Trying to bump changes from main into jax claude

.github/workflows/publish.yml

@@ -0,0 +1,42 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # full history so hatch-vcs reads the tag
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+
+      - name: Build package
+        run: uv build
+
+      - name: Upload dist artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write  # required for OIDC trusted publishing
+    steps:
+      - name: Download dist artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -1,7 +1,8 @@
 dev/
 __pycache__/
+src/pygenray/__about__.py
 .DS_Store
 docs/_build/
 dist/
 .vscode/
-uv.lock
+uv.lock

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v6.0.0"
+    hooks:
+      - id: check-added-large-files
+        args: ["--maxkb=5120"]
+      - id: check-merge-conflict
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: debug-statements
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.15.11"
+    hooks:
+      - id: ruff-check
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format

.readthedocs.yaml

@@ -23,4 +23,3 @@ python:
       path: .
       extra_requirements:
         - docs
-

docs/api.md

@@ -3,6 +3,7 @@
 ## Environment Specification
 ```{eval-rst}
 .. automodule:: pygenray.environment
+    :members:
 ```
 
 ## Launch Rays

docs/building_notes.md

@@ -38,4 +38,4 @@ actually... scipy might be worth it. Because I can have the ray code done in jus
     - use launched ray and previous bracketing rays and repeat until convergence
 
 
-**where I left off**: I have built out `shoot_rays` and `shoot_ray`, and created a single method that can be called from within the functions that take an environment as input, and when accessing shared memory. But I haven't tested all of that functionality yet.
+**where I left off**: I have built out `shoot_rays` and `shoot_ray`, and created a single method that can be called from within the functions that take an environment as input, and when accessing shared memory. But I haven't tested all of that functionality yet.

docs/conf.py

@@ -6,7 +6,7 @@
 import sys
 
 # Add the source directory to the path so Sphinx can import the modules
-sys.path.insert(0, os.path.abspath('../src'))
+sys.path.insert(0, os.path.abspath("../src"))
 
 project = "pygenray"
 copyright = "2025, John Ragland"

docs/quick_start.md

@@ -1 +0,0 @@
-

docs/ray_physics.md

@@ -4,4 +4,4 @@
 - Environment depth and source / receiver depths are specified with positive z, defined by distance from surface of ocean in meters.
 - The ray state, $y$, defined by $y = \left[\mathrm{T, z, p_z} \right]^T$, uses sign convention where z is negative and increases in z correspond to moving towards the surface.
     - Subsequently, a positive ray angle corresponds to a ray moving towards the surface.
-    - A positive ray ID corresponds to a positive launch angle (towards the surface)
+    - A positive ray ID corresponds to a positive launch angle (towards the surface)

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["hatchling"]
+requires = ["hatchling", "hatch-vcs"]
 build-backend = "hatchling.build"
 
 [project]
@@ -47,7 +47,10 @@ Issues = "https://github.com/John Ragland/pygenray/issues"
 Source = "https://github.com/John Ragland/pygenray"
 
 [tool.hatch.version]
-path = "src/pygenray/__about__.py"
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/pygenray/__about__.py"
 
 [tool.hatch.envs.types]
 extra-dependencies = [
@@ -75,6 +78,9 @@ exclude_lines = [
   "if TYPE_CHECKING:",
 ]
 
+[tool.ruff.lint.per-file-ignores]
+"src/pygenray/__init__.py" = ["F403"]
+
 [dependency-groups]
 dev = [
     "pytest>=8.3.5",