check ruff

.github/workflows/publish.yml

@@ -1,13 +1,11 @@
-name: Publish Package on PYPI
+name: Publish Package on PyPI
 
 on:
   release:
     types: [published]
 
-
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
 
     steps:
@@ -16,14 +14,19 @@ jobs:
       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: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        poetry install
     - name: Build package
-      run: python setup.py sdist bdist_wheel
+      run: |
+        poetry build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      env:
+        PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+      run: |
+        poetry config pypi-token.pypi $PYPI_TOKEN
+        poetry publish

.github/workflows/test.yml

@@ -3,8 +3,7 @@ name: Unit tests
 on:
   push:
     branches:
-      -dev
-      -main
+      - "**"
   pull_request:
     types: [opened, synchronize, reopened, ready_for_review]
   workflow_dispatch:
@@ -22,24 +21,23 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - name: Git clone
+      - name: Checkout
         uses: actions/checkout@v3
-      - name: Set up venv for ci
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Python
+        uses: actions/setup-python@v4
         with:
-          python-version: ${{matrix.python-version}}
-          environment-file: environment.ci.yml
-      - name: Lint with flake8
-        run: |
-          flake8
-      - name: Test with pytest
-        run: |
-          make coverage
-      - name: typing with mypy
-        run: |
-          mypy qolmat
-          echo you should uncomment mypy qolmat and delete this line
-      - name: Upload coverage reports to Codecov
+          python-version: ${{ 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 }}

.github/workflows/test_quick.yml

@@ -19,7 +19,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-      - name: Git clone
+      - name: Checkout
         uses: actions/checkout@v3
 
       # See caching environments
@@ -29,40 +29,27 @@ jobs:
         with:
             miniforge-variant: Mambaforge
             miniforge-version: latest
-            activate-environment: env_qolmat_ci
             use-mamba: true
+            python-version: ${{ matrix.python-version }}
 
       - name: Get Date
         id: get-date
         run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
 
-      - name: Cache Conda env
+      - name: Cache Poetry dependencies
         uses: actions/cache@v2
         with:
-          path: ${{ env.CONDA }}/envs
-          key:
-            conda-${{ runner.os }}--${{ runner.arch }}--${{
-            steps.get-date.outputs.today }}-${{
-            hashFiles('environment.ci.yml') }}-${{ env.CACHE_NUMBER
-            }}
-        env:
-          # Increase this value to reset cache if environment.ci.yml has not changed
-          CACHE_NUMBER: 0
-        id: cache
-
-      - name: Update environment
-        run: mamba env update -n env_qolmat_ci -f environment.ci.yml
-        if: steps.cache.outputs.cache-hit != 'true'
-
-      - name: Lint with flake8
-        run: |
-          flake8
-      - name: Test with pytest
-        run: |
-          make coverage
-      - name: Test docstrings
-        run: make doctest
-      - name: typing with mypy
-        run: |
-          mypy qolmat
-          echo you should uncomment mypy qolmat and delete this line
+          path: |
+            ~/.cache/pypoetry/cache
+            ~/.cache/pypoetry/artifacts
+          key: poetry-${{ runner.os }}-cache-${{ steps.get-date.outputs.today }}-${{ hashFiles('poetry.lock') }}
+          restore-keys: |
+            poetry-${{ runner.os }}-cache-
+
+      - name: Install Poetry
+        run :
+          mamba install -c conda-forge poetry -y
+          poetry install
+
+      - name: Checkers
+        run: make check-coverage check-types

.pre-commit-config.yaml

@@ -8,20 +8,8 @@ repos:
         exclude: (docs/)
       - id: trailing-whitespace
         exclude: (docs/)
-  - repo: https://github.com/psf/black
-    rev: 22.8.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.3.3
     hooks:
-      - id: black
-        args:
-          - "-l 99"
-  # Flake8
-  - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
-    hooks:
-      - id: flake8
-  - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.1.1
-    hooks:
-      - id: mypy
-        args: [--ignore-missing-imports]
-        additional_dependencies: [types-requests]
+      - id: ruff
+      - id: ruff-format

Makefile

@@ -1,13 +1,34 @@
-coverage:
-	pytest --cov-branch --cov=qolmat --cov-report=xml tests
 
-doctest:
-	pytest --doctest-modules --pyargs qolmat
+check-coverage:
+	poetry run pytest --cov-branch --cov=qolmat/ --cov-report=xml tests/
 
