[pre-commit.ci] pre-commit autoupdate (#219)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.6 → v0.6.3](astral-sh/ruff-pre-commit@v0.5.6...v0.6.3) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * lint settings --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Dan F-M <[email protected]>
dfm · Sep 7, 2024 · ef9fac4 · ef9fac4
1 parent 6c01d9f
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
     hooks:
       - id: black-jupyter
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.5.6"
+    rev: "v0.6.3"
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

diff --git a/docs/benchmarks.ipynb b/docs/benchmarks.ipynb
@@ -118,13 +118,12 @@
    "source": [
     "from functools import partial\n",
     "\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "\n",
+    "import celerite2\n",
+    "import george\n",
     "import jax\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
-    "import george\n",
-    "import celerite2\n",
     "import tinygp\n",
     "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",

diff --git a/docs/tutorials/derivative.ipynb b/docs/tutorials/derivative.ipynb
@@ -60,9 +60,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "\n",
+    "import numpy as np\n",
     "\n",
     "X = np.linspace(0.0, 5 * np.pi, 50)\n",
     "y = np.concatenate(\n",
@@ -97,10 +96,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import tinygp\n",
     "import jax\n",
     "import jax.numpy as jnp\n",
     "\n",
+    "import tinygp\n",
+    "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",
     "\n",
     "\n",
@@ -169,10 +169,10 @@
     "    )[0]\n",
     "\n",
     "    plt.figure()\n",
-    "    plt.plot(dt, k00, label=\"$\\mathrm{cov}(f,\\,f)$\", lw=1)\n",
-    "    plt.plot(dt, k01, label=\"$\\mathrm{cov}(f,\\,\\dot{f})$\", lw=1)\n",
-    "    plt.plot(dt, k10, label=\"$\\mathrm{cov}(\\dot{f},\\,f)$\", lw=1)\n",
-    "    plt.plot(dt, k11, label=\"$\\mathrm{cov}(\\dot{f},\\,\\dot{f})$\", lw=1)\n",
+    "    plt.plot(dt, k00, label=r\"$\\mathrm{cov}(f,\\,f)$\", lw=1)\n",
+    "    plt.plot(dt, k01, label=r\"$\\mathrm{cov}(f,\\,\\dot{f})$\", lw=1)\n",
+    "    plt.plot(dt, k10, label=r\"$\\mathrm{cov}(\\dot{f},\\,f)$\", lw=1)\n",
+    "    plt.plot(dt, k11, label=r\"$\\mathrm{cov}(\\dot{f},\\,\\dot{f})$\", lw=1)\n",
     "    plt.legend()\n",
     "    plt.xlabel(r\"$\\Delta t$\")\n",
     "    plt.xlim(dt.min(), dt.max())\n",

diff --git a/docs/tutorials/geometry.ipynb b/docs/tutorials/geometry.ipynb
@@ -47,11 +47,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
     "import jax\n",
     "import jax.numpy as jnp\n",
-    "from tinygp import kernels, GaussianProcess\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "\n",
+    "from tinygp import GaussianProcess, kernels\n",
     "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",
     "\n",

diff --git a/docs/tutorials/intro.ipynb b/docs/tutorials/intro.ipynb
@@ -82,8 +82,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "\n",
     "def plot_kernel(kernel, **kwargs):\n",

diff --git a/docs/tutorials/kernels.ipynb b/docs/tutorials/kernels.ipynb
@@ -48,10 +48,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import tinygp\n",
     "import jax\n",
     "import jax.numpy as jnp\n",
     "\n",
+    "import tinygp\n",
+    "\n",
     "\n",
     "class SpectralMixture(tinygp.kernels.Kernel):\n",
     "    weight: jax.Array\n",
@@ -85,8 +86,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "\n",
     "def build_gp(theta):\n",

diff --git a/docs/tutorials/likelihoods.ipynb b/docs/tutorials/likelihoods.ipynb
@@ -54,8 +54,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "random = np.random.default_rng(203618)\n",
     "x = np.linspace(-3, 3, 20)\n",
@@ -90,7 +90,8 @@
     "import jax.numpy as jnp\n",
     "import numpyro\n",
     "import numpyro.distributions as dist\n",
-    "from tinygp import kernels, GaussianProcess\n",
+    "\n",
+    "from tinygp import GaussianProcess, kernels\n",
     "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",
     "\n",

diff --git a/docs/tutorials/means.ipynb b/docs/tutorials/means.ipynb
@@ -52,10 +52,11 @@
    "outputs": [],
    "source": [
     "from functools import partial\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
+    "\n",
     "import jax\n",
     "import jax.numpy as jnp\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",
     "\n",
@@ -172,7 +173,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from tinygp import kernels, GaussianProcess\n",
+    "from tinygp import GaussianProcess, kernels\n",
     "\n",
     "\n",
     "def build_gp(params):\n",

