WIP on meson port

.cirrus.yml

@@ -46,6 +46,8 @@ cirrus_wheels_macos_arm64_task:
 
   build_script:
     - which python
+    # needed for discover_version.py
+    - git fetch --all
     # needed for submodules
     - git submodule update --init
     - uname -m

.github/workflows/build-wheels.yml

@@ -3,21 +3,42 @@ on:
     branches: [ master ]
     tags:
       - v*
+  pull_request:
+    branches: [ master ]    
 
 jobs:
   build_wheels:
     name: Build wheels on ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-12, windows-2019]
+        os: [ubuntu-22.04, macos-13, windows-2019]
       fail-fast: false
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0      
+
       - name: Checkout submodules
-        run: git submodule update --init --recursive      
+        run: git submodule update --init --recursive
+
+      - name: Install PCRE2 (Windows only)
+        if: matrix.os == 'windows-2019'
+        shell: bash        
+        run: |
+          pcre2_version=10.42
+          download_url=https://github.com/PCRE2Project/pcre2/releases/download/pcre2-${pcre2_version}/pcre2-${pcre2_version}.tar.gz
+          curl -L $download_url -o pcre2.tar.gz
+          tar xvzf pcre2.tar.gz
+          cd pcre2-${pcre2_version}
+          mkdir build
+          cd build
+          cmake ..
+          ninja
+          ninja install
+
       - name: Build wheels
         uses: pypa/cibuildwheel@v2.12.1
         env:
@@ -28,11 +49,11 @@ jobs:
            CIBW_TEST_REQUIRES: pytest 
            CIBW_TEST_COMMAND: "pytest -v {package}/tests"
 
-      # # Uncomment to get SSH access for testing
-      # - name: Setup tmate session
-      #   if: failure()
-      #   uses: mxschmitt/action-tmate@v3
-      #   timeout-minutes: 15
+      # Uncomment to get SSH access for testing
+      - name: Setup tmate session
+        if: failure()
+        uses: mxschmitt/action-tmate@v3
+        timeout-minutes: 15
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v2
@@ -50,10 +71,10 @@ jobs:
       - name: Check tag
         id: check-tag
         run: |
-          if [[ ${{ github.event.ref }} =~ ^refs/tags/v[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
-              echo ::set-output name=match::true
+          if [[ ${{ github.ref }} =~ ^refs/tags/v[0-9]+\.[0-9]+\.[0-9]+ ]]; then
+            echo "match=true" >> $GITHUB_OUTPUT
           fi
-    
+
       - name: Deploy to PyPI
         if: steps.check-tag.outputs.match == 'true'
         run: |

.github/workflows/python-package.yml

@@ -20,7 +20,9 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0      
     - name: Checkout submodules
       run: git submodule update --init --recursive
     - name: Set up Python ${{ matrix.python-version }}
@@ -60,8 +62,8 @@ jobs:
     - name: Test with pytest
       run: |
         USE_FORTRAN=T pytest -v --ignore QUIP
-    # # Uncomment to get SSH access for testing
-    # - name: Setup tmate session
-    #   if: failure()
-    #   uses: mxschmitt/action-tmate@v3
-    #   timeout-minutes: 15	
+    # Uncomment to get SSH access for testing
+    - name: Setup tmate session
+      if: failure()
+      uses: mxschmitt/action-tmate@v3
+      timeout-minutes: 15	

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "extxyz/libcleri"]
 	path = libcleri
-	url = https://github.com/transceptor-technology/libcleri
+	url = https://github.com/libAtoms/libcleri

discover_version.py

@@ -0,0 +1,94 @@
+#
+# Copyright 2022 Lars Pastewka
+#
+# ### MIT license
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+#
+
+#
+# This is the most minimal-idiotic way of discovering the version that I
+# could come up with. It deals with the following issues:
+# * If we are installed, we can get the version from package metadata,
+#   either via importlib.metadata or from pkg_resources. This also holds for
+#   wheels that contain the metadata. We are good! Yay!
+# * If we are not installed, there are two options:
+#   - We are working within the source git repository. Then
+#        git describe --tags --always
+#     yields a reasonable version descriptor, but that is unfortunately not
+#     PEP 440 compliant (see https://peps.python.org/pep-0440/). We need to
+#     mangle the version string to yield something compatible.
+# - If we install from a source tarball, we need to parse PKG-INFO manually.
+#
+
+import re
+import subprocess
+
+class CannotDiscoverVersion(Exception):
+    pass
+
+
+def get_version_from_pkg_info():
+    """
+    Discover version from PKG-INFO file.
+    """
+    f = open('PKG-INFO', 'r')
+    l = f.readline()
+    while l:
+        if l.startswith('Version:'):
+            return l[8:].strip()
+        l = f.readline()
+    raise CannotDiscoverVersion("No line starting with 'Version:' in 'PKG-INFO'.")
+
+
+def get_version_from_git():
+    """
+    Discover version from git repository.
+    """
+    git_describe = subprocess.run(
+        ['git', 'describe', '--tags', '--dirty', '--always'],
+        stdout=subprocess.PIPE)
+    if git_describe.returncode != 0:
+        raise CannotDiscoverVersion('git execution failed.')
+    version = git_describe.stdout.decode('latin-1').strip()
+
+    dirty = version.endswith('-dirty')
+
+    # Make version PEP 440 compliant
+    if dirty:
+        version = version.replace('-dirty', '')
+    version = version.strip('v')  # Remove leading 'v' if it exists
+    version = version.replace('-', '.dev', 1)
+    version = version.replace('-', '+', 1)
+    if dirty:
+        version += '.dirty'
+
+    return version
+
+
+try:
+    version = get_version_from_git()
+except CannotDiscoverVersion:
+    version = get_version_from_pkg_info()
+
+#
+# Print version to screen
+#
+
+print(version)

libextxyz/Makefile

@@ -22,13 +22,15 @@ else
 	dlext  ?= so
 endif
 
+.PHONY: default all libcleri install_libcleri install clean
+
 default: libextxyz.${dlext}
 
 all: libcleri extxyz_kv_grammar.c extxyz_kv_grammar.h libextxyz.${dlext}
 
 libcleri:
 	if [ -z ${LIBCLERI_PATH} ]; then echo "LIBCLERI_PATH must be defined" 1>&2; exit 1; fi
-	${MAKE} -C ${LIBCLERI_PATH} -f makefile
+	${MAKE} -C ${LIBCLERI_PATH} -f makefile libcleri.a
 
 install_libcleri: libcleri
 	${MAKE} -C ${LIBCLERI_PATH} -f makefile install INSTALL_PATH=${prefix}
@@ -53,11 +55,13 @@ install: libextxyz.${dlext}
 
 test_fortran_main.o: fextxyz.o extxyz.o extxyz_kv_grammar.o
 
-fextxyz: test_fortran_main.o fextxyz.o extxyz.o extxyz_kv_grammar.o
-	${F90} -g $^ -o $@ ${LIBCLERI_PATH}/libcleri.a  ${LDFLAGS} ${QUIP_LDFLAGS}
+FOBJS = test_fortran_main.o fextxyz.o extxyz.o extxyz_kv_grammar.o
+fextxyz: libcleri ${FOBJS}
+	${F90} -g ${FOBJS} -o $@ ${LIBCLERI_PATH}/libcleri.a  ${LDFLAGS} ${QUIP_LDFLAGS}
 
-cextxyz: test_C_main.o extxyz.o extxyz_kv_grammar.o
-	${F90} -g $^ -o $@ ${LIBCLERI_PATH}/libcleri.a  ${LDFLAGS}
+COBJS = test_C_main.o extxyz.o extxyz_kv_grammar.o
+cextxyz: libcleri ${COBJS}
+	${F90} -g ${COBJS} -o $@ ${LIBCLERI_PATH}/libcleri.a  ${LDFLAGS}
 
