Merge branch 'dev' into enh/add_oid_to_link_format

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others’ private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project’s leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,93 @@
+name: Bug Report
+description: File a bug report.
+title: "[Bug]: "
+labels: ["bug"]
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        # Thanks for taking the time to fill out this bug report!
+        ### The following information will help us resolve your issue.
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: What happened?
+      description: Also tell us, what did you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps to Reproduce
+      description: |
+        Please copy and paste the code you were trying to run that caused the error.
+
+        Feel free to include as little or as much as you think is relevant. This section will be automatically formatted into code, so no need for backticks.
+      render: shell
+    validations:
+      required: true
+  - type: textarea
+    id: traceback
+    attributes:
+      label: Traceback
+      description: |
+        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
+  - type: dropdown
+    id: os
+    attributes:
+      label: Operating System
+      options:
+        - Windows
+        - macOS
+        - Linux
+    validations:
+      required: true
+  - type: dropdown
+    id: executable
+    attributes:
+      label: Python Executable
+      options:
+        - Conda
+        - Python
+    validations:
+      required: true
+  - type: dropdown
+    id: python_version
+    attributes:
+      label: Python Version
+      options:
+        - "3.8"
+        - "3.9"
+        - "3.10"
+        - "3.11"
+    validations:
+      required: true
+  - type: textarea
+    id: package_versions
+    attributes:
+      label: Package Versions
+      description: |
+        Please share your currently installed Python package versions by calling `pip freeze > environment_for_issue.txt` and uploading the text file along with this issue.
+
+        This helps us determine if there are any secondary or tertiary issues caused by other dependencies.
+
+        You can attach images or log files by clicking this area to highlight it and then dragging files in.
+        If GitHub upload is not working, you can also copy and paste the output into this section.
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/.github/CODE_OF_CONDUCT.md)
+      options:
+        - label: I agree to follow this project's [Code of Conduct](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/.github/CODE_OF_CONDUCT.md)
+          required: true
+        - label: Have you checked the [Contributing](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/docs/CONTRIBUTING.rst) document?
+          required: true
+        - label: Have you ensured this bug was not already [reported](https://github.com/hdmf-dev/hdmf-zarr/issues)?
+          required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: true
+contact_links:
+  - name: Read the Documentation
+    url: https://hdmf-zarr.readthedocs.io/en/latest/
+    about: Check out the full documentation.

.github/ISSUE_TEMPLATE/documentation.yml

@@ -0,0 +1,46 @@
+name: Documentation
+description: Is the documentation of something missing, unclear, or lacking? This is the place.
+title: "[Documentation]: "
+labels: "documentation"
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## Thank you for your suggestion!
+
+        We welcome any ideas about how to make **HDMF-ZARR** better for the community.
+
+        Please keep in mind that new or improved documentation may not get implemented immediately.
+  - type: textarea
+    id: summary
+    attributes:
+      label: What would you like changed or added to the documentation and why?
+      description: Do you have any suggestions for the documents?
+    validations:
+      required: true
+  - type: dropdown
+    id: interest
+    attributes:
+      label: Do you have any interest in helping write or edit the documentation?
+      description: |
+        We appreciate any help you can offer!
+
+        For information on how to contribute, please refer to our [contributing guidelines](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/docs/CONTRIBUTING.rst).
+      options:
+        - Yes.
+        - Yes, but I would need guidance.
+        - No.
+    validations:
+      required: true
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/.github/CODE_OF_CONDUCT.md)
+      options:
+        - label: I agree to follow this project's [Code of Conduct](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/.github/CODE_OF_CONDUCT.md)
+          required: true
+        - label: Have you checked the [Contributing](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/docs/CONTRIBUTING.rst) document?
+          required: true
+        - label: Have you ensured this change was not already [requested](https://github.com/hdmf-dev/hdmf-zarr/issues)?
+          required: true

