Refactor to allow mixed Python Rust code

.github/workflows/pytest.yml

@@ -68,6 +68,6 @@ jobs:
       - name: Test Python
         working-directory: python
         run: |
-          uv run pytest
+          uv run pytest tests
         shell: bash
 

.github/workflows/website.yml

@@ -19,8 +19,8 @@ on:
       - crates/gp/examples/**
       - website/**
       - notebooks/**
-      - python/egobox/examples/*.py
-      - python/egobox/tests/test_examples.py
+      - python/examples/*.py
+      - python/tests/test_examples.py
   workflow_dispatch:
 
 permissions:
@@ -80,7 +80,7 @@ jobs:
 
       - name: Verify website examples
         working-directory: python
-        run: uv run pytest egobox/tests/test_examples.py
+        run: uv run pytest tests/test_examples.py
 
       - name: Install Zola
         uses: taiki-e/install-action@v2

README.md

@@ -71,7 +71,7 @@ plt.show()
 
 See also [this example written in Rust](crates/gp/examples/kriging.rs)
 
-See the [tutorial notebooks](https://github.com/relf/egobox/tree/master/notebooks/README.md) and [examples folder](https://github.com/relf/egobox/tree/d9db0248199558f23d966796737d7ffa8f5de589/python/egobox/examples) for more information on the usage of the optimizer and mixture of Gaussian processes surrogate model.
+See the [tutorial notebooks](https://github.com/relf/egobox/tree/master/notebooks/README.md) and [examples folder](https://github.com/relf/egobox/tree/master/python/examples) for more information on the usage of the optimizer and mixture of Gaussian processes surrogate model.
 
 ## The Rust libraries
 

python/Cargo.toml

@@ -11,7 +11,7 @@ readme = "README.md"
 publish = false
 
 [lib]
-name = "egobox"
+name = "_rust"
 crate-type = ["cdylib", "rlib"]
 doctest = false                 # do not doctest as doc uses Python style for Python API doc
 

