build: use pyproject.toml to declare configs

.github/workflows/checks.yaml

@@ -0,0 +1,61 @@
+name: checks
+on: [push, pull_request]
+jobs:
+  test:
+    name: test build py${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "${{ matrix.python-version }}"
+
+      - name: Install dependencies
+        run: |
+          python3 -m pip install ".[tests]"
+
+      # TODO -- build CI-ready unit tests
+
+  lint:
+    name: lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: python3 -m pip install ".[dev]"
+
+      - name: Check style
+        run: python3 -m flake8 src tests
+
+  precommit_hooks:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        cmd:
+          - "check-ast"
+          - "debug-statements"
+          - "end-of-file-fixer"
+          - "trailing-whitespace"
+          - "mixed-line-ending"
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - uses: pre-commit/action@v3.0.1
+        with:
+          extra_args: ${{ matrix.cmd }} --all-files

.github/workflows/release.yaml

@@ -0,0 +1,50 @@
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
+name: Publish Python distribution to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/vrs_anvil_toolkit
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
 
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v5.0.0
   hooks:
     - id: debug-statements #Check for debugger imports and breakpoint() in python files
     - id: check-ast #Simply check whether files parse as valid python
@@ -16,7 +16,7 @@ repos:
     - id: end-of-file-fixer #Makes sure files end in a newline and only a newline
     - id: trailing-whitespace
     - id: mixed-line-ending
-
+      args: [ --fix=lf ]
 - repo: local
   hooks:
   - id: run_tests
@@ -33,3 +33,4 @@ repos:
 #      language: system
 #      types: [python]
 #      exclude: ^venv/ ^.git/ ^.vscode/ ^.DS_Store
+minimum_pre_commit_version: 4.0.1

pyproject.toml

@@ -0,0 +1,79 @@
+[project]
+name = "vrs_anvil_toolkit"
+authors = [
+    {"name" = "GKS-AnVIL"}
+]
+readme = "README.md"
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Intended Audience :: Developers",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+requires-python = ">=3.10"
+description = "Useful tools and methods for applying GA4GH GKS and VRS models on the NHGRI AnVIL platform."
+license = {file = "LICENSE.md"}
+dependencies = [
+    "ga4gh.vrs[extras]==2.0.0a13",
+    "diskcache",
+    "biocommons.seqrepo",
+    "glom",
+    "click",
+    "pyyaml",
+    "google",
+    "requests",
+    "boto3",
+    "tqdm",
+    "google-cloud-storage",
+    "psutil",
+    # for CAF generation:
+    "firecloud",
+    "ga4gh.va_spec~=0.2.0a0",
+    "pandas",
+    "vrsix==0.1.1",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+tests = [
+    "pytest",
+]
+dev = [
+    "flake8",
+    "black",
+    "pre-commit>=4.0.1",
+]
+
+[project.urls]
+Homepage = "https://github.com/gks-anvil/vrs_anvil_toolkit"
+Documentation = "https://github.com/gks-anvil/vrs_anvil_toolkit"
+Changelog = "https://github.com/gks-anvil/vrs_anvil_toolkit/releases"
+Source = "https://github.com/gks-anvil/vrs_anvil_toolkit"
+"Bug Tracker" = "https://github.com/gks-anvil/vrs_anvil_toolkit/issues"
+
+[project.scripts]
+vrs_bulk = "vrs_anvil.cli:cli"
+
+[build-system]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+vrs_anvil_toolkit = ["**/*.yaml"]
+
+[tool.setuptools_scm]
+
+[tool.pytest.ini_options]
+filterwarnings = ["ignore::DeprecationWarning"]