From f6e1299712ecdb9261d5c3d42fb283c7635cab0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?R=C3=A9mi=20Lafage?= Date: Thu, 2 Jan 2025 20:30:43 +0100 Subject: [PATCH] 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 | 53 ++- .github/workflows/python.yml | 5 + .gitignore | 2 + .pre-commit-config.yaml | 9 + Cargo.lock | 16 - Cargo.toml | 61 ++- crates/doe/Cargo.toml | 44 ++ {doe => crates/doe}/README.md | 0 {doe => crates/doe}/benches/lhs.rs | 0 {doe => crates/doe}/benches/lhs_classics.rs | 0 {doe => crates/doe}/examples/samplings.rs | 0 {doe => crates/doe}/src/full_factorial.rs | 0 {doe => crates/doe}/src/lhs.rs | 0 {doe => crates/doe}/src/lib.rs | 0 {doe => crates/doe}/src/random.rs | 0 {doe => crates/doe}/src/traits.rs | 0 {doe => crates/doe}/src/utils.rs | 0 {ego => crates/ego}/Cargo.toml | 42 +- {ego => crates/ego}/README.md | 0 {ego => crates/ego}/benches/ego.rs | 0 {ego => crates/ego}/examples/ackley.rs | 0 {ego => crates/ego}/examples/g24.rs | 0 {ego => crates/ego}/examples/mopta08.rs | 0 {ego => crates/ego}/examples/rosenbrock.rs | 0 {ego => crates/ego}/src/criteria/ei.rs | 0 {ego => crates/ego}/src/criteria/mod.rs | 0 {ego => crates/ego}/src/criteria/wb2.rs | 0 {ego => crates/ego}/src/egor.rs | 0 {ego => crates/ego}/src/errors.rs | 0 {ego => crates/ego}/src/gpmix/mixint.rs | 0 {ego => crates/ego}/src/gpmix/mod.rs | 0 {ego => crates/ego}/src/gpmix/spec.rs | 0 {ego => crates/ego}/src/lib.rs | 0 .../ego}/src/optimizers/lhs_optimizer.rs | 0 {ego => crates/ego}/src/optimizers/mod.rs | 0 .../ego}/src/optimizers/optimizer.rs | 0 {ego => crates/ego}/src/solver/egor_config.rs | 0 {ego => crates/ego}/src/solver/egor_impl.rs | 0 .../ego}/src/solver/egor_service.rs | 0 {ego => crates/ego}/src/solver/egor_solver.rs | 0 {ego => crates/ego}/src/solver/egor_state.rs | 0 {ego => crates/ego}/src/solver/mod.rs | 0 {ego => crates/ego}/src/solver/trego.rs | 0 {ego => crates/ego}/src/types.rs | 0 {ego => crates/ego}/src/utils/find_result.rs | 0 {ego => crates/ego}/src/utils/hot_start.rs | 0 {ego => crates/ego}/src/utils/misc.rs | 0 {ego => crates/ego}/src/utils/mod.rs | 0 {ego => crates/ego}/src/utils/sort_axis.rs | 0 {gp => crates/gp}/Cargo.toml | 45 +- {gp => crates/gp}/README.md | 0 {gp => crates/gp}/benches/gp.rs | 0 {gp => crates/gp}/examples/kriging.rs | 0 {gp => crates/gp}/src/algorithm.rs | 0 {gp => crates/gp}/src/correlation_models.rs | 0 {gp => crates/gp}/src/errors.rs | 0 {gp => crates/gp}/src/lib.rs | 0 {gp => crates/gp}/src/mean_models.rs | 0 {gp => crates/gp}/src/metrics.rs | 0 {gp => crates/gp}/src/optimization.rs | 0 {gp => crates/gp}/src/parameters.rs | 0 {gp => crates/gp}/src/sparse_algorithm.rs | 0 {gp => crates/gp}/src/sparse_parameters.rs | 0 {gp => crates/gp}/src/utils.rs | 0 {moe => crates/moe}/Cargo.toml | 38 +- {moe => crates/moe}/README.md | 0 .../moe}/benches/bench_find_nb_clusters.rs | 0 {moe => crates/moe}/examples/clustering.rs | 0 {moe => crates/moe}/examples/moe_norm1.rs | 0 {moe => crates/moe}/examples/norm1.rs | 0 {moe => crates/moe}/examples/norm1_D2_200.csv | 0 {moe => crates/moe}/src/algorithm.rs | 0 {moe => crates/moe}/src/clustering.rs | 0 {moe => crates/moe}/src/errors.rs | 0 {moe => crates/moe}/src/expertise_macros.rs | 0 {moe => crates/moe}/src/gaussian_mixture.rs | 0 {moe => crates/moe}/src/lib.rs | 0 {moe => crates/moe}/src/parameters.rs | 0 {moe => crates/moe}/src/surrogates.rs | 0 {moe => crates/moe}/src/types.rs | 0 doe/Cargo.toml | 43 -- poetry.lock | 146 ------ python/.gitignore | 6 + python/Cargo.toml | 49 ++ python/egobox/__init__.py | 2 +- python/egobox/examples/optim_g24.py | 1 + python/egobox/tests/test_utils.py | 1 - pyproject.toml => python/pyproject.toml | 23 +- {src => python/src}/egor.rs | 0 {src => python/src}/gp_mix.rs | 0 {src => python/src}/lib.rs | 2 +- {src => python/src}/sampling.rs | 0 {src => python/src}/sparse_gp_mix.rs | 0 {src => python/src}/types.rs | 0 python/uv.lock | 426 ++++++++++++++++++ 95 files changed, 678 insertions(+), 336 deletions(-) create mode 100644 .pre-commit-config.yaml create mode 100644 crates/doe/Cargo.toml rename {doe => crates/doe}/README.md (100%) rename {doe => crates/doe}/benches/lhs.rs (100%) rename {doe => crates/doe}/benches/lhs_classics.rs (100%) rename {doe => crates/doe}/examples/samplings.rs (100%) rename {doe => crates/doe}/src/full_factorial.rs (100%) rename {doe => crates/doe}/src/lhs.rs (100%) rename {doe => crates/doe}/src/lib.rs (100%) rename {doe => crates/doe}/src/random.rs (100%) rename {doe => crates/doe}/src/traits.rs (100%) rename {doe => crates/doe}/src/utils.rs (100%) rename {ego => crates/ego}/Cargo.toml (70%) rename {ego => crates/ego}/README.md (100%) rename {ego => crates/ego}/benches/ego.rs (100%) rename {ego => crates/ego}/examples/ackley.rs (100%) rename {ego => crates/ego}/examples/g24.rs (100%) rename {ego => crates/ego}/examples/mopta08.rs (100%) rename {ego => crates/ego}/examples/rosenbrock.rs (100%) rename {ego => crates/ego}/src/criteria/ei.rs (100%) rename {ego => crates/ego}/src/criteria/mod.rs (100%) rename {ego => crates/ego}/src/criteria/wb2.rs (100%) rename {ego => crates/ego}/src/egor.rs (100%) rename {ego => crates/ego}/src/errors.rs (100%) rename {ego => crates/ego}/src/gpmix/mixint.rs (100%) rename {ego => crates/ego}/src/gpmix/mod.rs (100%) rename {ego => crates/ego}/src/gpmix/spec.rs (100%) rename {ego => crates/ego}/src/lib.rs (100%) rename {ego => crates/ego}/src/optimizers/lhs_optimizer.rs (100%) rename {ego => crates/ego}/src/optimizers/mod.rs (100%) rename {ego => crates/ego}/src/optimizers/optimizer.rs (100%) rename {ego => crates/ego}/src/solver/egor_config.rs (100%) rename {ego => crates/ego}/src/solver/egor_impl.rs (100%) rename {ego => crates/ego}/src/solver/egor_service.rs (100%) rename {ego => crates/ego}/src/solver/egor_solver.rs (100%) rename {ego => crates/ego}/src/solver/egor_state.rs (100%) rename {ego => crates/ego}/src/solver/mod.rs (100%) rename {ego => crates/ego}/src/solver/trego.rs (100%) rename {ego => crates/ego}/src/types.rs (100%) rename {ego => crates/ego}/src/utils/find_result.rs (100%) rename {ego => crates/ego}/src/utils/hot_start.rs (100%) rename {ego => crates/ego}/src/utils/misc.rs (100%) rename {ego => crates/ego}/src/utils/mod.rs (100%) rename {ego => crates/ego}/src/utils/sort_axis.rs (100%) rename {gp => crates/gp}/Cargo.toml (62%) rename {gp => crates/gp}/README.md (100%) rename {gp => crates/gp}/benches/gp.rs (100%) rename {gp => crates/gp}/examples/kriging.rs (100%) rename {gp => crates/gp}/src/algorithm.rs (100%) rename {gp => crates/gp}/src/correlation_models.rs (100%) rename {gp => crates/gp}/src/errors.rs (100%) rename {gp => crates/gp}/src/lib.rs (100%) rename {gp => crates/gp}/src/mean_models.rs (100%) rename {gp => crates/gp}/src/metrics.rs (100%) rename {gp => crates/gp}/src/optimization.rs (100%) rename {gp => crates/gp}/src/parameters.rs (100%) rename {gp => crates/gp}/src/sparse_algorithm.rs (100%) rename {gp => crates/gp}/src/sparse_parameters.rs (100%) rename {gp => crates/gp}/src/utils.rs (100%) rename {moe => crates/moe}/Cargo.toml (70%) rename {moe => crates/moe}/README.md (100%) rename {moe => crates/moe}/benches/bench_find_nb_clusters.rs (100%) rename {moe => crates/moe}/examples/clustering.rs (100%) rename {moe => crates/moe}/examples/moe_norm1.rs (100%) rename {moe => crates/moe}/examples/norm1.rs (100%) rename {moe => crates/moe}/examples/norm1_D2_200.csv (100%) rename {moe => crates/moe}/src/algorithm.rs (100%) rename {moe => crates/moe}/src/clustering.rs (100%) rename {moe => crates/moe}/src/errors.rs (100%) rename {moe => crates/moe}/src/expertise_macros.rs (100%) rename {moe => crates/moe}/src/gaussian_mixture.rs (100%) rename {moe => crates/moe}/src/lib.rs (100%) rename {moe => crates/moe}/src/parameters.rs (100%) rename {moe => crates/moe}/src/surrogates.rs (100%) rename {moe => crates/moe}/src/types.rs (100%) delete mode 100644 doe/Cargo.toml delete mode 100644 poetry.lock create mode 100644 python/.gitignore create mode 100644 python/Cargo.toml rename pyproject.toml => python/pyproject.toml (59%) rename {src => python/src}/egor.rs (100%) rename {src => python/src}/gp_mix.rs (100%) rename {src => python/src}/lib.rs (97%) rename {src => python/src}/sampling.rs (100%) rename {src => python/src}/sparse_gp_mix.rs (100%) rename {src => python/src}/types.rs (100%) create mode 100644 python/uv.lock diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index 1a4a37b8..ea509127 100644 --- a/.github/workflows/pytest.yml +++ b/.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 diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml index 352f2f80..7ddd2025 100644 --- a/.github/workflows/python.yml +++ b/.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 * diff --git a/.gitignore b/.gitignore index 9a2c5bda..368d7b41 100644 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,5 @@ mopta08_elf64.bin joss/paper.jats joss/paper.pdf +# Run history +history* \ No newline at end of file diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 00000000..85207fe6 --- /dev/null +++ b/.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 diff --git a/Cargo.lock b/Cargo.lock index bc61e1ca..90fef3f3 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -541,18 +541,13 @@ checksum = "0d6ef0072f8a535281e4876be788938b528e9a1d43900b82c2569af7da799125" name = "egobox" version = "0.25.0" dependencies = [ - "anyhow", - "approx", "argmin_testfunctions", - "criterion", "ctrlc", "egobox-doe", "egobox-ego", "egobox-gp", "egobox-moe", "env_logger", - "finitediff", - "libm", "linfa", "log", "ndarray", @@ -561,7 +556,6 @@ dependencies = [ "pyo3", "pyo3-log", "rand_xoshiro", - "rayon", "serde", "serde_json", ] @@ -679,7 +673,6 @@ dependencies = [ "ndarray-rand", "ndarray-stats", "paste", - "rand_isaac", "rand_xoshiro", "serde", "serde_json", @@ -1671,15 +1664,6 @@ dependencies = [ "rand", ] -[[package]] -name = "rand_isaac" -version = "0.3.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fac4373cd91b4f55722c553fb0f286edbb81ef3ff6eec7b99d1898a4110a0b28" -dependencies = [ - "rand_core", -] - [[package]] name = "rand_xoshiro" version = "0.6.0" diff --git a/Cargo.toml b/Cargo.toml index f9504066..30abe405 100644 --- a/Cargo.toml +++ b/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 "] -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"] diff --git a/crates/doe/Cargo.toml b/crates/doe/Cargo.toml new file mode 100644 index 00000000..10110c51 --- /dev/null +++ b/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 diff --git a/doe/README.md b/crates/doe/README.md similarity index 100% rename from doe/README.md rename to crates/doe/README.md diff --git a/doe/benches/lhs.rs b/crates/doe/benches/lhs.rs similarity index 100% rename from doe/benches/lhs.rs rename to crates/doe/benches/lhs.rs diff --git a/doe/benches/lhs_classics.rs b/crates/doe/benches/lhs_classics.rs similarity index 100% rename