Update to ruff, typer, and new type annotations

Author: gregorybchris

.github/workflows/ci.yaml

@@ -0,0 +1,54 @@
+name: Package CI
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version:
+          - "3.12"
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Python ${{ matrix.python-version }} setup
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: 0.6.14
+          enable-cache: true
+          cache-local-path: ~/.cache/uv
+          cache-dependency-glob: pyproject.toml
+
+      - name: Install package
+        run: uv sync --all-extras --dev
+
+      - name: Run ruff
+        shell: bash
+        run: |
+          uv run ruff check .
+          uv run ruff format . --check
+
+      - name: Run mypy
+        shell: bash
+        run: |
+          uv run mypy src --config pyproject.toml
+
+      - name: Run pytest
+        shell: bash
+        run: |
+          uv run pytest tests

.vscode/extensions.json

@@ -1,10 +1,8 @@
 {
   "recommendations": [
+    "charliermarsh.ruff",
     "esbenp.prettier-vscode",
-    "ms-python.black-formatter",
-    "ms-python.isort",
     "ms-python.mypy-type-checker",
-    "ms-python.pylint",
     "ms-python.python",
     "tamasfe.even-better-toml",
     "yzhang.markdown-all-in-one"

.vscode/settings.json

@@ -1,22 +1,21 @@
 {
-  "[json]": { "editor.defaultFormatter": "esbenp.prettier-vscode" },
   "[markdown]": { "editor.defaultFormatter": "esbenp.prettier-vscode" },
-  "[python]": { "editor.defaultFormatter": "ms-python.black-formatter" },
+  "[python]": { "editor.defaultFormatter": "charliermarsh.ruff" },
   "[toml]": { "editor.defaultFormatter": "tamasfe.even-better-toml" },
   "editor.codeActionsOnSave": {
-    "source.organizeImports": "explicit"
+    "source.organizeImports": "explicit",
+    "source.fixAll": "explicit"
   },
-  "black-formatter.args": ["--config", "pyproject.toml"],
-  "cSpell.words": ["randn"],
   "editor.defaultFormatter": "esbenp.prettier-vscode",
-  "flake8.args": ["--max-line-length", "120"],
   "editor.detectIndentation": true,
   "editor.formatOnSave": true,
   "editor.insertSpaces": true,
   "editor.rulers": [120],
-  "isort.args": ["--settings-file", "pyproject.toml"],
   "mypy-type-checker.args": ["--config-file", "pyproject.toml"],
   "prettier.printWidth": 120,
-  "pylint.path": ["pylint"],
-  "pylint.args": ["--rcfile", "pyproject.toml"]
+  "ruff.configuration": "pyproject.toml",
+  "ruff.nativeServer": true,
+  "python.testing.pytestArgs": ["tests"],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true
 }

pyproject.toml

@@ -2,69 +2,83 @@
 authors = [
     { name = "Chris Gregory", email = "christopher.b.gregory@gmail.com" },
 ]
-classifiers = [
-    "Intended Audience :: Developers",
-    "Topic :: Software Development",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Programming Language :: Python :: 3.13",
-]
-dependencies = ["click>=8.2.1", "numpy>=2.3.0"]
+dependencies = ["numpy>=2.3.0", "rich>=14.0.0", "typer>=0.16.0"]
 description = "Artificial genetics simulation."
 keywords = ["artificial", "genetics", "simulation"]
 name = "typogenetics"
 readme = "README.md"
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 version = "0.1.0"
 
-[project.urls]
-Repository = "https://github.com/gregorybchris/typogenetics"
-
-[project.scripts]
-typo = "typogenetics.cli:main"
-
-[dependency-groups]
-dev = ["black>=25.1.0", "mypy>=1.16.0", "pylint>=3.3.7", "pytest>=8.4.0"]
-
-[tool.hatch.build.targets.sdist]
-include = ["typogenetics"]
-
-[tool.hatch.build.targets.wheel]
-include = ["typogenetics"]
+[tool.uv]
+dev-dependencies = [
+    "mypy>=1.16.0",
+    "pytest>=8.4.0",
+    "ruff>=0.11.13",
+    "semver>=3.0.4",
+]
 
 [build-system]
 build-backend = "hatchling.build"
 requires = ["hatchling"]
 
-[tool.black]
-line-length = 120
+[project.urls]
+repository = "https://github.com/gregorybchris/typogenetics"
 
-[tool.isort]
-line_length = 120
-profile = "black"
-src_paths = "*"
+[project.scripts]
+typo = "typogenetics.cli:app"
 
 [tool.mypy]
 disallow_incomplete_defs = true
 disallow_untyped_calls = true
 disallow_untyped_defs = true
 ignore_missing_imports = true
 
-[tool.pylint.basic]
-good-names = ["f", "i"]
-notes = ["FIXME"]
+[tool.ruff]
+line-length = 120
+src = ["src"]
 
-[tool.pylint.format]
+[tool.ruff.lint]
+ignore = ["D100", "D104", "FIX002", "TD002", "TD003"]
+select = [
+    "A",
+    "ARG",
+    "B",
+    "BLE",
+    "C4",
+    "E",
+    "EM",
+    "ERA",
+    "F",
+    "FIX",
+    "G",
+    "I",
+    "ICN",
+    "ISC",
+    "LOG",
+    "N",
+    "PL",
+    "PT",
+    "PTH",
+    "PLR",
+    "RET",
+    "RUF",
+    "SIM",
+    "SLF",
+    "T20",
+    "TCH",
+    "TD",
+    "TID",
+    "W",
+]
+
+[tool.ruff.lint.pycodestyle]
 max-line-length = 120
 
-[tool.pylint.messages_control]
-disable = [
-    "missing-function-docstring",
-    "missing-module-docstring",
-    "missing-class-docstring",
-    "logging-fstring-interpolation",
-]
+[tool.ruff.lint.pydocstyle]
+convention = "google"
 
-[tool.pylint.reports]
-output-format = "colorized"
+[tool.ruff.lint.extend-per-file-ignores]
+"**/*.py" = ["A001", "A002"]
+"**/tests/**/*.py" = ["SLF", "PLR2004", "PLR6301"]
+"src/typogenetics/cli.py" = ["T201", "T203"]

typogenetics/__init__.py src/typogenetics/__init__.pytypogenetics/__init__.py renamed to src/typogenetics/__init__.py

@@ -0,0 +1,114 @@
+import logging
+from typing import Annotated, Optional
+
+import numpy as np
+from rich.console import Console
+from rich.logging import RichHandler
+from typer import Argument, Option, Typer
+
+from typogenetics.search import Search
+from typogenetics.typogenetics import Enzyme, Folder, Rewriter, Strand, Translator
+
+logger = logging.getLogger(__name__)
+
+app = Typer(pretty_exceptions_enable=False)
+console = Console()
+
+
+def set_logger_config(info: bool, debug: bool) -> None:
+    handlers = [RichHandler(rich_tracebacks=True)]
+    log_format = "%(message)s"
+
+    if info:
+        logging.basicConfig(level=logging.INFO, handlers=handlers, format=log_format)
+    if debug:
+        logging.basicConfig(level=logging.DEBUG, handlers=handlers, format=log_format)
+
+
+@app.command()
+def translate(
+    strand_str: Annotated[str, Argument(...)],
+    info: Annotated[bool, Option("--info/--no-info")] = True,
+    debug: Annotated[bool, Option("--debug/--no-debug")] = False,
+) -> None:
+    set_logger_config(info, debug)
+
+    strand = Strand.from_str(strand_str)
+    enzymes = Translator.translate(strand)
+    for enzyme in enzymes:
+        console.print(enzyme)
+
+
+@app.command()
+def rewrite(
+    enzyme_str: Annotated[str, Argument(...)],
+    strand_str: Annotated[str, Argument(...)],
+    info: Annotated[bool, Option("--info/--no-info")] = True,
+    debug: Annotated[bool, Option("--debug/--no-debug")] = False,
+) -> None:
+    set_logger_config(info, debug)
+
+    enzyme = Enzyme.from_str(enzyme_str)
+    strand = Strand.from_str(strand_str)
+    new_strands = Rewriter.rewrite(enzyme, strand)
+    console.print("New strands:")
+    for new_strand in new_strands:
+        console.print(f"- {new_strand}")
+
+
+@app.command()
+def simulate(  # noqa: PLR0913
+    init_strand_str: Annotated[str, Argument(...)],
+    n_iterations: Annotated[int, Option("--iter")] = 100_000,
+    seed: Annotated[Optional[int], Option("--seed")] = None,
+    print_strands: Annotated[bool, Option("--print-strands/--no-print-strands")] = False,
+    info: Annotated[bool, Option("--info/--no-info")] = True,
+    debug: Annotated[bool, Option("--debug/--no-debug")] = False,
+) -> None:
+    set_logger_config(info, debug)
+
+    rng = np.random.default_rng(seed)
+    init_strand = Strand.from_str(init_strand_str)
+
+    Search.random(init_strand, n_iterations, rng, print_strands=print_strands)
+
+
+@app.command()
+def search(  # noqa: PLR0913
+    init_strand_str: Annotated[str, Argument(...)],
+    apply_strand_str: Annotated[str, Argument(...)],
+    target_depth: Annotated[int, Option("--depth")] = 10,
+    seed: Annotated[Optional[int], Option("--seed")] = None,
+    n_edits: Annotated[int, Option("--edits")] = 10,
+    print_strands: Annotated[bool, Option("--print-strands/--no-print-strands")] = False,
+    info: Annotated[bool, Option("--info/--no-info")] = True,
+    debug: Annotated[bool, Option("--debug/--no-debug")] = False,
+) -> None:
+    set_logger_config(info, debug)
+
+    rng = np.random.default_rng(seed)
+    init_strand = Strand.from_str(init_strand_str)
+    apply_strand = Strand.from_str(apply_strand_str)
+
+    Search.bfs(init_strand, apply_strand, target_depth, n_edits, rng, print_strands=print_strands)
+
+
+@app.command()
+def go(
+    info: Annotated[bool, Option("--info/--no-info")] = True,
+    debug: Annotated[bool, Option("--debug/--no-debug")] = False,
+) -> None:
+    set_logger_config(info, debug)
+
+    strand = Strand.from_str("CAAGGGTATACCCCATATCCT")
+    console.print(strand)
+
+    enzymes = Translator.translate(strand)
+    console.print(enzymes)
+
+    enzyme = enzymes[0]
+    unit = Folder.get_binding_site(enzyme, strand)
+    console.print(unit)
+
+    new_strands = Rewriter.rewrite(enzyme, strand)
+    console.print(new_strands)