Add pre-commit hooks, Ruff formatting and linting (#42)

.github/workflows/pre-commit.yaml

@@ -0,0 +1,19 @@
+name: pre-commit hooks
+
+on:
+ pull_request:
+ push:
+ branches:
+ - main
+
+jobs:
+ pre-commit:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: actions/setup-python@v4
+ with:
+ python-version: 3.11.5
+
+ - uses: pre-commit/action@v3.0.0

.pre-commit-config.yaml

@@ -0,0 +1,17 @@
+repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v2.3.0
+ hooks:
+ - id: check-yaml
+ args: [--unsafe]
+ - id: end-of-file-fixer
+ - id: trailing-whitespace
+
+ - repo: https://github.com/astral-sh/ruff-pre-commit
+ rev: v0.1.11
+ hooks:
+ - id: ruff
+ # types_or: [ python, pyi, jupyter ]
+
+ - id: ruff-format
+ # types_or: [ python, pyi, jupyter ]

DEVELOPING.md

@@ -0,0 +1,34 @@
+# Developer's Guide
+
+This guide describes how to complete various tasks you'll encounter when working
+on the Bayes3D codebase.
+
+### Commit Hooks
+
+We use [pre-commit](https://pre-commit.com/) to manage a series of git
+pre-commit hooks for the project; for example, each time you commit code, the
+hooks will make sure that your python is formatted properly. If your code isn't,
+the hook will format it, so when you try to commit the second time you'll get
+past the hook.
+
+All hooks are defined in `.pre-commit-config.yaml`. To install these hooks,
+install `pre-commit` if you don't yet have it. I prefer using
+[pipx](https://github.com/pipxproject/pipx) so that `pre-commit` stays globally
+available.
+
+```bash
+pipx install pre-commit
+```
+
+Then install the hooks with this command:
+
+```bash
+pre-commit install
+```
+
+Now they'll run on every commit. If you want to run them manually, run the
+following command:
+
+```bash
+pre-commit run --all-files
+```

assets/sample_objs/bunny.obj

@@ -7469,4 +7469,4 @@ f 2411 1493 2503
 f 1493 1487 2503
 f 1487 1318 2503
 f 1318 1320 2503
-f 1320 2443 2503
+f 1320 2443 2503

assets/sample_objs/cube.obj

@@ -58,4 +58,4 @@ f 15//15 23//23 17//17
 f 3//3 14//14 16//16
 f 3//3 16//16 6//6
 f 4//4 18//18 22//22
-f 4//4 22//22 11//11
+f 4//4 22//22 11//11

assets/sample_objs/diamond.obj

@@ -13,4 +13,4 @@ f 6 5 4
 f 6 4 3
 f 6 3 2
 f 6 2 1
-f 6 1 5
+f 6 1 5

assets/sample_objs/icosahedron.obj

@@ -29,4 +29,4 @@ f 12 11 6
 f 10 9 5
 f 8 3 9
 f 10 8 9
-f 2 8 10
+f 2 8 10

assets/sample_objs/occulder.obj

@@ -26,4 +26,4 @@ f 4//4 8//8 3//3
 f 7//7 5//5 3//3
 f 3//3 8//8 7//7
 f 7//7 6//6 5//5
-f 8//8 6//6 7//7
+f 8//8 6//6 7//7

assets/sample_objs/pyramid.obj

@@ -9,4 +9,4 @@ f 3 4 2
 f 5 2 1
 f 4 5 1
 f 3 5 4
-f 5 3 2
+f 5 3 2

assets/sample_objs/sphere.obj

@@ -806,4 +806,4 @@ f 17/17/17 159/159/159 158/158/158
 f 13/13/13 157/157/157 159/159/159
 f 14/14/14 160/160/160 161/161/161
 f 15/15/15 161/161/161 162/162/162
-f 13/13/13 162/162/162 160/160/160
+f 13/13/13 162/162/162 160/160/160

bayes3d/__init__.py

@@ -1,24 +1,12 @@
 """
 .. include:: ./documentation.md
 """
-from .transforms_3d import *
+
+from .camera import *
+from .likelihood import *
 from .renderer import *
 from .rgbd import *
-from .likelihood import *
-from .camera import *
+from .transforms_3d import *
 from .viz import *
-from . import utils
-from . import distributions
-from . import scene_graph
-from . import colmap
-
-try:
- import genjax
- from .genjax import *
-except ImportError as e:
- print("GenJAX not installed. Importing bayes3d without genjax dependencies.")
- print(e)
-
-
 
 RENDERER = None

bayes3d/_mkl/gaussian_particle_system_v0.py

@@ -1,40 +1,39 @@
 # AUTOGENERATED! DO NOT EDIT! File to edit: ../../scripts/_mkl/notebooks/07a - Gaussian particle system v0.ipynb.
 
 # %% auto 0
-__all__ = ['normal_cdf', 'normal_pdf', 'normal_logpdf', 'inv', 'key', 'Array', 'Shape', 'Bool', 'Float', 'Int', 'Pose']
+__all__ = [
+ "normal_cdf",
+ "normal_pdf",
+ "normal_logpdf",
+ "inv",
+ "key",
+ "Array",
+ "Shape",
+ "Bool",
+ "Float",
+ "Int",
+ "Pose",
+]
 
 # %% ../../scripts/_mkl/notebooks/07a - Gaussian particle system v0.ipynb 2
-import bayes3d as b3d
-import trimesh
-import os
-from bayes3d._mkl.utils import *
-import matplotlib.pyplot as plt
-import numpy as np
 import jax
-from jax import jit, vmap
 import jax.numpy as jnp
-from jax.scipy.spatial.transform import Rotation as Rot
-from functools import partial
-import genjax
-from bayes3d.camera import Intrinsics, K_from_intrinsics, camera_rays_from_intrinsics
-from bayes3d.transforms_3d import transform_from_pos_target_up, add_homogenous_ones, unproject_depth
-import tensorflow_probability as tfp
-from tensorflow_probability.substrates.jax.math import lambertw
-
+import numpy as np
 
+from bayes3d._mkl.utils import *
 
-normal_cdf  = jax.scipy.stats.norm.cdf
-normal_pdf  = jax.scipy.stats.norm.pdf
+normal_cdf = jax.scipy.stats.norm.cdf
+normal_pdf = jax.scipy.stats.norm.pdf
 normal_logpdf = jax.scipy.stats.norm.logpdf
 inv = jnp.linalg.inv
 
 key = jax.random.PRNGKey(0)
 
 # %% ../../scripts/_mkl/notebooks/07a - Gaussian particle system v0.ipynb 4
-from typing import Any, NamedTuple
-import numpy as np
+from typing import NamedTuple
+
 import jax
-import jaxlib
+import numpy as np
 
 Array = np.ndarray | jax.Array
 Shape = int | tuple[int, ...]