from doe/benches/lhs_classics.rs rename to crates/doe/benches/lhs_classics.rs diff --git a/doe/examples/samplings.rs b/crates/doe/examples/samplings.rs similarity index 100% rename from doe/examples/samplings.rs rename to crates/doe/examples/samplings.rs diff --git a/doe/src/full_factorial.rs b/crates/doe/src/full_factorial.rs similarity index 100% rename from doe/src/full_factorial.rs rename to crates/doe/src/full_factorial.rs diff --git a/doe/src/lhs.rs b/crates/doe/src/lhs.rs similarity index 100% rename from doe/src/lhs.rs rename to crates/doe/src/lhs.rs diff --git a/doe/src/lib.rs b/crates/doe/src/lib.rs similarity index 100% rename from doe/src/lib.rs rename to crates/doe/src/lib.rs diff --git a/doe/src/random.rs b/crates/doe/src/random.rs similarity index 100% rename from doe/src/random.rs rename to crates/doe/src/random.rs diff --git a/doe/src/traits.rs b/crates/doe/src/traits.rs similarity index 100% rename from doe/src/traits.rs rename to crates/doe/src/traits.rs diff --git a/doe/src/utils.rs b/crates/doe/src/utils.rs similarity index 100% rename from doe/src/utils.rs rename to crates/doe/src/utils.rs diff --git a/ego/Cargo.toml b/crates/ego/Cargo.toml similarity index 70% rename from ego/Cargo.toml rename to crates/ego/Cargo.toml index 0cbec933..4331409f 100644 --- a/ego/Cargo.toml +++ b/crates/ego/Cargo.toml @@ -1,11 +1,12 @@ [package] name = "egobox-ego" -version = "0.25.0" -authors = ["Rémi Lafage "] -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]] diff --git a/ego/README.md b/crates/ego/README.md similarity index 100% rename from ego/README.md rename to crates/ego/README.md diff --git a/ego/benches/ego.rs b/crates/ego/benches/ego.rs similarity index 100% rename from ego/benches/ego.rs rename to crates/ego/benches/ego.rs diff --git a/ego/examples/ackley.rs b/crates/ego/examples/ackley.rs similarity index 100% rename from ego/examples/ackley.rs rename to crates/ego/examples/ackley.rs diff --git a/ego/examples/g24.rs b/crates/ego/examples/g24.rs similarity index 100% rename from ego/examples/g24.rs rename to crates/ego/examples/g24.rs diff --git a/ego/examples/mopta08.rs b/crates/ego/examples/mopta08.rs similarity index 100% rename from ego/examples/mopta08.rs rename to crates/ego/examples/mopta08.rs diff --git a/ego/examples/rosenbrock.rs b/crates/ego/examples/rosenbrock.rs similarity index 100% rename from ego/examples/rosenbrock.rs rename to crates/ego/examples/rosenbrock.rs diff --git a/ego/src/criteria/ei.rs b/crates/ego/src/criteria/ei.rs similarity index 100% rename from ego/src/criteria/ei.rs rename to crates/ego/src/criteria/ei.rs diff --git a/ego/src/criteria/mod.rs b/crates/ego/src/criteria/mod.rs similarity index 100% rename from ego/src/criteria/mod.rs rename to crates/ego/src/criteria/mod.rs diff --git a/ego/src/criteria/wb2.rs b/crates/ego/src/criteria/wb2.rs similarity index 100% rename from ego/src/criteria/wb2.rs rename to crates/ego/src/criteria/wb2.rs diff --git a/ego/src/egor.rs b/crates/ego/src/egor.rs similarity index 100% rename from ego/src/egor.rs rename to crates/ego/src/egor.rs diff --git a/ego/src/errors.rs b/crates/ego/src/errors.rs similarity index 100% rename from ego/src/errors.rs rename to crates/ego/src/errors.rs diff --git a/ego/src/gpmix/mixint.rs b/crates/ego/src/gpmix/mixint.rs similarity index 100% rename from ego/src/gpmix/mixint.rs rename to crates/ego/src/gpmix/mixint.rs diff --git a/ego/src/gpmix/mod.rs b/crates/ego/src/gpmix/mod.rs similarity index 100% rename from ego/src/gpmix/mod.rs rename to crates/ego/src/gpmix/mod.rs diff --git a/ego/src/gpmix/spec.rs b/crates/ego/src/gpmix/spec.rs similarity