qupled 0.0.4__tar.gz → 0.0.5__tar.gz

{qupled-0.0.4 → qupled-0.0.5}/.clang-format

@@ -47,7 +47,7 @@ BraceWrapping:
   SplitEmptyFunction: true
   SplitEmptyRecord: true
   SplitEmptyNamespace: true
-BreakBeforeBinaryOperators: None
+BreakBeforeBinaryOperators: NonAssignment
 BreakBeforeConceptDeclarations: true
 BreakBeforeBraces: Attach
 BreakBeforeInheritanceComma: false

qupled-0.0.4/.github/workflows/build-and-test-macos.yml → qupled-0.0.5/.github/workflows/build-and-test-base.yml

@@ -1,4 +1,4 @@
-name: Build & Test (macOS)
+name: Build & Test
 
 on:
   workflow_call:
@@ -15,39 +15,38 @@ env:
   PYTHON_VENV_ROOT: ${{ github.workspace }}/python-venv
 
 jobs:
-
   build_and_test:
-
-    runs-on: macos-latest
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-latest, ubuntu-latest]
 
     steps:
     - name: Checkout repository
       uses: actions/checkout@v2
 
     - name: Set up Python
+      if: ${{ matrix.os == 'macos-latest' }}
       uses: actions/setup-python@v4
       with:
         python-version: "3.12"
 
     - name: Install dependencies
       run: |
-        brew update
-        brew install cmake gsl libomp fmt boost-python3
+        ./devtool install-deps
         python3 -m venv ${PYTHON_VENV_ROOT}
 
     - name: Set build version
       if: ${{ inputs.build-version != '' }}
       run: |
-        BUILD_VERSION=${{ inputs.build-version }}
-        sed -i "" "s/^version = \".*\"/version = \"${BUILD_VERSION}\"/" pyproject.toml
+        ./devtool update-version ${{ inputs.build-version }}
 
     - name: Build
       run: |
         source ${PYTHON_VENV_ROOT}/bin/activate
         pip3 install --upgrade pip
         pip3 install build setuptools
-        export OpenMP_ROOT=$(brew --prefix)/opt/libomp	
-        ./devtool build --nompi
+        ./devtool build
 
     - name: Tests
       run: |
@@ -59,5 +58,5 @@ jobs:
       if: ${{ success() && inputs.upload-artifact == 'true' }}
       uses: actions/upload-artifact@v4
       with:
-        name: qupled-macos
+        name: qupled-${{ matrix.os }}
         path: dist

qupled-0.0.5/.github/workflows/build-and-test.yml

@@ -0,0 +1,13 @@
+name: Build & Test
+
+on:
+  push:
+  pull_request:
+    branches:
+      - master
+  
+jobs:
+  linux-MPI:
+    uses: ./.github/workflows/build-and-test-base.yml
+    with:
+      upload-artifact: false

{qupled-0.0.4 → qupled-0.0.5}/.github/workflows/release.yml

@@ -10,14 +10,8 @@ env:
 
 jobs:
 
-  build-and-test-linux:
-    uses: ./.github/workflows/build-and-test-linux-mpi.yml
-    with:
-      upload-artifact: true
-      build-version: ${GITHUB_REF#refs/tags/v}
-
-  build-and-test-macos:
-    uses: ./.github/workflows/build-and-test-macos-mpi.yml
+  build-and-test:
+    uses: ./.github/workflows/build-and-test-base.yml
     with:
       upload-artifact: true
       build-version: ${GITHUB_REF#refs/tags/v}
@@ -25,15 +19,15 @@ jobs:
   publish:
 
    runs-on: ubuntu-latest
-   needs: [build-and-test-linux, build-and-test-macos]
+   needs: [build-and-test]
 
    steps:
 
    - name: Download linux package
      uses: actions/download-artifact@v4
      with:
-       name: qupled-linux-mpi
-       path: qupled-linux-mpi
+       name: qupled-ubuntu-latest
+       path: qupled-ubuntu-latest
 
    - name: Set up Python environment
      run: |
@@ -44,8 +38,8 @@ jobs:
 
