chore: cleanup container and linting (#263)

## Changes

* Refresh container environment with actively-supported Dev Container
features.
* Refresh linting configuration.
* Apply listing configuration with fixes.

---

Reviewer: @cadojo

Author: cadojo

.devcontainer/devcontainer.json

@@ -1,27 +1,33 @@
 {
-	"name": "GeneralAstrodynamics",
-	"image": "mcr.microsoft.com/devcontainers/base:ubuntu",
-	"features": {
-		"ghcr.io/devcontainers/features/git": {},
-		"ghcr.io/devcontainers/features/git-lfs": {},
-		"ghcr.io/julialang/devcontainer-features/julia:1": {},
-		"ghcr.io/devcontainers/features/github-cli": {},
-		"ghcr.io/devcontainers-contrib/features/starship": {},
-		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {},
-		"ghcr.io/devcontainers/features/python:1": {"installJupyterlab": true}
+	"name": "general-astrodynamics",
+	"image": "mcr.microsoft.com/devcontainers/base:bookworm",
+	"containerEnv": {
+		"SHELL": "/bin/bash"
 	},
-	"postCreateCommand": {
-		"initialize starship": "echo 'eval $(starship init bash)' >> ~/.bashrc"
+	"remoteEnv": {
+		"JULIA_DEPOT_PATH": "/home/vscode/.julia"
 	},
-	"customizations": {
-		"vscode": {
-			"extensions": [
-				"GitHub.codespaces",
-				"github.vscode-github-actions",
-				"julialang.language-julia",
-				"ms-toolsai.jupyter",
-				"streetsidesoftware.code-spell-checker"
-			]
+	"features": {
+		"ghcr.io/devcontainers/features/python:1": {
+			"installTools": true,
+			"enableShared": true,
+			"installJupyterlab": true,
+			"version": "3.12"
+		},
+		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {},
+		"ghcr.io/julialang/devcontainer-features/julia:1": {},
+		"ghcr.io/devcontainer-community/devcontainer-features/starship.rs:1": {},
+		"ghcr.io/devcontainers/features/git:1": {},
+		"ghcr.io/devcontainers/features/git-lfs:1": {},
+		"ghcr.io/devcontainers-extra/features/pre-commit:2": {},
+		"ghcr.io/devcontainers/features/github-cli:1": {},
+		"ghcr.io/rocker-org/devcontainer-features/apt-packages:1": {
+			"packages": "jq"
 		}
+	},
+	"onCreateCommand": {
+		"initialize starship": "echo eval '$(starship init bash)' >> ~/.bashrc",
+		"configure starship": "starship preset no-runtime-versions -o ~/.config/starship.toml",
+		"initialize pre-commit": "pre-commit install --install-hooks"
 	}
-}
+}

.gitattributes

@@ -1,2 +1,2 @@
 paper/notebooks/*.ipynb filter=lfs diff=lfs merge=lfs -text
-*.ipynb linguist-vendored
+*.ipynb linguist-vendored

.github/ISSUE_TEMPLATE/enhancement.md

@@ -7,5 +7,4 @@ assignees: cadojo
 
 ---
 
-## Feature 
-
+## Feature

.github/ISSUE_TEMPLATE/question.md

@@ -8,4 +8,3 @@ assignees: cadojo
 ---
 
 ## Question
-

.github/workflows/Tests.yml

@@ -52,7 +52,7 @@ jobs:
           project: lib/${{ matrix.group }}
       - uses: julia-actions/julia-processcoverage@v1
         with:
-          directories: lib/${{ matrix.group }}/src
+          directories: lib/${{ matrix.group }}/src,lib/${{ matrix.group }}/test
       - uses: codecov/codecov-action@v5
         with:
           files: lcov.info
@@ -87,7 +87,7 @@ jobs:
           GROUP: "GeneralAstrodynamics"
       - uses: julia-actions/julia-processcoverage@v1
         with:
-          directories: src
+          directories: src,test
       - uses: codecov/codecov-action@v5
         with:
           files: lcov.info

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+exclude: '(^|/)pyproject\.toml$|(^|/)Project\.toml$|(^|/)Manifest\.toml$|^_extensions/|^_freeze/'
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+      - id: check-executables-have-shebangs
+      - id: check-symlinks
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.33.1
+    hooks:
+      - id: typos
+        args: ["--config", ".typos.toml", "--write-changes"]

.typos.toml

@@ -0,0 +1,2 @@
+[default.extend-words]
+Cloudfare = "Cloudfare"

.vscode/settings.json

@@ -1,3 +1,3 @@
 {
     "quarto.visualEditor.markdownWrap": "sentence"
-}
+}

README.md

@@ -63,4 +63,4 @@ orbit, T = let
 end
 
 trajectory = propagate(orbit, T)
-```
+```