to this PR and make sure all PRs to be included in this release have been merged
 - [ ] Check that the readthedocs build for this PR succeeds (build latest to pull the new branch, then activate and
   build docs for new branch): https://readthedocs.org/projects/hdmf/builds/

.github/pull_request_template.md

@@ -12,6 +12,6 @@ Show how to reproduce the new behavior (can be a bug fix or a new feature)
 - [ ] Did you update CHANGELOG.md with your changes?
 - [ ] Have you checked our [Contributing](https://github.com/hdmf-dev/hdmf/blob/dev/docs/CONTRIBUTING.rst) document?
 - [ ] Have you ensured the PR clearly describes the problem and the solution?
-- [ ] Is your contribution compliant with our coding style? This can be checked running `flake8` from the source directory.
+- [ ] Is your contribution compliant with our coding style? This can be checked running `ruff` from the source directory.
 - [ ] Have you checked to ensure that there aren't other open [Pull Requests](https://github.com/hdmf-dev/hdmf/pulls) for the same change?
 - [ ] Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

.github/workflows/check_external_links.yml

@@ -23,12 +23,12 @@ jobs:
       - name: Set up Python
         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-doc.txt
+          python -m pip install -r requirements-doc.txt -r requirements-opt.txt
           python -m pip install .
 
       - name: Check Sphinx external links

.github/workflows/codespell.yml

@@ -0,0 +1,19 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [dev]
+
+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

.github/workflows/deploy_release.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
 
       - name: Install build dependencies
         run: |
@@ -28,17 +28,21 @@ jobs:
 
       - name: Run tox tests
         run: |
-          tox -e py310-upgraded
+          tox -e py311-upgraded
 
       - name: Build wheel and source distribution
         run: |
-          tox -e build-py310-upgraded
+          tox -e build-py311-upgraded
           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 wheel and source distributions to PyPI
         run: |
           python -m pip install twine

.github/workflows/project_action.yml

@@ -0,0 +1,34 @@
+name: Add issues to Development Project Board
+
+on:
+  issues:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add issue to project
+    runs-on: ubuntu-latest
+    steps:
+      - name: GitHub App token
+        id: generate_token
+        uses: tibdex/[email protected]
+        with:
+          app_id: ${{ secrets.APP_ID }}
+          private_key: ${{ secrets.APP_PEM }}
+
+      - name: Add to Developer Board
+        env:
+          TOKEN: ${{ steps.generate_token.outputs.token }}
+        uses: actions/[email protected]
+        with:
+          project-url: https://github.com/orgs/hdmf-dev/projects/7
+          github-token: ${{ env.TOKEN }}
+
+      - name: Add to Community Board
+        env:
+          TOKEN: ${{ steps.generate_token.outputs.token }}
+        uses: actions/[email protected]
+        with:
+          project-url: https://github.com/orgs/hdmf-dev/projects/8
+          github-token: ${{ env.TOKEN }}

.github/workflows/ruff.yml

@@ -0,0 +1,9 @@
+name: Ruff
+on: pull_request
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1