    - name: Publish to PyPI
      env:
-       TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-       TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+       TWINE_USERNAME: __token__
+       TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
      run: |
        source ${PYTHON_VENV_ROOT}/bin/activate
-       twine upload --non-interactive qupled-linux-mpi/*.tar.gz
+       twine upload --non-interactive qupled-ubuntu-latest/*.tar.gz

{qupled-0.0.4 → qupled-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: qupled
-Version: 0.0.4
+Version: 0.0.5
 Summary: qupled: a package to investigate quantum plasmas via the dielectric formalism
 Author-email: Federico Lucco Castello <federico.luccocastello@gmail.com>
 Classifier: Programming Language :: Python :: 3.10
@@ -31,10 +31,8 @@ Requires-Dist: sphinxcontrib-serializinghtml~=2.0.0; extra == "docs"
 
 Qupled is a Python package designed for calculating the properties of quantum plasmas using the dielectric formalism. By combining a straightforward Python interface with the speed of C++, it allows for efficient and accurate computations of quantum plasma properties.
 
-<p align="center">
-  <img src="examples/readme/qupled_animation_light.svg#gh-light-mode-only" width="100%">
-  <img src="examples/readme/qupled_animation_dark.svg#gh-dark-mode-only" width="100%">
-<p>
+![](https://github.com/fedluc/qupled/blob/master/examples/readme/qupled_animation_light.svg#gh-light-mode-only)
+![](https://github.com/fedluc/qupled/blob/master/examples/readme/qupled_animation_dark.svg#gh-dark-mode-only)
 
 ## Status
 [![Build & Test](https://github.com/fedluc/qupled/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/fedluc/qupled/actions/workflows/build-and-test.yml)
@@ -62,11 +60,14 @@ Qupled has been used in the following publications:
 
 <ol>
   <li>
-    <a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.109.125134">Tolias, P., Lucco Castello, F., Kalkavouras, F., &#38; Dornheim, T. (2024). Revisiting the Vashishta-Singwi dielectric scheme for the warm dense uniform electron fluid. <i>Phys. Rev. B</i>, <i>109</i>(12)</a>
+    <a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.109.125134">Tolias, P., Lucco Castello, F., Kalkavouras, F., &#38; Dornheim, T. (2024). Revisiting the Vashishta-Singwi dielectric scheme for the warm dense uniform electron fluid. <i>Physical Review B</i>, <i>109</i>(12)</a>
   </li>
   <li>
     <a href="https://pubs.aip.org/aip/jcp/article/158/14/141102/2877795/Quantum-version-of-the-integral-equation-theory">Tolias, P., Lucco Castello, F., &#38; Dornheim, T. (2023). Quantum version of the integral equation theory-based dielectric scheme for strongly coupled electron liquids. <i>The Journal of Chemical Physics</i>, <i>158</i>(14)</a>
   </li>
+  <li>
+    <a href="https://iopscience.iop.org/article/10.1209/0295-5075/ac7166/meta">Lucco Castello, F., Tolias, P., &#38; Dornheim, T. (2022). Classical bridge functions in classical and quantum plasma liquids. <i>Europhysics Letters</i>, <i>138</i>(4)</a>
+  </li>
   <li>
     <a href="https://pubs.aip.org/aip/jcp/article/155/13/134115/353165/Integral-equation-theory-based-dielectric-scheme">Tolias, P., Lucco Castello, F., &#38; Dornheim, T. (2021). Integral equation theory based dielectric scheme for strongly coupled electron liquids. <i>The Journal of Chemical Physics</i>, <i>155</i>(13)</a>
   </li>

{qupled-0.0.4 → qupled-0.0.5}/README.md

@@ -2,10 +2,8 @@
 
 Qupled is a Python package designed for calculating the properties of quantum plasmas using the dielectric formalism. By combining a straightforward Python interface with the speed of C++, it allows for efficient and accurate computations of quantum plasma properties.
 
-<p align="center">
-  <img src="examples/readme/qupled_animation_light.svg#gh-light-mode-only" width="100%">
-  <img src="examples/readme/qupled_animation_dark.svg#gh-dark-mode-only" width="100%">
-<p>
+![](https://github.com/fedluc/qupled/blob/master/examples/readme/qupled_animation_light.svg#gh-light-mode-only)
+![](https://github.com/fedluc/qupled/blob/master/examples/readme/qupled_animation_dark.svg#gh-dark-mode-only)
 
 ## Status
 [![Build & Test](https://github.com/fedluc/qupled/actions/workflows/build-and-test.yml/badge.svg)](https://github.com/fedluc/qupled/actions/workflows/build-and-test.yml)
@@ -33,11 +31,14 @@ Qupled has been used in the following publications:
 
 <ol>
   <li>
-    <a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.109.125134">Tolias, P., Lucco Castello, F., Kalkavouras, F., &#38; Dornheim, T. (2024). Revisiting the Vashishta-Singwi dielectric scheme for the warm dense uniform electron fluid. <i>Phys. Rev. B</i>, <i>109</i>(12)</a>
+    <a href="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.109.125134">Tolias, P., Lucco Castello, F., Kalkavouras, F., &#38; Dornheim, T. (2024). Revisiting the Vashishta-Singwi dielectric scheme for the warm dense uniform electron fluid. <i>Physical Review B</i>, <i>109</i>(12)</a>
   </li>
   <li>
     <a href="https://pubs.aip.org/aip/jcp/article/158/14/141102/2877795/Quantum-version-of-the-integral-equation-theory">Tolias, P., Lucco Castello, F., &#38; Dornheim, T. (2023). Quantum version of the integral equation theory-based dielectric scheme for strongly coupled electron liquids. <i>The Journal of Chemical Physics</i>, <i>158</i>(14)</a>
   </li>
+  <li>
+    <a href="https://iopscience.iop.org/article/10.1209/0295-5075/ac7166/meta">Lucco Castello, F., Tolias, P., &#38; Dornheim, T. (2022). Classical bridge functions in classical and quantum plasma liquids. <i>Europhysics Letters</i>, <i>138</i>(4)</a>
+  </li>
   <li>
     <a href="https://pubs.aip.org/aip/jcp/article/155/13/134115/353165/Integral-equation-theory-based-dielectric-scheme">Tolias, P., Lucco Castello, F., &#38; Dornheim, T. (2021). Integral equation theory based dielectric scheme for strongly coupled electron liquids. <i>The Journal of Chemical Physics</i>, <i>155</i>(13)</a>
   </li>

