Merge staging into main

.ebextensions/01_download_data.config

@@ -3,46 +3,24 @@ commands:
         command: "yum install -y python-devel postgresql-devel"
     02_install_aws_cli:
         command: "yum install -y awscli"
-    03_install_p7zip:
-        command: "yum install -y p7zip"
-    04_eb_packages:
+    03_eb_packages:
        command: "/var/app/venv/staging-LQM1lest/bin/pip install uvloop websockets httptools typing-extensions"
-    05_export_eb_env_var:
+    04_export_eb_env_var:
         command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"
 
 container_commands:
-    01_cool_seq_tool_permissions:
-        test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool"
-        command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool/data"
+    01_s3_download:
+        test: test ! -d "/usr/local/share/seqrepo/2024-02-20"
+        command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.tar.gz --region us-east-2"
 
-    02_s3_download:
-        test: test ! -d "/usr/local/share/seqrepo"
-        command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.zip --region us-east-2"
+    02_extract_seqrepo:
+        test: test -f "/usr/local/share/seqrepo.tar.gz"
+        command: "mkdir -p /usr/local/share/seqrepo/2024-02-20 && tar -xzvf /usr/local/share/seqrepo.tar.gz -C /usr/local/share/seqrepo/2024-02-20"
 
-    03_p7zip_seqrepo:
-        test: test -f "/usr/local/share/seqrepo.zip"
-        command: "7za x /usr/local/share/seqrepo.zip -o/usr/local/share -y"
+    03_seqrepo_zip_permission:
+        test: test -f "/usr/local/share/seqrepo.tar.gz"
+        command: "chmod +wr /usr/local/share/seqrepo.tar.gz"
 
-    04_seqrepo_permission:
-        test: test -d "/usr/local/share/seqrepo"
-        command: "chmod -R 777 /usr/local/share/seqrepo"
-
-    05_macosx_permission:
-        test: test -d "/usr/local/share/__MACOSX"
-        command: "chmod -R +wr /usr/local/share/__MACOSX"
-
-    06_seqrepo_zip_permission:
-        test: test -f "/usr/local/share/seqrepo.zip"
-        command: "chmod +wr /usr/local/share/seqrepo.zip"
-
-    07_remove_macosx:
-        test: test -d "/usr/local/share/__MACOSX"
-        command: "rm -R /usr/local/share/__MACOSX"
-
-    08_remove_seqrepo_zip:
-        test: test -f "/usr/local/share/seqrepo.zip"
-        command: "rm /usr/local/share/seqrepo.zip"
-
-    9_data_permission:
-        test: test -d "/usr/local/share/seqrepo"
-        command: "chmod -R +wrx /usr/local/share/seqrepo"
+    04_remove_seqrepo_zip:
+        test: test -f "/usr/local/share/seqrepo.tar.gz"
+        command: "rm /usr/local/share/seqrepo.tar.gz"

.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/branch-warning.yaml

@@ -0,0 +1,19 @@
+name: PR branch check
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  check_branch:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check PR Source Branch
+        if: github.event.pull_request.head.ref != 'staging'
+        run: |
+          echo "Checking if PR is coming from 'staging' branch"
+          gh pr comment ${{ github.event.pull_request.number }} \
+            --body "Hey bud, you're opening a PR to main from a branch that isn't staging. Maybe you know what you're doing, but maybe you also just forgot to change the branch. Take a second to think about it."
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/checks.yml → .github/workflows/checks.yaml

@@ -7,12 +7,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -23,10 +23,10 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.11
 

.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/release.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - name: Install pypa/build
@@ -25,7 +25,7 @@ jobs:
       - name: Build a binary wheel and a source tarball
         run: python3 -m build
       - name: Store the distribution packages
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: python-package-distributions
           path: dist/
@@ -42,7 +42,7 @@ jobs:
       id-token: write # IMPORTANT: mandatory for trusted publishing
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: python-package-distributions
           path: dist/

.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@main
+    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@main
+    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@main
+    with:
+      days-before-issue-stale: 180
+      days-before-pr-stale: 7
+      labels: priority:low

.pre-commit-config.yaml

@@ -2,15 +2,19 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
+  rev: v4.6.0  # pre-commit-hooks version
   hooks:
   - id: check-added-large-files
   - id: detect-private-key
   - id: trailing-whitespace
   - id: end-of-file-fixer
+  - id: check-merge-conflict
+  - id: detect-aws-credentials
+    args: [ --allow-missing-credentials ]
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.2.0
+  rev: v0.5.0  # ruff version
   hooks:
     - id: ruff-format
     - id: ruff
       args: [ --fix, --exit-non-zero-on-fix ]
+minimum_pre_commit_version: 3.7.1

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2023 VICC
+Copyright (c) 2018-2024 VICC
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal