Configure python, CI, and pre-commit via PR#1

- Increase python version to 3.13 and lowered minimum supported version to 3.11.
- Add dependency groups for:
  - dev
  - test (no tests are set up yet)
  - docs (no docs are set up yet)
- Add `uv.lock`
  - After we accept this pull request, run `uv sync` to get the environment
- Configured pre-commit
  - I have pre-commit flag all print statements so that we don't accidentally push debugging code onto main. Do we want to require this and use some other logging solution for the code, or do we want to allow print statements?
- Added CI formatting for pull requests and pushes to main
- Add `dependabot.yml` to keep actions up to date

Author: budjensen

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/ci.yml

@@ -0,0 +1,25 @@
+name: CI
+
+on:
+  pull_request:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+
+
+jobs:
+  format:
+    name: Format code
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v5
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: "3.13"
+
+      - name: Download pre-commit
+        uses: pre-commit/[email protected]

.gitignore

@@ -182,9 +182,9 @@ cython_debug/
 .abstra/
 
 # Visual Studio Code
-#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
 #  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
 #  you could uncomment the following to ignore the entire vscode folder
 # .vscode/
 

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v6.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-toml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+
+  # Ruff configured in pyproject.toml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.14.0"
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: "0.8.1"
+    hooks:
+      - id: nbstripout

.python-version

@@ -1 +1 @@
-3.12
+3.13

pyproject.toml

@@ -1,7 +1,74 @@
 [project]
 name = "test-particle-sim-1d"
 version = "0.1.0"
-description = "Add your description here"
+description = "A 1D test particle tool for plasma applications"
+authors = [
+    { name = "budjensen", email = "[email protected]" },
+    { name = "lkadz", email = "[email protected]" },
+    { name = "SunnyNyhus" },
+]
 readme = "README.md"
-requires-python = ">=3.12"
-dependencies = []
+requires-python = ">=3.11,<3.14"
+dependencies = [
+    "numpy",
+    "scipy",
+]
+
+[dependency-groups]
+test = [
+    "pytest",
+]
+dev = [
+    { include-group = "test" },
+    "pre-commit",
+    "ruff",
+    "nox",
+]
+docs = [
+    "furo",
+    "myst_parser",
+    "sphinx",
+    "sphinx-markdown-builder",
+    "sphinx_copybutton",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.ruff.lint]
+extend-select = [
+  "ARG",      # flake8-unused-arguments
+  "B",        # flake8-bugbear
+  "C4",       # flake8-comprehensions
+  "EM",       # flake8-errmsg
+  "EXE",      # flake8-executable
+  "FURB",     # refurb
+  "G",        # flake8-logging-format
+  "I",        # isort
+  "ICN",      # flake8-import-conventions
+  "NPY",      # NumPy specific rules
+  "PD",       # pandas-vet
+  "PGH",      # pygrep-hooks
+  "PIE",      # flake8-pie
+  "PL",       # pylint
+  "PT",       # flake8-pytest-style
+  "PTH",      # flake8-use-pathlib
+  "PYI",      # flake8-pyi
+  "RET",      # flake8-return
+  "RUF",      # Ruff-specific
+  "SIM",      # flake8-simplify
+  "T20",      # flake8-print
+  "UP",       # pyupgrade
+  "YTT",      # flake8-2020
+]
+ignore = [
+  "PLR09",    # Too many <...>
+  "PLR2004",  # Magic value used in comparison
+]
+typing-modules = ["mypackage._compat.typing"]
+isort.required-imports = ["from __future__ import annotations"]
+
+[tool.ruff.lint.per-file-ignores]
+"tests/**" = ["T20"]
+"src/test_particle_sim_1d/__init__.py" = ["T201"]

src/__init__.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+
+def main() -> None:
+    print("Hello from test-particle-sim-1D!")