qupled-0.0.5/dev/devtool.py

@@ -0,0 +1,193 @@
+import os
+import argparse
+import subprocess
+import shutil
+from pathlib import Path
+
+
+def build(nompi):
+    # Build without MPI
+    if nompi:
+        os.environ["USE_MPI"] = "OFF"
+    # Set environment variable for OpenMP on macOS
+    if os.name == "posix" and shutil.which("brew"):
+        brew_prefix = subprocess.run(
+            ["brew", "--prefix"], capture_output=True, text=True
+        ).stdout.strip()
+        os.environ["OpenMP_ROOT"] = str(Path(brew_prefix, "opt", "libomp"))
+    subprocess.run(["python3", "-m", "build"], check=True)
+    print("Build completed.")
+
+
+def get_wheel_file():
+    wheel_file = list(Path().rglob("qupled*.whl"))
+    if not wheel_file:
+        print("No .whl files found. Ensure the package is built first.")
+        return None
+    else:
+        return str(wheel_file[0])
+
+
+def run_tox(environment):
+    tox_path = Path(".tox")
+    if tox_path.exists():
+        shutil.rmtree(tox_path)
+    wheel_file = get_wheel_file()
+    if wheel_file is not None:
+        os.environ["WHEEL_FILE"] = wheel_file
+        subprocess.run(["tox", "-e", environment], check=True)
+
+
+def test():
+    run_tox("test")
+
+
+def examples():
+    run_tox("examples")
+
+
+def format_code():
+    subprocess.run(["black", "."], check=True)
+    native_files_folder = Path("src", "qupled", "native")
+    cpp_files = list(native_files_folder.rglob("*.cpp"))
+    hpp_files = list(native_files_folder.rglob("*.hpp"))
+    for f in cpp_files + hpp_files:
+        subprocess.run(["clang-format", "--style=file", "-i", str(f)], check=True)
+
+
+def docs():
+    subprocess.run(["sphinx-build", "-b", "html", "docs", str(Path("docs", "_build"))])
+
+
+def clean():
+    folders_to_clean = [
+        Path("dist"),
+        Path("src", "qupled.egg-info"),
+        Path("docs", "_build"),
+    ]
+    for folder in folders_to_clean:
+        if folder.exists():
+            print(f"Removing folder: {folder}")
+            shutil.rmtree(folder)
+
+
+def install():
+    wheel_file = get_wheel_file()
+    if wheel_file is not None:
+        subprocess.run(["pip", "install", "--force-reinstall", wheel_file], check=True)
+
+
+def install_dependencies():
+    print("Installing dependencies...")
+    if os.name == "posix":
+        if shutil.which("apt-get"):
+            subprocess.run(["sudo", "apt-get", "update"], check=True)
+            subprocess.run(
+                [
+                    "sudo",
+                    "apt-get",
+                    "install",
+                    "-y",
+                    "cmake",
+                    "libboost-all-dev",
+                    "libopenmpi-dev",
+                    "libgsl-dev",
+                    "libomp-dev",
+                    "libfmt-dev",
+                    "python3-dev",
+                ],
+                check=True,
+            )
+        elif shutil.which("brew"):
+            subprocess.run(["brew", "update"], check=True)
+            subprocess.run(
+                [
+                    "brew",
+                    "install",
+                    "cmake",
+                    "gsl",
+                    "libomp",
+                    "openmpi",
+                    "fmt",
+                    "boost-python3",
+                ],
+                check=True,
+            )
+        else:
+            print("Unsupported package manager. Please install dependencies manually.")
+    else:
+        print("Unsupported operating system. Please install dependencies manually.")
+
+
+def update_version(build_version):
+    pyproject_file = Path("pyproject.toml")
+    if not pyproject_file.exists():
+        return
+    with pyproject_file.open("r") as file:
+        content = file.readlines()
+    with pyproject_file.open("w") as file:
+        for line in content:
+            if line.startswith("version = "):
+                file.write(f'version = "{build_version}"')
+                file.write("\n")
+            else:
+                file.write(line)
+
+
+def run():
+    parser = argparse.ArgumentParser(
+        description="""A utility script for building, testing, formatting,
+        and generating documentation for the qupled project."""
+    )
+
+    subparsers = parser.add_subparsers(dest="command", help="Sub-command to run")
+
+    # Build command
+    build_parser = subparsers.add_parser("build", help="Build the qupled package")
+    build_parser.add_argument(
+        "--nompi",
+        action="store_true",
+        help="Build without MPI support (default: False).",
+    )
+
+    # Update version command
+    version_parser = subparsers.add_parser(
+        "update-version", help="Update package version"
+    )
+    version_parser.add_argument("build_version", help="The new version number.")
+
+    # Other commands
+    subparsers.add_parser("clean", help="Clean up build artifacts")
+    subparsers.add_parser("docs", help="Generate documentation")
+    subparsers.add_parser("examples", help="Run tests for the examples")
+    subparsers.add_parser("format", help="Format the source code")
+    subparsers.add_parser("install", help="Install the qupled package")
+    subparsers.add_parser("install-deps", help="Install system dependencies")
+    subparsers.add_parser("test", help="Run tests")
+
+    args = parser.parse_args()
+
+    if args.command == "build":
+        build(args.nompi)
+    elif args.command == "clean":
+        clean()
+    elif args.command == "docs":
+        docs()
+    elif args.command == "examples":
+        examples()
+    elif args.command == "format":
+        format_code()
+    elif args.command == "install":
+        install()
+    elif args.command == "test":
+        test()
+    elif args.command == "install-deps":
+        install_dependencies()
+    elif args.command == "update-version":
+        update_version(args.build_version)
+    else:
+        parser.print_help()
+
+
+if __name__ == "__main__":
+    run()

