Maintenance updates, part 3: document changes to infrastructure + fix docker build

.github/workflows/lint.yml

@@ -0,0 +1,26 @@
+name: Gratopy Tests
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.13
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.13'
+    - name: Install the latest version of uv
+      uses: astral-sh/setup-uv@v5
+    - name: Check code formatting
+      run: uv tool run ruff format --check
+    - name: Run linting
+      run: uv tool run ruff check

.github/workflows/tests.yml

@@ -0,0 +1,35 @@
+# This workflow will install Python dependencies, run tests and lint with a multiple versions of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Gratopy Tests
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install the latest version of uv
+      uses: astral-sh/setup-uv@v5
+    - name: Install system dependencies
+      run: |
+        sudo apt-get install pocl-opencl-icd libopenblas-dev
+    - name: Install gratopy and Python dependencies
+      run: uv sync
+    - name: Run tests
+      run: uv run pytest

.gitignore

@@ -1,11 +1,11 @@
 # Compiled python modules.
 *.pyc
 
-# Setuptools distribution folder.
+# package distribution folder
 /dist/
 
-# Python egg metadata, regenerated from source files by setuptools.
-/*.egg-info
+# documentation
+doc/build
 
 # virtual environments
 .venv

README.md

@@ -37,29 +37,24 @@ Calling
 pip install .
 ```
 
-inside the main folder then installs the toolbox. 
-Gratopy supports setuptools for installation such that 
+inside the main folder then installs the toolbox.
+Gratopy uses [`uv`](https://docs.astral.sh/uv/) as its project and dependency
+management tool, which allows setting up a dedicated development environment
+by running
 
