Clean up build/release and move dependencies to pyproject.toml

.github/workflows/main.yml

@@ -4,11 +4,11 @@ on:
   push:
     branches:
     - main
-    - dev
+    - dev*
   pull_request:
     branches:
     - main
-    - dev
+    - dev*
 
 jobs:
   build:
@@ -43,7 +43,7 @@ jobs:
 
       - name: Install quality check dependencies
         run: |
-          pip install -r requirements.txt
+          pip install ".[dev]"
 
       - name: Run quality checks
         run: |

pyproject.toml

@@ -1,3 +1,60 @@
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "seqscore"
+dynamic = ["version"]
+description = "SeqScore: Scoring for named entity recognition and other sequence labeling tasks"
+readme = "README.md"
+license = {text = "MIT"}
+authors = [
+    {name = "Constantine Lignos", email = "lignos@brandeis.edu"},
+]
+requires-python = ">=3.10"
+dependencies = [
+    "attrs>=19.2.0",
+    "click",
+    "tabulate",
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+
+[project.urls]
+Homepage = "https://github.com/bltlab/seqscore"
+
+[project.scripts]
+seqscore = "seqscore.scripts.seqscore:cli"
+
+[project.optional-dependencies]
+dev = [
+    "types-tabulate",
+    "pytest==9.0.3",
+    "pytest-cov==7.1.0",
+    "mypy==2.1.0",
+    "ruff==0.15.15",
+    "flowmark",
+    "build",
+    "twine",
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "seqscore.__version__"}
+
+[tool.setuptools.packages.find]
+include = ["seqscore", "seqscore.*"]
+
+[tool.setuptools.package-data]
+seqscore = ["py.typed"]
+
 [tool.mypy]
 python_version = "3.10"
 strict_optional = false
@@ -6,7 +63,6 @@ disallow_untyped_calls = true
 
 [[tool.mypy.overrides]]
 module = [
-    "setuptools",
     "click.*",
 ]
 ignore_missing_imports = true

scripts/release.sh

@@ -0,0 +1,57 @@
+#!/usr/bin/env bash
+# Builds, uploads to PyPI, and tags the release.
+# Should only be run by project maintainers.
+set -euo pipefail
+
+VENV=".venv/bin"
+
+# Run pre-commit checks
+bash tests/check.sh
+
+# Must be on main with a clean working tree
+current_branch=$(git rev-parse --abbrev-ref HEAD)
+if [[ "$current_branch" != "main" ]]; then
+    echo "Error: must be on main branch (currently on '$current_branch')"
+    exit 1
+fi
+
+if ! git diff --quiet || ! git diff --cached --quiet; then
+    echo "Error: working tree is not clean"
+    exit 1
+fi
+
+# Read version from package
+version=$("$VENV/python" -c "import seqscore; print(seqscore.__version__)")
+tag="v$version"
+
+# Abort if tag already exists
+if git rev-parse "$tag" >/dev/null 2>&1; then
+    echo "Error: tag $tag already exists. Update __version__ in seqscore/__init__.py."
+    exit 1
+fi
+
+echo "Releasing $tag"
+
+# Build
+rm -rf dist/
+"$VENV/python" -m build
+
+# Tag and push
+git tag "$tag"
+git push origin "$tag"
+
+# Prompt to verify tag before uploading
+echo ""
+echo "Tag $tag pushed. Check the release on GitHub before uploading to PyPI:"
+echo "  https://github.com/bltlab/seqscore/releases/tag/$tag"
+echo ""
+read -r -p "Upload to PyPI? [y/N] " confirm
+if [[ "${confirm,,}" != "y" ]]; then
+    echo "Aborted. Re-run this script to retry the upload."
+    exit 1
+fi
+
+# Upload to PyPI
+"$VENV/twine" upload dist/*
+
+echo "Done: $tag released and pushed"

tests/check.sh

@@ -1,6 +1,7 @@
 #!/usr/bin/env bash
 set -euxo pipefail
 
-files=(seqscore/ tests/ setup.py)
+flowmark --check ./*.md
+files=(seqscore/ tests/)
 ruff check "${files[@]}"
 mypy "${files[@]}"

tests/pre_commit.sh

@@ -1,7 +1,8 @@
 #!/usr/bin/env bash
 set -euxo pipefail
 
-files=(seqscore/ tests/ *.py)
+flowmark -i --nobackup ./*.md
+files=(seqscore/ tests/)
 ruff check --fix "${files[@]}"
 ruff check --select I --fix "${files[@]}"  # Organize imports
 ruff format "${files[@]}"