Chore/patch history

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.9
+current_version = 0.2.0
 commit = True
 tag = True
 

.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

@@ -16,58 +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
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
         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
-        run: |
-          git fetch origin ${{ github.base_ref }}:${{ github.base_ref }} --depth=1
-          git diff --name-only ${{ github.base_ref }} > changed_files.txt
-      - name: Build Docs
-        if: contains(fromJSON('["docs/", ".rst"]').join(','), fromJSON('["${{ steps.changed-files.outputs.files }}"]').join(','))
+          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 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 @@
-env_qolmat_3.9

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

@@ -2,12 +2,18 @@
 History
 =======
 
-0.1.10 (2024-??-??)
+0.2.0 (2026-01-01)
+------------------
+* 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)
 ------------------
 * Long EM and RPCA operations wrapped with tqdm progress bars
 * Readme code sample updated, and results table made consistent
 
-0.1.9 (2024-08-29)
+0.1.9 (2025-08-29)
 ------------------
 * Tutorials reproducibility improved with random_state parameters
 * RPCA now accepts random_state parameters

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

@@ -27,7 +27,7 @@
 author = "Quantmetry"
 
 # The full version, including alpha/beta/rc tags
-version = "0.1.9"
+version = "0.2.0"
 release = version
 
 # -- General configuration ---------------------------------------------------
@@ -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
 
@@ -75,7 +73,7 @@
 source_suffix = ".rst"
 
 # Generate the plots for the gallery
-plot_gallery = True
+plot_gallery = "True"
 
 # The master toctree document.
 master_doc = "index"
@@ -156,9 +154,11 @@
     "gallery_dirs": ["examples/tutorials/"],
     "doc_module": "qolmat",
     "backreferences_dir": os.path.join("generated"),
-    "reference_url": {"qolmat": None},
+    "reference_url": {},
+    "inspect_global_variables": False,
 }
 
+
 suppress_warnings = ["autosectionlabel.*"]
 
 # doctest configuration

docs/sg_execution_times.rst

@@ -0,0 +1,52 @@
+
+:orphan:
+
+.. _sphx_glr_sg_execution_times:
+
+
+Computation times
+=================
+**01:04.897** total execution time for 6 files **from all galleries**:
+
+.. container::
+
+  .. raw:: html
+
+    <style scoped>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
+    <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
+    </style>
+    <script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script>
+    <script type="text/javascript" class="init">
+    $(document).ready( function () {
+        $('table.sg-datatable').DataTable({order: [[1, 'desc']]});
+    } );
+    </script>
+
+  .. list-table::
+   :header-rows: 1
+   :class: table table-striped sg-datatable
+
+   * - Example
+     - Time
+     - Mem (MB)
+   * - :ref:`sphx_glr_examples_tutorials_plot_tuto_benchmark_TS.py` (``../examples/tutorials/plot_tuto_benchmark_TS.py``)
+     - 00:21.381
+     - 0.0
+   * - :ref:`sphx_glr_examples_tutorials_plot_tuto_categorical.py` (``../examples/tutorials/plot_tuto_categorical.py``)
+     - 00:16.026
+     - 0.0
+   * - :ref:`sphx_glr_examples_tutorials_plot_tuto_diffusion_models.py` (``../examples/tutorials/plot_tuto_diffusion_models.py``)
+     - 00:11.896
+     - 0.0
+   * - :ref:`sphx_glr_examples_tutorials_plot_tuto_mcar.py` (``../examples/tutorials/plot_tuto_mcar.py``)
+     - 00:08.072
+     - 0.0
+   * - :ref:`sphx_glr_examples_tutorials_plot_tuto_mean_median.py` (``../examples/tutorials/plot_tuto_mean_median.py``)
+     - 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)