Refactor repository: sub-crates under crates directory (#226)

* Move sub-crates under crates directory

* Move python binding under python

* Adjust Python tools: use uv, ruff

* Adjust gitignore and remove poetry.lock

* Add uv lock

* Adjust pyproject, gitignore, pytest

* Adjust python action

* Adjust pytest action

* ruff format

* Adjust pytest action

* Fix ubuntu os name

* Adjust toml

* Use maturin action

* Adjust toml

* Import all rust symbols

* Add pre-commit

* Fix format

* DRY dependencies

.github/workflows/pytest.yml

@@ -23,35 +23,52 @@ jobs:
           - ubuntu-latest
           - windows-latest
           - macos-latest
+    env:
+      UV_CACHE_DIR: /tmp/.uv-cache
+      RUST_BACKTRACE: 1
 
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
+      - name: Set up uv
+        if: ${{ matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' }}
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Set up uv
+        if: ${{ matrix.os == 'windows-latest' }}
+        run: irm https://astral.sh/uv/install.ps1 | iex
+        shell: powershell
 
-      - name: Install Rust
-        uses: actions-rs/toolchain@v1
+      - name: Cache folder for uv
+        uses: actions/cache@v4
         with:
-          toolchain: stable
-          default: true
+          path: /tmp/.uv-cache
+          key: uv-${{ runner.os }}-${{ hashFiles('uv.lock') }}
+          restore-keys: |
+            uv-${{ runner.os }}-${{ hashFiles('uv.lock') }}
+            uv-${{ runner.os }}
 
-      - name: Log active toolchain
-        run: rustup show
+      - name: Install the project
+        working-directory: python
+        run: uv sync --all-extras --dev --python ${{ matrix.python-version }}
 
-      - name: Install test dependencies
+      - name: Build the wrapper
+        uses: PyO3/maturin-action@v1
+        with:
+          working-directory: python
+          command: develop
+          args: --release
+          sccache: 'true'
+
+      - name: Run linter and formatter
+        working-directory: python
         run: |
-          python -m pip install --upgrade pip
-          pip install maturin numpy pytest poetry
+          uv run ruff check
+          uv run ruff format --check
 
       - name: Test Python
+        working-directory: python
         run: |
-            poetry install
-            poetry run maturin develop --release
-            poetry run pytest
+          uv run pytest
         shell: bash
 
-    env:
-      RUST_BACKTRACE: 1

.github/workflows/python.yml

@@ -27,6 +27,7 @@ jobs:
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
+          working-directory: python
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
@@ -51,6 +52,7 @@ jobs:
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
+          working-directory: python
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
@@ -73,6 +75,7 @@ jobs:
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
+          working-directory: python
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
@@ -89,6 +92,7 @@ jobs:
       - name: Build sdist
         uses: PyO3/maturin-action@v1
         with:
+          working-directory: python
           command: build
           args: --sdist --out dist --release
       - name: Upload sdist
@@ -111,5 +115,6 @@ jobs:
         env:
           MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
         with:
+          working-directory: python
           command: upload
           args: --non-interactive --skip-existing *

.gitignore

@@ -31,3 +31,5 @@ mopta08_elf64.bin
 joss/paper.jats
 joss/paper.pdf
 
+# Run history
+history*

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+  rev: v0.8.5
+  hooks:
+    # Run the linter.
+    - id: ruff
+    # Run the formatter.
+    - id: ruff-format

Cargo.toml

@@ -1,67 +1,58 @@
-[package]
-name = "egobox"
+[workspace]
+members = ["crates/*", "python"]
+resolver = "2"
+
+[workspace.package]
+license = "Apache-2.0"
+edition = "2021"
+readme = "README.md"
 version = "0.25.0"
 authors = ["Rémi Lafage <[email protected]>"]
-edition = "2021"
+homepage = "https://github.com/relf/egobox"
+documentation = "https://pypi.org/project/egobox"
 description = "A toolbox for efficient global optimization"
-license = "Apache-2.0"
 repository = "https://github.com/relf/egobox"
 keywords = [
-  "machine-learning",
-  "doe",
-  "gaussian-process",
-  "mixture-of-experts",
-  "optimization",
+    "machine-learning",
+    "doe",
+    "gaussian-process",
+    "mixture-of-experts",
+    "optimization",
 ]
 categories = ["algorithms", "mathematics", "science"]
 rust-version = "1.74" # MSVR
 
 exclude = [".github/"]
 
-[lib]
-name = "egobox"
-crate-type = ["cdylib"]
-
-[features]
-default = []
-
-nlopt = ["egobox-ego/nlopt", "egobox-gp/nlopt"]
-serializable-gp = ["egobox-gp/serializable"]
-persistent-moe = ["egobox-moe/persistent"]
-blas = ["ndarray/blas", "egobox-gp/blas", "egobox-moe/blas", "egobox-ego/blas"]
-
-[dependencies]
-egobox-doe = { version = "0.25.0", path = "./doe" }
-egobox-gp = { version = "0.25.0", path = "./gp" }
-egobox-moe = { version = "0.25.0", path = "./moe", features = ["persistent"] }
-egobox-ego = { version = "0.25.0", path = "./ego", features = ["persistent"] }
+[workspace.metadata.release]
+shared-version = true
+tag-name = "{{version}}"
 