index 100% rename from ego/src/gpmix/spec.rs rename to crates/ego/src/gpmix/spec.rs diff --git a/ego/src/lib.rs b/crates/ego/src/lib.rs similarity index 100% rename from ego/src/lib.rs rename to crates/ego/src/lib.rs diff --git a/ego/src/optimizers/lhs_optimizer.rs b/crates/ego/src/optimizers/lhs_optimizer.rs similarity index 100% rename from ego/src/optimizers/lhs_optimizer.rs rename to crates/ego/src/optimizers/lhs_optimizer.rs diff --git a/ego/src/optimizers/mod.rs b/crates/ego/src/optimizers/mod.rs similarity index 100% rename from ego/src/optimizers/mod.rs rename to crates/ego/src/optimizers/mod.rs diff --git a/ego/src/optimizers/optimizer.rs b/crates/ego/src/optimizers/optimizer.rs similarity index 100% rename from ego/src/optimizers/optimizer.rs rename to crates/ego/src/optimizers/optimizer.rs diff --git a/ego/src/solver/egor_config.rs b/crates/ego/src/solver/egor_config.rs similarity index 100% rename from ego/src/solver/egor_config.rs rename to crates/ego/src/solver/egor_config.rs diff --git a/ego/src/solver/egor_impl.rs b/crates/ego/src/solver/egor_impl.rs similarity index 100% rename from ego/src/solver/egor_impl.rs rename to crates/ego/src/solver/egor_impl.rs diff --git a/ego/src/solver/egor_service.rs b/crates/ego/src/solver/egor_service.rs similarity index 100% rename from ego/src/solver/egor_service.rs rename to crates/ego/src/solver/egor_service.rs diff --git a/ego/src/solver/egor_solver.rs b/crates/ego/src/solver/egor_solver.rs similarity index 100% rename from ego/src/solver/egor_solver.rs rename to crates/ego/src/solver/egor_solver.rs diff --git a/ego/src/solver/egor_state.rs b/crates/ego/src/solver/egor_state.rs similarity index 100% rename from ego/src/solver/egor_state.rs rename to crates/ego/src/solver/egor_state.rs diff --git a/ego/src/solver/mod.rs b/crates/ego/src/solver/mod.rs similarity index 100% rename from ego/src/solver/mod.rs rename to crates/ego/src/solver/mod.rs diff --git a/ego/src/solver/trego.rs b/crates/ego/src/solver/trego.rs similarity index 100% rename from ego/src/solver/trego.rs rename to crates/ego/src/solver/trego.rs diff --git a/ego/src/types.rs b/crates/ego/src/types.rs similarity index 100% rename from ego/src/types.rs rename to crates/ego/src/types.rs diff --git a/ego/src/utils/find_result.rs b/crates/ego/src/utils/find_result.rs similarity index 100% rename from ego/src/utils/find_result.rs rename to crates/ego/src/utils/find_result.rs diff --git a/ego/src/utils/hot_start.rs b/crates/ego/src/utils/hot_start.rs similarity index 100% rename from ego/src/utils/hot_start.rs rename to crates/ego/src/utils/hot_start.rs diff --git a/ego/src/utils/misc.rs b/crates/ego/src/utils/misc.rs similarity index 100% rename from ego/src/utils/misc.rs rename to crates/ego/src/utils/misc.rs diff --git a/ego/src/utils/mod.rs b/crates/ego/src/utils/mod.rs similarity index 100% rename from ego/src/utils/mod.rs rename to crates/ego/src/utils/mod.rs diff --git a/ego/src/utils/sort_axis.rs b/crates/ego/src/utils/sort_axis.rs similarity index 100% rename from ego/src/utils/sort_axis.rs rename to crates/ego/src/utils/sort_axis.rs diff --git a/gp/Cargo.toml b/crates/gp/Cargo.toml similarity index 62% rename from gp/Cargo.toml rename to crates/gp/Cargo.toml index d035cb80..cacef318 100644 --- a/gp/Cargo.toml +++ b/crates/gp/Cargo.toml @@ -1,11 +1,12 @@ [package] name = "egobox-gp" -version = "0.25.0" -authors = ["Rémi Lafage "] -edition = "2021" +authors.workspace = true +version.workspace = true +license.workspace = true +edition.workspace = true +homepage.workspace = true description = "A library for gaussian process modeling" -license = "Apache-2.0" -repository = "https://github.com/relf/egobox" +repository = "https://github.com/relf/egobox/crates/gp" keywords = ["machine-learning", "gaussian-process", "kriging", "surrogate"] categories = ["algorithms", "mathematics", "science"] @@ -20,36 +21,40 @@ blas = ["ndarray-linalg", "linfa/ndarray-linalg", "linfa-pls/blas"] [dependencies] egobox-doe = { version = "0.25.0", path = "../doe" } -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-stats.workspace = true +ndarray-rand.workspace = true + +num-traits.workspace = true + +rand_xoshiro.workspace = true +thiserror.workspace = true +log.workspace = true +rayon.workspace = true + ndarray-linalg = { version = "0.15", optional = true } -ndarray-stats = "0.5" ndarray_einsum_beta = "0.7" -ndarray-rand = "0.14" -ndarray-npy = "0.8" + +ndarray-npy.workspace = true nlopt = { version = "0.7.0", optional = true } cobyla = { version = "0.6" } -rand_xoshiro = "0.6" paste = "1.0" -num-traits = "0.2" -thiserror = "1" -log = "0.4" -rayon = "1" serde = { version = "1", features = ["derive"], optional = true } serde_json = { version = "1", optional = true } typetag = { version = "0.2", optional = true } -finitediff = { version = "0.1", features = ["ndarray"] } +finitediff.workspace = true [dev-dependencies] -criterion = "0.5" -serde_json = "1" -approx = "0.4" -argmin_testfunctions = "0.2" +criterion.workspace = true +serde_json.workspace = true +approx.workspace = true +argmin_testfunctions.workspace = true [[bench]] name = "gp" diff --git a/gp/README.md b/crates/gp/README.md similarity index 100% rename from gp/README.md rename to crates/gp/README.md diff --git a/gp/benches/gp.rs b/crates/gp/benches/gp.rs similarity index 100% rename from gp/benches/gp.rs rename to crates/gp/benches/gp.rs diff --git a/gp/examples/kriging.rs b/crates/gp/examples/kriging.rs similarity index 100% rename from gp/examples/kriging.rs rename to crates/gp/examples/kriging.rs diff --git a/gp/src/algorithm.rs b/crates/gp/src/algorithm.rs similarity index 100% rename from gp/src/algorithm.rs rename to crates/gp/src/algorithm.rs diff --git a/gp/src/correlation_models.rs b/crates/gp/src/correlation_models.rs similarity index 100% rename from gp/src/correlation_models.rs rename to crates/gp/src/correlation_models.rs diff --git a/gp/src/errors.rs b/crates/gp/src/errors.rs similarity index 100% rename from gp/src/errors.rs rename to crates/gp/src/errors.rs diff --git a/gp/src/lib.rs b/crates/gp/src/lib.rs similarity index 100% rename from gp/src/lib.rs rename to crates/gp/src/lib.rs diff --git a/gp/src/mean_models.rs b/crates/gp/src/mean_models.rs similarity index 100% rename from gp/src/mean_models.rs rename to crates/gp/src/mean_models.rs diff --git a/gp/src/metrics.rs b/crates/gp/src/metrics.rs similarity index 100% rename from gp/src/metrics.rs rename to crates/gp/src/metrics.rs diff --git a/gp/src/optimization.rs b/crates/gp/src/optimization.rs similarity index 100% rename from gp/src/optimization.rs rename to crates/gp/src/optimization.rs diff --git a/gp/src/parameters.rs b/crates/gp/src/parameters.rs similarity index 100% rename from gp/src/parameters.rs rename to crates/gp/src/parameters.rs diff --git a/gp/src/sparse_algorithm.rs b/crates/gp/src/sparse_algorithm.rs similarity index 100% rename from gp/src/sparse_algorithm.rs rename to crates/gp/src/sparse_algorithm.rs diff --git a/gp/src/sparse_parameters.rs b/crates/gp/src/sparse_parameters.rs similarity index 100% rename from gp/src/sparse_parameters.rs rename to crates/gp/src/sparse_parameters.rs diff --git a/gp/src/utils.rs b/crates/gp/src/utils.rs similarity index 100% rename