Install with pip

.github/workflows/python-publish.yml

@@ -0,0 +1,101 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  push:
+    branches:
+      - "master"
+
+permissions:
+  contents: read
+
+jobs:
+  #build_wheels:
+
+    #runs-on: ${{ matrix.os }}
+
+    #strategy:
+    #  matrix:
+    #    os: [ubuntu-latest]
+
+    #steps:
+    #- uses: actions/checkout@v4
+    #- name: Set up Python
+    #  uses: actions/setup-python@v5
+
+    #- name: Install dependencies
+    #  run: |
+    #    python -m pip install --upgrade pip
+    #    python -m pip install cibuildwheel==2.20.0
+
+    #- name: Build wheels
+    #  run: python -m cibuildwheel --output-dir dist
+    #  env:
+    #    CIBW_SKIP: cp36-*
+    #    CIBW_BEFORE_BUILD_LINUX: yum install -y fftw-devel || apk add --upgrade fftw-dev || apt-get install libfftw3-dev
+    #    CIBW_BEFORE_BUILD_MACOS: brew install fftw
+
+    #- uses: actions/upload-artifact@v4
+    #  with:
+    #    name: dist-${{ matrix.os }}-${{ strategy.job-index }}
+    #    path: dist/*.whl
+
+  build_sdist:
+
+    runs-on: [ubuntu-latest]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+
+    - name: Install FFTW3 on Linux
+      run: sudo apt-get install libfftw3-dev
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+
+    - name: Build package
+      run: python -m build
+
+    - name: Upload sdist
+      uses: actions/upload-artifact@v4
+      with:
+        name: dist-sdist
+        path: dist/*.tar.gz
+
+  publish-to-pypi:
+    name: Publish Python 🐍 distribution 📦 to PyPI
+    needs:
+    #- build_wheels
+    - build_sdist
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+
+    environment:
+      name: pypi
+      url: https://pypi.org/p/galario
+
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v4
+      with:
+        path: dist
+        pattern: dist-*
+        merge-multiple: true
+    - name: Publish distribution 📦 to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/unit-tests.yml

@@ -6,7 +6,11 @@ name: tests and docs
 # workflows running on Linux and MacOS have passwordless sudo rights:
 # https://stackoverflow.com/questions/57982945/how-to-apt-get-install-in-a-github-actions-workflow
 
-on: push
+on: 
+  push:
+    branches:
+      - "master"
+      - "unit-tests_workflow_updates"
 
 jobs:
   test:
@@ -18,7 +22,7 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: [ 3.6, 3.7, 3.8, 3.9 ]
+        python-version: [ 3.8, 3.9, '3.10', 3.11 ]
     env:
       OMP_NUM_THREADS: 2
     steps:
@@ -45,27 +49,23 @@ jobs:
       - name: Build and install galario, build docs
         run: |
           conda activate test
-          conda install astropy cython nomkl numpy pytest scipy sphinx
+          conda install astropy cython nomkl numpy pytest scipy sphinx scikit-build-core
           pip install coverage codecov pytest-cov
-          mkdir build && cd build
-          cmake -DCMAKE_INSTALL_PREFIX=/tmp -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} ..
-          make
-          make install
+          pip install .
       - name: Run unit tests
-        run: python/py.test.sh -sv --cov=./ python/test_galario.py
-        working-directory: build
+        run: pytest -sv --cov=./ 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'
       - name: build docs
         run: |
           conda activate test
           pip install sphinx_py3doc_enhanced_theme sphinxcontrib-fulltoc
-          cd build
-          make docs
+          sphinx-build -M html docs docs/build
       - name: deploy docs
         if: github.ref == 'refs/heads/master' && matrix.python-version == '3.7'
         uses: JamesIves/[email protected]
         with:
           branch: gh-pages  # The branch the action should deploy to.
-          folder: build/docs/html  # The folder the action should deploy.
+          folder: docs/build/html  # The folder the action should deploy.
           dry-run: false

CMakeLists.txt

@@ -99,12 +99,12 @@ else()
   message(STATUS "Skipping the ${PROJECT_NAME} python wrapper")
 endif()
 
-find_package(Sphinx)
-if(SPHINX_FOUND)
-  add_subdirectory(docs)
-else()
-  message(STATUS "Cannot build the documentation without sphinx")
-endif()
+#find_package(Sphinx)
+#if(SPHINX_FOUND)
+#  add_subdirectory(docs)
+#else()
+#  message(STATUS "Cannot build the documentation without sphinx")
+#endif()
 
 ###
 # uninstall target

docs/conf.py.in → docs/conf.py

@@ -72,7 +72,7 @@
 #
 # 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 @@
 
 # override CSS file
 def setup(app):
-    app.add_stylesheet('css/custom.css')
+    app.add_css_file('css/custom.css')

pyproject.toml

@@ -0,0 +1,24 @@
+[build-system]
+requires = [
+    "scikit-build-core",
+    "numpy",
+    "Cython",
+    "pytest",
+]
+build-backend="scikit_build_core.build"
+
+[project]
+name = "galario"
+version = "1.2.2"
+authors = [
+    { name="Marco Tazzari", email="[email protected]" },
+]
+description = "Gpu Accelerated Library for Analysing Radio Interferometer Observations"
+readme = "README.md"
+
+[tool.scikit-build]
+cmake.args = ['-DGALARIO_CHECK_CUDA=0']
+
+[[tool.scikit-build.overrides]]
+if.env.GALARIO_CHECK_CUDA = true
+cmake.args = ['-DGALARIO_CHECK_CUDA=1']

python/CMakeLists.txt

@@ -56,7 +56,7 @@ set(GALARIO_PYTHON_PKG_DIR "${PYTHON_PKG_DIR}" CACHE PATH "Current python instal
 
 # on unix: install .py and .so relative to ${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT}
 install(DIRECTORY ${PYGALARIO_DIR}
-  DESTINATION "${GALARIO_PYTHON_PKG_DIR}"
+  DESTINATION ${SKBUILD_PLATLIB_DIR}
   FILES_MATCHING REGEX ".*py$|.*so$"
   )
 

python/libcommon.pyx

@@ -29,6 +29,9 @@ include "galario_config.pxi"
 
 cimport galario_defs as cpp
 
+cdef extern from "numpy/arrayobject.h":
+    int PyArray_SetBaseObject(np.ndarray arr, PyObject* obj)
+
 __all__ = ['arcsec', 'deg', 'cgs_to_Jy', 'pc', 'au',
            '_init', '_cleanup', 'set_v_origin',
            'ngpus', 'use_gpu', 'threads',
@@ -82,7 +85,8 @@ 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
+        #ndarray.base = <PyObject*> self
+        PyArray_SetBaseObject(ndarray, <PyObject*> self)
 
         # without this, data would be cleaned up right away
         Py_INCREF(self)

python/utils.py

@@ -25,7 +25,7 @@
 import numpy as np
 
 from scipy.interpolate import interp1d, RectBivariateSpline
-from scipy.integrate import trapz, quadrature
+from scipy.integrate import trapezoid, quadrature
 
 __all__ = ["py_sampleImage", "py_sampleProfile", "py_chi2Profile", "py_chi2Image",
            "radial_profile", "g_sweep_prototype", "sweep_ref",
@@ -217,7 +217,7 @@ 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 +227,7 @@ 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 +394,10 @@ 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)

src/CMakeLists.txt

@@ -127,11 +127,11 @@ endif() # cuda
 # it would be nice if directory would let me access all libraries but there is no such property
 # https://cmake.org/cmake/help/v3.0/manual/cmake-properties.7.html
 install (TARGETS ${install_libs}
-  ARCHIVE DESTINATION lib
-  LIBRARY DESTINATION lib
-  RUNTIME DESTINATION bin
+  ARCHIVE DESTINATION ${SKBUILD_DATA_DIR}/lib
+  LIBRARY DESTINATION ${SKBUILD_DATA_DIR}/lib
+  RUNTIME DESTINATION ${SKBUILD_DATA_DIR}/bin
   )
-install(FILES galario.h galario_py.h galario_defs.h DESTINATION include)
+install(FILES galario.h galario_py.h galario_defs.h DESTINATION ${SKBUILD_DATA_DIR}/include)
 
 ###
 # testing