Refactor CI workflows and migration to Hatchling 🎉

- `.github/workflows/release-cli.yml`: Added PyPI environment info, updated
build and publish steps to use `uv`.
- `.github/workflows/test-cli.yml`: Modified test platform to use `uv`
instead of `poetry`.
- `cli/pyproject.toml`: Replaced `[tool.poetry]` with `[project]`, updated
dependencies format, set build system to `hatchling`.

.github/workflows/release-cli.yml

@@ -13,14 +13,27 @@ jobs:
   release:
     runs-on: ubuntu-latest
 
+    environment:
+      name: pypi
+      url: https://pypi.org/p/deciphon-cli
+
+    permissions:
+      id-token: write
+
     steps:
       - uses: actions/checkout@v4
 
-      - name: Build
-        run: pipx run build
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Deploy
+        run: |
+          uv sync --all-extras --dev
+          uv build
+          uv publish
 
       - uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          password: ${{secrets.PYPI_API_TOKEN}}
           packages-dir: cli/dist
           skip-existing: true
+          verbose: true

.github/workflows/test-cli.yml

@@ -14,15 +14,18 @@ defaults:
 
 jobs:
   test:
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13]
+        os: [ubuntu-latest, macos-latest]
 
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
       - name: Run tests
         run: |
-          pipx run poetry install
-          pipx run poetry run pytest
+          uv sync --all-extras --dev
+          uv run pytest

cli/pyproject.toml

@@ -1,39 +1,44 @@
-[tool.poetry]
+[project]
 name = "deciphon"
 version = "1.0.3"
 description = "Individually annotate long, error-prone nucleotide sequences into proteins"
-authors = ["Danilo Horta <[email protected]>"]
-license = "MIT"
+authors = [{ name = "Danilo Horta", email = "[email protected]" }]
+requires-python = "~=3.9"
 readme = "README.md"
-packages = [{ include = "deciphon" }]
+license = "MIT"
+dependencies = [
+    "cffi~=1.17",
+    "fasta-reader>=3.0.3,<4",
+    "hmmer~=3.4",
+    "ijson~=3.3",
+    "pydantic~=2.9",
+    "typer>=0.12,<0.13",
+    "rich~=13.8",
+    "deciphon-snap>=1.0.3,<2",
+    "more-itertools~=10.5",
+    "psutil>=6.1.0,<7",
+    "deciphon-core>=1.0.5,<2",
+    "h3daemon>=0.14.8,<0.15",
+    "h3result>=1.0.3,<2",
+    "loguru>=0.7.2,<0.8",
+    "deciphon-worker>=0.3.1,<0.4",
+]
 
-[tool.poetry.dependencies]
-python = "^3.9"
-cffi = "^1.17"
-fasta-reader = "^3.0.3"
-hmmer = "^3.4"
-ijson = "^3.3"
-pydantic = "^2.9"
-typer = "^0.12"
-rich = "^13.8"
-deciphon-snap = "^1.0.3"
-more-itertools = "^10.5"
-psutil = "^6.1.0"
-deciphon-core = "^1.0.5"
-h3daemon = "^0.14.8"
-h3result = "^1.0.3"
-loguru = "^0.7.2"
-deciphon-worker = "^0.3.1"
+[project.scripts]
+deciphon = "deciphon.cli:app"
 
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.2"
+[dependency-groups]
+dev = ["pytest~=8.2"]
 
-[tool.pytest.ini_options]
-pythonpath = ["."]
+[tool.hatch.build.targets.sdist]
+include = ["deciphon"]
 
-[tool.poetry.scripts]
-deciphon = 'deciphon.cli:app'
+[tool.hatch.build.targets.wheel]
+include = ["deciphon"]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.pytest.ini_options]
+pythonpath = ["."]