Updating testing and building infrastructure (#184)

* don't run news check on bot PR * applying updated pre-commit * switching to nox for testing * removing setup.py * news * version for news check * copyright in docs * font on rtds
dfm · Sep 27, 2023 · dbb6bc2 · dbb6bc2
1 parent 1b7798a
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diff --git a/.github/workflows/news.yml b/.github/workflows/news.yml
@@ -2,11 +2,10 @@ name: News
 
 on:
   pull_request:
-    paths-ignore:
-      - ".pre-commit-config.yaml"
 
 jobs:
   news:
+    if: ${{ github.actor != 'dependabot[bot]' && github.actor != 'pre-commit-ci[bot]' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
@@ -15,11 +14,10 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: "3.9"
+          python-version: "3.10"
       - name: Install dependencies
         run: |
           python -m pip install -U pip
-          # FIXME: using github towncrier until next release
-          python -m pip install https://github.com/twisted/towncrier/archive/6b1527b6bf2cbb293ef411ac4f300bd50a5c98ae.zip
+          python -m pip install towncrier
       - name: Check for news
         run: python -m towncrier check --compare-with origin/main
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -13,7 +13,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
+        nox-session: ["test"]
+        include:
+          - python-version: "3.10"
+            nox-session: "doctest"
 
     steps:
       - name: Checkout
@@ -27,68 +31,11 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install -U pip
-          python -m pip install -U coveralls coverage[toml] tox tox-gh-actions
+          python -m pip install nox
       - name: Run tests
-        run: python -m tox
-      - name: Combine and upload coverage
         run: |
-          python -m coverage combine
-          python -m coverage xml -i
-          python -m coveralls --service=github
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_PARALLEL: true
-          COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
-
-  coverage:
-    needs: tests
-    runs-on: ubuntu-latest
-    steps:
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.9"
-      - name: Finish coverage collection
-        run: |
-          python -m pip install -U pip
-          python -m pip install -U coveralls
-          python -m coveralls --finish
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-  doctest:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.9"
-      - name: Install dependencies
-        run: |
-          python -m pip install -U pip
-          python -m pip install tox
-      - name: Lint the code
-        run: python -m tox -e doctest
-
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: "3.9"
-      - name: Install dependencies
-        run: |
-          python -m pip install -U pip
-          python -m pip install tox
-      - name: Lint the code
-        run: python -m tox -e lint
+          python -m nox --non-interactive --error-on-missing-interpreter \
+            --session ${{ matrix.nox-session }} --python ${{ matrix.python-version }}
 
   build:
     runs-on: ubuntu-latest
@@ -99,27 +46,31 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: "3.9"
-      - name: Build sdist and wheel
+          python-version: "3.10"
+      - name: Install dependencies
         run: |
           python -m pip install -U pip
-          python -m pip install -U build
-          python -m build .
+          python -m pip install -U build twine
+      - name: Build the distribution
+        run: python -m build .
+      - name: Check the distribution
+        run: python -m twine check --strict dist/*
       - uses: actions/upload-artifact@v3
         with:
           path: dist/*
 
-  upload_pypi:
-    needs: [tests, lint, build]
+  publish:
+    environment:
+      name: pypi
+      url: https://pypi.org/p/tinygp
+    permissions:
+      id-token: write
+    needs: [tests, build]
     runs-on: ubuntu-latest
-    if: startsWith(github.ref, 'refs/tags/')
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/')
     steps:
       - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
-
       - uses: pypa/[email protected]
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,6 @@
 *_version.py
 .coverage
+.nox
 .tox
 .coverage*
 /*.ipynb

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,31 +3,22 @@ ci:
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: "v4.4.0"
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
         exclude_types: [json, binary]
-  - repo: https://github.com/PyCQA/isort
-    rev: "5.12.0"
-    hooks:
-      - id: isort
-        additional_dependencies: [toml]
-        exclude: docs/tutorials
   - repo: https://github.com/psf/black
-    rev: "23.7.0"
+    rev: "23.9.1"
     hooks:
       - id: black-jupyter
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.0.291"
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/kynan/nbstripout
     rev: "0.6.1"
     hooks:
       - id: nbstripout
         exclude: docs/benchmarks.ipynb
-  - repo: https://github.com/hadialqattan/pycln
-    rev: "v2.2.2"
-    hooks:
-      - id: pycln
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.5.1"
-    hooks:
-      - id: mypy
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,7 +1,13 @@
 version: 2
 
+build:
+  os: ubuntu-20.04
+  apt_packages:
+    - fonts-liberation
+  tools:
+    python: "3.10"
+
 python:
-  version: 3.8
   install:
     - method: pip
       path: .

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -34,8 +34,8 @@ Tracker](https://github.com/dfm/tinygp/issues).
 ## How to test the project
 
 ```bash
-python -m pip install tox
-python -m tox
+python -m pip install nox
+python -m nox -s test -p 3.10
 ```
 
 ## How to submit changes

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright 2021, 2022 Simons Foundation, Inc.
+Copyright 2021, 2022, 2023 Simons Foundation, Inc.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/docs/benchmarks.ipynb b/docs/benchmarks.ipynb
@@ -145,9 +145,7 @@
     "    return gp.log_likelihood(y)\n",
     "\n",
     "\n",
-    "hodlr_loglike = partial(\n",
-    "    george_loglike, solver=george.solvers.HODLRSolver, tol=0.5\n",
-    ")\n",
+    "hodlr_loglike = partial(george_loglike, solver=george.solvers.HODLRSolver, tol=0.5)\n",
     "\n",
     "\n",
     "def celerite_loglike(x, y):\n",
@@ -340,9 +338,7 @@
     "    lw=1,\n",
     "    label=\"george (approx)\",\n",
     ")\n",
-    "plt.loglog(\n",
-    "    ns, celerite_time, \"^--\", color=\"k\", lw=0.75, label=\"celerite2 (struct)\"\n",
-    ")\n",
+    "plt.loglog(ns, celerite_time, \"^--\", color=\"k\", lw=0.75, label=\"celerite2 (struct)\")\n",
     "\n",
     "plt.loglog(\n",
     "    ns[: len(cpu_time)],\n",
@@ -360,9 +356,7 @@
     "    lw=2,\n",
     "    label=\"tinygp (exact; GPU)\",\n",
     ")\n",
-    "plt.loglog(\n",
-    "    ns, quasisep_time, \"^--\", color=\"C2\", lw=2, label=\"tinygp (struct; CPU)\"\n",
-    ")\n",
+    "plt.loglog(ns, quasisep_time, \"^--\", color=\"C2\", lw=2, label=\"tinygp (struct; CPU)\")\n",
     "\n",
     "plt.legend(fontsize=10)\n",
     "plt.xlabel(\"number of data points\")\n",

diff --git a/docs/conf.py b/docs/conf.py
@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 import tinygp
 
 extensions = [
@@ -22,7 +20,7 @@
 
 # General information about the project.
 project = "tinygp"
-copyright = tinygp.__copyright__
+copyright = "2021, 2022, 2023 Simons Foundation, Inc."
 version = tinygp.__version__
 release = tinygp.__version__
 

diff --git a/docs/index.md b/docs/index.md
@@ -41,7 +41,7 @@ GitHub Repository <https://github.com/dfm/tinygp>
 
 ## Authors & license
 
-Copyright 2021, 2022 Simons Foundation, Inc.
+Copyright 2021, 2022, 2023 Simons Foundation, Inc.
 
 Built by [Dan Foreman-Mackey](https://github.com/dfm) and contributors (see [the
 contribution graph](https://github.com/dfm/tinygp/graphs/contributors) for the

diff --git a/docs/install.md b/docs/install.md
@@ -34,6 +34,6 @@ If you installed from source, you can run the unit tests. From the root of the
 source directory, run:
 
 ```bash
-python -m pip install tox
-python -m tox
+python -m pip install nox
+python -m nox -s test -p 3.10
 ```
diff --git a/docs/tutorials/derivative.ipynb b/docs/tutorials/derivative.ipynb
@@ -71,9 +71,7 @@
     "        -np.sin(X) + 2 * np.cos(2 * X),\n",
     "    )\n",
     ")\n",
-    "flag = np.concatenate(\n",
-    "    (np.zeros(len(X), dtype=bool), np.ones(len(X), dtype=bool))\n",
-    ")\n",
+    "flag = np.concatenate((np.zeros(len(X), dtype=bool), np.ones(len(X), dtype=bool)))\n",
     "X = np.concatenate((X, X))\n",
     "y += 0.1 * np.random.default_rng(1234).normal(size=len(y))\n",
     "\n",
@@ -215,9 +213,7 @@
     "    kernel = DerivativeKernel(base_kernel)\n",
     "\n",
     "    # Note that we're passing in (X, flag) as the input coordinates.\n",
-    "    return tinygp.GaussianProcess(\n",
-    "        kernel, (X, flag), diag=jnp.exp(params[\"log_diag\"])\n",
-    "    )\n",
+    "    return tinygp.GaussianProcess(kernel, (X, flag), diag=jnp.exp(params[\"log_diag\"]))\n",
     "\n",
     "\n",
     "@jax.jit\n",
@@ -337,12 +333,7 @@
     "        b2 = self.coeff_deriv[label2]\n",
     "\n",
     "        # Construct the matrix element\n",
-    "        return (\n",
-    "            a1 * a2 * K\n",
-    "            + a1 * b2 * dK_dx2\n",
-    "            + b1 * a2 * dK_dx1\n",
-    "            + b1 * b2 * d2K_dx1dx2\n",
-    "        )"
+    "        return a1 * a2 * K + a1 * b2 * dK_dx2 + b1 * a2 * dK_dx1 + b1 * b2 * d2K_dx1dx2"
    ]
   },
   {
@@ -363,9 +354,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "base_kernel = tinygp.kernels.ExpSquared(\n",
-    "    scale=1.5\n",
-    ") * tinygp.kernels.ExpSineSquared(scale=2.5, gamma=0.5)\n",
+    "base_kernel = tinygp.kernels.ExpSquared(scale=1.5) * tinygp.kernels.ExpSineSquared(\n",
+    "    scale=2.5, gamma=0.5\n",
+    ")\n",
     "kernel = LatentKernel(base_kernel, [1.0, 0.5], [-0.1, 0.3])\n",
     "\n",
     "random = np.random.default_rng(5678)\n",
@@ -424,12 +415,8 @@
     "    ) * tinygp.kernels.ExpSineSquared(\n",
     "        scale=jnp.exp(params[\"log_period\"]), gamma=params[\"gamma\"]\n",
     "    )\n",
-    "    kernel = LatentKernel(\n",
-    "        base_kernel, params[\"coeff_prim\"], params[\"coeff_deriv\"]\n",
-    "    )\n",
-    "    return tinygp.GaussianProcess(\n",
-    "        kernel, X_obs, diag=jnp.exp(params[\"log_diag\"])\n",
-    "    )\n",
+    "    kernel = LatentKernel(base_kernel, params[\"coeff_prim\"], params[\"coeff_deriv\"])\n",
+    "    return tinygp.GaussianProcess(kernel, X_obs, diag=jnp.exp(params[\"log_diag\"]))\n",
     "\n",
     "\n",
     "@jax.jit\n",

diff --git a/docs/tutorials/geometry.ipynb b/docs/tutorials/geometry.ipynb
@@ -83,19 +83,15 @@
     "random = np.random.default_rng(456)\n",
     "X_obs = random.normal(size=(100, 3))\n",
     "X_obs /= np.sqrt(np.sum(X_obs**2, axis=1))[:, None]\n",
-    "theta_obs = np.arctan2(\n",
-    "    X_obs[:, 2], np.sqrt(X_obs[:, 0] ** 2 + X_obs[:, 1] ** 2)\n",
-    ")\n",
+    "theta_obs = np.arctan2(X_obs[:, 2], np.sqrt(X_obs[:, 0] ** 2 + X_obs[:, 1] ** 2))\n",
     "phi_obs = np.arctan2(X_obs[:, 1], X_obs[:, 0])\n",
     "\n",
     "# Our kernel is parameterized by a length scale in **radians**\n",
     "ell = 0.5\n",
     "kernel = 1.5 * kernels.Matern52(ell, distance=GreatCircleDistance())\n",
     "\n",
     "# Sample a simulated dataset\n",
-    "gp = GaussianProcess(\n",
-    "    kernel, np.concatenate((X_grid, X_obs), axis=0), diag=0.01\n",
-    ")\n",
+    "gp = GaussianProcess(kernel, np.concatenate((X_grid, X_obs), axis=0), diag=0.01)\n",
     "y_samp = gp.sample(jax.random.PRNGKey(10))\n",
     "y_grid = y_samp[: len(X_grid)]\n",
     "y_obs = y_samp[len(X_grid) :] + 0.5 * random.normal(size=len(X_obs))\n",

diff --git a/docs/tutorials/ipython_kernel_config.py b/docs/tutorials/ipython_kernel_config.py
@@ -1,3 +1 @@
-# mypy: ignore-errors
-
-c.InlineBackend.rc = {}
+c.InlineBackend.rc = {}  # noqa