Add tests

.github/workflows/CI.yml

@@ -1,14 +1,15 @@
-# This file is autogenerated by maturin v1.3.0
+# This file is autogenerated by maturin v1.4.0
 # To update, run
 #
-#    maturin generate-ci github
+#    maturin generate-ci github --pytest
 #
 name: CI
 
 on:
   push:
     branches:
       - main
+      - master
     tags:
       - '*'
   pull_request:
@@ -40,6 +41,29 @@ jobs:
         with:
           name: wheels
           path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.target, 'x86_64') }}
+        shell: bash
+        run: |
+          set -e
+          pip install rebop --find-links dist --force-reinstall
+          pip install pytest
+          pytest
+      - name: pytest
+        if: ${{ !startsWith(matrix.target, 'x86') && matrix.target != 'ppc64' }}
+        uses: uraimo/run-on-arch-action@v2.5.0
+        with:
+          arch: ${{ matrix.target }}
+          distro: ubuntu22.04
+          githubToken: ${{ github.token }}
+          install: |
+            apt-get update
+            apt-get install -y --no-install-recommends python3 python3-pip
+            pip3 install -U pip pytest
+          run: |
+            set -e
+            pip3 install rebop --find-links dist --force-reinstall
+            pytest
 
   windows:
     runs-on: windows-latest
@@ -63,6 +87,14 @@ jobs:
         with:
           name: wheels
           path: dist
+      - name: pytest
+        if: ${{ !startsWith(matrix.target, 'aarch64') }}
+        shell: bash
+        run: |
+          set -e
+          pip install rebop --find-links dist --force-reinstall
+          pip install pytest
+          pytest
 
   macos:
     runs-on: macos-latest
@@ -85,6 +117,14 @@ jobs:
         with:
           name: wheels
           path: dist
+      - name: pytest
+        if: ${{ !startsWith(matrix.target, 'aarch64') }}
+        shell: bash
+        run: |
+          set -e
+          pip install rebop --find-links dist --force-reinstall
+          pip install pytest
+          pytest
 
   sdist:
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -12,6 +12,8 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
       - id: mixed-line-ending
+      - id: name-tests-test
+        args: [--pytest-test-first]
   - repo: https://github.com/crate-ci/typos
     rev: v1.17.2
     hooks:

pyproject.toml

@@ -15,6 +15,7 @@ extend-exclude = ["benches/*"]
 target-version = "py39"
 
 [tool.ruff.per-file-ignores]
+"tests/test_*.py" = ["D", "S101", "PLR2004", "ANN201"]
 "examples/*" = ["INP001"]
 "examples/sir.py" = ["T201"]
 "python/rebop/__init__.py" = ["D104"]

tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for the python bindings."""

tests/test_rebop.py

@@ -0,0 +1,36 @@
+import numpy as np
+import numpy.testing as npt
+import pytest
+import rebop
+import xarray as xr
+
+
+def sir_model(transmission: float = 1e-4, recovery: float = 0.01) -> rebop.Gillespie:
+    sir = rebop.Gillespie()
+    sir.add_reaction(transmission, ["S", "I"], ["I", "I"])
+    sir.add_reaction(recovery, ["I"], ["R"])
+    return sir
+
+
+@pytest.mark.parametrize("seed", [None, *range(10)])
+def test_sir(seed: int):
+    sir = sir_model()
+    ds = sir.run({"S": 999, "I": 1}, tmax=250, nb_steps=250, seed=seed)
+    assert isinstance(ds, xr.Dataset)
+    npt.assert_array_equal(ds.time, np.arange(251))
+    assert all(ds.S >= 0)
+    assert all(ds.I >= 0)
+    assert all(ds.R >= 0)
+    assert all(ds.S <= 1000)
+    assert all(ds.I <= 1000)
+    assert all(ds.R <= 1000)
+    npt.assert_array_equal(ds.S + ds.I + ds.R, [1000] * 251)
+
+
+def test_fixed_seed():
+    sir = sir_model()
+    ds = sir.run({"S": 999, "I": 1}, tmax=250, nb_steps=250, seed=42)
+
+    assert ds.S[-1] == 0
+    assert ds.I[-1] == 166
+    assert ds.R[-1] == 834