pyvpmr 231126__tar.gz → 240307__tar.gz

pyvpmr-240307/.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly

pyvpmr-240307/.github/workflows/coverage.yml

@@ -0,0 +1,40 @@
+name: Coverage
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+jobs:
+  ubuntu:
+    runs-on: ubuntu-22.04
+    timeout-minutes: 10
+    steps:
+      - name: Setup
+        run: |
+          sudo apt-get update && sudo apt-get install -y cmake git g++ libtbb-dev libmpfr-dev libgmp-dev libpython3-dev python3 python3-distutils
+      - name: Clone
+        uses: actions/checkout@v4
+      - name: Compile
+        run: |
+          git config --global --add safe.directory /__w/vpmr/vpmr
+          git submodule update --init --recursive
+          sed -i 's/3.24/3.13/g' CMakeLists.txt
+          mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Debug ..
+          make -j"$(nproc)"
+          ./vpmr -h
+          echo "exp(-t^2/2)" > k
+          ./vpmr -nc 5 -n 20 -d 100 -q 400 -e 1e-9 -k k -w -s
+          for SRC in `find . | egrep '\.o'`; do gcov -n $SRC > /dev/null; done
+          python3 -c "import _pyvpmr;print(_pyvpmr.vpmr())"
+      - name: Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Build
+        run: pip install --verbose .
+      - name: Test
+        run: python3 test/test.py
+      - name: Upload
+        uses: codecov/codecov-action@v4
+        with:
+          plugin: pycoverage

