build: added support for uv

.github/workflows/build.yaml

@@ -1,34 +1,32 @@
-name: PyProx
+name: PyProximal-testing
 
-on: [push, pull_request]
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+  push:
+    branches:
+      - main
+      - dev
 
 jobs:
   build:
     strategy:
       matrix:
         platform: [ ubuntu-latest, macos-latest ]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     runs-on: ${{ matrix.platform }}
     steps:
-    - uses: actions/checkout@v4
-    - name: Get history and tags for SCM versioning to work
-      run: |
-        git fetch --prune --unshallow
-        git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        pip install flake8 pytest
-        if [ -f requirements.txt ]; then pip install -r requirements-dev.txt; fi
-    - name: Install pyproximal
-      run: |
-        python -m setuptools_scm
-        pip install .
-    - name: Test with pytest
-      run: |
-        pytest
+      - uses: actions/checkout@v4
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+      - name: Install uv with Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies and pyproximal
+        run: uv sync --locked --all-extras --all-groups
+      - name: Test with pytest
+        run: uv run pytest --color=yes pytests/

.github/workflows/codacy-coverage-reporter.yaml

@@ -0,0 +1,52 @@
+# This workflow uploads PyProximal coverage analysis on Codacy
+# For more information see: https://github.com/codacy/codacy-coverage-reporter-action
+name: PyProximal-coverage
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        platform: [ubuntu-latest]
+        python-version: ["3.11"]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+
+      - name: Install uv with Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies and pyproximal
+        run: uv sync --locked --all-extras --all-groups
+
+      - name: Coverage with pytest
+        run: |
+          uv run coverage run -m pytest
+          uv run coverage xml
+          uv run coverage html
+
+      - name: Upload HTML coverage report
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-html
+          path: htmlcov/
+
+      - name: Run codacy-coverage-reporter
+        if: github.event_name == 'push'
+        uses: codacy/codacy-coverage-reporter-action@v1
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: coverage.xml

.github/workflows/deploy.yaml

@@ -1,6 +1,6 @@
 # This workflow uploads PyProx on PyPI using Twine when a release is created
 # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-name: PyProx-deploy
+name: PyProximal-deploy
 
 on:
   release:

.github/workflows/mypy.yaml

@@ -0,0 +1,22 @@
+# This workflow runs MyPy on the PR
+name: PyProximal-mypy
+
+on: [push, pull_request]
+
+jobs:
+  mypy:
+    runs-on: ubuntu-latest
+    name: MyPy
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v4
+      - name: Install uv with Python
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.11"
+          enable-cache: true
+      - name: Install dependencies and pyproximal
+        run: uv sync --locked --all-extras --all-groups
+      - name: Run Mypy
+        run: |
+          uv run mypy pyproximal/

.github/workflows/ruff.yaml

@@ -0,0 +1,17 @@
+# This workflow runs Ruff on the PR
+# For more information see: https://github.com/marketplace/actions/ruff-action
+name: PyProximal-ruff
+
+on: [push, pull_request]
+
+jobs:
+  ruff-lint:
+    runs-on: ubuntu-latest
+    name: Lint
+    steps:
+      - name: Check out source repository
+        uses: actions/checkout@v4
+      - name: ruff Lint
+        uses: astral-sh/ruff-action@v3
+        with:
+           src: "./pyproximal"

.pre-commit-config.yaml

@@ -5,26 +5,29 @@ repos:
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: requirements-txt-fixer
+      - id: check-toml
       - id: check-yaml
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
 
-  - repo: https://github.com/psf/black
-    rev: 25.1.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.14.14
     hooks:
-      - id: black
-        args: # arguments to configure black
-          - --line-length=88
+      - id: ruff-check
+        args: [ --fix ]
+      - id: ruff-format
 
-  - repo: https://github.com/pycqa/isort
-    rev: 6.0.1
+  - repo: https://github.com/astral-sh/uv-pre-commit
+    rev: 0.9.28
     hooks:
-      - id: isort
-        name: isort (python)
-        args:
-          [
-            "--profile",
-            "black",
-            "--skip",
-            "__init__.py",
-            "--filter-files",
-            "--line-length=88",
-          ]
+      - id: uv-lock
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.23"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]

.readthedocs.yaml

@@ -5,19 +5,21 @@
 # Required
 version: 2
 
-# Set the version of Python and other tools you might need
-build:
-  os: ubuntu-20.04
-  tools:
-    python: "3.11"
-
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
-# Declare the Python requirements required to build your docs
-python:
-  install:
-    - requirements: requirements-doc.txt
-    - method: pip
-      path: .
+# Set the version of environment using UV
+build:
+   os: ubuntu-24.04
+   tools:
+      python: "3.13"
+   jobs:
+      pre_create_environment:
+         - asdf plugin add uv
+         - asdf install uv latest
+         - asdf global uv latest
+      create_environment:
+         - uv venv "${READTHEDOCS_VIRTUALENV_PATH}"
+      install:
+         - UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --locked --all-extras --all-groups