+[workspace.dependencies]
 linfa = { version = "0.7", default-features = false }
 
 ndarray = { version = "0.15", features = ["rayon", "approx"] }
 ndarray-rand = "0.14"
+ndarray-stats = "0.5"
+ndarray-npy = "0.8"
+
+num-traits = "0.2"
+
+thiserror = "1"
 anyhow = "1"
 rayon = "1"
 
 rand_xoshiro = "0.6"
-libm = "0.2"
 finitediff = { version = "0.1.4", features = ["ndarray"] }
 env_logger = "0.11"
 log = "0.4"
 
-pyo3 = { version = "0.22", features = ["extension-module"] }
-pyo3-log = "0.11"
-numpy = "0.22.1"
-
 serde = "1"
 serde_json = "1"
 
 ctrlc = "3.4"
 
-[dev-dependencies]
+# dev dependencies 
 criterion = "0.5"
 approx = "0.4"
 argmin_testfunctions = "0.2"
-
-[workspace]
-members = ["doe", "gp", "moe", "ego"]

crates/doe/Cargo.toml

@@ -0,0 +1,44 @@
+[package]
+name = "egobox-doe"
+authors.workspace = true
+version.workspace = true
+license.workspace = true
+edition.workspace = true
+homepage.workspace = true
+description = "A library for design of experiments"
+repository = "https://github.com/relf/egobox/crates/doe"
+keywords = [
+    "machine-learning",
+    "design",
+    "experiments",
+    "lhs",
+    "full-factorial",
+]
+readme = "README.md"
+
+[features]
+default = []
+
+serializable = ["serde", "rand_xoshiro/serde1"]
+
+[dependencies]
+linfa.workspace = true
+ndarray.workspace = true
+ndarray-rand.workspace = true
+ndarray-stats.workspace = true
+num-traits.workspace = true
+rand_xoshiro.workspace = true
+serde = { version = "1", optional = true }
+
+[dev-dependencies]
+criterion.workspace = true
+serde_json.workspace = true
+approx.workspace = true
+
+[[bench]]
+name = "lhs"
+harness = false
+
+[[bench]]
+name = "lhs_classics"
+harness = false

ego/Cargo.toml → crates/ego/Cargo.toml

@@ -1,11 +1,12 @@
 [package]
 name = "egobox-ego"
-version = "0.25.0"
-authors = ["Rémi Lafage <[email protected]>"]
-edition = "2021"
+authors.workspace = true
+version.workspace = true
+license.workspace = true
+edition.workspace = true
+homepage.workspace = true
 description = "A library for efficient global optimization"
-license = "Apache-2.0"
-repository = "https://github.com/relf/egobox"
+repository = "https://github.com/relf/egobox/crates/ego"
 keywords = ["machine-learning", "bayesian", "optimization"]
 categories = ["algorithms", "mathematics", "science"]
 
@@ -24,16 +25,16 @@ egobox-moe = { version = "0.25.0", path = "../moe", features = [
     "serializable",
 ] }
 
-linfa = { version = "0.7", default-features = false }
+linfa.workspace = true
 linfa-pls = { version = "0.7", default-features = false }
 linfa-linalg = { version = "0.1", default-features = false }
 
-ndarray = { version = "0.15", features = ["rayon", "approx"] }
+ndarray.workspace = true
 ndarray-linalg = { version = "0.15", optional = true }
-ndarray-stats = "0.5"
-ndarray-rand = "0.14"
-ndarray-npy = "0.8"
-rayon = "1"
+ndarray-stats.workspace = true
+ndarray-rand.workspace = true
+ndarray-npy.workspace = true
+rayon.workspace = true
 
 cobyla = { version = "0.6" }
 slsqp = { version = "0.1" }
@@ -44,25 +45,24 @@ argmin = { version = "0.10.0", features = ["serde1", "ctrlc"] }
 bincode = { version = "1.3.0" }
 web-time = "1.1.0"
 libm = "0.2.6"
-finitediff = { version = "0.1", features = ["ndarray"] }
+finitediff.workspace = true
 # sort-axis
 rawpointer = { version = "0.2" }
-log = "0.4"
-env_logger = "0.11.3"
-thiserror = "1"
-anyhow = "1"
+log.workspace = true
+env_logger.workspace = true
+thiserror.workspace = true
+anyhow.workspace = true
 clap = { version = "4", features = ["derive"] }
 
 serde = { version = "1", features = ["derive", "rc"] }
-serde_json = "1"
+serde_json.workspace = true
 typetag = { version = "0.2" }
 dyn-clonable = { version = "0.9" }
 
-
 [dev-dependencies]
-criterion = "0.5"
-approx = "0.4"
-argmin_testfunctions = "0.2"
+criterion.workspace = true
+approx.workspace = true
+argmin_testfunctions.workspace = true
 serial_test = "3.1.0"
 
 [[bench]]