Fix * imports

.github/workflows/code-style.yaml

@@ -0,0 +1,25 @@
+name: Code style
+
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+    types:
+      - opened
+      - reopened
+      - synchronize
+      - ready_for_review
+  workflow_dispatch:
+
+jobs:
+  codestyle:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: chartboost/ruff-action@v1
+      with:
+        changed-files: 'true'

.pre-commit-config.yaml

@@ -0,0 +1,12 @@
+# 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: v0.5.2
+    hooks:
+      - id: ruff
+        args: [--fix]
+        types_or: [python, pyi]
+      # - id: ruff-format
+      #   types_or: [python, pyi]

CONTRIBUTING.md

@@ -28,9 +28,41 @@ conda activate proteus
 pip install -e .[develop]
 ```
 
+### Linting
+
+Linting is a term for static code analysis to flag programming errors,
+bugs, stylistic errors and [suspicious constructs](https://en.wikipedia.org/wiki/Lint_(software)).
+PROTEUS uses [`ruff`](https://astral.sh/ruff) for linting.
+The linting [rules](https://docs.astral.sh/ruff/rules/) are defined in [`pyproject.toml`](https://github.com/FormingWorlds/PROTEUS/blob/master/pyproject.toml).
+
+This check are run automatically via a Github Action: [codestyle](https://github.com/FormingWorlds/PROTEUS/blob/master/.github/workflows/codestyle.yaml).
+
+You can `ruff` on locally using one of these commands:
+
+```console
+ruff check start_proteus.py  # single file
+ruff check src/proteus       # directory
+ruff check .                 # everything
+```
+
+If you prepend `--fix`, it can also fix some issues for you:
+
+```console
+ruff check . --fix
+```
+
+You can also use [pre-commit](https://pre-commit.com/#usage) to automatically run `ruff` on every commit, e.g.:
+
+```console
+pre-commit install
+```
+
 ### Running tests
 
 PROTEUS uses [pytest](https://docs.pytest.org/en/latest/) to run the tests.
+
+The tests are run automatically via a Github Action: [tests](https://github.com/FormingWorlds/PROTEUS/blob/master/.github/workflows/tests.yaml).
+
 You can run the tests for yourself using:
 
 ```console

README.md

@@ -1,4 +1,4 @@
-[![Tests for PROTEUS](https://github.com/FormingWorlds/actions/workflows/tests.yaml/badge.svg)](https://github.com/FormingWorlds/actions/workflows/tests.yaml)
+[![Tests for PROTEUS](https://github.com/FormingWorlds/PROTEUS/actions/workflows/tests.yaml/badge.svg)](https://github.com/FormingWorlds/PROTEUS/actions/workflows/tests.yaml)
 ![Coverage](https://gist.githubusercontent.com/stefsmeets/b4ee7dab92e20644bcb3a5ad09f71165/raw/covbadge.svg)
 [![Documentation Status](https://readthedocs.org/projects/fwl-proteus/badge/?version=latest)](https://fwl-proteus.readthedocs.io/en/latest/?badge=latest)
 [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

pyproject.toml

@@ -66,6 +66,8 @@ develop = [
     "coverage[toml]",
     "pip-tools",
     "pytest >= 8.1",
+    "pre-commit",
+    "ruff",
 ]
 
 docs = [
@@ -86,6 +88,33 @@ source = ["proteus"]
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 
+[tool.ruff]
+line-length = 96
+target-version = "py310"
+extend-exclude = ["*ipynb"]
+
+[tool.ruff.lint]
+select = [
+	# "F",  # Pyflakes
+	# "E",  # pycodestyle (error)
+	# "W",  # pycodestyle (warning)
+    "I",    # isort
+    "F401", # {name} imported but unused
+    "F402", # from __future__ imports must occur at the beginning of the file
+    "F403", # from {name} import * only allowed at module level
+    "F404", # from {name} import * only allowed at module level
+    "E401", # Multiple imports on one line
+    "E402", # Module level import not at top of cell
+]
+
+[tool.ruff.lint.isort]
+known-first-party=["proteus"]
+required-imports = ["from __future__ import annotations"]
+
+[tool.ruff.format]
+quote-style = "single"
+indent-style = "space"
+
 [tool.bumpversion]
 # https://callowayproject.github.io/bump-my-version/howtos/calver/
 current_version = "24.07.25"

src/proteus/__init__.py

@@ -1 +1,3 @@
+from __future__ import annotations
+
 __version__ = '24.07.25'

src/proteus/atmos_clim/__init__.py

@@ -1,2 +1,7 @@
+from __future__ import annotations
 
 from .wrapper_atmosphere import RunAtmosphere
+
+__all__ = [
+    'RunAtmosphere',
+]