{qupled-0.0.4 → qupled-0.0.5}/docs/conf.py

@@ -14,7 +14,7 @@ author = "Federico Lucco Castello"
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath(".."))
+sys.path.insert(0, os.path.abspath(os.path.join("..", "src")))
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration

qupled-0.0.4/examples/readme/animation.py → qupled-0.0.5/examples/readme/create_cover.py

@@ -1,74 +1,47 @@
 import os
+import tempfile
+import shutil
 import numpy as np
 import matplotlib as mpl
 from matplotlib import pyplot as plt
 from matplotlib import colormaps as cm
-from scour.scour import start, getInOut, parse_args
-import qupled.classic as qpc
-import qupled.quantum as qpq
+from qupled.util import Hdf
+from qupled.quantum import Qstls
 
 
 def main():
-    darkmode = True
-    nIterations = 33
-    svg_files = create_all_svg_files(nIterations, darkmode)
-    combine_svg_files(svg_files, darkmode)
+    with tempfile.TemporaryDirectory() as temp_dir:
+        original_dir = os.getcwd()
+        os.chdir(temp_dir)
+        try:
+            svg_files = create_svg_files()
+            for svg_file in svg_files:
+                shutil.copy(svg_file, original_dir)
+        finally:
+            os.chdir(original_dir)
+
+
+def create_svg_files():
+    plot_data, error = get_plot_data()
+    if plot_data is not None:
+        svg_files = []
+        for darkmode in [True, False]:
+            svg_files.append(create_one_svg_file(darkmode, plot_data, error))
+        return svg_files
+    else:
+        return []
+
+
+def get_plot_data():
+    plot_data = None
+    error = []
+    while plot_data is None or plot_data.error > 1e-5:
+        plot_data = solve_qstls()
+        error.append(plot_data.error)
+    return plot_data, error
 
 
-def create_all_svg_files(nFiles, darkmode):
-    fig, ax = plt.subplots()
-    images = []
-    error = []
-    file_names = []
-    for i in range(nFiles):
-        file_names.append(create_one_svg_file(i, error, darkmode))
-    return file_names
-
-
-def combine_svg_files(svg_files, darkmode):
-    svg_template = """
-    <svg width="864pt" height="576pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
-     {}
-    </svg>
-    """
-    image_template = """
-    <g visibility="hidden">
-     {}
-    </g>
-    """
-    image_duration = 0.18  # in seconds
-    svg_image = ""
-    animation_file = "qupled_animation_light.svg"
-    if darkmode:
-        animation_file = "qupled_animation_dark.svg"
-    for i in range(len(svg_files)):
-        svg_file = svg_files[i]
-        begin_visible = i * image_duration
-        begin_hidden = begin_visible + image_duration
-        with open(svg_file, "r") as f:
-            svg_content = f.read()
-            svg_content = svg_content[svg_content.index("<svg") :]
-            svg_content = add_animation(svg_content, begin_visible, begin_hidden)
-            svg_image += image_template.format(svg_content)
-        os.remove(svg_file)
-    with open(animation_file, "w") as fw:
-        fw.write(svg_template.format(svg_image))
-    optimise_svg(animation_file)
-
-
-def add_animation(svg_content, begin, end):
-    animation_xml = f"""
-     <animate attributeName="visibility" values="hidden;visible" begin="{begin}s"/>
-     <animate attributeName="visibility" values="visible;hidden" begin="{end}s"/>
-    """
-    index = svg_content.index("</svg>")
-    modified_svg_content = svg_content[:index] + animation_xml + svg_content[index:]
-    return modified_svg_content
-
-
-def create_one_svg_file(i, errorList, darkmode):
-    # Solve scheme
-    plot_data = solve_qstls(i)
+def create_one_svg_file(darkmode, plot_data, error):
     # Get plot settings
     settings = PlotSettings(darkmode)
     plt.figure(figsize=settings.figure_size)
@@ -78,39 +51,39 @@ def create_one_svg_file(i, errorList, darkmode):
     # Plot quantities of interest
     plot_density_response(plt, plot_data, settings)
     plot_ssf(plt, plot_data, settings)
-    plot_error(plt, i, errorList, plot_data.error, settings)
+    plot_error(plt, error, settings)
     # Combine plots
     plt.tight_layout()
     # Save figure
-    file_name = f"plot{i:03}.svg"
+    file_name = settings.figure_name
     plt.savefig(file_name)
     plt.close()
-    # Optimise svg file
-    optimise_svg(file_name)
     return file_name
 
