Merge pull request #117 from libAtoms/22_meson

BUILD: Switch to Meson for building

.gitattributes

@@ -1,4 +1,3 @@
-matscipy/_version.py export-subst
 *.fs -linguist-detectable
 .gitattributes text eol=lf
 *.py text eol=lf

.github/workflows/build-wheels.yml

@@ -1,3 +1,7 @@
+# This is partially adopted from scipy.
+# See: https://github.com/scipy/scipy/blob/main/.github/workflows/wheels.yml
+# License: 3-clause BSD, https://github.com/scipy/scipy/blob/main/LICENSE.txt
+
 name: Build wheels
 
 # Controls when the action will run.
@@ -15,49 +19,42 @@ on:
 
 jobs:
   build_wheels:
-    name: Build wheels on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+    name: Build wheel for ${{ matrix.python }}-${{ matrix.buildplat[1] }} ${{ matrix.buildplat[2] }}
+    runs-on: ${{ matrix.buildplat[0] }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        buildplat:
+        - [ubuntu-20.04, manylinux, x86_64]
+        - [macos-10.15, macosx, x86_64]
+        - [windows-2019, win, AMD64]
+
+        python: ["cp38", "cp39", "cp310", "cp311"]
       fail-fast: false
 
+    env:
+      IS_32_BIT: ${{ matrix.buildplat[2] == 'x86' }}
+
     steps:
-      - uses: actions/checkout@v2
-
-      - uses: ilammy/msvc-dev-cmd@v1      
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
       - uses: actions/setup-python@v2
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.9.0
+        with:
+          python-version: '3.8'
 
       - name: Build wheels
-        run: |
-           if [[ $RUNNER_OS == "Linux" ]]; then
-              for image in manylinux2010 manylinux2014; do
-                 export CIBW_MANYLINUX_X86_64_IMAGE=$image
-                 python -m cibuildwheel --output-dir wheelhouse           
-              done
-           else
-              python -m cibuildwheel --output-dir wheelhouse
-           fi
+        uses: pypa/cibuildwheel@v2.11.3
         env:
-           CIBW_SKIP: cp27-* cp35-* cp36-* cp311-* pp* *musllinux*
-           CIBW_ARCHS_MACOS: "x86_64 arm64"
-           CIBW_BEFORE_BUILD: "pip install oldest-supported-numpy"
-           CIBW_TEST_COMMAND: "cd {project}/tests; pip install -r ../requirements.txt; pytest"
-           CIBW_TEST_SKIP: "*"
-
-      # Uncomment to get SSH access for testing
-#       - name: Setup tmate session
-#         if: failure()
-#         uses: mxschmitt/action-tmate@v3
-#         timeout-minutes: 15
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}*
+          CIBW_ARCHS: ${{ matrix.buildplat[2] }}
+          CIBW_ENVIRONMENT_PASS_LINUX: RUNNER_OS
+          CIBW_TEST_COMMAND: python {project}/tests/test_ffi.py
 
       - uses: actions/upload-artifact@v2
         with:
           path: ./wheelhouse/*.whl
+          name: ${{ matrix.python }}-${{ matrix.buildplat[1] }}-${{ matrix.buildplat[2] }}
 
       - name: Release wheels
         uses: softprops/action-gh-release@v1
@@ -73,7 +70,8 @@ jobs:
           if [[ ${{ github.ref }} =~ ^refs/tags/v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
               echo ::set-output name=match::true
           fi
-          
+        shell: bash
+
       - name: Deploy to PyPI
         if: steps.check-tag.outputs.match == 'true'
         run: |
@@ -82,3 +80,4 @@ jobs:
         env:
           TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        shell: bash

.github/workflows/publish.yml

@@ -2,7 +2,7 @@ name: Test compilation and publish documentation
 
 on:
   push:
-    branches:    
+    branches:
       - master
     tags:
       - '*'
@@ -13,59 +13,61 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
-    - name: install_python
-      run: |
-        sudo apt-get update -qy
-        sudo apt-get install -y python3-dev python3-pip libxml2-dev libxslt-dev zlib1g-dev
-        sudo pip3 install -r requirements.txt
+      - name: install_python
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y python3-dev python3-pip libxml2-dev libxslt-dev zlib1g-dev
+          sudo pip install --upgrade sphinxcontrib-napoleon sphinx_rtd_theme
 
-    - name: build
-      run: |
-        python3 setup.py build
-        sudo python3 setup.py install
-        
-    - name: pytest
-      run: |
-        cd tests
-        pytest -s --verbose
+      - name: build
+        run: |
+          sudo pip install .[test]
 
-    - name: package_dist
-      run: |
-        sudo python3 setup.py sdist
+      - name: pytest
+        run: |
+          cd tests
+          pytest -s --verbose
 
-    # Standard drop-in approach that should work for most people.
-    - name: build_doc
-      run: |
-        cd docs
-        make html
-        cd ..
+      - name: package_dist
+        run: |
+          sudo pip install build
+          sudo python3 -m build . -s
 
-    # Publish built docs to gh-pages branch.
-    # ===============================
-    - name: Commit documentation changes
-      run: |
-        git clone https://github.com/libAtoms/matscipy.git --branch gh-pages --single-branch gh-pages
-        cp -r docs/_build/html/* gh-pages/
-        cd gh-pages
-        git config --local user.email "action@github.com"
-        git config --local user.name "GitHub Action"
-        git add .
-        git commit -m "Update documentation" -a || true
-        # The above command will fail if no changes were present, so we ignore
-        # that.
+      # Standard drop-in approach that should work for most people.
+      - name: build_doc
+        run: |
+          cd docs
+          make html
+          cd ..
 
-    - name: Push changes
-      uses: ad-m/github-push-action@master
-      with:
-        branch: gh-pages
-        directory: gh-pages
-        github_token: ${{ secrets.GITHUB_TOKEN }}
+      # Publish built docs to gh-pages branch.
+      # ===============================
+      - name: Commit documentation changes
+        run: |
+          git clone https://github.com/libAtoms/matscipy.git --branch gh-pages --single-branch gh-pages
+          cp -r docs/_build/html/* gh-pages/
+          cd gh-pages
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add .
+          git commit -m "Update documentation" -a || true
+          # The above command will fail if no changes were present, so we ignore
+          # that.
 
-    - name: Publish package
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
-      with:
-        user: __token__
-        password: ${{ secrets.pypi_password }}
+      - name: Push changes
+        uses: ad-m/github-push-action@master
+        with:
+          branch: gh-pages
+          directory: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Publish package
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

.github/workflows/run_tests.yml

@@ -16,26 +16,26 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v1
-
-    - name: install_python
-      run: |
-        sudo apt-get update -qy
-        sudo apt-get install -y python3-dev python3-pip libxml2-dev libxslt-dev zlib1g-dev
-        sudo pip3 install -r requirements.txt
-
-    - name: build_c
-      run: |
-        python3 setup.py build
-        sudo python3 setup.py install
-
-    - name: pytest
-      run: |
-        cd tests
-        pytest -v --junitxml=report.xml --durations=20
-
-    - name: report
-      uses: mikepenz/action-junit-report@v2
-      if: always()
-      with:
-        report_paths: "**/report.xml"
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: install_python
+        run: |
+          sudo apt-get update -qy
+          sudo apt-get install -y python3-dev python3-pip python3-venv libxml2-dev libxslt-dev zlib1g-dev meson
+
+      - name: build_c
+        run: |
+          sudo pip install .[test]
+
+      - name: pytest
+        run: |
+          cd tests
+          pytest -v --junitxml=report.xml --durations=20
+
+      - name: report
+        uses: mikepenz/action-junit-report@v2
+        if: always()
+        with:
+          report_paths: "**/report.xml"

.gitignore

@@ -1,6 +1,9 @@
 .gitignore
 .idea
 
+# Meson files
+.mesonpy-native-file.ini
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

CONTRIBUTING.md

@@ -15,14 +15,15 @@ work in 2018, the branch could be called "18_line_scans".
 Commits
 -------
 Prepend you commits with a shortcut indicating the type of changes they contain:
+* API: changes to the user exposed API
 * BUG: Bug fix
+* BUILD: Changes to the build system
 * CI: Changes to the CI configuration
 * DOC: Changes to documentation strings or documentation in general (not only typos)
 * ENH: Enhancement (e.g. a new feature)
-* MAINT: Maintenance (e.g. fixing a typo)
+* MAINT: Maintenance (e.g. fixing a typo, or changing code without affecting function)
 * TST: Changes to the unit test environment
 * WIP: Work in progress
-* API: changes to the user exposed API
 
 The changelog will be based on the content of the commits with tag BUG, API and ENH.
 

ChangeLog.md

@@ -7,6 +7,7 @@ v0.8.0 (not yet released)
 - Calculator for traditional Ewald summation 
 - Analytic computation of Hessian and zero-temperature elastic constants for potentials with electrostatic interaction
 - Writing and reading inhomogenous (and non numeric) data with savetbl/readtbl
+- Changed build system to Meson
 
 v0.7.0 (29Jul21)
 ----------------

c/angle_distribution.c → c/angle_distribution.cpp

@@ -27,6 +27,11 @@
 #define NPY_NO_DEPRECATED_API NPY_1_5_API_VERSION
 #include <numpy/arrayobject.h>
 
+#ifdef _MSC_VER
+#define _USE_MATH_DEFINES
+#include <cmath>
+#endif
+
 #include "angle_distribution.h"
 
 /*
@@ -72,11 +77,11 @@ py_angle_distribution(PyObject *self, PyObject *args)
   PyObject *h_arr = PyArray_ZEROS(1, &dim, NPY_INT, 1);
   PyObject *tmp_arr = PyArray_ZEROS(1, &dim, NPY_INT, 1);
 
-  npy_int *i = PyArray_DATA(i_arr);
-  npy_int *j = PyArray_DATA(j_arr);
-  double *r = PyArray_DATA(r_arr);
-  npy_int *h = PyArray_DATA(h_arr);
-  npy_int *tmp = PyArray_DATA(tmp_arr);
+  npy_int *i = (npy_int*)PyArray_DATA(i_arr);
+  npy_int *j = (npy_int*)PyArray_DATA(j_arr);
+  double *r = (double*)PyArray_DATA(r_arr);
+  npy_int *h = (npy_int*)PyArray_DATA(h_arr);
+  npy_int *tmp = (npy_int*)PyArray_DATA(tmp_arr);
 
   npy_int last_i = i[0], i_start = 0;
   memset(tmp, 0, nbins*sizeof(npy_int));

c/meson.build

@@ -0,0 +1,33 @@
+# Find numpy include directory
+include_numpy = run_command(python,
+  ['-c', 'import os; os.chdir(".."); import numpy; print(numpy.get_include())'],
+  check : true
+).stdout().strip()
+
+link_args = []
+
+# Statically linking gcc components if on windows
+if build_machine.system() == 'windows'
+    link_args = ['-static-libstdc++', '-static-libgcc', '-static']
+endif
+
+
+# Build and install the extension module
+module = python.extension_module(
+    '_matscipy', # Name of the module
+    [  # List of sources
+        'angle_distribution.cpp',
+        'islands.cpp',
+        'neighbours.c',
+        'ring_statistics.cpp',
+        'tools.c',
+        'matscipymodule.c'
+    ],
+    install: true,  # Install it
+    subdir: 'matscipy',
+    include_directories: include_directories(include_numpy),
+    dependencies: [ # List of dependencies
+        python.dependency(), # Add Python.h as dependency
+    ],
+    link_args: link_args,
+)