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,64 @@
+name: Feature Request
+description: Suggest an idea for a brand new feature, or a change to an existing one.
+title: "[Feature]: "
+labels: ["enhancement"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        ## Thank you for your suggestion!
+
+        We welcome any ideas about how to make **HDMF-ZARR** better for the community.
+
+        Please keep in mind that new features may not get implemented immediately.
+  - type: textarea
+    id: summary
+    attributes:
+      label: What would you like to see added to HDMF-ZARR?
+      description: |
+        What are you trying to achieve with **HDMF-ZARR**?
+
+        Is this a more convenient way to do something that is already possible, or is a workaround currently unfeasible?
+    validations:
+      required: true
+  - type: textarea
+    id: problem
+    attributes:
+      label: Is your feature request related to a problem?
+      description: A clear and concise description of what the problem is.
+  - type: textarea
+    id: solution
+    attributes:
+      label: What solution would you like?
+      description: |
+        A clear and concise description of what you want to happen.
+
+        Describe alternative solutions you have considered.
+    validations:
+      required: true
+  - type: dropdown
+    id: interest
+    attributes:
+      label: Do you have any interest in helping implement the feature?
+      description: |
+        We appreciate any help you can offer!
+
+        For information on how to contribute, please refer to our [contributing guidelines](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/docs/CONTRIBUTING.rst).
+      options:
+        - Yes.
+        - Yes, but I would need guidance.
+        - No.
+    validations:
+      required: true
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Code of Conduct
+      description: By submitting this issue, you agree to follow our [Code of Conduct](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/.github/CODE_OF_CONDUCT.md)
+      options:
+        - label: I agree to follow this project's [Code of Conduct](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/.github/CODE_OF_CONDUCT.md)
+          required: true
+        - label: Have you checked the [Contributing](https://github.com/hdmf-dev/hdmf-zarr/blob/dev/docs/CONTRIBUTING.rst) document?
+          required: true
+        - label: Have you ensured this change was not already [requested](https://github.com/hdmf-dev/hdmf-zarr/issues)?
+          required: true

.github/PULL_REQUEST_TEMPLATE/release.md

@@ -0,0 +1,24 @@
+Prepare for release of HDMF-Zarr [version]
+
+### Before merging:
+- [ ] Major and minor releases: Update package versions in `requirements.txt`, `requirements-dev.txt`,
+  `requirements-doc.txt`, `requirements-min.txt`, and `setup.py` 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 `README.rst` as needed
+- [ ] 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`)
+- [ ] Test docs locally by going into the `docs` directory and running the following: `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-zarr/builds/
+
+### After merging:
+1. Create release by following steps in `docs/source/make_a_release.rst` or use alias `git pypi-release [tag]` if set up
+2. After the CI bot creates the new release (wait ~10 min), update the release notes on the
+   [GitHub releases page](https://github.com/hdmf-dev/hdmf-zarr/releases) with the changelog
+3. Check that the readthedocs "latest" and "stable" builds run and succeed
+4. Update [conda-forge/hdmf_zarr-feedstock](https://github.com/conda-forge/hdmf_zarr-feedstock) with the latest version number
+   and SHA256 retrieved from PyPI > HDMF-Zarr > Download Files > View hashes for the `.tar.gz` file. Re-render as needed

.github/pull_request_template.md

@@ -0,0 +1,17 @@
+## Motivation
+
+What was the reasoning behind this change? Please explain the changes briefly.
+
+## How to test the behavior?
+```
+Show how to reproduce the new behavior (can be a bug fix or a new feature)
+```
+
+## Checklist
+
+- [ ] Did you update CHANGELOG.md with your changes?
+- [ ] Have you checked our [Contributing](https://github.com/hdmf-dev/hdmf-zarr/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 `ruff` from the source directory.
+- [ ] Have you checked to ensure that there aren't other open [Pull Requests](https://github.com/hdmf-dev/hdmf-zarr/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

@@ -22,12 +22,12 @@ 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 -r requirements.txt
+          python -m pip install -r requirements-doc.txt -r requirements.txt -r requirements-opt.txt
           python -m pip install .
       - name: Check Sphinx external links
         run: sphinx-build -b linkcheck ./docs/source ./test_build

.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: |
@@ -28,11 +28,11 @@ 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

.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 }}