qupled 1.2.0__tar.gz → 1.3.0__tar.gz

qupled-1.2.0/.github/workflows/build-and-test-base.yml → qupled-1.3.0/.github/workflows/build-and-test.yml

@@ -1,15 +1,12 @@
 name: Build & Test
 
 on:
-  workflow_call:
-    inputs:
-      upload-artifact:
-        required: true
-        type: string
-      build-version:
-        required: false
-        type: string
-        default: ""
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
 
 env:
   PYTHON_VENV_ROOT: ${{ github.workspace }}/python-venv
@@ -30,11 +27,6 @@ jobs:
         ./devtool install-deps
         python3 -m venv ${PYTHON_VENV_ROOT}
 
-    - name: Set build version
-      if: ${{ inputs.build-version != '' }}
-      run: |
-        ./devtool update-version ${{ inputs.build-version }}
-
     - name: Build
       run: |
         source ${PYTHON_VENV_ROOT}/bin/activate
@@ -46,11 +38,4 @@ jobs:
       run: |
         source ${PYTHON_VENV_ROOT}/bin/activate
         pip3 install tox
-        ./devtool test
-
-    - name: Upload artifact
-      if: ${{ success() && inputs.upload-artifact == 'true' }}
-      uses: actions/upload-artifact@v4
-      with:
-        name: qupled-${{ matrix.os }}
-        path: dist
+        ./devtool test

{qupled-1.2.0 → qupled-1.3.0}/.github/workflows/formatting.yml

@@ -2,6 +2,10 @@ name: Code Formatting
 
 on:
   push:
+    branches:
+      - '**'
+    tags-ignore:
+      - 'v*'
   pull_request:
 
 jobs:

qupled-1.3.0/.github/workflows/release.yml

@@ -0,0 +1,117 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  build-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source code
+        uses: actions/checkout@v4
+
+      - name: Set build version
+        run: ./devtool update-version ${{ github.ref_name }}
+
+      - name: Build sdist
+        run: |
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip install build
+          python -m build --sdist --outdir dist
+
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  build-wheels:
+    name: Build ${{ matrix.arch }} wheels
+    runs-on: ubuntu-latest
+    needs: build-sdist
+
+    strategy:
+      matrix:
+        arch: [x86_64] # add also aarch64
+
+    steps:
+      - name: Checkout source code
+        uses: actions/checkout@v4
+
+      - name: Set build version
+        run: ./devtool update-version ${{ github.ref_name }}
+
+      - name: Set up QEMU (for aarch64 emulation)
+        if: matrix.arch == 'aarch64'
+        uses: docker/setup-qemu-action@v3
+
+      - name: Authenticate with GHCR
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+
+      - name: Pull correct manylinux image
+        run: |
+          docker pull --platform linux/${{ matrix.arch }} ghcr.io/fedluc/qupled/qupled_manylinux_${{ matrix.arch }}
+
+      - name: Build wheels using cibuildwheel
+        uses: pypa/cibuildwheel@v2.16.5
+        with:
+          output-dir: wheelhouse
+        env:
+          CIBW_PLATFORM: linux
+          CIBW_ARCHS: ${{ matrix.arch }}
+          CIBW_CONTAINER_PLATFORM: linux/${{ matrix.arch }}
+
+      - name: Upload built wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.arch }}
+          path: wheelhouse/*.whl
+
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    needs: [build-sdist, build-wheels]
+
+    steps:
+      - name: Prepare dist folder
+        run: mkdir -p dist
+
+      - name: Download sdist
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: temp-sdist
+
+      - name: Download wheels (x86_64)
+        uses: actions/download-artifact@v4
+        with:
+          name: wheels-x86_64
+          path: temp-wheels-x86_64
+
+      # - name: Download wheels (aarch64)
+      #   uses: actions/download-artifact@v4
+      #   with:
+      #     name: wheels-aarch64
+      #     path: temp-wheels-aarch64
+
+      - name: Move all files to dist/
+        run: |
+          mv temp-sdist/* dist/ || true
+          mv temp-wheels-*/* dist/ || true
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: |
+          python3 -m venv .venv
+          source .venv/bin/activate
+          pip3 install --upgrade pip
+          pip3 install twine
+          twine check dist/*
+          twine upload dist/* --non-interactive

{qupled-1.2.0 → qupled-1.3.0}/.gitignore

@@ -10,4 +10,5 @@ Makefile
 dist
 dist-native-only
 docs/_build
-qupled.egg-info
+qupled.egg-info
+wheelhouse

{qupled-1.2.0 → qupled-1.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qupled
-Version: 1.2.0
+Version: 1.3.0
 Summary: qupled: a package to investigate quantum plasmas via the dielectric formalism
 Author-email: Federico Lucco Castello <federico.luccocastello@gmail.com>
 License-Expression: GPL-3.0-or-later

{qupled-1.2.0 → qupled-1.3.0}/dev/requirements-apt.txt

@@ -1,6 +1,5 @@
 clang-format
 cmake
-libboost-all-dev
 libopenmpi-dev
 libgsl-dev
 libomp-dev

{qupled-1.2.0 → qupled-1.3.0}/dev/requirements-brew.txt

@@ -3,6 +3,5 @@ brew "cmake"
 brew "gsl"
 brew "libomp"
 brew "open-mpi"
-brew "boost-python3"
 brew "sqlite"
 brew "sqlitecpp"

{qupled-1.2.0 → qupled-1.3.0}/dev/requirements-pip.txt

@@ -1,5 +1,6 @@
 black
 build
+cibuildwheel
 pytest
 pytest-mock
 setuptools

{qupled-1.2.0 → qupled-1.3.0}/docs/introduction.rst

@@ -56,13 +56,13 @@ For linux distributions all these dependencies can be installed with
 
 .. code-block:: console
 
-   sudo apt-get install -y cmake libboost-all-dev libopenmpi-dev libgsl-dev libomp-dev python3-dev libsqlite3-dev libsqlitecpp-dev
+   sudo apt-get install -y cmake libopenmpi-dev libgsl-dev libomp-dev python3-dev libsqlite3-dev libsqlitecpp-dev
 
 For macOS they can be installed directly from homebrew
 
 .. code-block:: console
 
-   brew install cmake gsl libomp openmpi boost-python3 sqlite sqlitecpp
+   brew install cmake gsl libomp openmpi sqlite sqlitecpp
 
 Install with pip
 ~~~~~~~~~~~~~~~~
@@ -78,13 +78,13 @@ This will also install all the python packages that are necessary for running th
 Install from source
 ~~~~~~~~~~~~~~~~~~~
 
-Qupled and all its python dependencies can also be installed from source by running
+Qupled and all its dependencies can also be installed from source by running
 
 .. code-block:: console
 
    git clone https://github.com/fedluc/qupled.git
    cd qupled
-   pip install -r dev/requirements.txt
+   ./devtool install-deps
    ./devtool build
    ./devtool test
    ./devtool install

qupled-1.3.0/manylinux/Dockerfile.manylinux_2_28

@@ -0,0 +1,24 @@
+ARG ARCH=x86_64
+FROM quay.io/pypa/manylinux_2_28_${ARCH}
+
+# Install dev tools and system dependencies
+RUN dnf -y update && \
+    dnf -y groupinstall "Development Tools" && \
+    dnf -y install \
+        gsl-devel \
+        sqlite-devel \
+        git \
+        wget \
+        cmake \
+    && dnf clean all
+
+# Build SQLiteCpp from source
+RUN cd /tmp && \
+    git clone https://github.com/SRombauts/SQLiteCpp.git && \
+    cd SQLiteCpp && \
+    mkdir build && cd build && \
+    cmake .. && \
+    make -j$(nproc) && \
+    make install && \
+    ldconfig && \
+    cd / && rm -rf /tmp/SQLiteCpp

qupled-1.3.0/manylinux/build_manylinux_2_28

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+docker buildx create --use
+
+ARCH="x86_64"
+docker buildx build \
+  --platform linux/amd64 \
+  -f manylinux/Dockerfile.manylinux_2_28 \
+  --build-arg ARCH=${ARCH} \
+  --push \
+  -t  "ghcr.io/fedluc/qupled/qupled_manylinux_${ARCH}" \
+  .
+
+ARCH="aarch64"
+docker buildx build \
+  --platform linux/arm64 \
+  -f manylinux/Dockerfile.manylinux_2_28 \
+  --build-arg ARCH=${ARCH} \
+  --push \
+  -t "ghcr.io/fedluc/qupled/qupled_manylinux_${ARCH}" \
+  .

{qupled-1.2.0 → qupled-1.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "qupled"
-version = "1.2.0"
+version = "v1.3.0"
 description = "qupled: a package to investigate quantum plasmas via the dielectric formalism"
 readme = "README.md"
 requires-python = ">=3.10, <3.14"
@@ -44,3 +44,20 @@ docs = [
 include-package-data = false
 packages = ["qupled", "qupled.native"]
 package-dir = { "" = "src" }
+
+[tool.cibuildwheel]
+manylinux-x86_64-image = "ghcr.io/fedluc/qupled/qupled_manylinux_x86_64"
+manylinux-aarch64-image = "ghcr.io/fedluc/qupled/qupled_manylinux_aarch64"
+build = [
+    "cp310-manylinux_x86_64",
+    "cp311-manylinux_x86_64",
+    "cp312-manylinux_x86_64",
+    "cp313-manylinux_x86_64",
+    "cp310-manylinux_aarch64",
+    "cp311-manylinux_aarch64",
+    "cp312-manylinux_aarch64",
+    "cp313-manylinux_aarch64",
+]
+environment = "USE_MPI=OFF"
+test-command = "pytest {project}/tests --ignore={project}/tests/native"
+before-test = "pip install pytest pytest-mock"

{qupled-1.2.0 → qupled-1.3.0}/src/qupled/mpi.py

@@ -6,24 +6,21 @@ from qupled import native
 class MPI:
     """Class to handle the calls to the MPI API"""
 
-    def __init__(self):
-        self.qp_mpi = native.MPI()
-
     def rank(self):
         """Get rank of the process"""
-        return self.qp_mpi.rank()
+        return native.MPI.rank()
 
     def is_root(self):
         """Check if the current process is root (rank 0)"""
-        return self.qp_mpi.is_root()
+        return native.MPI.is_root()
 
     def barrier(self):
         """Setup an MPI barrier"""
-        self.qp_mpi.barrier()
+        native.MPI.barrier()
 
     def timer(self):
         """Get wall time"""
-        return self.qp_mpi.timer()
+        return native.MPI.timer()
 
     @staticmethod
     def run_only_on_root(func):
@@ -31,7 +28,7 @@ class MPI:
 
         @functools.wraps(func)
         def wrapper(*args, **kwargs):
-            if MPI().is_root():
+            if native.MPI.is_root():
                 return func(*args, **kwargs)
 
         return wrapper
@@ -43,7 +40,7 @@ class MPI:
         @functools.wraps(func)
         def wrapper(*args, **kwargs):
             func(*args, **kwargs)
-            MPI().barrier()
+            native.MPI.barrier()
 
         return wrapper
 
@@ -53,7 +50,7 @@ class MPI:
 
         @functools.wraps(func)
         def wrapper(*args, **kwargs):
-            mpi = MPI()
+            mpi = native.MPI
             tic = mpi.timer()
             func(*args, **kwargs)
             toc = mpi.timer()

{qupled-1.2.0 → qupled-1.3.0}/src/qupled/native/include/python_interface/inputs.hpp

@@ -1,9 +1,11 @@
 #ifndef PYTHON_INTERFACE_INPUTS_HPP
 #define PYTHON_INTERFACE_INPUTS_HPP
 
+#include <pybind11/pybind11.h>
+
 namespace pythonWrappers {
 
-  void exposeInputs();
+  void exposeInputs(pybind11::module_ &m);
 
 }
 

{qupled-1.2.0 → qupled-1.3.0}/src/qupled/native/include/python_interface/schemes.hpp

@@ -1,10 +1,12 @@
 #ifndef PYTHON_INTERFACE_SCHEMES_HPP
 #define PYTHON_INTERFACE_SCHEMES_HPP
 
+#include <pybind11/pybind11.h>
+
 namespace pythonWrappers {
 
   // Function to expose schemes to Python
-  void exposeSchemes();
+  void exposeSchemes(pybind11::module_ &m);
 
 } // namespace pythonWrappers
 

qupled-1.3.0/src/qupled/native/include/python_interface/util.hpp

@@ -0,0 +1,37 @@
+#ifndef PYTHON_INTERFACE_UTIL_HPP
+#define PYTHON_INTERFACE_UTIL_HPP
+
+#include "vector2D.hpp"
+#include "vector3D.hpp"
+#include <pybind11/numpy.h>
+#include <pybind11/pybind11.h>
+#include <vector>
+
+namespace pythonUtil {
+
+  namespace py = pybind11;
+  using py::array;
+  using py::array_t;
+  using py::list;
+
+  // Check if a numpy array is stored in row-major order
+  void CheckRowMajor(const py::array &arr);
+
+  // Convert Python list or 1D array to std::vector<double>
+  std::vector<double> toVector(const py::array_t<double> &arr);
+  std::vector<double> toVector(const py::list &list);
+
+  // Convert 2D array to Vector2D or std::vector<std::vector<double>>
+  Vector2D toVector2D(const py::array_t<double> &arr);
+  std::vector<std::vector<double>>
+  toDoubleVector(const py::array_t<double> &arr);
+
+  // Convert native C++ containers to numpy arrays
+  py::array toNdArray(const std::vector<double> &v);
+  py::array toNdArray2D(const Vector2D &v);
+  py::array toNdArray2D(const std::vector<std::vector<double>> &v);
+  py::array toNdArray3D(const Vector3D &v);
+
+} // namespace pythonUtil
+
+#endif // PYTHON_INTERFACE_UTIL_HPP

{qupled-1.2.0 → qupled-1.3.0}/src/qupled/native/include/python_interface/utilities.hpp

@@ -1,10 +1,12 @@
 #ifndef PYTHON_INTERFACE_UTILITIES_HPP
 #define PYTHON_INTERFACE_UTILITIES_HPP
 
+#include <pybind11/pybind11.h>
+
 namespace pythonWrappers {
 
   // Function to expose utility functions to Python
-  void exposeUtilities();
+  void exposeUtilities(pybind11::module_ &m);
 
 } // namespace pythonWrappers
 

qupled-1.3.0/src/qupled/native/src/CMakeLists.txt

@@ -0,0 +1,91 @@
+# Set cmake version
+cmake_minimum_required(VERSION 3.28)
+
+# Define project name
+project(native LANGUAGES CXX)
+
+# Setup python environment
+find_package(Python3 REQUIRED COMPONENTS Development.Module)
+
+# Setup pybind11
+include(FetchContent)
+FetchContent_Declare(
+  pybind11
+  GIT_REPOSITORY https://github.com/pybind/pybind11.git
+  GIT_TAG v2.13.6
+)
+FetchContent_MakeAvailable(pybind11)
+
+# Setup MPI environment
+option(USE_MPI "Compile with MPI support" ON)
+if(USE_MPI)
+	set(MPI_CXX_SKIP_MPICXX TRUE)
+	find_package(MPI REQUIRED)
+	add_compile_definitions(USE_MPI)
+	set(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER})
+endif()
+
+# Additional external libraries
+find_package(OpenMP REQUIRED)
+find_package(GSL REQUIRED)
+find_package(SQLite3 REQUIRED)
+find_package(SQLiteCpp REQUIRED)
+
+# Set compiler flags
+set(CMAKE_CXX_STANDARD 20)
+add_compile_options(-Wall -Wextra -Wpedantic -O3)
+
+# Source code
+pybind11_add_module(native
+	logger.cpp
+	numerics.cpp
+	vector2D.cpp
+	vector3D.cpp
+	internal_energy.cpp
+	free_energy.cpp
+	rdf.cpp
+	mpi_util.cpp
+	num_util.cpp
+	vector_util.cpp
+	thermo_util.cpp
+	input.cpp
+	chemical_potential.cpp
+	hf.cpp
+	rpa.cpp
+	esa.cpp
+	stls.cpp
+	iet.cpp
+	stlsiet.cpp
+	qstls.cpp
+	qstlsiet.cpp
+	vsbase.cpp
+	vsstls.cpp
+	qvsstls.cpp
+	python_interface/util.cpp
+	python_interface/inputs.cpp
+	python_interface/schemes.cpp
+	python_interface/utilities.cpp
+	python_interface/native.cpp
+)
+
+# Include directories
+target_include_directories(native PUBLIC
+	../include
+)
+
+# Link external libraries
+if(USE_MPI)
+	target_link_libraries(native PUBLIC MPI::MPI_CXX)
+endif()
+target_link_libraries(native PUBLIC
+	OpenMP::OpenMP_CXX
+	GSL::gsl
+	GSL::gslcblas
+	SQLiteCpp
+	SQLite::SQLite3
+)
+
+# Install
+install(TARGETS native
+	DESTINATION .
+)