CONTRIBUTING.md

@@ -58,14 +58,21 @@ Ready to contribute?
     ```
     make tests
     ```
+    or
+    ```
+    make tests_uv
+    ```
 
-4. Run flake8 to check the quality of your code:
+4. Run ruff to check the quality of your code:
     ```
     make lint
     ```
-    Note that PyLops does not enforce full compliance with flake8, rather this is used as a
-guideline and will also be run as part of our CI.
-Make sure to limit to a minimum flake8 warnings before making a PR.
+    or
+    ```
+    make lint_uv
+    ```
+
+    Note that PyProximal enforces full compliance with ruff and it will also be run as part of our CI.
 
 5. Update the docs
    ```

Makefile

@@ -1,7 +1,10 @@
 PIP := $(shell command -v pip3 2> /dev/null || command which pip 2> /dev/null)
 PYTHON := $(shell command -v python3 2> /dev/null || command which python 2> /dev/null)
+UV := $(shell command -v uv 2> /dev/null || command which uv 2> /dev/null)
 
-.PHONY: install dev-install install_conda dev-install_conda tests doc docupdate servedoc lint typeannot
+.PHONY: install dev-install install_conda dev-install_conda
+.PHONY: tests tests_uv doc doc_uv docupdate docupdate_uv servedoc
+.PHONY: lint lint_uv typeannot typeannot_uv coverage, coverage_uv
 
 pipcheck:
 ifndef PIP
@@ -15,6 +18,12 @@ ifndef PYTHON
 endif
 	@echo Using python: $(PYTHON)
 
+uvcheck:
+ifndef UV
+	$(error "Ensure uv is in your PATH")
+endif
+	@echo Using uv: $(UV)
+
 install:
 	make pipcheck
 	$(PIP) install -r requirements.txt && $(PIP) install .
@@ -36,19 +45,56 @@ tests:
 	make pythoncheck
 	pytest
 
+tests_uv:
+	make uvcheck
+	$(UV) run pytest
+
 doc:
 	cd docs  && rm -rf source/api/generated && rm -rf source/gallery &&\
 	rm -rf source/tutorials && rm -rf source/examples &&\
 	rm -rf build && make html && cd ..
 
+doc_uv:
+	make uvcheck
+	cd docs  && rm -rf source/api/generated && rm -rf source/gallery &&\
+	rm -rf source/tutorials && rm -rf source/examples &&\
+	rm -rf build && $(UV) run make html && cd ..
+
 docupdate:
 	cd docs && make html && cd ..
 
+docupdate_uv:
+	make uvcheck
+	cd docs && $(UV) run make html && cd ..
+
 servedoc:
+	make pythoncheck
 	$(PYTHON) -m http.server --directory docs/build/html/
 
+servedoc_uv:
+	make uvcheck
+	$(UV) run python -m http.server --directory docs/build/html/
+
 lint:
-	flake8 docs/source examples/ pyproximal/ pytests/ tutorials/
+	ruff check docs/source examples/ pyproximal/ pytests/ tutorials/
+
+lint_uv:
+	make uvcheck
+	$(UV) run ruff check docs/source examples/ pyproximal/ pytests/ tutorials/
 
 typeannot:
 	mypy pyproximal/
+
+typeannot_uv:
+	make uvcheck
+	$(UV) run mypy pyproximal/
+
+coverage:
+	coverage run -m pytest && coverage xml && coverage html && $(PYTHON) -m http.server --directory htmlcov/
+
+coverage_uv:
+	make uvcheck
+	$(UV) run coverage run -m pytest  &&\
+	$(UV) run coverage xml &&\
+	$(UV) run coverage html  &&\
+	$(UV) run python -m http.server --directory htmlcov/

docs/source/adding.rst

@@ -2,9 +2,9 @@
 
 .. _numpydoc-docstring: https://numpydoc.readthedocs.io/en/latest/
 
+|:paintbrush:| Implementing new operators
+#########################################
 
-Implementing new operators
-==========================
 Users are welcome to create new operators and add them to the PyProximal library.
 
 In this tutorial, we will go through the key steps in the definition of an operator, using the

docs/source/api/index.rst

@@ -1,7 +1,7 @@
 .. _api:
 
-PyProximal API
-==============
+|:wrench:| PyProximal API
+=========================
 
 The Application Programming Interface (API) of PyProximal is composed of 3 elements: