Migrate build system from Makefile to Meson

.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

@@ -3,40 +3,86 @@ on:
     branches: [ master ]
     tags:
       - v*
+  pull_request:
+    branches: [ master ]    
 
 jobs:
   build_wheels:
-    name: Build wheels on ${{ matrix.os }}
+    name: Build wheels on ${{ matrix.os }} for Python ${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macos-12, windows-2019]
+        os: [ubuntu-22.04, macos-latest, macos-15-intel]
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        exclude:
+          # macOS ARM64 (macos-latest) doesn't support Python 3.8
+          - os: macos-latest
+            python-version: '3.8'
+          # Windows builds disabled due to meson-python issue with .lib import libraries
+          # See: https://github.com/libAtoms/extxyz/pull/17
       fail-fast: false
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
       - name: Checkout submodules
-        run: git submodule update --init --recursive      
+        run: git submodule update --init --recursive
+
+      - name: Set Python version for cibuildwheel
+        id: set-py-version
+        shell: bash
+        run: |
+          PY_VERSION="${{ matrix.python-version }}"
+          CIBW_PYTHON="cp${PY_VERSION//.}"
+          echo "cibw-python=${CIBW_PYTHON}" >> $GITHUB_OUTPUT
+
+      - name: Install PCRE2 via vcpkg (Windows only)
+        if: runner.os == 'Windows'
+        shell: bash
+        run: |
+          # Install pkg-config lite (ensures working pkg-config before Strawberry Perl)
+          choco install pkgconfiglite -y
+
+          # Install PCRE2 using vcpkg
+          vcpkg install pcre2:x64-windows
+
+          # Set up environment for meson/pkg-config
+          VCPKG_ROOT="C:/vcpkg"
+          PCRE2_DIR="${VCPKG_ROOT}/installed/x64-windows"
+
+          # Add pkgconfiglite to PATH first (before Strawberry Perl)
+          echo "C:/ProgramData/chocolatey/lib/pkgconfiglite/tools/bin" >> $GITHUB_PATH
+
+          echo "CMAKE_PREFIX_PATH=${PCRE2_DIR}" >> $GITHUB_ENV
+          echo "PKG_CONFIG_PATH=${PCRE2_DIR}/lib/pkgconfig" >> $GITHUB_ENV
+          echo "PCRE2_ROOT=${PCRE2_DIR}" >> $GITHUB_ENV
+          echo "LIB=${PCRE2_DIR}/lib;$LIB" >> $GITHUB_ENV
+          echo "INCLUDE=${PCRE2_DIR}/include;$INCLUDE" >> $GITHUB_ENV
+          echo "PATH=${PCRE2_DIR}/bin;$PATH" >> $GITHUB_ENV
+
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.1
+        uses: pypa/cibuildwheel@v2.22.0
         env:
-           CIBW_SKIP: cp27-* cp35-* pp* *musl* "*-macosx_arm64"
+           CIBW_BUILD: ${{ steps.set-py-version.outputs.cibw-python }}-*
+           CIBW_SKIP: pp* *musl*
            CIBW_ARCHS_LINUX: "auto64"
-           CIBW_ARCHS_MACOS: "x86_64"
-           CIBW_BEFORE_ALL_LINUX: "which yum && yum install -y pcre2-devel zlib-devel"
-           CIBW_TEST_REQUIRES: pytest 
-           CIBW_TEST_COMMAND: "pytest -v {package}/tests"
+           CIBW_ARCHS_MACOS: ${{ matrix.os == 'macos-latest' && 'arm64' || 'x86_64' }}
+           CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=${{ matrix.os == 'macos-latest' && '15.0' || '14.0' }}"
+           CIBW_ARCHS_WINDOWS: "AMD64"
 
-      # # Uncomment to get SSH access for testing
+      # 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
+        uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.os }}-py${{ matrix.python-version }}
           path: ./wheelhouse/*.whl
 
       - name: Release wheels
@@ -50,10 +96,10 @@ 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

@@ -16,22 +16,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.7, 3.8, 3.9, "3.10", "3.11", "3.12"]
+        python-version: [3.8, 3.9, "3.10", "3.11", "3.12"]
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
     - name: Checkout submodules
       run: git submodule update --init --recursive
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update -y
+        sudo apt-get install -y libpcre2-dev
     - name: Install Python dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
-        python -m pip install -e . --verbose
+        python -m pip install . --verbose
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -63,7 +69,7 @@ jobs:
     - name: Test with pytest
       run: |
         USE_FORTRAN=T pytest -v --ignore QUIP
-    # # Uncomment to get SSH access for testing
+    # Uncomment to get SSH access for testing
     # - name: Setup tmate session
     #   if: failure()
     #   uses: mxschmitt/action-tmate@v3

.gitignore

@@ -6,4 +6,8 @@ extxyz.egg-info/
 .DS_Store
 *.o
 pcre2-10.37/
-venv/
+venv/
+
+# Claude notes (don't commit)
+MESON_BUILD_STATUS.md
+CLAUDE.md

.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 +1,105 @@
+#
+# 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.
+    """
+    try:
+        git_describe = subprocess.run(
+            ['git', 'describe', '--tags', '--dirty', '--always'],
+            stdout=subprocess.PIPE)
+    except (FileNotFoundError, OSError) as e:
+        # git command not found in PATH (common in isolated build environments like Windows cibuildwheel)
+        raise CannotDiscoverVersion(f'git command not found: {e}')
+
+    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:
+    try:
+        version = get_version_from_pkg_info()
+    except (CannotDiscoverVersion, FileNotFoundError):
+        # Fallback for isolated build environments (e.g., Windows cibuildwheel)
+        # where neither git nor PKG-INFO is available
+        # Use a development version that will be replaced by the build system
+        version = '0.0.0+unknown'
+
+#
+# Print version to screen
+#
+
+print(version)

libcleri_meson.build

@@ -0,0 +1,32 @@
+inc_dir = include_directories('inc')
+
+libcleri = static_library('cleri',
+  'src/children.c',
+  'src/choice.c',
+  'src/dup.c',
+  'src/expecting.c',
+  'src/grammar.c',
+  'src/keyword.c',
+  'src/kwcache.c',
+  'src/list.c',
+  'src/node.c',
+  'src/cleri.c',
+  'src/olist.c',
+  'src/optional.c',
+  'src/parse.c',
+  'src/prio.c',
+  'src/ref.c',
+  'src/regex.c',
+  'src/repeat.c',
+  'src/rule.c',
+  'src/sequence.c',
+  'src/this.c',
+  'src/token.c',
+  'src/tokens.c', 
+  'src/version.c', 
+  dependencies: pcre2, 
+  include_directories: inc_dir)
+
+cleri = declare_dependency(
+  link_with: libcleri,
+  include_directories: inc_dir)

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/extxyz.c

@@ -235,9 +235,9 @@ int parse_tree(cleri_node_t *node, DictEntry **cur_entry, int *in_seq, int *in_k
     }
 
     //DEBUG printf("looping over children\n"); //DEBUG
-    for (cleri_children_t *child = node->children; child; child = child->next) {
+    for (cleri_node_t *child = node->children; child; child = child->next) {
         //DEBUG printf("child\n"); //DEBUG
-        int err = parse_tree(child->node, cur_entry, in_seq, in_kv_pair, in_old_one_d, error_message);
+        int err = parse_tree(child, cur_entry, in_seq, in_kv_pair, in_old_one_d, error_message);
         if (err) {
             return err;
         }
@@ -319,8 +319,8 @@ void dump_tree(cleri_node_t *node, char *prefix) {
         printf("%snode NULL\n", prefix);
     }
 
-    for (cleri_children_t *child = node->children; child; child = child->next) {
-        dump_tree(child->node, new_prefix);
+    for (cleri_node_t *child = node->children; child; child = child->next) {
+        dump_tree(child, new_prefix);
     }
 
     free(new_prefix);