New updates detected with Cruft

.github/dependabot.yml

@@ -20,7 +20,7 @@ updates:
       default-days: 7
 
   - package-ecosystem: pip
-    directory: /CI
+    directory: /.github
     schedule:
       interval: daily
       time: '12:00'

CI/requirements_ci.txt → .github/requirements_ci.txt

@@ -31,7 +31,10 @@ cachetools==7.0.4 \
 certifi==2024.7.4 \
     --hash=sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b \
     --hash=sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90
-    # via requests
+    # via
+    #   httpcore
+    #   httpx
+    #   requests
 charset-normalizer==3.3.2 \
     --hash=sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027 \
     --hash=sha256:06a81e93cd441c56a9b65d8e1d043daeb97a3d0856d177d5c90ba85acb3db087 \
@@ -598,12 +601,7 @@ tomli==2.4.1 \
     --hash=sha256:fd0409a3653af6c147209d267a0e4243f0ae46b011aa978b1080359fddc9b6cf \
     --hash=sha256:ff18e6a727ee0ab0388507b89d1bc6a22b138d1e2fa56d1ad494586d61d2eae9 \
     --hash=sha256:ff2983983d34813c1aeb0fa89091e76c3a22889ee83ab27c5eeb45100560c049
-    # via
-    #   -r requirements_ci.in
-    #   deptry
-    #   pylint
-    #   pyproject-api
-    #   tox
+    # via requests
 tomli-w==1.2.0 \
     --hash=sha256:188306098d013b691fcadc011abd66727d3c414c571bb01b1a174ba8c983cf90 \
     --hash=sha256:2dd14fac5a47c27be9cd4c976af5a12d87fb1f0b4512f81d69cce3b35ae25021

.github/workflows/bump-version.yml

@@ -14,14 +14,14 @@ on:
       - .cruft.json
       - .editorconfig
       - .github/**.yml
+      - .github/*.in
+      - .github/*.txt
       - .gitignore
       - .pre-commit-config.yaml
       - .yamllint.yaml
       - .zenodo.json
       - AUTHORS.rst
       - CHANGELOG.rst
-      - CI/**/*.in
-      - CI/**/*.txt
       - CITATION.cff
       - CODE_OF_CONDUCT.md
       - CONTRIBUTING.rst
@@ -45,7 +45,6 @@ jobs:
     runs-on: ubuntu-latest
     environment: automation
     permissions:
-      actions: read
       contents: write
     strategy:
       matrix:
@@ -76,7 +75,7 @@ jobs:
           git config --local user.name "bumpversion[bot]"
       - name: Install CI libraries
         run: |
-          python -m pip install --require-hashes -r CI/requirements_ci.txt
+          python -m pip install --require-hashes -r .github/requirements_ci.txt
       - name: Conditional Bump Version
         run: |
           CURRENT_VERSION=$(bump-my-version show current_version)

.github/workflows/first-pull-request.yml

@@ -57,6 +57,5 @@ jobs:
               we ask that you add your information to the \`AUTHORS.rst\` and \`.zenodo.json\`:
                - [ ] The relevant author information has been added to \`AUTHORS.rst\` and \`.zenodo.json\`
 
-              Please make sure you've read our [contributing guide](CONTRIBUTING.rst).
-              We look forward to reviewing your Pull Request shortly ✨`
+              Please make sure you've read our [contributing guide](https://github.com/glamod/cdm_reader_mapper/blob/main/CONTRIBUTING.rst). We look forward to reviewing your Pull Request shortly ✨`
             })

.github/workflows/publish-pypi.yml

@@ -41,7 +41,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install packaging libraries
         run: |
-          python -m pip install -r CI/requirements_ci.txt
+          python -m pip install -r .github/requirements_ci.txt
       - name: Build a binary wheel and a source tarball
         run: |
           python -m flit build

.github/workflows/tag-testpypi.yml

@@ -74,7 +74,7 @@ jobs:
 
       - name: Install CI libraries
         run: |
-          python -m pip install --require-hashes -r CI/requirements_ci.txt
+          python -m pip install --require-hashes -r .github/requirements_ci.txt
       - name: Build a binary wheel and a source tarball
         run: |
           python -m flit build

.github/workflows/testing-suite.yml

@@ -39,7 +39,7 @@ jobs:
           cache: pip
       - name: Install CI libraries
         run: |
-          python -m pip install --require-hashes -r CI/requirements_ci.txt
+          python -m pip install --require-hashes -r .github/requirements_ci.txt
       - name: Environment Caching
         uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:

.github/workflows/workflow-warning.yml

@@ -15,12 +15,16 @@ on:
 permissions:
   contents: read
 
+concurrency:
+  group: workflow-warning-${{ github.event.pull_request.number }}
+  cancel-in-progress: true
+
+
 jobs:
   comment-concerning-workflow-changes:
     name: Comment Concerning Workflow Changes
     runs-on: ubuntu-latest
-    if: |
-      (github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name)
+    if: github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
     permissions:
       contents: read
       pull-requests: write
@@ -33,60 +37,58 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
 
-      - name: Manage Warning / Note Comments
+      - name:  Create or Update Warning Comment
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          APPROVED: ${{ contains(github.event.pull_request.labels.*.name, 'approved') }}
-          PR_NUMBER: ${{ github.event.pull_request.number }}
           REPO: ${{ github.repository }}
+          PR_NUMBER: ${{ github.event.pull_request.number }}
         run: |
-          WARNING_TEXT="This Pull Request modifies GitHub workflows and is coming from a fork."
-          NOTE_TEXT="Workflow changes in this Pull Request have been approved!"
+          set -euo pipefail
 
-          # Fetch existing comments
-          COMMENTS=$(gh api repos/$REPO/issues/$PR_NUMBER/comments)
+          MARKER="<!-- workflow-changes-warning -->"
 
-          # Find warning comment ID
-          WARNING_COMMENT_ID=$(echo "$COMMENTS" | jq -r \
-            '.[] | select(.user.login=="github-actions[bot]") | select(.body | contains("'"$WARNING_TEXT"'")) | .id' | head -n 1)
+          BODY=$(cat <<EOF
+          $MARKER
 
-          # Find note comment ID
-          NOTE_COMMENT_ID=$(echo "$COMMENTS" | jq -r \
-            '.[] | select(.user.login=="github-actions[bot]") | select(.body | contains("'"$NOTE_TEXT"'")) | .id' | head -n 1)
+          > [!WARNING]
+          > This pull request modifies GitHub Actions workflows and originates from a fork.
+          >
+          > Review the workflow changes carefully before approving or merging.
+          EOF
+          )
 
-          if [ "$APPROVED" = "true" ]; then
-            BODY="> [!NOTE]
-          > Workflow changes in this Pull Request have been approved!"
+          COMMENTS=$(gh api repos/$REPO/issues/$PR_NUMBER/comments)
 
-            if [ -n "$NOTE_COMMENT_ID" ] && [ "$NOTE_COMMENT_ID" != "null" ]; then
-              # Append to existing note comment
-              EXISTING=$(gh api repos/$REPO/issues/comments/$NOTE_COMMENT_ID --jq .body)
-              gh api \
-                --method PATCH \
-                repos/$REPO/issues/comments/$NOTE_COMMENT_ID \
-                -f body="$EXISTING
+          mapfile -t IDS < <(
+            echo "$COMMENTS" |
+            jq -r '
+              .[]
+              | select(.body | contains("<!-- workflow-changes-warning -->"))
+              | .id
+            '
+          )
+
+          COMMENT_ID=""
 
-          $BODY"
-            else
-              # Create new note comment
-              gh pr comment "$PR_NUMBER" --body "$BODY"
-            fi
+          if [ "${#IDS[@]}" -gt 0 ]; then
+            COMMENT_ID="${IDS[0]}"
 
-            # Add reaction (hooray)
-            if [ -n "$NOTE_COMMENT_ID" ] && [ "$NOTE_COMMENT_ID" != "null" ]; then
+            # Remove duplicate managed comments if they exist.
+            for id in "${IDS[@]:1}"; do
               gh api \
-                --method POST \
-                repos/$REPO/issues/comments/$NOTE_COMMENT_ID/reactions \
-                -f content='hooray' \
-                -H "Accept: application/vnd.github+json"
-            fi
+                --method DELETE \
+                repos/$REPO/issues/comments/$id
+            done
+          fi
 
+          if [ -n "$COMMENT_ID" ]; then
+            gh api \
+              --method PATCH \
+              repos/$REPO/issues/comments/$COMMENT_ID \
+              -f body="$BODY"
           else
-            BODY="> [!WARNING]
-          > This Pull Request modifies GitHub Workflows and is coming from a fork.
-          **It is very important for the reviewer to ensure that the workflow changes are appropriate.**"
-
-            if [ -z "$WARNING_COMMENT_ID" ] || [ "$WARNING_COMMENT_ID" = "null" ]; then
-              gh pr comment "$PR_NUMBER" --body "$BODY"
-            fi
-          fi
+            gh api \
+              --method POST \
+              repos/$REPO/issues/$PR_NUMBER/comments \
+              -f body="$BODY"
+           fi

.pre-commit-config.yaml

@@ -85,7 +85,7 @@ repos:
       - id: check-github-workflows
       - id: check-readthedocs
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.23.1
+    rev: v1.24.1
     hooks:
       - id: zizmor
         args: [ '--config=.zizmor.yml' ]

AGENTS.md

@@ -0,0 +1,62 @@
+# Agents
+
+Rules for AI coding agents working in this repository.
+
+## General
+
+- Follow existing code conventions and patterns
+- Do not modify files outside the scope of the current task
+- Prefer editing existing files over creating new ones
+- Do not add dependencies without explicit approval
+- Keep changes atomic -- one concern per commit
+- Ask for clarification when requirements are ambiguous
+- Do not generate PR descriptions or review comments on others' code
+
+## Code Style
+
+- Follow the linting patterns provided via `$ make lint` in the `Makefile` alongside the configurations found in the top-level `pyproject.toml` and `.pre-commit-config.yaml` files.
+- All functions should be typed and new functions must have `numpydoc`-like docstrings.
+
+## Setup
+
+The package can be installed in developer mode in Python using the `$ make develop` recipe.
+
+## Testing
+
+- Write tests for new functionality.
+- Any `pytest` fixtures common to tests across multiple `test_*.py` files should be found within `conftest.py`.
+- Run the full suite before submitting.
+- Test coverage must not significantly drop between PRs and main.
+
+## Restricted Paths
+
+Do not modify:
+
+- `.*`
+- `.github`
+- `docs`
+- `tox.toml`
+
+## Changelog
+
+- Changes must be summarized in one or two sentences within the `CHANGELOG.rst` file.
+- New additions must be placed under the section labelled "(unreleased)".
+- Acceptable category types are all previously categories found in `CHANGELOG.rst`
+- Entries must end with the issue number and PR number appended to the end: "(:issue:`#`, :pull:`#`)".
+
+## Commits
+
+- Use clear, descriptive commit messages
+- One logical change per commit
+- Do not bundle unrelated changes
+- Reference relevant issues when applicable
+- Never push directly to main
+- Always use a PR branch and get human approval before merging
+- Include `Assisted-by: <tool name>` trailer on AI-assisted commits
+
+## Review
+
+All changes to code require human review.
+
+---
+*Generated by [aipolicy.1mb.dev](https://aipolicy.1mb.dev) · v1.0*

AI_POLICY.md

@@ -0,0 +1,63 @@
+# AI Policy
+
+## Accountability
+
+You are responsible for every line of code you submit, regardless of how it was produced. If you use AI tools, review and verify all output before committing.
+
+## Pull Requests
+
+Pull Requests descriptions must be drafted by a human and adhere to the template selected on creation.
+Summaries of changes posted by AI are not accepted in Pull Requests.
+
+## AI Tool Usage
+
+AI tools are permitted. Standard review process applies to all contributions.
+
+## AI-Generated Code
+
+AI-generated code must be reviewed by a human maintainer before merging. Keep changes atomic -- you must be able to explain any line on request.
+
+## Disclosure
+
+Mark AI involvement in commit messages with a trailer:
+
+```text
+Assisted-by: <tool name>
+```
+
+Code changes from less sophisticated phrase-completion tools do not require an AI disclosure.
+
+## Prohibited Uses
+
+- Submitting AI output you have not read and understood
+- Using AI to generate code that circumvents tests or CI checks
+- Feeding reviewer feedback back into AI without understanding it first
+- AI-generated PR descriptions -- describe your own work
+- AI-generated reviews on other contributors' PRs
+
+## AI in CI/CD
+
+AI tools may be used in CI/CD pipelines for code analysis, test generation, and deployment.
+
+## Training Data
+
+This project requests that its code not be used for AI model training. We ask that AI tool providers honor this preference.
+
+## Low Effort Contributions
+
+AI-generated low-effort contributions are unacceptable; Human and AI contributors must be capable of explaining their changes, responding to review comments, and precisely adapting their contributions as requested.
+
+## Licensing
+
+AI-generated contributions must be compatible with this project's license. Contributors must be able to certify their submissions under the project's contribution terms.
+
+## Enforcement
+
+Maintainers may close AI-generated PRs that do not meet these standards without detailed feedback.
+
+## Policy Evolution
+
+This policy will evolve as tooling and conventions change. Contributions to the policy itself are welcome.
+
+---
+*Generated by [aipolicy.1mb.dev](https://aipolicy.1mb.dev) · v1.0*