 
-def solve_qstls(i):
-    qstls = qpq.Qstls(
-        15.0,
-        1.0,
-        mixing=0.3,
-        resolution=0.1,
-        cutoff=10,
-        matsubara=16,
-        threads=16,
-        iterations=0,
+def solve_qstls():
+    qstls = Qstls()
+    rs = 15.0
+    theta = 1.0
+    inputs = Qstls.Input(rs, theta)
+    inputs.mixing = 0.3
+    inputs.resolution = 0.1
+    inputs.cutoff = 10
+    inputs.matsubara = 16
+    inputs.threads = 16
+    inputs.iterations = 0
+    guess_file = f"rs{rs:.3f}_theta{theta:.3f}_QSTLS.h5"
+    adr_file = f"adr_fixed_theta{theta:.3f}_matsubara{inputs.matsubara}_QSTLS.bin"
+    inputs.guess = (
+        Qstls.getInitialGuess(guess_file)
+        if os.path.exists(guess_file)
+        else inputs.guess
     )
-    if i > 0:
-        qstls.setGuess("rs15.000_theta1.000_QSTLS.h5")
-        qstls.inputs.fixed = "adr_fixed_theta1.000_matsubara16.bin"
-    qstls.compute()
+    inputs.fixed = adr_file if os.path.exists(adr_file) else inputs.fixed
+    qstls.compute(inputs)
+    results = Hdf().read(qstls.hdfFileName, ["wvg", "adr", "ssf", "idr", "error"])
     return QStlsData(
-        qstls.scheme.wvg,
-        qstls.scheme.adr,
-        qstls.scheme.idr,
-        qstls.scheme.ssf,
-        qstls.scheme.error,
+        results["wvg"], results["adr"], results["idr"], results["ssf"], results["error"]
     )
 
 
@@ -161,14 +134,12 @@ def plot_ssf(plt, plot_data, settings):
     plt.yticks(fontsize=settings.ticksz)
 
 
-def plot_error(plt, iteration, errorList, error, settings):
-    errorList.append(error)
+def plot_error(plt, error, settings):
+    iterations = range(len(error))
     horizontalLineColor = mpl.rcParams["text.color"]
     plt.subplot(2, 1, 1)
-    plt.plot(
-        range(iteration + 1), errorList, color=settings.color, linewidth=settings.width
-    )
-    plt.scatter(iteration, error, color="red", s=150, alpha=1)
+    plt.plot(iterations, error, color=settings.color, linewidth=settings.width)
+    plt.scatter(iterations[-1], error[-1], color="red", s=150, alpha=1)
     plt.axhline(y=1.0e-5, color=horizontalLineColor, linestyle="--")
     plt.text(
         3, 1.5e-5, "Convergence", horizontalalignment="center", fontsize=settings.ticksz
@@ -223,14 +194,14 @@ class PlotSettings:
         self.labelsz = 16
         self.ticksz = 14
         self.width = 2.0
-        self.theme = "ggplot"
-        self.colormap = cm["viridis"].reversed()
+        self.theme = "dark_background" if darkmode else "ggplot"
+        self.colormap = cm["plasma"] if darkmode else cm["viridis"].reversed()
         self.xlim = 6
-        if darkmode:
-            self.theme = "dark_background"
-            self.colormap = cm["plasma"]
         self.color = self.colormap(1.0)
         self.figure_size = (12, 8)
+        self.figure_name = (
+            "qupled_animation_dark.svg" if darkmode else "qupled_animation_light.svg"
+        )
 
 
 if __name__ == "__main__":