[INFRA] Configure tools (#2)

* configure pre-commit and add some metadata to pyproject

* add linting ci workflow

* add pytest in dev dependencies

* add basic example functions and tests with CI

.github/workflows/lint.yaml

@@ -0,0 +1,20 @@
+name: Lint
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+      - uses: pre-commit/[email protected]

.github/workflows/unit_test.yaml

@@ -0,0 +1,29 @@
+name: Unit Tests
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["maint"]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: Run unit tests on ${{ matrix.os }} with Python ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ['3.9', '3.10', '3.11', '3.12']
+    steps:
+      - uses: actions/checkout@v4
+      - uses: snok/install-poetry@v1
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: poetry
+      - name: Run unit tests
+        run: make test

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-yaml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.2.2
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+  - repo: https://github.com/python-poetry/poetry
+    rev: '1.7.1'
+    hooks:
+      - id: poetry-check
+
+default_language_version:
+  python: python3

Makefile

@@ -0,0 +1,13 @@
+POETRY ?= poetry
+
+.PHONY: check.lock
+check.lock:
+	@$(POETRY) check --lock
+
+.PHONY: install
+install: check.lock
+	@$(POETRY) install
+
+.PHONY: test
+test: install
+	@$(POETRY) run python -m pytest -v tests/unittests

pyproject.toml

@@ -1,15 +1,58 @@
 [tool.poetry]
 name = "clinicaio"
 version = "0.1.0"
-description = ""
+description = "A Python library for input/output management of all Clinica projects."
+license = "MIT"
 authors = ["ARAMIS Lab"]
+maintainers = ["Clinica developers <[email protected]>"]
 readme = "README.md"
+repository = "https://github.com/aramis-lab/clinicaio.git"
 packages = [{include = "clinicaio", from = "src"}]
+keywords = [
+    "bids",
+    "image processing",
+    "machine learning",
+    "neuroimaging",
+    "neuroscience"
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: End Users/Desktop",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Medical Science Apps.",
+    "Topic :: Scientific/Engineering :: Image Processing"
+]
 
 [tool.poetry.dependencies]
-python = "^3.12"
+python = ">=3.9,<3.13"
 
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.3"
 
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.ruff]
+target-version = "py39"
+line-length = 88
+
+[tool.ruff.lint]
+select = [
+    "E",
+    "W",
+    "I001",
+    "PTH",
+]
+ignore = ["E203", "E501"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["clinicaio"]
+
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"

src/clinicaio/hello.py

@@ -0,0 +1,16 @@
+__all__ = ["greet"]
+
+
+def greet(name: str):
+    """Greet the person with provided name.
+
+    Parameters
+    ----------
+    name : str
+        The name of the person to greet.
+    """
+    print(_build_greeting_message(name))
+
+
+def _build_greeting_message(name: str) -> str:
+    return f"Hello {name} !"

tests/unittests/test_hello.py

@@ -0,0 +1,16 @@
+def test_build_greeting_message():
+    from clinicaio.hello import _build_greeting_message
+
+    assert (
+        _build_greeting_message("ClinicaIO developers")
+        == "Hello ClinicaIO developers !"
+    )
+
+
+def test_greet(capsys):
+    from clinicaio.hello import greet
+
+    greet("John Doe")
+
+    captured = capsys.readouterr()
+    assert captured.out == "Hello John Doe !\n"