python/README.md

@@ -55,4 +55,4 @@ plt.plot(xtrain, ytrain, "o")
 plt.show()
 ```
 
-See the [tutorial notebooks](https://github.com/relf/egobox/tree/master/notebooks/README.md) and [examples folder](https://github.com/relf/egobox/tree/d9db0248199558f23d966796737d7ffa8f5de589/python/egobox/examples) for more information on the usage of the optimizer and mixture of Gaussian processes surrogate model.
+See the [tutorial notebooks](https://github.com/relf/egobox/tree/master/notebooks/README.md) and [examples folder](https://github.com/relf/egobox/tree/master/python/examples) for more information on the usage of the optimizer and mixture of Gaussian processes surrogate model.

python/egobox/__init__.py

@@ -1 +1,36 @@
-from .egobox import *  # noqa
+# Public API - re-export all symbols from the Rust extension
+# ruff: noqa: F405
+from ._rust import *  # noqa
+
+__all__ = [
+    "ConstraintStrategy",
+    "CorrelationSpec",
+    "CstrSpec",
+    "Egor",
+    "EgorOptim",
+    "ExitStatus",
+    "FailsafeStrategy",
+    "FeasibleInfillStrategy",
+    "GpConfig",
+    "GpMix",
+    "Gpx",
+    "InfillOptimizer",
+    "InfillStrategy",
+    "OptimResult",
+    "QEiConfig",
+    "QEiStrategy",
+    "Recombination",
+    "RegressionSpec",
+    "RunInfo",
+    "RunStatus",
+    "Sampling",
+    "SparseGpMix",
+    "SparseGpx",
+    "SparseMethod",
+    "TregoConfig",
+    "Verbose",
+    "XSpec",
+    "XType",
+    "lhs",
+    "sampling",
+]  # noqa

python/egobox/examples/kriging.py → python/examples/kriging.py

@@ -3,11 +3,14 @@
 import matplotlib
 import numpy as np
 import matplotlib.pyplot as plt
+import egobox as egx
+import warnings
+
+warnings.filterwarnings("ignore", category=UserWarning)
 
 # Comment out the following line to display the plot in a window
 matplotlib.use("Agg")
 
-import egobox as egx
 
 xt = np.array([[0.0, 1.0, 1.5, 2.0, 3.0, 4.0]]).T
 yt = np.array([[0.0, 1.0, 1.7, 1.5, 0.9, 1.0]]).T

python/egobox/examples/rastrigin.py → python/examples/rastrigin.py

@@ -9,6 +9,10 @@
 import egobox as egx
 import matplotlib.pyplot as plt
 
+import warnings
+
+warnings.filterwarnings("ignore", category=UserWarning)
+
 # Comment out the following line to display the plot in a window
 matplotlib.use("Agg")
 

python/pyproject.toml

@@ -38,7 +38,8 @@ dev = [
 ]
 
 [tool.maturin]
-module-name = "egobox"
+python-source = "."
+module-name = "egobox._rust"
 features = ["pyo3/extension-module"]
 # Optional usage of BLAS backend 
 # cargo-extra-args = "--features linfa/intel-mkl-static"

python/src/bin/stub_gen.rs

@@ -2,7 +2,16 @@ use pyo3_stub_gen::Result;
 
 fn main() -> Result<()> {
     env_logger::Builder::from_env(env_logger::Env::default().filter_or("RUST_LOG", "info")).init();
-    let stub = egobox::stub_info()?;
+    let stub = _rust::stub_info()?;
     stub.generate()?;
+
+    // The Rust stub generator generates a stub file in the python/egobox/_rust directory,
+    // As Python API is the same as core Rust API, we move the stub file to python/egobox/egobox.pyi
+    log::info!("Moving stub file to egobox/egobox.pyi");
+    let from = std::path::Path::new("python/egobox/_rust/__init__.pyi");
+    let to = std::path::Path::new("python/egobox/egobox.pyi");
+    std::fs::rename(from, to).expect(
+        "Should move stub file to egobox/egobox.pyi. Ensure to run this command from the root of the repository, and that the stub file exists.",
+    );
     Ok(())
 }

python/src/lib.rs

@@ -29,7 +29,7 @@ fn _run_gpx_cli(args: Vec<String>) -> i32 {
 
 #[doc(hidden)]
 #[pymodule]
-fn egobox(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
+fn _rust(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
     // egobox version
     m.add("__version__", env!("CARGO_PKG_VERSION"))?;
 

python/egobox/tests/test_gpx_cli.py → python/tests/test_gpx_cli.py

@@ -1,8 +1,8 @@
-from egobox import egobox as native
+import egobox as egx
 
 
 def test_gpx_help_exit_code_zero(capfd):
-    code = native._run_gpx_cli(["--help"])
+    code = egx._rust._run_gpx_cli(["--help"])
 
     assert code == 0
     out, err = capfd.readouterr()

website/content/examples/index.md

@@ -5,15 +5,15 @@ weight = 20
 
 # Examples
 
-The Python snippets below are included directly from source files under [`python/egobox/examples`](https://github.com/relf/EGObox/tree/master/python/egobox/examples/).
+The Python snippets below are included directly from source files under [`python/examples`](https://github.com/relf/EGObox/tree/master/python/examples/).
 Here you can just copy-paste the code to run it locally, or click on the links to open the source files in a new tab.
 
 ## Optimization with _Egor_
 
-### Unconstrained optimization: [Rastrigin](https://github.com/relf/EGObox/blob/master/python/egobox/examples/rastrigin.py)
+### Unconstrained optimization: [Rastrigin](https://github.com/relf/EGObox/blob/master/python/examples/rastrigin.py)
 
 {{ include_code(
-    url="https://raw.githubusercontent.com/relf/EGObox/master/python/egobox/examples/rastrigin.py",
+    url="https://raw.githubusercontent.com/relf/EGObox/master/python/examples/rastrigin.py",
     lang="python")
 }}
 
@@ -27,10 +27,10 @@ Best point (x*): [ 0.00415341 -0.00058284]
 
 ![Rastrigin function optimization](img/rastrigin.png)
 
-### Constrained optimization: [G24](https://github.com/relf/EGObox/blob/master/python/egobox/examples/g24.py)
+### Constrained optimization: [G24](https://github.com/relf/EGObox/blob/master/python/examples/g24.py)
 
 {{ include_code(
-    url="https://raw.githubusercontent.com/relf/EGObox/master/python/egobox/examples/g24.py",
+    url="https://raw.githubusercontent.com/relf/EGObox/master/python/examples/g24.py",
     lang="python")
 }}
 
@@ -40,10 +40,10 @@ Optimization f=[-5.50853583e+00  8.65985077e-04  3.83913510e-04] at [2.32948272
 
 ## Surrogate modeling with _Gpx_
 
-### Simple surrogate model: [Kriging](https://github.com/relf/EGObox/blob/master/python/egobox/examples/kriging.py)
+### Simple surrogate model: [Kriging](https://github.com/relf/EGObox/blob/master/python/examples/kriging.py)
 
 {{ include_code(
-    url="https://raw.githubusercontent.com/relf/EGObox/master/python/egobox/examples/kriging.py",
+    url="https://raw.githubusercontent.com/relf/EGObox/master/python/examples/kriging.py",
     lang="python")
 }}
 

website/content/reference.md

@@ -22,5 +22,5 @@ weight = 60
 
 - [Github repository](https://github.com/relf/EGObox)
 - [Notebook index](https://github.com/relf/EGObox/blob/master/notebooks/README.md)
-- [Python examples directory](https://github.com/relf/EGObox/tree/master/python/egobox/examples)
+- [Python examples directory](https://github.com/relf/EGObox/tree/master/python/examples)
 - [Rust crate directory](https://github.com/relf/EGObox/tree/master/crates)