Major Upgrade v1.0.0

.github/workflows/ci.yml

@@ -14,35 +14,30 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependent tools for CLI workflow
-        run: |
-          sudo apt update -y
-          sudo apt install -y mummer progressivemauve
-        if: ${{ matrix.os=='ubuntu-latest'}}
+      - name: Install python dependencies
+        run: pip install -e . pytest pytest-cov ruff streamlit
 
-      - name: Install Poetry
+      - name: Install external dependencies
         run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
-
-      - name: Install Dependencies
-        run: poetry install -n
-
-      - name: Run black format check
-        run: poetry run black src tests --check --diff --verbose
+          sudo apt update -y
+          sudo apt install -y ncbi-blast+ mmseqs2 mummer progressivemauve
+        if: ${{ matrix.os=='ubuntu-latest' }}
 
       - name: Run ruff lint check
-        run: poetry run ruff .
+        run: ruff check --diff
+
+      - name: Run ruff format check
+        run: ruff format --check --diff
 
       - name: Run pytest
-        run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term
+        run: pytest

.github/workflows/publish_mkdocs.yml

@@ -10,12 +10,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
 
       - name: Install MkDocs & Plugins
         run: |

.github/workflows/publish_to_pypi.yml

@@ -13,12 +13,12 @@ jobs:
       PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
+      - name: Setup Python 3.11
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: "3.11"
 
       - name: Install Poetry
         run: |

.github/workflows/push_docker_image.yml

@@ -13,17 +13,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Login to GHCR
-        uses: docker/login-action@v2
+        uses: docker/login-action@v3
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Docker Build & Push
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           push: true

.github/workflows/stale_issues.yml

@@ -0,0 +1,23 @@
+name: Close inactive issues
+on:
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v9
+        with:
+          days-before-issue-stale: 14
+          days-before-issue-close: 14
+          exempt-issue-labels: "bug,documentation,enhancement"
+          stale-issue-label: "stale"
+          stale-issue-message: "This issue is stale because it has been open for 14 days with no activity."
+          close-issue-message: "This issue was closed because it has been inactive for 14 days since being marked as stale."
+          days-before-pr-stale: -1
+          days-before-pr-close: -1
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,11 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+      - id: ruff
+        name: ruff lint check
+        args: [--fix]
+      - id: ruff-format
+        name: ruff format check

.streamlit/config.toml

@@ -0,0 +1,13 @@
+[theme]
+base = "dark"
+
+[browser]
+gatherUsageStats = false
+
+[server]
+runOnSave = true
+maxUploadSize = 1
+
+[logger]
+messageFormat = "%(asctime)s | %(levelname)s | %(message)s"
+level = "info"

CITATION.cff

@@ -4,5 +4,5 @@ authors:
   - family-names: Shimoyama
     given-names: Yuki
 title: "pyGenomeViz: A genome visualization python package for comparative genomics"
-date-released: 2022-06-20
+date-released: 2024-05-18
 url: https://github.com/moshi4/pyGenomeViz

Dockerfile

@@ -1,12 +1,15 @@
-FROM python:3.10-slim
+FROM python:3.12-slim
 
+# Install dependent aligner tools
 RUN apt-get update && \
-    apt-get install -y mummer mmseqs2 progressivemauve
+    apt-get install -y ncbi-blast+ mummer mmseqs2 progressivemauve
 
+# Install pyGenomeViz
 RUN pip install -U pip && \
     pip install pygenomeviz[gui] --no-cache-dir
 
 # Download example dataset in advance
-RUN pgv-download-dataset -n enterobacteria_phage
+RUN pgv-download enterobacteria_phage --cache_only && \
+    pgv-download mycoplasma_mycoides --cache_only
 
 CMD ["/bin/bash"]