Bump to v2.0.0

.github/workflows/ci.yml

@@ -13,30 +13,33 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python ${{ matrix.python-version}}
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Install Poetry
+      - name: Install Rye
         run: |
-          curl -sSL https://install.python-poetry.org | python3 -
-          echo "$HOME/.local/bin" >> $GITHUB_PATH
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
-      - name: Install Dependencies
-        run: poetry install -n
+      - name: Setup Python ${{matrix.python-version}} & Dependencies
+        run: |
+          rye pin ${{ matrix.python-version }}
+          rye sync --update-all --all-features
 
-      - name: Run black format check
-        run: poetry run black src tests --check --diff --verbose
+      - name: Install external tool dependencies
+        run: |
+          sudo apt update -y
+          sudo apt install -y ncbi-blast+
+        if: ${{ matrix.os=='ubuntu-latest' }}
 
       - name: Run ruff lint check
-        run: poetry run ruff .
+        run: rye run ruff check --diff
+
+      - name: Run ruff format check
+        run: rye run ruff format --check --diff
 
       - name: Run pytest
-        run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term
+        run: rye run pytest

.github/workflows/publish_to_pypi.yml

@@ -2,6 +2,7 @@ name: Publish to PyPI
 on:
   release:
     types: [released]
+  workflow_dispatch:
 
 jobs:
   publish_to_pypi:
@@ -12,19 +13,15 @@ jobs:
       PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v4
-        with:
-          python-version: 3.9
-
-      - name: Install Dependencies
+      - name: Install Rye
         run: |
-          python -m pip install --upgrade pip
-          pip install poetry poetry-dynamic-versioning
+          curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
+          echo "$HOME/.rye/shims" >> $GITHUB_PATH
+
       - name: Build
-        run: poetry build
+        run: rye build
 
       - name: Publish
-        run: poetry publish -u $PYPI_USERNAME -p $PYPI_PASSWORD
+        run: rye publish -u $PYPI_USERNAME --token $PYPI_PASSWORD -y

.gitignore

@@ -1,6 +1,6 @@
 cog_download/
-example/
-output/
+# example/
+# output/
 .vscode/
 
 # Byte-compiled / optimized / DLL files

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+# 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: v0.11.6
+    hooks:
+      - id: ruff
+        name: ruff lint check
+        types_or: [python, pyi]
+        args: [--fix]
+      - id: ruff-format
+        name: ruff format check
+        types_or: [python, pyi]