Update pyproject.toml to use PEP-621 dependency specification (#584)

jameskrach · web-flow · commit 7875b9702d9a · 2025-07-19T10:03:00.000+02:00
* Update pyproject.toml to use PEP-621 dependency specification

* Remove requirements files

* Merge dependency groups, sort dependencies within groups

* Remove upper bound constraints, update workflow

* Update run_tests.yml

* Use just uv instead of uv and poetry

* Appease the new version of ruff

* Fix workflow bugs

* Fix numpy version issue on build
diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
@@ -18,25 +18,20 @@ jobs:
       contents: write
     steps:
       - uses: actions/checkout@v3
-      - name: Setup Python
-        uses: actions/setup-python@v3
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: '3.10'
+          python-version: "3.10"
       - name: Get tag
         uses: olegtarasov/get-tag@v2.1
       - name: Install pandoc
         run: sudo apt-get install -y pandoc
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 'latest'
       - name: Install package and test dependencies
-        run: |
-          poetry install --with dev,nbtools
+        run: uv sync --extra dev
       - name: build sphinx docs
         run: |
           cd docsrc
-          poetry run make github
+          uv run make github
       - name: Determine directory to publish docs to
         id: docs-publish-dir
         uses: jannekem/run-python-script-action@v1
diff --git a/.github/workflows/format_and_lint.yml b/.github/workflows/format_and_lint.yml
@@ -13,16 +13,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v3
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
         python-version: "3.9"
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: 'latest'
     - name: Install dependencies
-      run: |
-        poetry install --with dev
+      run: uv sync --extra dev
     - name: Run pre-commit
-      run : poetry run pre-commit run --all-files --show-diff-on-failure --color=always
+      run: uv run pre-commit run --all-files --show-diff-on-failure --color=always
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -1,4 +1,4 @@
-# This workflow will upload a Python Package using poetry when a release is created
+# This workflow will upload a Python Package using uv when a release is created
 # Note that you must manually update the version number in pyproject.toml before attempting this.
 
 name: Upload Python Package
@@ -14,10 +14,10 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
-    - name: Build and publish to pypi
-      uses: JRubics/poetry-publish@v2.0
-      with:
-        pypi_token: ${{ secrets.PYPI_API_TOKEN }}
-        # python_version: "3.10"
-        # poetry_version: "==1.8" # can lock versions if we want
+    - uses: actions/checkout@v4
+    - uses: astral-sh/setup-uv@v6
+    - run: uv build
+    - name: Publish to pypi
+      env:
+        PYPI_API_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+      run: uv publish --token "$PYPI_API_TOKEN"
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# This workflow will install Python dependencies and run tests in multiple versions of Python
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
 name: tests
@@ -25,31 +25,16 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v3
+    - name: Install uv and set the python version
+      uses: astral-sh/setup-uv@v6
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install the latest version of uv
-      uses: astral-sh/setup-uv@v5
-      with:
-        version: "latest"
-    - name: Install Poetry
-      uses: snok/install-poetry@v1
-      with:
-        version: 'latest'
     - name: Install test dependencies
       run: |
-        poetry self add poetry-plugin-export
-        poetry export -f requirements.txt --with dev,nbtools --without-hashes --output requirements-dev.txt
-        echo "numpy${{ matrix.numpy-version }}" >> constraints.txt
-        uv pip compile requirements-dev.txt --output-file requirements.txt \
-          --python-version ${{ matrix.python-version }} \
-          --override constraints.txt
-        poetry run pip install -r requirements.txt
-        poetry install --only-root
-    - name: Test with pytest
-      run: |
-        poetry run pytest --cov-report xml --cov=bayes_opt/
+        uv sync --extra dev
+        uv pip install "numpy${{ matrix.numpy-version}}"
+    - name: Run pytest
+      run: uv run --no-sync pytest --cov-report xml --cov=bayes_opt/
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
diff --git a/.gitignore b/.gitignore
@@ -37,6 +37,7 @@ docsrc/static/*
 docsrc/README.md
 
 poetry.lock
+uv.lock
 
 # Add log files and optimizer state files to gitignore
 examples/logs.log
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,4 +6,4 @@ repos:
         name: ruff-format
         args: [--check]
     repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.6
+    rev: v0.12.3
diff --git a/bayes_opt/__init__.py b/bayes_opt/__init__.py
@@ -15,10 +15,10 @@
 
 
 __all__ = [
-    "acquisition",
     "BayesianOptimization",
-    "TargetSpace",
     "ConstraintModel",
     "ScreenLogger",
     "SequentialDomainReductionTransformer",
+    "TargetSpace",
+    "acquisition",
 ]
diff --git a/bayes_opt/constraint.py b/bayes_opt/constraint.py
@@ -240,7 +240,7 @@ def approx(self, X: NDArray[Float]) -> NDArray[Float]:
             return self._model[0].predict(X).reshape(X_shape[:-1])
 
         result = np.column_stack([gp.predict(X) for gp in self._model])
-        return result.reshape(X_shape[:-1] + (len(self._lb),))
+        return result.reshape(*X_shape[:-1], len(self._lb))
 
     def allowed(self, constraint_values: NDArray[Float]) -> NDArray[np.bool_]:
         """Check whether `constraint_values` fulfills the specified limits.
diff --git a/bayes_opt/exception.py b/bayes_opt/exception.py
@@ -4,9 +4,9 @@
 
 __all__ = [
     "BayesianOptimizationError",
-    "NotUniqueError",
     "ConstraintNotSupportedError",
     "NoValidPointRegisteredError",
+    "NotUniqueError",
     "TargetSpaceEmptyError",
 ]
 
diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ description = "Bayesian Optimization package"
 authors = [{ name = "Fernando Nogueira", email = "fmfnogueira@gmail.com" }]
 license = { file = "LICENSE" }
 readme = "README.md"
-requires-python = ">=3.9,<4.0"
+requires-python = ">=3.9"
 classifiers = [
     "License :: OSI Approved :: MIT License",
     "Programming Language :: Python",
@@ -17,51 +17,40 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "scikit-learn>=1.0.0,<2.0.0",
+    "colorama>=0.4.6",
     "numpy>=1.25; python_version<'3.13'",
     "numpy>=2.1.3; python_version>='3.13'",
-    "scipy>=1.0.0,<2.0.0; python_version<'3.13'",
-    "scipy>=1.14.1,<2.0.0; python_version>='3.13'",
-    "colorama>=0.4.6,<1.0.0",
+    "scikit-learn>=1.0.0",
+    "scipy>=1.0.0; python_version<'3.13'",
+    "scipy>=1.14.1; python_version>='3.13'",
 ]
 
-[tool.poetry]
-requires-poetry = ">=2.0"
-packages = [{ include = "bayes_opt" }]
-
-
-[tool.poetry.group.dev] # for testing/developing
-optional = true
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.0.0"
-pytest-cov = "^4.1.0"
-coverage = "^7.4.1"
-ruff = "0.6.6"
-pre-commit = "^3.7.1"
-
-
-[tool.poetry.group.nbtools] # for running/converting notebooks
-optional = true
-[tool.poetry.group.nbtools.dependencies]
-nbformat = "^5.9.2"
-nbconvert = "^7.14.2"
-jupyter = "^1.0.0"
-matplotlib = "^3.0"
-nbsphinx = "^0.9.4"
-sphinx-immaterial = "^0.12.0"
-sphinx = [
-    { version = "^7.0.0", python = "<3.10" },
-    { version = "^8.0.0", python = ">=3.10" },
+[project.optional-dependencies]
+dev = [
+    "coverage>=7.4.1",
+    "jupyter>=1.0.0",
+    "matplotlib>=3.0",
+    "nbconvert>=7.14.2",
+    "nbformat>=5.9.2",
+    "nbsphinx>=0.9.4",
+    "pre-commit>=3.7.1",
+    "pytest>=8.0.0",
+    "pytest-cov>=4.1.0",
+    "ruff>=0.12.3",
+    "sphinx-immaterial>=0.12.0",
+    "sphinx>=7.0.0; python_version<'3.10'",
+    "sphinx>=8.0.0; python_version>='3.10'",
+    "sphinx-autodoc-typehints>=2.3.0; python_version<'3.10'",
+    "sphinx-autodoc-typehints>=2.4.0; python_version>='3.10'",
 ]
-sphinx-autodoc-typehints = [
-    { version = "^2.3.0", python = "<3.10" },
-    { version = "^2.4.0", python = ">=3.10" },
-]
-
 
 [build-system]
-requires = ["poetry-core>=2.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["uv_build>=0.7.21,<0.8.0"]
+build-backend = "uv_build"
+
+[tool.uv.build-backend]
+module-name = "bayes_opt"
+module-root = ""
 
 [tool.coverage.report]
 exclude_lines = [
diff --git a/scripts/check.sh b/scripts/check.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env sh
 set -ex
 
-poetry run ruff format --check bayes_opt tests
-poetry run ruff check bayes_opt tests
+uv run ruff format --check bayes_opt tests
+uv run ruff check bayes_opt tests
diff --git a/scripts/check_precommit.sh b/scripts/check_precommit.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env sh
 set -ex
 
-poetry run pre-commit install
-poetry run pre-commit run --all-files --show-diff-on-failure
+uv run pre-commit install
+uv run pre-commit run --all-files --show-diff-on-failure
diff --git a/scripts/format.sh b/scripts/format.sh
@@ -1,6 +1,5 @@
 #!/usr/bin/env sh
 set -ex
 
-poetry run ruff format bayes_opt tests
-poetry run ruff check bayes_opt --fix
-
+uv run ruff format bayes_opt tests
+uv run ruff check bayes_opt --fix
diff --git a/tests/test_seq_domain_red.py b/tests/test_seq_domain_red.py
@@ -156,14 +156,14 @@ def verify_bounds_in_range(new_bounds, global_bounds):
 
     # test if both (upper/lower) bounds for a parameter exceed the global bounds
     new_bounds = np.array([[-50, -20], [20, 50]])
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match="A parameter's lower bound is greater than the global upper bound"):
         trimmed_bounds = bounds_transformer._trim(new_bounds, global_bounds)
     assert verify_bounds_in_range(trimmed_bounds, global_bounds)
 
     # test if both (upper/lower) bounds for a parameter exceed the global bounds
     # while they are out of order
     new_bounds = np.array([[-20, -50], [-10, 10]])
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match="A parameter's lower bound is greater than the global upper bound"):
         trimmed_bounds = bounds_transformer._trim(new_bounds, global_bounds)
     assert verify_bounds_in_range(trimmed_bounds, global_bounds)
 
diff --git a/tests/test_target_space.py b/tests/test_target_space.py
@@ -125,7 +125,7 @@ def test_register_point_beyond_bounds():
     PBOUNDS = {"p1": (0, 1), "p2": (1, 10)}
     space = TargetSpace(target_func, PBOUNDS)
 
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match="is outside the bounds of the parameter"):
         space.register(params={"p1": 0.5, "p2": 20}, target=2.5)
 
 
@@ -209,7 +209,7 @@ def test_y_max_within_pbounds():
     assert space._target_max() is None
     space.probe(params={"p1": 1, "p2": 2})
     space.probe(params={"p1": 0, "p2": 1})
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match="is outside the bounds of the parameter"):
         space.probe(params={"p1": 5, "p2": 1})
     assert space._target_max() == 3
 

Original file line number	Diff line number	Diff line change
`@@ -4,9 +4,9 @@`
`4`	`4`
`5`	`5`	`__all__ = [`
`6`	`6`	`"BayesianOptimizationError",`
`7`		`- "NotUniqueError",`
`8`	`7`	`"ConstraintNotSupportedError",`
`9`	`8`	`"NoValidPointRegisteredError",`
	`9`	`+ "NotUniqueError",`
`10`	`10`	`"TargetSpaceEmptyError",`
`11`	`11`	`]`
`12`	`12`