-doc:
-	make html -C docs
+check-poetry:
+	poetry check --lock
+
+check-quality:
+	poetry run ruff check qolmat/ tests/
+
+check-security:
+	poetry run bandit --recursive --configfile=pyproject.toml qolmat/
+
+check-tests:
+	poetry run pytest tests/
+
+check-types:
+	poetry run mypy qolmat/ tests/
+
+checkers: check-coverage check-types
 
 clean:
 	rm -rf .mypy_cache .pytest_cache .coverage*
 	rm -rf **__pycache__
 	make clean -C docs
+
+coverage:
+	poetry run pytest --cov-branch --cov=qolmat --cov-report=xml tests
+
+doc:
+	make html -C docs
+
+doctest:
+	poetry run pytest --doctest-modules --pyargs qolmat

examples/tutorials/plot_tuto_benchmark_TS.py

@@ -1,5 +1,4 @@
-"""
-=========================
+"""=========================
 Benchmark for time series
 =========================
 
@@ -14,18 +13,18 @@
 # First import some libraries
 
 import numpy as np
-import pandas as pd
 
 np.random.seed(1234)
-from matplotlib import pyplot as plt
 import matplotlib.ticker as plticker
+from matplotlib import pyplot as plt
 
 tab10 = plt.get_cmap("tab10")
 
+from sklearn.linear_model import LinearRegression
+
 from qolmat.benchmark import comparator, missing_patterns
 from qolmat.imputations import imputers
 from qolmat.utils import data, plot
-from sklearn.linear_model import LinearRegression
 
 # %%
 # 1. Data

examples/tutorials/plot_tuto_categorical.py

@@ -1,5 +1,4 @@
-"""
-==============================
+"""==============================
 Benchmark for categorical data
 ==============================
 
@@ -8,14 +7,13 @@
 It comprehends passengers features as well as if they survived the accident.
 """
 
-from qolmat.imputations import preprocessing, imputers
+from sklearn.pipeline import Pipeline
+
+from qolmat.benchmark import comparator, missing_patterns
+from qolmat.imputations import imputers, preprocessing
 from qolmat.imputations.imputers import ImputerRegressor
-from qolmat.benchmark import missing_patterns
-from qolmat.benchmark import comparator
 from qolmat.utils import data
 
-from sklearn.pipeline import Pipeline
-
 # %%
 # 1. Titanic dataset
 # ---------------------------------------------------------------

examples/tutorials/plot_tuto_diffusion_models.py

@@ -1,21 +1,19 @@
-"""
-===============================================
+"""===============================================
 Tutorial for imputers based on diffusion models
 ===============================================
 
 In this tutorial, we show how to use :class:`~qolmat.imputations.diffusions.ddpms.TabDDPM`
 and :class:`~qolmat.imputations.diffusions.ddpms.TsDDPM` classes.
 """
 
-import pandas as pd
-import numpy as np
 import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
 
-from qolmat.utils import data
 from qolmat.benchmark import comparator, missing_patterns
-
-from qolmat.imputations.imputers_pytorch import ImputerDiffusion
 from qolmat.imputations.diffusions.ddpms import TabDDPM, TsDDPM
+from qolmat.imputations.imputers_pytorch import ImputerDiffusion
+from qolmat.utils import data
 
 # %%
 # 1. Time-series data

examples/tutorials/plot_tuto_hole_generator.py

@@ -1,5 +1,4 @@
-"""
-============================================
+"""============================================
 Tutorial for hole generation in tabular data
 ============================================
 
@@ -17,13 +16,10 @@
 """
 from typing import List
 
-from io import BytesIO
 import matplotlib
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import requests
-import zipfile
 
 from qolmat.benchmark import missing_patterns
 from qolmat.utils import data
@@ -90,6 +86,7 @@ def visualise_missing_values(df_init: pd.DataFrame, df_mask: pd.DataFrame):
         initial dataframe
     df_mask : pd.DataFrame
         masked dataframe
+
     """
     df_tot = df_init.copy()
     df_tot[df_init.notna()] = 0
@@ -117,6 +114,7 @@ def get_holes_sizes_column_wise(data: np.ndarray) -> List[List[int]]:
     -------
     List[List[int]]
         List of hole size for each column.
+
     """
     hole_sizes = []
     for col in range(data.shape[1]):
@@ -153,6 +151,7 @@ def plot_cdf(
         list of labels
     colors : List[str]
         list of colors
+
     """
     _, axs = plt.subplots(1, df.shape[1], sharey=True, figsize=(15, 3))
 

examples/tutorials/plot_tuto_mcar.py

@@ -1,5 +1,4 @@
-"""
-============================================
+"""============================================
 Tutorial for Testing the MCAR Case
 ============================================
 
@@ -8,10 +7,9 @@
 
 # %%
 # First import some libraries
-from matplotlib import pyplot as plt
-
 import numpy as np
 import pandas as pd
+from matplotlib import pyplot as plt
 from scipy.stats import norm
 
 from qolmat.analysis.holes_characterization import LittleTest