Update code to re-enable dev

.github/workflows/ci.yml

@@ -0,0 +1,106 @@
+name: CI
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+    - uses: pre-commit/action@v3.0.1
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+      with:
+        version: "latest"
+
+    - name: Set up Python ${{ matrix.python-version }}
+      run: uv python install ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        uv sync --dev
+        # Install additional system dependencies for documentation
+        sudo apt-get update
+        sudo apt-get install -y graphviz
+
+    # - name: Lint with flake8
+    #   run: |
+    #     # Replicate: flake8 --doctests --exclude=doc, also exclude .venv
+    #     uv run flake8 --doctests --exclude=doc,.venv
+
+    - name: Test with pytest
+      run: |
+        # Set matplotlib backend for headless testing
+        export MPLBACKEND=agg
+        # Run tests with pytest and coverage
+        uv run pytest --cov=pyunlocbox --cov-report=term-missing --cov-report=html --cov-report=xml -v
+
+    - name: Upload coverage to Coveralls
+      if: matrix.python-version == '3.11'  # Only upload once
+      uses: coverallsapp/github-action@v2
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+        file: coverage.xml
+      continue-on-error: true
+
+    - name: Build documentation
+      if: matrix.python-version == '3.11'  # Only build docs once
+      run: |
+        # Replicate: sphinx-build commands from Makefile
+        uv run sphinx-build -b html -d doc/_build/doctrees doc doc/_build/html
+        uv run sphinx-build -b linkcheck -d doc/_build/doctrees doc doc/_build/linkcheck
+
+    - name: Upload documentation artifacts
+      if: matrix.python-version == '3.11'
+      uses: actions/upload-artifact@v4
+      with:
+        name: documentation
+        path: doc/_build/html/
+
+  # Separate job for building and checking distribution
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
+
+    - name: Set up Python
+      run: uv python install 3.11
+
+    - name: Install dependencies
+      run: uv sync --dev
+
+    - name: Build package
+      run: |
+        uv build
+        ls -lh dist/*
+
+    - name: Check package
+      run: |
+        uv run twine check dist/*
+
+    - name: Upload build artifacts
+      uses: actions/upload-artifact@v4
+      with:
+        name: dist
+        path: dist/

.gitignore

@@ -1,3 +1,6 @@
+uv.lock
+.venv/
+coverage.xml
 __pycache__/
 
 # Packages

.pre-commit-config.yaml

@@ -0,0 +1,64 @@
+repos:
+  # Standard pre-commit hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-added-large-files
+      - id: check-merge-conflict
+      - id: debug-statements
+      - id: check-docstring-first
+
+  # Python code formatting with black
+  - repo: https://github.com/psf/black
+    rev: 24.10.0
+    hooks:
+      - id: black
+        language_version: python3
+        args: [--line-length=88]
+
+  # Import sorting with isort
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: [--profile=black]
+
+  # Linting with flake8
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
+    hooks:
+      - id: flake8
+        args: [--max-line-length=88, --extend-ignore=E203]
+        exclude: ^(doc/|\.venv/)
+
+  # Modern Python upgrade suggestions
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.19.0
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+
+  # Check for common security issues
+  - repo: https://github.com/pycqa/bandit
+    rev: 1.7.10
+    hooks:
+      - id: bandit
+        args: [-c, pyproject.toml]
+        additional_dependencies: ["bandit[toml]"]
+        exclude: ^tests/
+
+ci:
+  autofix_commit_msg: |
+    [pre-commit.ci] auto fixes from pre-commit.com hooks
+
+    for more information, see https://pre-commit.ci
+  autofix_prs: true
+  autoupdate_branch: ''
+  autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+  autoupdate_schedule: weekly
+  skip: []
+  submodules: false

.travis.yml

@@ -1,24 +1,28 @@
-language: python
+# DEPRECATED: This project has migrated to GitHub Actions
+# See .github/workflows/ci.yml for the new CI configuration
+# This file is kept for reference and can be removed once migration is complete
 
-python:
-  - 3.6
-  - 3.7
-  - 3.8
-  - 3.9
-
-addons:
-  apt:
-    packages:
-      - graphviz  # sphinx inheritance diagrams
-
-install:
-  - pip install --upgrade pip setuptools wheel  # install with latest tools
-  - pip install --upgrade --upgrade-strategy eager .[dev]  # get latest deps
-
-script:
-  - make lint
-  - make test
-  - make doc
-
-after_success:
-  - coveralls
+# language: python
+#
+# python:
+#   - 3.6
+#   - 3.7
+#   - 3.8
+#   - 3.9
+#
+# addons:
+#   apt:
+#     packages:
+#       - graphviz  # sphinx inheritance diagrams
+#
+# install:
+#   - pip install --upgrade pip setuptools wheel  # install with latest tools
+#   - pip install --upgrade --upgrade-strategy eager .[dev]  # get latest deps
+#
+# script:
+#   - make lint
+#   - make test
+#   - make doc
+#
+# after_success:
+#   - coveralls

CHANGELOG.rst

@@ -6,14 +6,16 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <https://keepachangelog.com>`_
 and this project adheres to `Semantic Versioning <https://semver.org>`_.
 
-Unreleased
-----------
-
-* New function: proj_lineq.
-* New function: proj_sdsp.
-* New function: proj_positive.
-* New function: structured_sparsity.
-* Continuous integration with Python 3.6, 3.7, 3.8, 3.9. Dropped 2.7, 3.4, 3.5.
+0.6.0 (2025-09-10)
+------------------
+
+* Update to use pytest instead of unittest.
+* Update to use UV instead of conda.
+* New function: `proj_lineq`.
+* New function: `proj_sdsp`.
+* New function: `proj_positive`.
+* New function: `structured_sparsity`.
+* Continuous integration with Python 3.8 to 3.13.
 * Merged all the extra requirements in a single dev requirement.
 
 0.5.2 (2017-12-15)

Makefile

@@ -14,25 +14,22 @@ clean:
 	jupyter nbconvert --inplace --ClearOutputPreprocessor.enabled=True $(NB)
 
 lint:
-	flake8 --doctests --exclude=doc
+	uv run flake8 --doctests --exclude=doc,.venv
 
 # Matplotlib doesn't print to screen. Also faster.
 export MPLBACKEND = agg
 
 test:
-	coverage run --branch --source pyunlocbox setup.py test
-	coverage report
-	coverage html
+	uv run pytest --cov=pyunlocbox --cov-report=term-missing --cov-report=html --cov-report=xml -v
 
 doc:
-	sphinx-build -b html -d doc/_build/doctrees doc doc/_build/html
-	sphinx-build -b linkcheck -d doc/_build/doctrees doc doc/_build/linkcheck
+	uv run sphinx-build -b html -d doc/_build/doctrees doc doc/_build/html
+	uv run sphinx-build -b linkcheck -d doc/_build/doctrees doc doc/_build/linkcheck
 
 dist: clean
-	python setup.py sdist
-	python setup.py bdist_wheel --universal
+	uv build
 	ls -lh dist/*
-	twine check dist/*
+	uv run twine check dist/*
 
 release: dist
-	twine upload dist/*
+	uv run twine upload dist/*

README.rst

@@ -125,10 +125,33 @@ for an exhaustive documentation of the API. Enjoy!
 Installation
 ------------
 
+UV (Recommended)
+~~~~~~~~~~~~~~~~
+
+For the fastest installation and dependency management, use `UV <https://docs.astral.sh/uv/>`_::
+
+    $ uv add pyunlocbox
+
+Or install directly::
+
+    $ uv pip install pyunlocbox
+
+To set up a development environment with UV::
+
+    $ git clone https://github.com/epfl-lts2/pyunlocbox.git
+    $ cd pyunlocbox
+    $ uv sync --dev
+
+Pip
+~~~
+
 The PyUNLocBoX is available on PyPI::
 
     $ pip install pyunlocbox
 
+Conda
+~~~~~
+
 The PyUNLocBoX is available on `conda-forge <https://github.com/conda-forge/pyunlocbox-feedstock>`_::
 
     $ conda install -c conda-forge pyunlocbox
@@ -138,6 +161,67 @@ Contributing
 
 See the guidelines for contributing in ``CONTRIBUTING.rst``.
 
+For development, we recommend using UV for fast dependency management::
+
+    $ git clone https://github.com/epfl-lts2/pyunlocbox.git
+    $ cd pyunlocbox
+    $ uv sync --dev
+    $ source .venv/bin/activate  # On Windows: .venv\Scripts\activate
+
+**Quick setup with just** (modern command runner)::
+
+    $ just setup  # Installs dependencies and sets up pre-commit hooks
+
+Set up pre-commit hooks (recommended)::
+
+    $ uv run pre-commit install
+
+This will automatically run code formatting and linting checks before each commit.
+
+**Pre-commit hooks include:**
+
+* **Code formatting**: ``black`` for consistent Python code style
+* **Import sorting**: ``isort`` for organized imports
+* **Linting**: ``flake8`` for code quality and style checks
+* **Security scanning**: ``bandit`` for common security issues
+* **Modern Python**: ``pyupgrade`` for upgrading syntax to newer Python versions
+* **General checks**: trailing whitespace, file endings, YAML/TOML validation
+
+Run tests with pytest::
+
+    $ uv run pytest
+
+Run tests with coverage::
+
+    $ uv run pytest --cov=pyunlocbox --cov-report=html
+
+Run specific test files::
+
+    $ uv run pytest pyunlocbox/tests/test_acceleration.py
+
+**Note**: All tests have been successfully migrated from unittest to pytest! The complete test
+suite now uses modern pytest conventions: `test_acceleration.py`, `test_functions.py`,
+`test_operators.py`, `test_solvers.py`, and `test_docstrings.py`.
+
+Run pre-commit checks manually::
+
+    $ uv run pre-commit run --all-files
+
+Run linting::
+
+    $ uv run flake8 --doctests --exclude=doc,.venv
+
+Format code::
+
+    $ uv run black .
+    $ uv run isort .
+
+Build documentation::
+
+    $ uv run sphinx-build -b html doc/ doc/_build/
+
+Note: This project has migrated from Travis CI to GitHub Actions. The ``.travis.yml`` file can be removed once the migration is complete.
+
 Similar libraries
 -----------------