diff --git a/docs/tutorials/mixture.ipynb b/docs/tutorials/mixture.ipynb
@@ -66,9 +66,8 @@
    "source": [
     "import jax\n",
     "import jax.numpy as jnp\n",
-    "\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "from tinygp import GaussianProcess, kernels, transforms\n",
     "\n",

diff --git a/docs/tutorials/modeling.ipynb b/docs/tutorials/modeling.ipynb
@@ -67,8 +67,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "random = np.random.default_rng(42)\n",
     "\n",
@@ -120,15 +120,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from tinygp import kernels, GaussianProcess\n",
-    "\n",
+    "import flax.linen as nn\n",
     "import jax\n",
     "import jax.numpy as jnp\n",
-    "\n",
-    "import flax.linen as nn\n",
+    "import optax\n",
     "from flax.linen.initializers import zeros\n",
     "\n",
-    "import optax\n",
+    "from tinygp import GaussianProcess, kernels\n",
     "\n",
     "\n",
     "class GPModule(nn.Module):\n",

diff --git a/docs/tutorials/multivariate.ipynb b/docs/tutorials/multivariate.ipynb
@@ -74,8 +74,9 @@
    "outputs": [],
    "source": [
     "import jax\n",
-    "import numpy as np\n",
     "import jax.numpy as jnp\n",
+    "import numpy as np\n",
+    "\n",
     "from tinygp import kernels\n",
     "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",
@@ -117,8 +118,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "random = np.random.default_rng(48392)\n",
     "X = random.uniform(-5, 5, (100, 2))\n",
@@ -163,6 +164,7 @@
    "outputs": [],
    "source": [
     "import jaxopt\n",
+    "\n",
     "from tinygp import GaussianProcess, kernels, transforms\n",
     "\n",
     "\n",

diff --git a/docs/tutorials/quasisep-custom.ipynb b/docs/tutorials/quasisep-custom.ipynb
@@ -131,8 +131,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "random = np.random.default_rng(394)\n",
     "t = np.sort(random.uniform(0, 10, 700))\n",

diff --git a/docs/tutorials/quasisep.ipynb b/docs/tutorials/quasisep.ipynb
@@ -57,8 +57,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "random = np.random.default_rng(42)\n",
     "\n",
@@ -108,7 +108,7 @@
     "import jax\n",
     "import jax.numpy as jnp\n",
     "\n",
-    "from tinygp import kernels, GaussianProcess\n",
+    "from tinygp import GaussianProcess, kernels\n",
     "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",
     "\n",

diff --git a/docs/tutorials/quickstart.ipynb b/docs/tutorials/quickstart.ipynb
@@ -48,8 +48,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "from statsmodels.datasets import co2\n",
     "\n",
     "data = co2.load_pandas().data\n",
@@ -102,8 +102,7 @@
     "import jax\n",
     "import jax.numpy as jnp\n",
     "\n",
-    "from tinygp import kernels, GaussianProcess\n",
-    "\n",
+    "from tinygp import GaussianProcess, kernels\n",
     "\n",
     "jax.config.update(\"jax_enable_x64\", True)\n",
     "\n",

diff --git a/docs/tutorials/transforms.ipynb b/docs/tutorials/transforms.ipynb
@@ -61,8 +61,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
     "\n",
     "random = np.random.default_rng(567)\n",
     "\n",
@@ -99,12 +99,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import flax.linen as nn\n",
     "import jax\n",
-    "import optax\n",
     "import jax.numpy as jnp\n",
-    "import flax.linen as nn\n",
+    "import optax\n",
     "from flax.linen.initializers import zeros\n",
-    "from tinygp import kernels, transforms, GaussianProcess"
+    "\n",
+    "from tinygp import GaussianProcess, kernels, transforms"
    ]
   },
   {

diff --git a/pyproject.toml b/pyproject.toml
@@ -50,6 +50,8 @@ line-length = 88
 [tool.ruff]
 target-version = "py39"
 line-length = 88
+
+[tool.ruff.lint]
 select = ["F", "I", "E", "W", "YTT", "B", "Q", "PLE", "PLR", "PLW", "UP"]
 ignore = [
     "E741",    # Allow ambiguous variable names
@@ -60,7 +62,15 @@ ignore = [
 ]
 exclude = []
 
-[tool.ruff.isort]
+[tool.ruff.lint.per-file-ignores]
+"docs/tutorials/*.ipynb" = [
+    "B007",  # Loop variable is not used
+    "E501",  # Line too long
+    "E731",  # Do not assign a lambda expression
+    "F401",  # Unused imports
+]
+
+[tool.ruff.lint.isort]
 known-first-party = ["tinygp"]
 combine-as-imports = true