Switch to Ruff for linting and formatting

.devcontainer.json

@@ -6,7 +6,9 @@
     "customizations": {
         "vscode": {
             "extensions": [
-                "github.vscode-github-actions"
+                "github.vscode-github-actions",
+                "ms-python.mypy-type-checker",
+                "charliermarsh.ruff"
             ]
         }
     }

.github/workflows/ci.yml

@@ -10,15 +10,19 @@ on:
   workflow_dispatch:
 
 jobs:
-  format:
+  lint:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
       uses: actions/checkout@v4
-    - name: Format code with Black
-      uses: psf/black@stable
+    - name: Lint with Ruff
+      uses: chartboost/ruff-action@v1
+    - name: Format with Ruff
+      uses: chartboost/ruff-action@v1
+      with:
+        args: 'format --check'
 
-  type:
+  typing:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout
@@ -29,7 +33,7 @@ jobs:
         python-version: '3.x'
     - name: Install typing dependencies
       run: |
-        pip install .[type]
+        pip install .[typing]
     - name: Check types with mypy
       run: |
         mypy

README.md

@@ -4,7 +4,7 @@
 [![Codecov](https://codecov.io/gh/microfluidica/electrolytes/branch/main/graph/badge.svg)](https://codecov.io/gh/microfluidica/electrolytes)
 [![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
 [![Pydantic v2](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/pydantic/pydantic/5697b1e4c4a9790ece607654e6c02a160620c7e1/docs/badge/v2.json)](https://pydantic.dev)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![PyPI](https://img.shields.io/pypi/v/electrolytes)](https://pypi.org/project/electrolytes/)
 [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/electrolytes)](https://pypi.org/project/electrolytes/)
 [![Docker image](https://img.shields.io/badge/docker%20image-microfluidica%2Felectrolytes-0085a0)](https://hub.docker.com/r/microfluidica/electrolytes/)

electrolytes/__init__.py

@@ -23,18 +23,18 @@
 class Constituent(BaseModel, populate_by_name=True, frozen=True):
     id: Optional[int] = None
     name: str
-    u_neg: Annotated[list[float], Field(alias="uNeg")] = (
-        []
-    )  # [-neg_count, -neg_count+1, -neg_count+2, ..., -1]
-    u_pos: Annotated[list[float], Field(alias="uPos")] = (
-        []
-    )  # [+1, +2, +3, ..., +pos_count]
-    pkas_neg: Annotated[list[float], Field(alias="pKaNeg")] = (
-        []
-    )  # [-neg_count, -neg_count+1, -neg_count+2, ..., -1]
-    pkas_pos: Annotated[list[float], Field(alias="pKaPos")] = (
-        []
-    )  # [+1, +2, +3, ..., +pos_count]
+    u_neg: Annotated[
+        list[float], Field(alias="uNeg")
+    ] = []  # [-neg_count, -neg_count+1, -neg_count+2, ..., -1]
+    u_pos: Annotated[
+        list[float], Field(alias="uPos")
+    ] = []  # [+1, +2, +3, ..., +pos_count]
+    pkas_neg: Annotated[
+        list[float], Field(alias="pKaNeg")
+    ] = []  # [-neg_count, -neg_count+1, -neg_count+2, ..., -1]
+    pkas_pos: Annotated[
+        list[float], Field(alias="pKaPos")
+    ] = []  # [+1, +2, +3, ..., +pos_count]
     neg_count: Annotated[int, Field(alias="negCount", validate_default=True)] = None  # type: ignore
     pos_count: Annotated[int, Field(alias="posCount", validate_default=True)] = None  # type: ignore
 

electrolytes/__main__.py

@@ -21,18 +21,54 @@ def complete_name_user_defined(incomplete: str) -> list[str]:
 @app.command()
 def add(
     name: Annotated[str, typer.Argument(autocompletion=complete_name_user_defined)],
-    p1: Annotated[tuple[float, float], typer.Option("+1", help="Mobility (*1e-9) and pKa for +1", show_default=False)] = (None, None),  # type: ignore
-    p2: Annotated[tuple[float, float], typer.Option("+2", help="Mobility (*1e-9) and pKa for +2", show_default=False)] = (None, None),  # type: ignore
-    p3: Annotated[tuple[float, float], typer.Option("+3", help="Mobility (*1e-9) and pKa for +3", show_default=False)] = (None, None),  # type: ignore
-    p4: Annotated[tuple[float, float], typer.Option("+4", help="Mobility (*1e-9) and pKa for +4", show_default=False)] = (None, None),  # type: ignore
-    p5: Annotated[tuple[float, float], typer.Option("+5", help="Mobility (*1e-9) and pKa for +5", show_default=False)] = (None, None),  # type: ignore
-    p6: Annotated[tuple[float, float], typer.Option("+6", help="Mobility (*1e-9) and pKa for +6", show_default=False)] = (None, None),  # type: ignore
-    m1: Annotated[tuple[float, float], typer.Option("-1", help="Mobility (*1e-9) and pKa for -1", show_default=False)] = (None, None),  # type: ignore
-    m2: Annotated[tuple[float, float], typer.Option("-2", help="Mobility (*1e-9) and pKa for -2", show_default=False)] = (None, None),  # type: ignore
-    m3: Annotated[tuple[float, float], typer.Option("-3", help="Mobility (*1e-9) and pKa for -3", show_default=False)] = (None, None),  # type: ignore
-    m4: Annotated[tuple[float, float], typer.Option("-4", help="Mobility (*1e-9) and pKa for -4", show_default=False)] = (None, None),  # type: ignore
-    m5: Annotated[tuple[float, float], typer.Option("-5", help="Mobility (*1e-9) and pKa for -5", show_default=False)] = (None, None),  # type: ignore
-    m6: Annotated[tuple[float, float], typer.Option("-6", help="Mobility (*1e-9) and pKa for -6", show_default=False)] = (None, None),  # type: ignore
+    p1: Annotated[
+        tuple[float, float],
+        typer.Option("+1", help="Mobility (*1e-9) and pKa for +1", show_default=False),
+    ] = (None, None),  # type: ignore
+    p2: Annotated[
+        tuple[float, float],
+        typer.Option("+2", help="Mobility (*1e-9) and pKa for +2", show_default=False),
+    ] = (None, None),  # type: ignore
+    p3: Annotated[
+        tuple[float, float],
+        typer.Option("+3", help="Mobility (*1e-9) and pKa for +3", show_default=False),
+    ] = (None, None),  # type: ignore
+    p4: Annotated[
+        tuple[float, float],
+        typer.Option("+4", help="Mobility (*1e-9) and pKa for +4", show_default=False),
+    ] = (None, None),  # type: ignore
+    p5: Annotated[
+        tuple[float, float],
+        typer.Option("+5", help="Mobility (*1e-9) and pKa for +5", show_default=False),
+    ] = (None, None),  # type: ignore
+    p6: Annotated[
+        tuple[float, float],
+        typer.Option("+6", help="Mobility (*1e-9) and pKa for +6", show_default=False),
+    ] = (None, None),  # type: ignore
+    m1: Annotated[
+        tuple[float, float],
+        typer.Option("-1", help="Mobility (*1e-9) and pKa for -1", show_default=False),
+    ] = (None, None),  # type: ignore
+    m2: Annotated[
+        tuple[float, float],
+        typer.Option("-2", help="Mobility (*1e-9) and pKa for -2", show_default=False),
+    ] = (None, None),  # type: ignore
+    m3: Annotated[
+        tuple[float, float],
+        typer.Option("-3", help="Mobility (*1e-9) and pKa for -3", show_default=False),
+    ] = (None, None),  # type: ignore
+    m4: Annotated[
+        tuple[float, float],
+        typer.Option("-4", help="Mobility (*1e-9) and pKa for -4", show_default=False),
+    ] = (None, None),  # type: ignore
+    m5: Annotated[
+        tuple[float, float],
+        typer.Option("-5", help="Mobility (*1e-9) and pKa for -5", show_default=False),
+    ] = (None, None),  # type: ignore
+    m6: Annotated[
+        tuple[float, float],
+        typer.Option("-6", help="Mobility (*1e-9) and pKa for -6", show_default=False),
+    ] = (None, None),  # type: ignore
     force: Annotated[
         bool,
         typer.Option(
@@ -100,7 +136,7 @@ def info(
     names: Annotated[
         Optional[list[str]],
         typer.Argument(help="Component names", autocompletion=complete_name),
-    ] = None
+    ] = None,
 ) -> None:
     """
     Show the properties of components.
@@ -158,7 +194,7 @@ def ls(
         typer.Option(
             "--user/--default", help="List only user-defined/default components"
         ),
-    ] = None
+    ] = None,
 ) -> None:
     """List components in the database."""
 
@@ -244,7 +280,7 @@ def common(
         typer.Option(
             "--version", help="Show version and exit.", callback=version_callback
         ),
-    ] = False
+    ] = False,
 ) -> None:
     """Database of electrolytes and their properties."""
     pass

pyproject.toml

@@ -37,8 +37,8 @@ dependencies = [
 dynamic = ["version"]
 
 [project.optional-dependencies]
-lint = ["black"]
-type = [
+lint = ["ruff"]
+typing = [
     "mypy==1.*",
     "pytest>=7,<9",
 ]

tests/test_api.py

@@ -1,7 +1,7 @@
 import pytest
 
 import electrolytes
-from electrolytes import *
+from electrolytes import Constituent, database
 
 
 def test_version() -> None:
@@ -10,13 +10,13 @@ def test_version() -> None:
 
 def test_list_components() -> None:
     assert database
-    l = list(database)
-    assert len(l) == len(database)
-    assert isinstance(l[0], str)
-    assert l == sorted(l)
-    assert "LYSINE" in l
-    assert "CYSTINE" in l
-    assert "SILVER" in l
+    lst = list(database)
+    assert len(lst) == len(database)
+    assert isinstance(lst[0], str)
+    assert lst == sorted(lst)
+    assert "LYSINE" in lst
+    assert "CYSTINE" in lst
+    assert "SILVER" in lst
 
 
 def test_get_component() -> None:

tests/test_cli.py

@@ -3,7 +3,7 @@
 from typer.testing import CliRunner
 
 import electrolytes
-from electrolytes import *
+from electrolytes import Constituent, database
 from electrolytes.__main__ import app
 
 

tests/test_lock.py

@@ -1,9 +1,7 @@
-import pytest
-
 import subprocess
 from time import sleep
 
-from electrolytes import *
+from electrolytes import Constituent, database
 
 
 def test_lock_api_cli() -> None: