Merge pull request #370 from BvB93/wheels

BLD: Add workflows for building linux aarch64 and macos x86_68 wheels

.github/workflows/pypi.yaml

@@ -22,6 +22,8 @@ jobs:
       matrix:
         buildplat:
         - [ubuntu-20.04, manylinux_x86_64]
+        - [ubuntu-20.04, manylinux_aarch64]
+        - [macos-10.15, macosx_x86_64]
         version:
         - "cp37"
         - "cp38"
@@ -31,11 +33,37 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Build wheels
+      - name: Set up QEMU
+        if: matrix.buildplat[1] == 'manylinux_aarch64'
+        uses: docker/setup-qemu-action@v1
+        with:
+          platforms: arm64
+
+      - name: Get MacOS build dependencies
+        if: matrix.buildplat[1] == 'macosx_x86_64'
+        run: |
+          git clone https://github.com/nlesc-nano/nano-qmflows-manylinux
+
+          cd nano-qmflows-manylinux/macos
+          tar -xzf macos_deps.tar.gz
+          cp -r output/bin/* /usr/local/bin/
+          cp -r output/lib/* /usr/local/lib/
+          cp -r output/include/* /usr/local/include/
+          cp -r output/share/* /usr/local/share/
+
+      - name: Build wheels (x86_64)
         uses: pypa/[email protected]
+        if: matrix.buildplat[1] != 'manylinux_aarch64'
         env:
           CIBW_BUILD: ${{ matrix.version }}-${{ matrix.buildplat[1] }}
 
+      - name: Build wheels (aarch64)
+        uses: pypa/[email protected]
+        if: matrix.buildplat[1] == 'manylinux_aarch64'
+        env:
+          CIBW_BUILD: ${{ matrix.version }}-${{ matrix.buildplat[1] }}
+          CIBW_ARCHS_LINUX: aarch64
+
       - uses: actions/upload-artifact@v3
         with:
           name: wheels
@@ -82,7 +110,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Install CP2K
-      run: bash scripts/download_cp2k.sh 9.1
+      run: bash scripts/download_cp2k.sh x86_64 9.1
 
     - name: Info CP2K
       run: cp2k.popt --version
@@ -151,6 +179,7 @@ jobs:
           twine check dist/*
 
       - name: Publish wheels
+        if: github.event_name == 'release'
         uses: pypa/gh-action-pypi-publish@master
         with:
           user: __token__

.github/workflows/pythonapp.yml

@@ -80,7 +80,7 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Install CP2K
-      run: bash scripts/download_cp2k.sh "${{ matrix.cp2k }}"
+      run: bash scripts/download_cp2k.sh x86_64 "${{ matrix.cp2k }}"
 
     - name: Info CP2K
       run: cp2k.popt --version
@@ -157,7 +157,7 @@ jobs:
           python-version: "3.10"
 
       - name: Install linters
-        run: pip install pydocstyle pycodestyle mypy qmflows "numpy>=1.21" types-pyyaml types-setuptools "pyparsing>=3.0.8"
+        run: pip install -r ./linting_requirements.txt
 
       - name: Python info
         run: |

CHANGELOG.md

@@ -3,7 +3,7 @@
 # 0.13.2 (unreleased)
 
 ## New
-* *Placeholder**.
+* Add MacOS x86_64 and Linux aarch64 wheels.
 
 
 # 0.13.1 (21/04/2022)

CITATION.cff

@@ -17,8 +17,8 @@ keywords:
  - materials-science
  - python
  - Workflows
-version: '0.13.1'
-date-released: "2022-04-21"
+version: '0.13.2'
+date-released: "2022-04-26"
 repository-code: https://github.com/SCM-NV/nano-qmflows
 license: "Apache-2.0"
 doi: 10.5281/zenodo.2576893

README.rst

@@ -21,15 +21,11 @@ For further information on the theory behind nano-qmflows and how to use the pro
 
 Installation
 ------------
+Pre-compiled binaries are available on pypi and can be installed via ``pip install nano-qmflows`` on MacOS and Linux.
 
-In order to install the **nano-qmflows** library there two options:
-
-1. Install pre-compiled binaries.
-2. Build Nano-QMFlows from source.
-
-Pre-compiled linux binaries are available on pypi. In order to use them all one needs is a linux machine and then issue the ``pip install nano-qmflows`` command.
-
-On the other hand, other operating systems (and source builds in general) first require an installation of *Miniconda* as is detailed here_.
+Building from source
+--------------------
+Building Nano-QMFlows from source first requires an installation of *Miniconda* as is detailed here_.
 
 .. _here: https://docs.conda.io/en/latest/miniconda.html
 

linting_requirements.txt

@@ -0,0 +1,11 @@
+pydocstyle
+pycodestyle
+
+# Mypy-related stuff
+mypy
+qmflows
+numpy>=1.21
+types-pyyaml
+types-setuptools
+pyparsing>=3.0.8
+Nano-Utils>=2.0.0

nanoqm/_version.py

@@ -1,3 +1,3 @@
 """The Nano-QMFlows version."""
 
-__version__ = '0.13.2.dev0'
+__version__ = '0.13.2'

pyproject.toml

@@ -20,21 +20,39 @@ module = [
 ignore_missing_imports = true
 
 [tool.cibuildwheel]
-build = "cp*-manylinux_x86_64"
+build = [
+    "cp*-manylinux_aarch64",
+    "cp*-manylinux_x86_64",
+    "cp*-macosx_x86_64",
+]
 build-verbosity = "3"
 before-all = "cp licenses/LICENSE*.txt ."
-repair-wheel-command = "auditwheel -v repair -w {dest_dir} {wheel}"
-manylinux-x86_64-image = "ghcr.io/nlesc-nano/manylinux2014_x86_64-qmflows"
-environment = { QMFLOWS_INCLUDEDIR="", QMFLOWS_LIBDIR="", CFLAGS="-Werror", LDFLAGS="-Wl,--strip-debug" }
-before-test = [
-    "bash {project}/scripts/download_cp2k.sh 9.1",
+test-command = [
     "mkdir /tmp/nanoqm",
     "cp {project}/setup.cfg /tmp/nanoqm/",
     "cp {project}/conftest.py /tmp/nanoqm/conftest.py",
     "cp -r {project}/test /tmp/nanoqm/test",
-]
-test-command = [
     "cd /tmp/nanoqm",
     "pytest -m 'not (slow or long)' test",
 ]
 test-extras = ["test"]
+
+[tool.cibuildwheel.linux]
+environment = { QMFLOWS_INCLUDEDIR="", QMFLOWS_LIBDIR="", CFLAGS="-Werror", LDFLAGS="-Wl,--strip-debug" }
+manylinux-x86_64-image = "ghcr.io/nlesc-nano/manylinux2014_x86_64-qmflows"
+manylinux-aarch64-image = "ghcr.io/nlesc-nano/manylinux2014_aarch64-qmflows"
+repair-wheel-command = "auditwheel -v repair -w {dest_dir} {wheel}"
+before-test = "bash {project}/scripts/download_cp2k.sh x86_64 9.1"
+test-skip = "cp310-manylinux_aarch64"  # TODO: Remove once aarch64 python 3.10 wheels are available for h5py
+
+[[tool.cibuildwheel.overrides]]
+select = "*-manylinux_aarch64"
+before-test = "bash {project}/scripts/download_cp2k.sh arm64 9.1"
+
+[tool.cibuildwheel.macos]
+# TODO: Install CP2K for the tests once a workaround can be found for SCM-NV/qmflows#295
+environment = { QMFLOWS_INCLUDEDIR="", QMFLOWS_LIBDIR="", CFLAGS="-Werror -Wno-sign-compare", LDFLAGS="-Wl", MACOSX_DEPLOYMENT_TARGET="10.14" }
+repair-wheel-command = [
+    "delocate-listdeps {wheel}",
+    "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}",
+]

scripts/download_cp2k.sh

@@ -2,10 +2,11 @@
 
 set -euo pipefail
 
-VERSION="$1"
+ARCH="$1"
+VERSION="$2"
 VERSION_LONG=v"$VERSION".0
 
-echo "Installing CP2K $VERSION binaries"
-curl -Ls https://github.com/cp2k/cp2k/releases/download/$VERSION_LONG/cp2k-$VERSION-Linux-x86_64.ssmp -o cp2k.ssmp
+echo "Installing CP2K $ARCH $VERSION binaries"
+curl -Lsf https://github.com/cp2k/cp2k/releases/download/$VERSION_LONG/cp2k-$VERSION-Linux-$ARCH.ssmp -o cp2k.ssmp
 chmod u+rx cp2k.ssmp
 mv cp2k.ssmp /usr/local/bin/cp2k.popt

setup.py

@@ -182,10 +182,17 @@ def get_paths() -> "tuple[list[str], list[str]]":
     classifiers=[
         'License :: OSI Approved :: Apache Software License',
         'Natural Language :: English',
+        'Operating System :: MacOS',
+        'Operating System :: POSIX :: Linux',
+        'Programming Language :: C++',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3 :: Only',
         'Programming Language :: Python :: 3.7',
         'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
+        'Programming Language :: Python :: Implementation :: CPython',
         'Development Status :: 4 - Beta',
         'Intended Audience :: Science/Research',
         'Topic :: Scientific/Engineering :: Chemistry',
@@ -198,6 +205,7 @@ def get_paths() -> "tuple[list[str], list[str]]":
     extras_require={
         'test': parse_requirements("test_requirements.txt"),
         'doc': parse_requirements("doc_requirements.txt"),
+        'lint': parse_requirements("linting_requirements.txt"),
     },
     package_data={
         'nanoqm': ['basis/*.json', 'basis/BASIS*', 'basis/GTH_POTENTIALS', 'py.typed', '*.pyi']

test/test_absorption_spectrum.py

@@ -7,13 +7,15 @@
 import pytest
 import qmflows
 import numpy as np
+from qmflows.test_utils import requires_cp2k
 from nanoqm.common import retrieve_hdf5_data
 from nanoqm.workflows import workflow_stddft
 from nanoqm.workflows.input_validation import process_input
 
 from .utilsTest import PATH_TEST, remove_files
 
 
+@requires_cp2k
 class TestComputeOscillators:
     _PARAMS = {
         "MOLOPT": ("Cd", "input_test_absorption_spectrum.yml", ""),
@@ -75,4 +77,4 @@ def check_properties(self, path: Path, orbitals_type: str, name: str) -> None:
         # Compare with reference data
         with h5py.File(PATH_TEST / "test_files.hdf5", "r") as f:
             ref = f[f"test_absorption_spectrum/TestComputeOscillators/{name}/dipole"][...]
-        np.testing.assert_allclose(dipole_matrices, ref)
+        np.testing.assert_allclose(dipole_matrices, ref, rtol=0, atol=1e-08)

test/test_input_validation.py

@@ -5,6 +5,7 @@
 import yaml
 import pytest
 from qmflows import cp2k, run
+from qmflows.test_utils import requires_cp2k
 from qmflows.type_hints import PathLike
 from qmflows.packages import CP2K_Result
 from scm import plams
@@ -13,7 +14,7 @@
 from nanoqm.common import read_cell_parameters_as_array
 from nanoqm.workflows.input_validation import process_input, schema_workflows, InputSanitizer
 
-from .utilsTest import PATH_TEST, cp2k_available, remove_files, validate_status
+from .utilsTest import PATH_TEST, remove_files, validate_status
 
 
 class TestInputValidation:
@@ -105,8 +106,7 @@ def test_functional(self, functional_c: bool, functional_x: bool) -> None:
         assert dft.xc.xc_functional == ref
 
 
-@pytest.mark.skipif(
-    not cp2k_available(), reason="CP2K is not install or not loaded")
+@requires_cp2k
 def test_call_cp2k_pbe() -> None:
     """Check if the input for a PBE cp2k job is valid."""
     try:

test/test_workflow_single_points.py

@@ -9,7 +9,7 @@
 from nanoqm.workflows.input_validation import process_input
 from nanoqm.workflows.workflow_single_points import workflow_single_points
 
-from .utilsTest import PATH_TEST, cp2k_available, remove_files
+from .utilsTest import PATH_TEST, remove_files
 
 
 def run_single_point(tmp_path: Path, input_file: str):
@@ -28,8 +28,6 @@ def run_single_point(tmp_path: Path, input_file: str):
         remove_files()
 
 
-# @pytest.mark.skipif(
-#     not cp2k_available(), reason="CP2K is not install or not loaded")
 @pytest.mark.slow
 def test_single_point(tmp_path: Path):
     """Check that the couplings run."""