Merge pull request #182 from scikit-learn-contrib/feat/migration-uv

tests updated

Author: JulienRoussel77

.github/workflows/publish.yml

@@ -4,29 +4,22 @@ on:
   release:
     types: [published]
 
+permissions:
+  id-token: write
+
 jobs:
   deploy:
     runs-on: ubuntu-latest
+    environment: pypi
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-    - name: Install Poetry
-      run: |
-        curl -sSL https://install.python-poetry.org | python3 -
-        echo "$HOME/.local/bin" >> $GITHUB_PATH
-    - name: Install dependencies
-      run: |
-        poetry install
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v3
+
     - name: Build package
-      run: |
-        poetry build
-    - name: Publish package
-      env:
-        PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
-      run: |
-        poetry config pypi-token.pypi $PYPI_TOKEN
-        poetry publish
+      run: uv build
+
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yml

@@ -16,61 +16,39 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.11", "3.12"]
+        # Full matrix only for PRs to main
+        os: ${{ github.event_name == 'pull_request' && github.base_ref == 'main' && fromJSON('["ubuntu-latest", "windows-latest"]') || fromJSON('["ubuntu-latest"]') }}
+        python-version: ${{ github.event_name == 'pull_request' && github.base_ref == 'main' && fromJSON('["3.9", "3.11", "3.12"]') || fromJSON('["3.12"]') }}
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-      - name: Set OS and Python version
-        id: set-vars
-        run: |
-          if [[ "${GITHUB_REF}" == "refs/heads/main" || "${GITHUB_REF}" == "refs/heads/dev" ]]; then
-            echo "os-matrix=ubuntu-latest,windows-latest" >> $GITHUB_ENV
-            echo "python-matrix=3.9,3.11,3.12" >> $GITHUB_ENV
-          else
-            echo "os-matrix=ubuntu-latest" >> $GITHUB_ENV
-            echo "python-matrix=3.12" >> $GITHUB_ENV
-          fi
-      - name: Checkout
-        uses: actions/checkout@v3
-      - name: Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Cache Poetry
-        uses: actions/cache@v3
-        with:
-          path: |
-            ~/.cache/pypoetry
-            ~/.cache/pip
-          key: ${{ runner.os }}-poetry-${{ matrix.python-version }}-${{ hashFiles('**/poetry.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-poetry-${{ matrix.python-version }}-
-      - name: Poetry
-        uses: snok/install-poetry@v1
-        with:
-          version: 1.8.3
-      - name: Lock
-        run: poetry lock --no-update
-      - name: Install
-        run: poetry install
-      - name: Checkers
-        run: make checkers
-      - name: Codecov
-        uses: codecov/codecov-action@v3
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-      - name: Check Changed Files
-        id: changed-files
-        uses: tj-actions/changed-files@v40
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         with:
-          files: |
-            docs/**
-            **.rst
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: make install
+
+      - name: Check with ruff
+        run: make check-quality
+
+      - name: Test with pytest
+        run: make check-tests
+
+      - name: Check types
+        run: make check-types
 
-      - name: Build Docs
-        if: matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest' && steps.changed-files.outputs.any_changed == 'true'
+      - name: Build and test docs
+        if: matrix.python-version == '3.12' && matrix.os == 'ubuntu-latest'
         run: |
-          poetry run sphinx-build -b html docs/ _build/html
+          make doc
+          make doctest

.gitignore

@@ -28,7 +28,6 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
-poetry.lock
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

.python-version

@@ -1 +0,0 @@
-3.12.10

CONTRIBUTING.rst

@@ -25,15 +25,12 @@ Local setup
 
 We encourage you to use a virtual environment. You'll want to activate it every time you want to work on `Qolmat`.
 
-You can create a virtual environment via `conda`:
+You can create a virtual environment and install dependencies with `uv`:
 
 .. code:: sh
 
-    $ pip install poetry
-    $ poetry config virtualenvs.in-project true
-    $ poetry lock
-    $ poetry install
-    $ poetry shell
+    $ uv sync
+    $ uv run pytest
 
 Once the environment is installed, pre-commit is installed, but need to be activated using the following command:
 

HISTORY.rst

@@ -5,6 +5,8 @@ History
 0.1.11 (2025-12-30)
 ------------------
 * PLKM test implemented and documented in the holes_characterization module
+* Dependency management improved with uv
+* Migrated from hyperopt to skopt for hyperparameter optimization
 
 0.1.10 (2025-08-30)
 ------------------

Makefile

@@ -1,34 +1,45 @@
+# Install dependencies
+install:
+	uv sync --all-extras
 
+# Code quality checks
 check-coverage:
-	poetry run pytest --cov-branch --cov=qolmat/ --cov-report=xml tests/
-
-check-poetry:
-	poetry check --lock
+	uv run pytest --cov-branch --cov=qolmat/ --cov-report=xml tests/
 
 check-quality:
-	poetry run ruff check qolmat/ tests/
+	uv run ruff check qolmat/ tests/
 
 check-security:
-	poetry run bandit --recursive --configfile=pyproject.toml qolmat/
+	uv run bandit --recursive --configfile=pyproject.toml qolmat/
 
 check-tests:
-	poetry run pytest tests/
+	uv run pytest tests/
 
 check-types:
-	poetry run mypy qolmat/ tests/
+	uv run mypy qolmat/ tests/
 
 checkers: check-coverage check-types
 
+# Formatting
+format:
+	uv run ruff format qolmat/ tests/
+	uv run ruff check --fix qolmat/ tests/
+
+# Cleaning
 clean:
-	rm -rf .mypy_cache .pytest_cache .coverage*
+	rm -rf .mypy_cache .pytest_cache .coverage* .ruff_cache
 	rm -rf **__pycache__
-	make clean -C docs
-
-coverage:
-	poetry run pytest --cov-branch --cov=qolmat --cov-report=xml tests
+	uv run make clean -C docs
 
