merge: merge latest changes from upstream/main and resolve conflicts

.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_unzip:
-        command: "yum install -y unzip"
-    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_uta_permissions:
-        test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/uta_tools"
-        command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/uta_tools/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_unzip_seqrepo:
-        test: test -f "/usr/local/share/seqrepo.zip"
-        command: "unzip /usr/local/share/seqrepo.zip -d /usr/local/share"
+    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"

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+ignore = E129,E133,E203,E221,E241,E251,E303,E266,H106,H904,W291
+max-line-length = 100
+max-complexity = 15
+hang-closing = true
+exclude =
+    .eggs
+    .tox
+    build
+    dist
+    docs/conf.py
+    tests/*

.git-blame-ignore-revs

@@ -0,0 +1,3 @@
+# .git-blame-ignore-revs
+# Initial formatting with Ruff
+2b56cd434a129fe0ab1311f7fe9a65767ed88b9e

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @GenomicMedLab/wagner-lab-developers

.github/labels.yml

@@ -0,0 +1,3 @@
+# file must contain an array, which may be empty
+
+[]

.github/workflows/build-and-push-image.yml

@@ -0,0 +1,48 @@
+# https://josephrodriguezg.medium.com/build-and-publish-docker-images-with-github-actions
+
+
+name: Build and publish a Docker image
+on:
+  push:
+    branches:
+      - 'main'
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+      - '[0-9]+.[0-9]+.[0-9]+rc[0-9]+'
+jobs:
+  build:
+    name: Build & push docker image
+    runs-on: ubuntu-latest
+    env:
+      IMG_NAME: ${{ github.repository }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Debug
+        run: |
+          echo "github.ref -> {{ github.ref }}"
+
+      - name: Docker metadata
+        id: metadata
+        uses: docker/metadata-action@v3
+        with:
+          images: ${{ env.IMG_NAME }}
+          tags: |
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=raw,value={{sha}},enable=${{ github.ref_type != 'tag' }}
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v1
+        if: ${{ github.ref_type == 'tag' }}
+        with:
+          username: ${{ vars.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          push: ${{ github.event.base_ref =='refs/heads/main' && github.ref_type == 'tag' }}
+          tags: ${{ steps.metadata.outputs.tags }}
+          labels: ${{ steps.metadata.outputs.labels }}

.github/workflows/labels.yml

@@ -0,0 +1,29 @@
+name: Sync labels
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '.github/labels.yml'
+      - '.github/workflows/labels.yml'
+
+permissions:
+  issues: write
+
+jobs:
+  labels:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: .github/labels.yml
+
+      - uses: EndBug/label-sync@v2
+        with:
+          config-file: |
+            https://raw.githubusercontent.com/biocommons/.github/main/etc/labels.yml
+            .github/labels.yml
+
+          delete-other-labels: false

.github/workflows/python-package.yml

@@ -0,0 +1,68 @@
+name: Python package
+
+on:
+  push:
+
+jobs:
+  cqa:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: awalsh128/cache-apt-pkgs-action@latest
+      with:
+        packages: zsh
+        version: 1.0
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
+        cache: pip
+        cache-dependency-path: '**/pyproject.yaml'
+
+    - name: Install test dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install --use-deprecated=legacy-resolver -e '.[dev]'
+
+    - name: Lint with Ruff
+      run: |
+        ruff check .
+
+    - name: Format check with Ruff
+      run: |
+        ruff format --check .
+
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: awalsh128/cache-apt-pkgs-action@latest
+      with:
+        packages: zsh
+        version: 1.0
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: '**/pyproject.yaml'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        make develop
+
+    - name: Test with pytest
+      run: |
+        make test

.github/workflows/stale.yml

@@ -1,24 +1,11 @@
-name: Mark stale issues and pull requests
+# https://github.com/actions/stale
 
+name: 'Close stale issues and PRs'
 on:
+  workflow_dispatch:
   schedule:
-  - cron: "30 1 * * *"
+    - cron: '1 1 * * *'
 
 jobs:
   stale:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/stale@v1
-      with:
-        repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-issue-label: Stale
-        stale-issue-message: >-
-          This issue was marked stale due to inactivity.
-        stale-pr-label: Stale
-        stale-pr-message: >-
-          This pull request was marked stale due to inactivity.
-        days-before-stale: 60
-        days-before-close: 14
-        exempt-issue-labels: "Stayin' Alive"
+    uses: biocommons/.github/.github/workflows/stale.yml@main

.gitignore

@@ -1,108 +1,22 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
+*.bak
 *.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
+*.egg-info
 *.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# IPython Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# dotenv
-.env
-
-# virtualenv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-
-# Rope project settings
-.ropeproject
-
-# PyCharm
-.idea
-
-*~
-*.bak
+*.manifest
 *.orig
-doc/_build
+*.sqlite3
+*~
+.cache
+.coverage
 .eggs
-archive
-misc/docker
-.pytest_cache
-
-doc/changelog/*/.tags
-doc/changelog/*/.tags.mk
-doc/changelog/*/hg-git-remap.pl
+.idea
+.ipynb_checkpoints
+.tox
 .vscode
-web_*
-refget-compliance-suite/
+__pycache__
+archive
+build
+dist
+docs/_build
+nosetests.xml
+venv

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.4
+  hooks:
+    - id: ruff-format
+      args: [ --check ]
+