cicd: update github workflows/templates

.github/ISSUE_TEMPLATE/bug-report.yaml

@@ -0,0 +1,85 @@
+name: Bug Report
+description: Report a bug.
+labels: ["bug"]
+body:
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: Provide a clear and concise description of what the bug is.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      description: Provide detailed steps to replicate the bug.
+      placeholder: |
+        1. In this environment...
+        2. With this config...
+        3. Run '...'
+        4. See error...
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Expected behavior
+      description: What did you expect to happen?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Current behavior
+      description: |
+        What actually happened?
+
+        Include full errors, stack traces, and/or relevant logs.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Possible reason(s)
+      description: Provide any insights into what might be causing the issue.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Suggested fix
+      description: Provide any suggestions on how to resolve the bug.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Branch, commit, and/or version
+      description: Provide the branch, commit, and/or version you're using.
+      placeholder: |
+        branch: issue-1
+        commit: abc123d
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Screenshots
+      description: If applicable, add screenshots with descriptions to help explain your problem.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Environment details
+      description: Provide environment details (OS name and version, etc).
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional details
+      description: Provide any other additional details about the problem.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this fix."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/feature-request.yaml

@@ -0,0 +1,60 @@
+name: Feature Request
+description: Suggest an idea for this project.
+labels: ["enhancement"]
+body:
+  - type: textarea
+    attributes:
+      label: Feature description
+      description: Provide a clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Use case
+      description: |
+        Why do you need this feature? For example: "I'm always frustrated when..."
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Proposed solution
+      description: Provide proposed solution.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Alternatives considered
+      description: Describe any alternative solutions you've considered.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Implementation details
+      description: Provide any technical details on how the feature might be implemented.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Potential Impact
+      description: |
+        Discuss any potential impacts of this feature on existing functionality or performance, if known.
+        Will this feature cause breaking changes?
+        What challenges might arise?
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Provide any other context or screenshots about the feature.
+    validations:
+      required: false
+  - type: dropdown
+    attributes:
+      label: Contribution
+      description: Can you contribute to the development of this feature?
+      options:
+        - "Yes, I can create a PR for this feature."
+        - "Yes, but I can only provide ideas and feedback."
+        - "No, I cannot contribute."
+    validations:
+      required: false

.github/workflows/backend_checks.yml

@@ -7,8 +7,8 @@ jobs:
     strategy:
       fail-fast: false
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.11
 
@@ -18,7 +18,7 @@ jobs:
     name: lint
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: black
         uses: psf/black@stable

.github/workflows/pr-priority-label.yaml

@@ -0,0 +1,23 @@
+name: Pull Request Has Priority Label
+on:
+  pull_request:
+    types: [opened, labeled, unlabeled, synchronize]
+jobs:
+  pr-priority-label:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    outputs:
+      status: { { "${{ steps.check-labels.outputs.status }}" } }
+    steps:
+      - id: check-labels
+        uses: mheap/github-action-required-labels@v5
+        with:
+          mode: exactly
+          count: 1
+          labels: "priority:*"
+          use_regex: true
+          add_comment: true
+          message: "PRs require a priority label. Please add one."
+          exit_type: failure

.github/workflows/stale.yaml

@@ -0,0 +1,27 @@
+name: "Stalebot for issues and PRs"
+
+on:
+  schedule:
+    - cron: "30 13 * * 1-5"
+
+jobs:
+  stale-high-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml
+    with:
+      days-before-issue-stale: 90
+      days-before-pr-stale: 1
+      labels: priority:high
+
+  stale-medium-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml
+    with:
+      days-before-issue-stale: 135
+      days-before-pr-stale: 3
+      labels: priority:medium
+
+  stale-low-priority:
+    uses: genomicmedlab/software-templates/.github/workflows/reusable-stale.yaml
+    with:
+      days-before-issue-stale: 180
+      days-before-pr-stale: 7
+      labels: priority:low