 ```bash
-python setup.py install
+uv sync
 ```
 
-has the same effect.
 For more details we refer to the [documentation](https://gratopy.readthedocs.io/).
 
-As a further alternative, if no dedicated installation is needed for the toolbox, the code can simply be downloaded and the contents of the `gratopy` directory can be imported as a module. Please make sure to have the following Python modules installed, most of which should be standard.
-
 ## Requirements
+Most notably, `gratopy` is built using [PyOpenCL](https://pypi.org/project/pyopencl/), which
+might require additional care in order to correctly install and configure it: depending on the
+used platform and GPU, suitable drivers must be installed. We refer to
+[PyOpenCL's documentation](https://documen.tician.de/pyopencl/) for detailed instructions.
 
-* [pyopencl>=2019.1](https://pypi.org/project/pyopencl/)
-* [numpy>=1.17.0](https://pypi.org/project/numpy/)
-* [scipy>=1.3.0](https://pypi.org/project/scipy/)
-* [matplotlib>=3.2.0](https://pypi.org/project/matplotlib/)
-* [Pillow>=6.0.0](https://pypi.org/project/Pillow/)
-* [Mako>=1.1.0](https://pypi.org/project/Mako/)
-
-Note that in particular, correctly installing and configuring PyOpenCL might take some time, as dependent on the used platform/GPU, suitable drivers must be installed. We refer to [PyOpenCL's documentation](https://documen.tician.de/pyopencl/).
-
+The full list of requirements can be found in [`pyproject.toml`](/pyproject.toml).
 
 ## Getting started
 We refer to the extensive [documentation](https://gratopy.readthedocs.io/), in particular to the [getting started](https://gratopy.readthedocs.io/en/latest/getting_started.html) guide, as well as to the test files for the [Radon transform](https://gratopy.readthedocs.io/en/latest/_modules/test_radon.html) and [fanbeam transform](https://gratopy.readthedocs.io/en/latest/_modules/test_fanbeam.html). The following [rudimentary example](https://gratopy.readthedocs.io/en/latest/getting_started.html#first-example-radon-transform) is also included in the documentation.

doc/source/conf.py

@@ -12,30 +12,36 @@
 #
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../..'))
+
+sys.path.insert(0, os.path.abspath("../.."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'gratopy'
-copyright = '2021, Kristian Bredies, Richard Huber'
-author = 'Kristian Bredies, Richard Huber'
+project = "gratopy"
+copyright = "2021, Kristian Bredies, Richard Huber"
+author = "Kristian Bredies, Richard Huber"
 
 # The full version, including alpha/beta/rc tags
-release = '0.1.0'
+release = "0.1.0"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosectionlabel', 'sphinx.ext.viewcode', 'sphinx.ext.intersphinx']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosectionlabel",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.intersphinx",
+]
 
 autosectionlabel_prefix_document = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -48,7 +54,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -57,9 +63,9 @@
 html_static_path = []
 
 intersphinx_mapping = {
-    "https://docs.python.org/dev": None,
-    "https://numpy.org/doc/stable/": None,
-    "https://documen.tician.de/pyopencl/": None,
-    "https://matplotlib.org/stable/": None,
-    "https://docs.scipy.org/doc/scipy/": None
+    "python": ("https://docs.python.org/dev", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pyopencl": ("https://documen.tician.de/pyopencl/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
 }

doc/source/installation.rst

@@ -3,10 +3,12 @@
 Installation
 ============
 
-Gratopy supports common Python package distribution frameworks such as
-setuptools_ or pip_.
+Stable releases can be found on the
+`GitHub Release page <https://github.com/kbredies/gratopy/releases>`__
+and are distributed via the
+`Python Packaging Index, PyPI <https://pypi.org/project/gratopy/>`__.
+
 
-.. _setuptools: https://pypi.org/project/setuptools/
 .. _pip: https://pypi.org/project/pip/
 
 Installation in Python
@@ -22,32 +24,39 @@ Alternatively, the release can be downloaded from https://github.com/kbredies/gr
 
     pip install .
 
-Also, setuptools_ can be used for installation via
-::
-
-    python setup.py install
+In case installation fails due to the dependency on other packages
+(see `pyproject.toml <https://github.com/kbredies/gratopy/blob/master/pyproject.toml>`_),
+it is advised to install the packages by hand before retrying to install gratopy.
 
-In case installation fails due to the dependency on other packages (see `requirements.txt <https://github.com/kbredies/gratopy/blob/master/requirements.txt>`_), it is advised to install the packages by hand before retrying to install gratopy. In particular, the PyOpenCL package may require some additional
+In particular, the PyOpenCL package may require some additional
 effort as it depends on additional drivers and C libraries which might needed to be installed by hand. We refer to the documentation of PyOpenCL_.
 
 .. _pyopencl: https://documen.tician.de/pyopencl/
 
+For development, we recommend installing the project and dependency management
+tool `uv <https://docs.astral.sh/uv/>`__. The local development environment
+is then setup from within the cloned repository by running
+
+::
+
+    uv sync
 
 
 Testing correct installation
 ----------------------------
 
+
+
 The release archive (or GitHub repository) includes a ``tests`` folder which contains a variety of tests that allow to observe visually and numerically whether gratopy was installed correctly and works as desired.
 
-One can perform these tests by using, for instance, pytest_
+One can perform these tests by using, for instance, pytest_ (which, if you are not using ``uv``
+for managing a local development environment, needs to be installed by running
+``pip install pytest``). The tests are then executed by running
 ::
 
     pytest
 
-or nose_
-::
-
-    nosetests
+or ``uv run pytest`` when using ``uv``.
 
 In case multiple OpenCL devices are registered in :mod:`pyopencl`, but the default device is not suitably configured for the tests to work, one might need to choose the context to use manually. This a-priori choice of context to use in :mod:`pyopencl` can be done via
 ::
@@ -70,20 +79,19 @@ By default, the plots of the tests are disabled, but can be activated, e.g., by
 Moreover, the :ref:`getting-started` guide contains two example code segments which can be executed to quickly check that no errors occur and the output is as desired.
 
 .. _pytest: https://pypi.org/project/pytest/
-.. _nose: https://pypi.org/project/nose/
 
 Requirements
 ------------
 
-The `requirements.txt <https://github.com/kbredies/gratopy/blob/master/requirements.txt>`_ file specifies Python packages
-required for the use of gratopy. Amongst them the most relevant are
+The `pyproject.toml <https://github.com/kbredies/gratopy/blob/master/pyproject.toml>`_ file specifies Python packages
+required for the use of ``gratopy``. Amongst them the most relevant are
 
-* `pyopencl>=2019.1 <https://pypi.org/project/pyopencl/>`_
-* `numpy>=1.17.0 <https://pypi.org/project/numpy/>`_
-* `scipy>=1.3.0 <https://pypi.org/project/scipy/>`_
-* `matplotlib>=3.2.0 <https://pypi.org/project/matplotlib/>`_
-* `Pillow>=6.0.0 <https://pypi.org/project/Pillow/>`_
-* `Mako>=1.1.0 <https://pypi.org/project/Mako/>`_
+* `pyopencl <https://pypi.org/project/pyopencl/>`_
+* `numpy <https://pypi.org/project/numpy/>`_
+* `scipy <https://pypi.org/project/scipy/>`_
+* `matplotlib <https://pypi.org/project/matplotlib/>`_
+* `Pillow <https://pypi.org/project/Pillow/>`_
+* `Mako <https://pypi.org/project/Mako/>`_
 
 Most users aiming for scientific computing applications will probably have these packages already installed as they can be considered standard for numerical computations in Python.
 Let us again point out that correctly installing PyOpenCL might take some time and effort though, as dependent on the used hardware/GPU, the installation of suitable drivers might be required, see, for instance, https://documen.tician.de/pyopencl/.

docker/Dockerfile

@@ -38,12 +38,11 @@ ENV NVIDIA_DRIVER_CAPABILITIES compute,utility
 
 # Install gratopy
 
-RUN pip install -U pip
+RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 
 WORKDIR /usr/local/gratopy
 ADD . .
 
-RUN pip install -r requirements.txt && pip install pytest notebook
-RUN pip install .
+RUN uv sync && uv pip install notebook
 
-CMD ["/usr/bin/python3"]
+CMD ["uv", "run", "python"]

docker/readme.md

@@ -61,7 +61,7 @@ It is also possible to spin up a local Jupyter server in order to
 interact with `gratopy` in a Jupyter notebook from a browser on your
 host machine. To do so, run the image with
 ```
-docker run --rm [GPU options] -p 8888:8888 gratopy:latest jupyter notebook --ip=0.0.0.0 --allow-root
+docker run --rm [GPU options] -p 8888:8888 gratopy:latest uv run jupyter notebook --ip=0.0.0.0 --allow-root
 ```
 and navigate to the link to `http://127.0.0.1:8888/?token=...` that is
 shown in your terminal.
@@ -80,7 +80,7 @@ from the repository root.
 The docker container ships with `gratopy`s test suite, which can be
 run via
 ```sh
-docker run --rm -it [GPU options] gratopy:latest pytest
+docker run --rm -it [GPU options] gratopy:latest uv run pytest
 ```
 
 

gratopy/__init__.py

@@ -19,10 +19,27 @@
 #    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
 from .gratopy import RADON, PARALLEL, FAN, FANBEAM, VERSION
-from .gratopy import forwardprojection, backprojection, ProjectionSettings, \
-    landweber, conjugate_gradients, total_variation, normest, weight_sinogram
+from .gratopy import (
+    forwardprojection,
+    backprojection,
+    ProjectionSettings,
+    landweber,
+    conjugate_gradients,
+    total_variation,
+    normest,
+    weight_sinogram,
+)
 from .phantom import ct_shepp_logan as phantom
 
 
 # internal functions
-from .gratopy import radon, radon_ad, radon_struct, fanbeam, fanbeam_ad, fanbeam_struct, create_code, read_angles
+from .gratopy import (
+    radon,
+    radon_ad,
+    radon_struct,
+    fanbeam,
+    fanbeam_ad,
+    fanbeam_struct,
+    create_code,
+    read_angles,
+)