+# Documentation
 doc:
-	make html -C docs
+	uv run make html -C docs
 
 doctest:
-	poetry run pytest --doctest-modules --pyargs qolmat
+	uv run pytest --doctest-modules --pyargs qolmat
+
+# Development helpers
+lock:
+	uv lock
+
+.PHONY: install check-coverage check-quality check-security check-tests check-types checkers format clean doc doctest lock

docs/conf.py

@@ -53,8 +53,6 @@
 # see https://github.com/numpy/numpydoc/issues/69
 numpydoc_show_class_members = False
 
-from distutils.version import LooseVersion
-
 # pngmath / imgmath compatibility layer for different sphinx versions
 # import sphinx
 

docs/sg_execution_times.rst

@@ -6,7 +6,7 @@
 
 Computation times
 =================
-**00:00.000** total execution time for 6 files **from all galleries**:
+**01:04.897** total execution time for 6 files **from all galleries**:
 
 .. container::
 
@@ -33,20 +33,20 @@ Computation times
      - Time
      - Mem (MB)
    * - :ref:`sphx_glr_examples_tutorials_plot_tuto_benchmark_TS.py` (``../examples/tutorials/plot_tuto_benchmark_TS.py``)
-     - 00:00.000
+     - 00:21.381
      - 0.0
    * - :ref:`sphx_glr_examples_tutorials_plot_tuto_categorical.py` (``../examples/tutorials/plot_tuto_categorical.py``)
-     - 00:00.000
+     - 00:16.026
      - 0.0
    * - :ref:`sphx_glr_examples_tutorials_plot_tuto_diffusion_models.py` (``../examples/tutorials/plot_tuto_diffusion_models.py``)
-     - 00:00.000
-     - 0.0
-   * - :ref:`sphx_glr_examples_tutorials_plot_tuto_hole_generator.py` (``../examples/tutorials/plot_tuto_hole_generator.py``)
-     - 00:00.000
+     - 00:11.896
      - 0.0
    * - :ref:`sphx_glr_examples_tutorials_plot_tuto_mcar.py` (``../examples/tutorials/plot_tuto_mcar.py``)
-     - 00:00.000
+     - 00:08.072
      - 0.0
    * - :ref:`sphx_glr_examples_tutorials_plot_tuto_mean_median.py` (``../examples/tutorials/plot_tuto_mean_median.py``)
-     - 00:00.000
+     - 00:04.939
+     - 0.0
+   * - :ref:`sphx_glr_examples_tutorials_plot_tuto_hole_generator.py` (``../examples/tutorials/plot_tuto_hole_generator.py``)
+     - 00:02.583
      - 0.0

examples/benchmark.md

@@ -22,9 +22,7 @@ First, import some useful libraries
 ```python tags=[]
 import warnings
 # warnings.filterwarnings('error')
-```
 
-```python tags=[]
 %reload_ext autoreload
 %autoreload 2
 
@@ -33,21 +31,21 @@ from IPython.display import Image
 import pandas as pd
 from datetime import datetime
 import numpy as np
-import hyperopt as ho
+from skopt.space import Real, Integer, Categorical
 np.random.seed(1234)
 from matplotlib import pyplot as plt
 import matplotlib.ticker as plticker
 
 tab10 = plt.get_cmap("tab10")
 plt.rcParams.update({'font.size': 18})
 
-
 from sklearn.linear_model import LinearRegression
 
 from qolmat.benchmark import comparator, missing_patterns
 from qolmat.imputations import imputers
 from qolmat.utils import data, utils, plot
 
+
 ```
 
 ### **I. Load data**
@@ -124,15 +122,15 @@ imputer_residuals = imputers.ImputerResiduals(groups=("station",), period=365, m
 imputer_rpca = imputers.ImputerRpcaNoisy(groups=("station",), columnwise=False, max_iterations=500, tau=.01, lam=5, rank=1)
 imputer_rpca_opti = imputers.ImputerRpcaNoisy(groups=("station",), columnwise=False, max_iterations=256)
 dict_config_opti["RPCA_opti"] = {
-    "tau": ho.hp.uniform("tau", low=.5, high=5),
-    "lam": ho.hp.uniform("lam", low=.1, high=1),
+    "tau": Real(0.5, 5.0, name="tau"),
+    "lam": Real(0.1, 1.0, name="lam"),
 }
 imputer_rpca_opticw = imputers.ImputerRpcaNoisy(groups=("station",), columnwise=False, max_iterations=256)
 dict_config_opti["RPCA_opticw"] = {
-    "tau/TEMP": ho.hp.uniform("tau/TEMP", low=.5, high=5),
-    "tau/PRES": ho.hp.uniform("tau/PRES", low=.5, high=5),
-    "lam/TEMP": ho.hp.uniform("lam/TEMP", low=.1, high=1),
-    "lam/PRES": ho.hp.uniform("lam/PRES", low=.1, high=1),
+    "tau/TEMP": Real(0.5, 5.0, name="tau/TEMP"),
+    "tau/PRES": Real(0.5, 5.0, name="tau/PRES"),
+    "lam/TEMP": Real(0.1, 1.0, name="lam/TEMP"),
+    "lam/PRES": Real(0.1, 1.0, name="lam/PRES"),
 }
 
 imputer_normal_sample = imputers.ImputerEM(groups=("station",), model="multinormal", method="sample", max_iter_em=8, n_iter_ou=128, dt=4e-2)