 clean:
-	rm -rf libextxyz.${dlext} *.o
+	rm -rf libextxyz.${dlext} *.o

libextxyz/meson.build

@@ -0,0 +1,16 @@
+python3 = find_program('python3')
+
+run_command(
+    python3,
+    '..' / 'python' / 'extxyz' / 'extxyz_kv_grammar.py'
+)
+
+# Build and install the extension module
+module = python.extension_module(
+    '_extxyz', # Name of the module
+    ['extxyz.c', 'extxyz_kv_grammar.c'], 
+    install: true,  # Install it
+    subdir: 'extxyz',
+    gnu_symbol_visibility: 'default', # keep symbols public
+    dependencies: [cleri, pcre2]
+)

meson.build

@@ -0,0 +1,55 @@
+# https://mesonbuild.com/
+project(
+    'extxyz', # Project name
+    'c',
+    version: run_command('python3', 'discover_version.py', check: true).stdout().strip(), # Project version
+)
+
+# https://mesonbuild.com/Python-module.html
+pymod = import('python')
+python = pymod.find_installation('python3',
+    required: true,
+    pure: false
+)
+
+host_system = host_machine.system()
+cc = meson.get_compiler('c')
+
+# adapted from https://gitlab.gnome.org/GNOME/glib/-/blob/cd9a5c173a154e326a3ebaa28cfe41a7444625c5/meson.build#L2020-L2052
+pcre2 = dependency('libpcre2-8', version: '>= 10.23', required : false)
+if not pcre2.found()
+  if cc.get_id() == 'msvc' or cc.get_id() == 'clang-cl'
+  # MSVC: Search for the PCRE2 library by the configuration, which corresponds
+  # to the output of CMake builds of PCRE2.  Note that debugoptimized
+  # is really a Release build with .PDB files.
+    if vs_crt == 'debug'
+      pcre2 = cc.find_library('pcre2d-8', required : false)
+    else
+      pcre2 = cc.find_library('pcre2-8', required : false)
+    endif
+  endif
+endif
+
+# Try again with the fallback
+if not pcre2.found()
+  pcre2 = dependency('libpcre2-8', required : true, fallback : ['pcre2', 'libpcre2_8'])
+  use_pcre2_static_flag = true
+elif host_system == 'windows'
+  pcre2_static = cc.links('''#define PCRE2_STATIC
+                             #define PCRE2_CODE_UNIT_WIDTH 8
+                             #include <pcre2.h>
+                             int main() {
+                               void *p = NULL;
+                               pcre2_code_free(p);
+                               return 0;
+                             }''',
+                         dependencies: pcre2,
+                         name : 'Windows system PCRE2 is a static build')
+  use_pcre2_static_flag = pcre2_static
+else
+  use_pcre2_static_flag = false
+endif
+
+subdir('libcleri')
+subdir('libextxyz')
+subdir('python/extxyz')

pyproject.toml

@@ -1,4 +1,31 @@
 [build-system]
-# Minimum requirements for the build system to execute.
-requires = ["setuptools", "wheel", "pyleri>=1.3.3"]
-build-backend = "setuptools.build_meta"
+requires = ["meson>=1.0.0", "meson-python>=0.13.0", "ninja", "pyleri>=1.3.3", "oldest-supported-numpy"]
+build-backend = "mesonpy"
+
+[project]
+name = "extxyz"
+description = "Extended XYZ file format tools"
+readme = "README.md"
+license = { file = "LICENSE" }
+authors = [
+    { name = "James Kermode", email = "james.kermode@gmail.com"},
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Programming Language :: Python"
+]
+requires-python = ">=3.7.0"
+dynamic = [ "version" ]
+dependencies = [
+    "numpy>=1.13.0", 'pyleri>=1.3.3', 'ase>=3.17'
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+
+]
+
+[project.urls]
+documentation = "http://libatoms.github.io/extxyz/"
+repository = "https://github.com/libAtoms/extxyz"

python/extxyz/_version.py.in

@@ -0,0 +1,27 @@
+#
+# Copyright 2017 Lars Pastewka (U. Freiburg)
+#
+# matscipy - Materials science with Python at the atomic-scale
+# https://github.com/libAtoms/matscipy
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+__version__ = '@VERSION@'