pyvpmr-240307/.github/workflows/release.yml

@@ -0,0 +1,94 @@
+name: Release
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+jobs:
+  debian:
+    runs-on: ubuntu-22.04
+    timeout-minutes: 10
+    container: debian:buster
+    steps:
+      - name: Setup
+        run: |
+          echo "VPMR_VERSION=$(date +''%y%m%d'')" >> $GITHUB_ENV
+          apt-get update && apt-get install -y cmake git g++ libtbb-dev libmpfr-dev libgmp-dev libpython3-dev python3 python3-distutils wget gtk-update-icon-cache
+      - name: Clone
+        uses: actions/checkout@v4
+      - name: Compile
+        run: |
+          git config --global --add safe.directory /__w/vpmr/vpmr
+          git submodule update --init --recursive
+          cd eigen && git apply ../patch_size.patch && cd ..
+          sed -i 's/3.24/3.13/g' CMakeLists.txt
+          mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release ..
+          make -j"$(nproc)"
+      - name: AppImage
+        run: |
+          echo "version: 1" >> AppImageBuilder.yml
+          echo "AppDir:" >> AppImageBuilder.yml
+          echo "  path: build/AppDir" >> AppImageBuilder.yml
+          echo "  app_info:" >> AppImageBuilder.yml
+          echo "    id: io.github.tlcfem.vpmr" >> AppImageBuilder.yml
+          echo "    name: vpmr" >> AppImageBuilder.yml
+          echo "    version: '${{ env.VPMR_VERSION }}'" >> AppImageBuilder.yml
+          echo "    icon: vpmr" >> AppImageBuilder.yml
+          echo "    exec: usr/bin/vpmr" >> AppImageBuilder.yml
+          echo "    exec_args: \$@" >> AppImageBuilder.yml
+          echo "  files:" >> AppImageBuilder.yml
+          echo "    include:" >> AppImageBuilder.yml
+          echo "    - lib64/ld-linux-x86-64.so.2" >> AppImageBuilder.yml
+          echo "    exclude:" >> AppImageBuilder.yml
+          echo "    - usr/share/man" >> AppImageBuilder.yml
+          echo "    - usr/share/doc/*/README.*" >> AppImageBuilder.yml
+          echo "    - usr/share/doc/*/changelog.*" >> AppImageBuilder.yml
+          echo "    - usr/share/doc/*/NEWS.*" >> AppImageBuilder.yml
+          echo "    - usr/share/doc/*/TODO.*" >> AppImageBuilder.yml
+          echo "  test:" >> AppImageBuilder.yml
+          echo "    fedora-30:" >> AppImageBuilder.yml
+          echo "      image: appimagecrafters/tests-env:fedora-30" >> AppImageBuilder.yml
+          echo "      command: ./AppRun -h" >> AppImageBuilder.yml
+          echo "    debian-stable:" >> AppImageBuilder.yml
+          echo "      image: appimagecrafters/tests-env:debian-stable" >> AppImageBuilder.yml
+          echo "      command: ./AppRun -h" >> AppImageBuilder.yml
+          echo "    archlinux-latest:" >> AppImageBuilder.yml
+          echo "      image: appimagecrafters/tests-env:archlinux-latest" >> AppImageBuilder.yml
+          echo "      command: ./AppRun -h" >> AppImageBuilder.yml
+          echo "    centos-7:" >> AppImageBuilder.yml
+          echo "      image: appimagecrafters/tests-env:centos-7" >> AppImageBuilder.yml
+          echo "      command: ./AppRun -h" >> AppImageBuilder.yml
+          echo "    ubuntu-xenial:" >> AppImageBuilder.yml
+          echo "      image: appimagecrafters/tests-env:ubuntu-xenial" >> AppImageBuilder.yml
+          echo "      command: ./AppRun -h" >> AppImageBuilder.yml
+          echo "AppImage:" >> AppImageBuilder.yml
+          echo "  arch: x86_64" >> AppImageBuilder.yml
+          echo "  update-information: guess" >> AppImageBuilder.yml
+          cat AppImageBuilder.yml
+      - name: Package
+        run: |
+          wget -q https://github.com/linuxdeploy/linuxdeploy/releases/download/1-alpha-20220822-1/linuxdeploy-x86_64.AppImage
+          chmod +x linuxdeploy-x86_64.AppImage
+          wget -q https://github.com/AppImageCrafters/appimage-builder/releases/download/v1.1.0/appimage-builder-1.1.0-x86_64.AppImage
+          chmod +x appimage-builder-1.1.0-x86_64.AppImage
+
+          ./linuxdeploy-x86_64.AppImage --appimage-extract-and-run --appdir AppDir --executable build/vpmr -i resource/vpmr.svg
+          ./appimage-builder-1.1.0-x86_64.AppImage --appimage-extract-and-run --recipe AppImageBuilder.yml --skip-tests
+          
+          chmod +x vpmr-${{ env.VPMR_VERSION }}-x86_64.AppImage
+          ./vpmr-${{ env.VPMR_VERSION }}-x86_64.AppImage --appimage-extract-and-run -h
+      - name: Release
+        if: contains(github.event.head_commit.message, '[publish]')
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: vpmr-${{ env.VPMR_VERSION }}-x86_64.AppImage
+          asset_name: vpmr-${{ env.VPMR_VERSION }}-x86_64.AppImage
+          tag: v${{ env.VPMR_VERSION }}
+          prerelease: false
+          overwrite: true
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: vpmr-${{ env.VPMR_VERSION }}-x86_64.AppImage
+          path: vpmr-${{ env.VPMR_VERSION }}-x86_64.AppImage

pyvpmr-240307/.github/workflows/wheels.yml

@@ -0,0 +1,63 @@
+name: Wheels
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+jobs:
+  build_sdist:
+    name: Build
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup
+        run: |
+          git submodule update --init --recursive
+          cd eigen && git apply ../patch_size.patch && cd ..
+      - name: Build
+        run: pipx run build --sdist
+      - name: Check
+        run: pipx run twine check dist/*
+      - uses: actions/upload-artifact@v4
+        with:
+          name: pyvpmr-sdist
+          path: dist/*.tar.gz
+  build_wheels:
+    name: Wheels
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, macos-latest ]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Setup
+        run: |
+          git submodule update --init --recursive
+          cd eigen && git apply ../patch_size.patch && cd ..
+      - name: CI Build Wheel
+        uses: pypa/cibuildwheel@v2.16
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: pyvpmr-${{ matrix.os }}
+          path: wheelhouse/*.whl
+  upload_all:
+    name: Upload
+    needs: [ build_wheels, build_sdist ]
+    runs-on: ubuntu-latest
+    if: contains(github.event.head_commit.message, '[publish]')
+    steps:
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - uses: actions/download-artifact@v4
+        with:
+          pattern: pyvpmr*
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI }}

pyvpmr-240307/.github/workflows/windows.yml

@@ -0,0 +1,60 @@
+name: Windows
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+jobs:
+  windows:
+    runs-on: windows-2022
+    timeout-minutes: 120
+    steps:
+      - name: MSYS
+        uses: msys2/setup-msys2@v2
+        with:
+          msystem: mingw64
+          update: true
+          install: git mingw-w64-x86_64-cmake mingw-w64-x86_64-tbb mingw-w64-x86_64-gcc mingw-w64-x86_64-ninja mingw-w64-x86_64-gmp mingw-w64-x86_64-mpfr mingw-w64-x86_64-7zip
+      - name: Clone
+        uses: actions/checkout@v4
+      - name: Version
+        run: |
+          echo ("VPMR_VERSION="+(get-date -format "yyMMdd")) >> $env:GITHUB_ENV
+      - name: Compile
+        shell: msys2 {0}
+        run: |
+          git submodule update --init --recursive
+          cd eigen && git apply --ignore-space-change --ignore-whitespace ../patch_size.patch && cd ..
+          sed -i 's/3.24/3.13/g' CMakeLists.txt
+          mkdir build && cd build
+          cmake -G Ninja -DCMAKE_BUILD_TYPE=Release ..
+          cmake --build .
+          mkdir release
+          ldd vpmr.exe
+          cp vpmr.exe release
+          cmake -G Ninja -DCMAKE_BUILD_TYPE=RelWithDebInfo ..
+          cmake --build .
+          cp vpmr.exe release/vpmr-dbg.exe
+          cp /mingw64/bin/libgcc_s_seh-1.dll release
+          cp /mingw64/bin/libstdc++-6.dll release
+          cp /mingw64/bin/libwinpthread-1.dll release
+          cp /mingw64/bin/libgmp-10.dll release
+          cp /mingw64/bin/libmpfr-6.dll release
+          cp /mingw64/bin/libtbb12.dll release
+          cd release
+          7z a ../../vpmr-${{ env.VPMR_VERSION }}-win.7z *
+      - name: Release
+        if: contains(github.event.head_commit.message, '[publish]')
+        uses: svenstaro/upload-release-action@v2
+        with:
+          repo_token: ${{ secrets.GITHUB_TOKEN }}
+          file: vpmr-${{ env.VPMR_VERSION }}-win.7z
+          asset_name: vpmr-${{ env.VPMR_VERSION }}-win.7z
+          tag: v${{ env.VPMR_VERSION }}
+          prerelease: false
+          overwrite: true
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: vpmr-${{ env.VPMR_VERSION }}-win.7z
+          path: vpmr-${{ env.VPMR_VERSION }}-win.7z

pyvpmr-240307/PKG-INFO

@@ -0,0 +1,263 @@
+Metadata-Version: 2.1
+Name: pyvpmr
+Version: 240307
+Summary: The VPMR Algorithm
+Home-page: https://github.com/TLCFEM/vpmr
+Author: Theodore Chang
+Author-email: tlcfem@gmail.com
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+
+# VPMR C++ Implementation
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7770193.svg)](https://doi.org/10.5281/zenodo.7770193)
+[![codecov](https://codecov.io/gh/TLCFEM/vpmr/branch/master/graph/badge.svg?token=9QE6SQC3ZG)](https://codecov.io/gh/TLCFEM/vpmr)
+[![PyPI version](https://badge.fury.io/py/pyvpmr.svg)](https://pypi.org/project/pyvpmr/)
+
+[![gplv3-or-later](https://www.gnu.org/graphics/gplv3-or-later.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
+
+## Call For Help
+
+- [ ] **more performant parallel SVD algorithm**: `eigen` only provides sequential SVD
+- [ ] **alternative integration**: currently only Gauss-Legendre quadrature is available
+
+## What Is This?
+
+This is a C++ implementation of the VPMR algorithm to compute the approximation of arbitrary smooth kernel.
+A Python package is also provided.
+
+Check the reference paper [10.1007/s10915-022-01999-1](https://doi.org/10.1007/s10915-022-01999-1) and
+the [original](https://github.com/ZXGao97/VPMR) MATLAB implementation for more details.
+
+In short, the algorithm tries to find a summation of exponentials to approximate a given kernel function.
+In mathematical terms, it looks for a set of $m_j$ and $s_j$ such that
+
+```math
+\max_{t\in{}I}\left\|g(t)-\sum_jm_j\exp(-s_jt)\right\|<\epsilon.
+```
+
+In the above, $g(t)$ is the given kernel function and $\epsilon$ is the prescribed tolerance.
+
+## Dependency
+
+The following libraries are required:
+
+1. [gmp](https://gmplib.org/) for multiple precision arithmetic
+2. [mpfr](https://www.mpfr.org/) for multiple-precision floating-point computations
+3. [tbb](https://github.com/oneapi-src/oneTBB) for parallel computing
+
+The following libraries are included:
+
+1. [mpreal](http://www.holoborodko.com/pavel/mpfr/) `mpreal` type C++ wrapper, included
+2. [BigInt](https://github.com/faheel/BigInt) `BigInt` arbitrary large integer for combinatorial number, included
+3. [Eigen](https://eigen.tuxfamily.org/) for matrix decomposition, included
+4. [exprtk](https://github.com/ArashPartow/exprtk.git) for expression parsing, included
+5. [exprtk-custom-types](https://github.com/ArashPartow/exprtk-custom-types.git) for `mpreal` support, included
+
+## How To
+
+### Python Package
+
+> [!WARNING]
+> The Python module needs external libraries to be installed.
+
+> [!WARNING]
+> Windows users need to have a working [MSYS2](https://www.msys2.org/) environment. See below for more details.
+> For other environments, you need to figure out how to install `gmp` and `mpfr` on your own.
+
+On RPM-based Linux distributions (using `dnf`), if you are:
+
+1. compiling the application from source (or wheels are not
+   available), `sudo dnf install -y gcc-c++ tbb-devel mpfr-devel gmp-devel`
+2. using the packaged binary (wheels are available), `sudo dnf install -y gmp mpfr tbb`
+
+On DEB-based Linux distributions (using `apt`), you need to `sudo apt install -y libtbb-dev libmpfr-dev libgmp-dev`.
+
+On macOS, you need to `brew install tbb mpfr gmp`.
+
+Then install the package with `pip`.
+
+```
+pip install pyvpmr
+```
+
+If the corresponding wheel is not available, the package will be compiled, which takes a few minutes.
+The execution of the algorithm always requires available `gmp`, `mpfr` and `tbb` libraries.
+
+#### Jumpstart
+
+```python
+import numpy as np
+
+from pyvpmr import vpmr, plot
+
+
+def kernel(x):
+    return np.exp(-x ** 2 / 4)
+
+
+if __name__ == '__main__':
+    m, s = vpmr(n=50, k='exp(-t^2/4)')
+    plot(m, s, kernel)
+```
+
+### Compile Binary
+
+> [!WARNING]
+> The application relies on `eigen` and `exprtk`, which depend on very heavy usage of templates.
+> The compilation would take minutes and around 2 GB memory.
+> You need to install libraries `gmp`, `mpfr` and `tbb` before compiling.
+
+#### Windows
+
+Use the following instructions based on [MSYS2](https://www.msys2.org/), or follow the Linux instructions below with
+WSL.
+
+```bash
+# install necessary packages
+pacman -S git mingw-w64-x86_64-cmake mingw-w64-x86_64-tbb mingw-w64-x86_64-gcc mingw-w64-x86_64-ninja mingw-w64-x86_64-gmp mingw-w64-x86_64-mpfr
+# clone the repository
+git clone --depth 1 https://github.com/TLCFEM/vpmr.git
+# initialise submodules
+cd vpmr
+git submodule update --init --recursive
+# apply patch to enable parallel evaluation of some loops in SVD
+cd eigen && git apply --ignore-space-change --ignore-whitespace ../patch_size.patch && cd ..
+# configure and compile
+cmake -G Ninja -DCMAKE_BUILD_TYPE=Release .
+ninja
+```
+
+#### Linux
+
+The following is based on Fedora.
+
+```bash
+sudo dnf install gcc g++ gfortran cmake git -y
+sudo dnf install tbb-devel mpfr-devel gmp-devel -y
+git clone --depth 1 https://github.com/TLCFEM/vpmr.git
+cd vpmr
+git submodule update --init --recursive
+cd eigen && git apply --ignore-space-change --ignore-whitespace ../patch_size.patch && cd ..
+cmake -DCMAKE_BUILD_TYPE=Release .
+make
+```
+
+### Usage
+
+All available options are:
+
+```text
+Usage: vpmr [options]
+
+Options:
+
+   -n <int>     number of terms (default: 10)
+   -d <int>     number of precision bits (default: 512)
+   -q <int>     quadrature order (default: 500)
+   -m <int>     precision multiplier (default: 6)
+   -nc <int>    controls the maximum exponent (default: 4)
+   -e <float>   tolerance (default: 1E-8)
+   -k <string>  file name of kernel function (default: exp(-t^2/4))
+   -s           print singular values
+   -w           print weights
+   -h           print this help message
+```
+
+#### Example
+
+The default kernel is `exp(-t^2/4)`. One can run the application with the following command:
+
+```bash
+./vpmr -n 30
+```
+
+The output is:
+
+```text
+Using the following parameters:
+        nc = 4.
+         n = 30.
+     order = 500.
+ precision = 336.
+ tolerance = 1.0000e-08.
+    kernel = exp(-t*t/4).
+
+[1/6] Computing weights... [60/60]
+[2/6] Solving Lyapunov equation...
+[3/6] Solving SVD...
+[4/6] Transforming (P=+9)...
+[5/6] Solving eigen decomposition...
+[6/6] Done.
+
+M = 
++1.1745193571738943e+01-1.4261645574068720e-100j
+-5.5143304351134397e+00+5.7204056791636839e+00j
+-5.5143304351134397e+00-5.7204056791636839e+00j
+-1.6161617424833762e-02+2.3459542440459513e+00j
+-1.6161617424833762e-02-2.3459542440459513e+00j
++1.6338578576177487e-01+1.9308431539218418e-01j
++1.6338578576177487e-01-1.9308431539218418e-01j
+-5.4905134221689715e-03+2.2104939243740062e-03j
+-5.4905134221689715e-03-2.2104939243740062e-03j
+S = 
++1.8757961592204051e+00-0.0000000000000000e+00j
++1.8700580506914817e+00+6.2013413918954552e-01j
++1.8700580506914817e+00-6.2013413918954552e-01j
++1.8521958553280000e+00-1.2601975249082220e+00j
++1.8521958553280000e+00+1.2601975249082220e+00j
++1.8197653300065935e+00+1.9494562062795735e+00j
++1.8197653300065935e+00-1.9494562062795735e+00j
++1.7655956664692953e+00-2.7555720406099038e+00j
++1.7655956664692953e+00+2.7555720406099038e+00j
+
+Running time: 3 s.
+```
+
+![exp(-t^2/4)](https://raw.githubusercontent.com/TLCFEM/vpmr/master/resource/example.png)
+
+#### Arbitrary Kernel
+
+For arbitrary kernel, it is necessary to provide the kernel function in a text file.
+The file should contain the kernel expressed as a function of variable `t`.
+
+The `exprtk` is used to parse the expression and compute the value.
+The provided kernel function must be valid and supported by `exprtk`.
+
+For example, to compute the approximation of `exp(-t^2/10)`, one can create a file `kernel.txt` with the following
+content:
+
+```text
+exp(-t*t/10)
+```
+
+In the following, the kernel function is echoed to a file and then used as an input to the application.
+
+```bash
+echo "exp(-t*t/10)" > kernel.txt
+ ./vpmr -n 60 -k kernel.txt -e 1e-12
+```
+
+![exp(-t^2/10)](https://raw.githubusercontent.com/TLCFEM/vpmr/master/resource/arbitrary.png)
+
+## Binary
+
+The binary requires available `gmp`, `mpfr` and `tbb` libraries.
+
+```bash
+❯ ldd vpmr
+     linux-vdso.so.1 (0x00007ffcf3121000)
+     libgmp.so.10 => /lib64/libgmp.so.10 (0x00007f72087e8000)
+     libmpfr.so.6 => /lib64/libmpfr.so.6 (0x00007f7208736000)
+     libtbb.so.2 => /lib64/libtbb.so.2 (0x00007f72086f2000)
+     libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f7208400000)
+     libm.so.6 => /lib64/libm.so.6 (0x00007f7208320000)
+     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f72086d0000)
+     libc.so.6 => /lib64/libc.so.6 (0x00007f7208143000)
+     /lib64/ld-linux-x86-64.so.2 (0x00007f72088a1000)
+```
+
+The distributed `appimage` is portable.