from gp/src/utils.rs rename to crates/gp/src/utils.rs diff --git a/moe/Cargo.toml b/crates/moe/Cargo.toml similarity index 70% rename from moe/Cargo.toml rename to crates/moe/Cargo.toml index 08f2081e..1dc1d109 100644 --- a/moe/Cargo.toml +++ b/crates/moe/Cargo.toml @@ -1,11 +1,12 @@ [package] name = "egobox-moe" -version = "0.25.0" -authors = ["Rémi Lafage "] -edition = "2021" +authors.workspace = true +version.workspace = true +license.workspace = true +edition.workspace = true +homepage.workspace = true description = "A library for mixture of expert gaussian processes" -license = "Apache-2.0" -repository = "https://github.com/relf/egobox" +repository = "https://github.com/relf/egobox/crates/moe" keywords = [ "machine-learning", "mixture", @@ -32,22 +33,22 @@ blas = ["ndarray-linalg", "linfa/ndarray-linalg", "linfa-pls/blas"] egobox-doe = { version = "0.25.0", path = "../doe" } egobox-gp = { version = "0.25.0", path = "../gp" } -linfa = { version = "0.7", default-features = false } +linfa.workspace = true linfa-clustering = { version = "0.7", default-features = false } 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" -rand_xoshiro = "0.6" +ndarray-stats.workspace = true +ndarray-rand.workspace = true +ndarray-npy.workspace = true +rand_xoshiro.workspace = true paste = "1.0" bitflags = { version = "2.4.1", features = ["serde"] } -log = "0.4" -env_logger = "0.11.3" -thiserror = "1" +log.workspace = true +env_logger.workspace = true +thiserror.workspace = true serde = { version = "1", features = ["derive"], optional = true } serde_json = { version = "1", optional = true } @@ -56,13 +57,12 @@ bincode = { version = "1.3.3", optional = true } typetag = { version = "0.2", optional = true } [dev-dependencies] -criterion = "0.5" -approx = "0.4" -ndarray-npy = "0.8" +criterion.workspace = true +approx.workspace = true +ndarray-npy.workspace = true ndarray-csv = "0.5" csv = "1.1" -argmin_testfunctions = "0.2" -rand_isaac = "0.3" +argmin_testfunctions.workspace = true [[bench]] name = "bench_find_nb_clusters" diff --git a/moe/README.md b/crates/moe/README.md similarity index 100% rename from moe/README.md rename to crates/moe/README.md diff --git a/moe/benches/bench_find_nb_clusters.rs b/crates/moe/benches/bench_find_nb_clusters.rs similarity index 100% rename from moe/benches/bench_find_nb_clusters.rs rename to crates/moe/benches/bench_find_nb_clusters.rs diff --git a/moe/examples/clustering.rs b/crates/moe/examples/clustering.rs similarity index 100% rename from moe/examples/clustering.rs rename to crates/moe/examples/clustering.rs diff --git a/moe/examples/moe_norm1.rs b/crates/moe/examples/moe_norm1.rs similarity index 100% rename from moe/examples/moe_norm1.rs rename to crates/moe/examples/moe_norm1.rs diff --git a/moe/examples/norm1.rs b/crates/moe/examples/norm1.rs similarity index 100% rename from moe/examples/norm1.rs rename to crates/moe/examples/norm1.rs diff --git a/moe/examples/norm1_D2_200.csv b/crates/moe/examples/norm1_D2_200.csv similarity index 100% rename from moe/examples/norm1_D2_200.csv rename to crates/moe/examples/norm1_D2_200.csv diff --git a/moe/src/algorithm.rs b/crates/moe/src/algorithm.rs similarity index 100% rename from moe/src/algorithm.rs rename to crates/moe/src/algorithm.rs diff --git a/moe/src/clustering.rs b/crates/moe/src/clustering.rs similarity index 100% rename from moe/src/clustering.rs rename to crates/moe/src/clustering.rs diff --git a/moe/src/errors.rs b/crates/moe/src/errors.rs similarity index 100% rename from moe/src/errors.rs rename to crates/moe/src/errors.rs diff --git a/moe/src/expertise_macros.rs b/crates/moe/src/expertise_macros.rs similarity index 100% rename from moe/src/expertise_macros.rs rename to crates/moe/src/expertise_macros.rs diff --git a/moe/src/gaussian_mixture.rs b/crates/moe/src/gaussian_mixture.rs similarity index 100% rename from moe/src/gaussian_mixture.rs rename to crates/moe/src/gaussian_mixture.rs diff --git a/moe/src/lib.rs b/crates/moe/src/lib.rs similarity index 100% rename from moe/src/lib.rs rename to crates/moe/src/lib.rs diff --git a/moe/src/parameters.rs b/crates/moe/src/parameters.rs similarity index 100% rename from moe/src/parameters.rs rename to crates/moe/src/parameters.rs diff --git a/moe/src/surrogates.rs b/crates/moe/src/surrogates.rs similarity index 100% rename from moe/src/surrogates.rs rename to crates/moe/src/surrogates.rs diff --git a/moe/src/types.rs b/crates/moe/src/types.rs similarity index 100% rename from moe/src/types.rs rename to crates/moe/src/types.rs diff --git a/doe/Cargo.toml b/doe/Cargo.toml deleted file mode 100644 index 710d37c5..00000000 --- a/doe/Cargo.toml +++ /dev/null @@ -1,43 +0,0 @@ -[package] -name = "egobox-doe" -version = "0.25.0" -authors = ["Rémi Lafage "] -edition = "2021" -description = "A library for design of experiments" -license = "Apache-2.0" -repository = "https://github.com/relf/egobox" -keywords = [ - "machine-learning", - "design", - "experiments", - "lhs", - "full-factorial", -] -categories = ["algorithms", "mathematics", "science"] - -[features] -default = [] - -serializable = ["serde", "rand_xoshiro/serde1"] - -[dependencies] -linfa = { version 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+[dependencies] +egobox-doe = { version = "0.25.0", path = "../crates/doe" } +egobox-gp = { version = "0.25.0", path = "../crates/gp" } +egobox-moe = { version = "0.25.0", path = "../crates/moe", features = [ + "persistent", +] } +egobox-ego = { version = "0.25.0", path = "../crates/ego", features = [ + "persistent", +] } + +pyo3 = { version = "0.22", features = ["extension-module"] } +pyo3-log = "0.11" +numpy = "0.22.1" + +linfa.workspace = true +ndarray.workspace = true +ndarray-rand.workspace = true + +rand_xoshiro.workspace = true +env_logger.workspace = true +log.workspace = true + +serde.workspace = true +serde_json.workspace = true +ctrlc.workspace = true + +argmin_testfunctions.workspace = true diff --git a/python/egobox/__init__.py b/python/egobox/__init__.py index 5f8f5a98..e8e30997 100644 --- a/python/egobox/__init__.py +++ b/python/egobox/__init__.py @@ -1 +1 @@ -from .egobox import * +from .egobox import * # noqa diff --git a/python/egobox/examples/optim_g24.py b/python/egobox/examples/optim_g24.py index d1c285b3..9d63f517 100644 --- a/python/egobox/examples/optim_g24.py +++ b/python/egobox/examples/optim_g24.py @@ -9,6 +9,7 @@ xspecs_g24 = egx.to_specs([[0.0, 3.0], [0.0, 4.0]]) n_cstr_g24 = 2 + # Objective def G24(point): """ diff --git a/python/egobox/tests/test_utils.py b/python/egobox/tests/test_utils.py index 34f0b6ab..e87d3438 100644 --- a/python/egobox/tests/test_utils.py +++ b/python/egobox/tests/test_utils.py @@ -1,5 +1,4 @@ import unittest -import numpy as np import egobox as egx diff --git a/pyproject.toml b/python/pyproject.toml similarity index 59% rename from pyproject.toml rename to python/pyproject.toml index 18cae1be..b72829eb 100644 --- a/pyproject.toml +++ b/python/pyproject.toml @@ -12,26 +12,19 @@ classifiers = [ "Operating System :: Microsoft :: Windows", "Operating System :: Unix", ] +requires-python = ">=3.9" +dependencies = ["numpy"] +dynamic = ["version"] [build-system] build-backend = "maturin" -requires = 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