Fix cmake and Cython compile issues; update GH Action CI; extend support for python 3.12, 3.13, 3.14

.dockerignore

@@ -0,0 +1,5 @@
+.git
+.DS_Store
+build
+docs/_build
+quickstart

.github/workflows/unit-tests.yml

@@ -11,29 +11,28 @@ on: push
 jobs:
   test:
     name: Run Unit Tests
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     defaults:
       run:
         # pinning the shell name helps to properly set conda
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: [ 3.7, 3.8, 3.9]
+        python-version: [ 3.7, 3.8, 3.9, '3.12', '3.13', '3.14' ]
     env:
       OMP_NUM_THREADS: 2
     steps:
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v6
       - name: Setup conda for Python ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2
+        uses: conda-incubator/setup-miniconda@v4
         with:
           activate-environment: test
           python-version: ${{ matrix.python-version }}
           channels: conda-forge
           allow-softlinks: true
           channel-priority: flexible
           show-channel-urls: true
-          use-only-tar-bz2: true
       - name: Print conda config
         run: |
           conda info
@@ -45,17 +44,21 @@ jobs:
       - name: Build and install galario, build docs
         run: |
           conda activate test
-          conda install astropy cython nomkl numpy pytest scipy sphinx
+          conda install cython nomkl numpy pytest scipy sphinx
           pip install coverage codecov pytest-cov
           mkdir build && cd build
           cmake -DCMAKE_INSTALL_PREFIX=/tmp -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} ..
           make
           make install
       - name: Run unit tests
-        run: python/py.test.sh -sv --cov=./ python/test_galario.py
+        run: python/py.test.sh -sv --cov=./ --cov-report=xml:coverage.xml python/test_galario.py
         working-directory: build
       - name: Upload code coverage report
-        run: bash <(curl -s https://codecov.io/bash) || echo 'Codecov failed to upload'
+        uses: codecov/codecov-action@v5
+        with:
+          files: ./build/coverage.xml
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}
       - name: build docs
         run: |
           conda activate test

CMakeLists.txt

@@ -17,7 +17,9 @@
 # For documentation see https://mtazzari.github.io/galario/                   #
 ###############################################################################
 
-cmake_minimum_required(VERSION 3.0)
+# CMake 4 no longer provides compatibility for projects declaring a version
+# older than 3.5.  3.10 still supports the legacy FindCUDA-based GPU build.
+cmake_minimum_required(VERSION 3.10)
 project(galario)
 set(PACKAGE_VERSION "'1.2.2'")
 

Dockerfile

@@ -0,0 +1,39 @@
+# Reproduce the Linux CPU installation with pip-managed Python dependencies.
+# CUDA is intentionally disabled here: a CUDA build requires an NVIDIA toolkit
+# and is covered by the same CMake path when GALARIO_CHECK_CUDA is enabled.
+FROM ubuntu:22.04
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    OMP_NUM_THREADS=2 \
+    PYTHONPATH=/opt/galario/lib/python3.10/site-packages \
+    PYTHONDONTWRITEBYTECODE=1
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        build-essential \
+        cmake \
+        git \
+        libfftw3-dev \
+        python3 \
+        python3-dev \
+        python3-pip \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN python3 -m pip install --no-cache-dir \
+        'Cython>=3' \
+        numpy \
+        pytest \
+        pytest-cov \
+        scipy
+
+WORKDIR /src
+COPY . .
+
+RUN cmake -S . -B build \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=/opt/galario \
+        -DGALARIO_CHECK_CUDA=OFF \
+    && cmake --build build --parallel \
+    && cmake --install build \
+    && python3 -c 'import galario; print(galario.__file__)' \
+    && ctest --test-dir build --output-on-failure

Dockerfile.conda

@@ -0,0 +1,37 @@
+# Reproduce the documented and GitHub Actions Linux CPU build in a Conda
+# environment.  CUDA is intentionally disabled because this image has neither
+# an NVIDIA toolkit nor GPU access.
+FROM continuumio/miniconda3:latest
+
+ENV DEBIAN_FRONTEND=noninteractive \
+    OMP_NUM_THREADS=2 \
+    PYTHONDONTWRITEBYTECODE=1
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+        build-essential \
+        cmake \
+        git \
+        libfftw3-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN conda create -y --name galario --channel conda-forge \
+        python=3.12 \
+        cython \
+        numpy \
+        pytest \
+        pytest-cov \
+        scipy \
+    && conda clean --all --yes
+
+WORKDIR /src
+COPY . .
+
+RUN conda run --no-capture-output --name galario \
+        cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DGALARIO_CHECK_CUDA=OFF \
+    && conda run --no-capture-output --name galario cmake --build build --parallel \
+    && conda run --no-capture-output --name galario cmake --install build \
+    && conda run --no-capture-output --name galario \
+        python -c 'import galario; print(galario.__file__)' \
+    && conda run --no-capture-output --name galario \
+        ctest --test-dir build --output-on-failure

docs/conf.py.in

@@ -72,7 +72,7 @@ release = str(galario.__version__)
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -307,4 +307,4 @@ texinfo_documents = [
 
 # override CSS file
 def setup(app):
-    app.add_stylesheet('css/custom.css')
+    app.add_css_file('css/custom.css')

docs/install.rst

@@ -27,6 +27,30 @@ To create a conda environment for |galario|, see Section 1.4, step 2.
 Due to technical limitations, the conda package does not support GPUs at the
 moment. If you want to use a GPU, read on as you have to build |galario| by hand.
 
+Linux installation test containers
+----------------------------------
+
+The repository includes two Linux CPU test containers.  The Conda container
+mirrors the manual and GitHub Actions installation path, using system FFTW and
+a Conda environment for Python and its build dependencies:
+
+.. code-block:: bash
+
+   ./scripts/build-linux-conda-container.sh
+
+The pip container provides complementary coverage for a future PyPI release:
+
+.. code-block:: bash
+
+   ./scripts/build-linux-container.sh
+
+It builds an ``linux/amd64`` image by default, matching the usual Linux
+research-server target.  Set ``DOCKER_PLATFORM`` to build another platform.
+The image deliberately configures ``-DGALARIO_CHECK_CUDA=OFF`` because Docker
+Desktop on a non-NVIDIA host cannot compile or run CUDA.  The production CUDA
+configuration remains available by enabling ``GALARIO_CHECK_CUDA`` on a host
+with a compatible NVIDIA toolkit.
+
 Build requirements
 ------------------
 

python/CMakeLists.txt

@@ -48,8 +48,19 @@ endif()
 ###
 # installation
 ###
-# to set ${PYTHON_PKG_DIR}. It is prepended by ${CMAKE_INSTALL_PREFIX} if set
-include(PythonInstall)
+# PythonInstall from GreatCMakeCookOff imports distutils, which was removed in
+# Python 3.12.  Use the conventional installation layout relative to
+# CMAKE_INSTALL_PREFIX instead.
+execute_process(
+  COMMAND "${PYTHON_EXECUTABLE}" -c
+    "import sys; print('lib/python{}.{}{}'.format(sys.version_info[0], sys.version_info[1], '/site-packages'))"
+  OUTPUT_VARIABLE PYTHON_PKG_DIR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+if(PYTHON_PKG_DIR MATCHES "^\\.\\.")
+  message(FATAL_ERROR "Could not determine a Python package directory relative to ${PYTHON_EXECUTABLE}")
+endif()
+message(STATUS "Python install path (PYTHON_PKG_DIR): ${PYTHON_PKG_DIR}")
 
 # I guess variable has to be in cache to survive reinvocations of cmake that happen during building
 set(GALARIO_PYTHON_PKG_DIR "${PYTHON_PKG_DIR}" CACHE PATH "Current python install path")
@@ -77,13 +88,14 @@ configure_file("${galario_test}" "${CMAKE_CURRENT_BINARY_DIR}" COPYONLY)
 add_test(NAME CanImport COMMAND ${PYTHON_EXECUTABLE} -c "import ${PROJECT_NAME}")
 
 # https://github.com/UCL/GreatCMakeCookOff/wiki/Adding-py.test-to-ctest
-include(AddPyTest)
-
-# I don't understand the first arg but it seems to work if py.test already installed
-setup_pytest("${CMAKE_CURRENT_BINARY_DIR}" "${CMAKE_CURRENT_BINARY_DIR}/py.test.sh")
+# Keep a small compatibility wrapper for documented/manual test commands.
+configure_file("${CMAKE_CURRENT_SOURCE_DIR}/py.test.sh.in"
+  "${CMAKE_CURRENT_BINARY_DIR}/py.test.sh" @ONLY)
+if(UNIX)
+  execute_process(COMMAND chmod +x "${CMAKE_CURRENT_BINARY_DIR}/py.test.sh")
+endif()
 
-# the source name has to match test_*.py
-# https://github.com/UCL/GreatCMakeCookOff/issues/56
-#
-# need to run in binary_dir so import of pygalario works
-add_pytest("${CMAKE_CURRENT_BINARY_DIR}/${galario_test}" NOINSTALL CMDLINE --cov=./)
+# Run in the binary directory so the generated galario package is importable.
+add_test(NAME galario
+  COMMAND "${PYTHON_EXECUTABLE}" -m pytest "${CMAKE_CURRENT_BINARY_DIR}/${galario_test}" --cov=./)
+set_tests_properties(galario PROPERTIES WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")

python/libcommon.pyx

@@ -18,7 +18,7 @@
 ###############################################################################
 
 cimport numpy as np
-from cpython cimport PyObject, Py_INCREF
+from cpython cimport Py_INCREF
 
 # Numpy must be initialized. When using numpy from C or Cython you must
 # _always_ do that, or you will have segfaults
@@ -82,10 +82,12 @@ cdef class ArrayWrapper:
 
         # Create a 2D array, of length `nx*ny/2+1`
         ndarray = np.PyArray_SimpleNewFromData(2, shape, complex_typenum, self.data_ptr)
-        ndarray.base = <PyObject*> self
 
-        # without this, data would be cleaned up right away
+        # NumPy owns a reference to its base object.  Assigning ``.base`` was
+        # accepted by older Cython releases, but is a read-only property in
+        # Cython 3.  PyArray_SetBaseObject steals the reference passed to it.
         Py_INCREF(self)
+        np.PyArray_SetBaseObject(ndarray, self)
         return ndarray
 
     def __dealloc__(self):

python/py.test.sh.in

@@ -0,0 +1,2 @@
+#!/usr/bin/env sh
+exec "@PYTHON_EXECUTABLE@" -m pytest "$@"

python/utils.py

@@ -25,7 +25,6 @@
 import numpy as np
 
 from scipy.interpolate import interp1d, RectBivariateSpline
-from scipy.integrate import trapz, quadrature
 
 __all__ = ["py_sampleImage", "py_sampleProfile", "py_chi2Profile", "py_chi2Image",
            "radial_profile", "g_sweep_prototype", "sweep_ref",
@@ -217,7 +216,7 @@ def g_sweep_prototype(I, Rmin, dR, nrow, ncol, dxy, inc, dtype_image='float64'):
     inc_cos = np.cos(inc)
 
     # radial extent in number of image pixels covered by the profile
-    rmax = min(np.int(np.ceil((Rmin+nrad*dR)/dxy)), irow_center)
+    rmax = min(int(np.ceil((Rmin+nrad*dR)/dxy)), irow_center)
     row_offset = irow_center-rmax
     col_offset = icol_center-rmax
     for irow in range(rmax*2):
@@ -227,7 +226,7 @@ def g_sweep_prototype(I, Rmin, dR, nrow, ncol, dxy, inc, dtype_image='float64'):
             rr = np.sqrt((x/inc_cos)**2. + (y)**2.)
 
             # interpolate 1D
-            iR = np.int(np.floor((rr-Rmin) / dR))
+            iR = int(np.floor((rr-Rmin) / dR))
             if iR >= nrad-1:
                 image[irow+row_offset, jcol+col_offset] = 0.
             else:
@@ -394,10 +393,10 @@ def int_bilin_MT(f, x, y):
     for i in range(len(x)):
         t = y[i] - np.floor(y[i])
         u = x[i] - np.floor(x[i])
-        y0 = f[np.int(np.floor(y[i])), np.int(np.floor(x[i]))]
-        y1 = f[np.int(np.floor(y[i])) + 1, np.int(np.floor(x[i]))]
-        y2 = f[np.int(np.floor(y[i])) + 1, np.int(np.floor(x[i])) + 1]
-        y3 = f[np.int(np.floor(y[i])), np.int(np.floor(x[i])) + 1]
+        y0 = f[int(np.floor(y[i])), int(np.floor(x[i]))]
+        y1 = f[int(np.floor(y[i])) + 1, int(np.floor(x[i]))]
+        y2 = f[int(np.floor(y[i])) + 1, int(np.floor(x[i])) + 1]
+        y3 = f[int(np.floor(y[i])), int(np.floor(x[i])) + 1]
 
         vis_int[i] = t * u * (y0 - y1 + y2 - y3)
         vis_int[i] += t * (y1 - y0)

scripts/build-linux-conda-container.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env sh
+# Build the Linux/amd64 Conda installation test image from the repository root.
+set -eu
+
+image_tag=${1:-galario-linux-conda-test:local}
+platform=${DOCKER_PLATFORM:-linux/amd64}
+exec docker build --quiet --platform "$platform" --file Dockerfile.conda --tag "$image_tag" .

scripts/build-linux-container.sh

@@ -0,0 +1,7 @@
+#!/usr/bin/env sh
+# Build the Linux CPU installation test image from the repository root.
+set -eu
+
+image_tag=${1:-galario-linux-test:local}
+platform=${DOCKER_PLATFORM:-linux/amd64}
+exec docker build --quiet --platform "$platform" --tag "$image_tag" .