major changes - LorentzAttractor should again work

Author: kadeslu

.github/workflows/build.yml

@@ -1,98 +0,0 @@
-name: Build and Test
-
-on:
-  push:
-    branches: [ main, master, develop ]
-  pull_request:
-    branches: [ main, master ]
-  release:
-    types: [published]
-
-jobs:
-  test:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        cuda-version: ["11.8", "12.1"]
-
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: recursive
-
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install CUDA Toolkit
-      if: matrix.os == 'ubuntu-latest'
-      uses: Jimver/[email protected]
-      with:
-        cuda: ${{ matrix.cuda-version }}
-
-    - name: Install system dependencies
-      if: matrix.os == 'ubuntu-latest'
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y cmake build-essential ninja-build libboost-all-dev
-        
-    - name: Install Python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build wheel setuptools cmake pybind11 ninja
-        pip install pytest pytest-cov numpy matplotlib scipy
-
-    - name: Build package (superbuild)
-      run: |
-        python -m build --wheel
-        
-    - name: Install package
-      run: |
-        pip install dist/*.whl
-
-    - name: Run tests
-      run: |
-        pytest odevis/python/tests/ -v
-
-  build-wheel:
-    if: github.event_name == 'release'
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: recursive
-
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"
-
-    - name: Install CUDA Toolkit
-      uses: Jimver/[email protected]
-      with:
-        cuda: "12.1"
-
-    - name: Install system dependencies
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y cmake build-essential ninja-build libboost-all-dev
-
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build twine cmake pybind11 ninja
-
-    - name: Build wheel
-      run: |
-        python -m build
-
-    - name: Upload to PyPI
-      env:
-        TWINE_USERNAME: __token__
-        TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
-      run: |
-        twine upload dist/*

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: C++ CI
+name: CI
 
 on:
   # We run CI on pushes to the main branch
@@ -14,35 +14,31 @@ on:
 
 jobs:
   build-and-test:
-    name: C++ Testing on ${{matrix.os}}
+    name: Testing on ${{matrix.os}}
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-18.04, macos-10.15]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v2
+
       with:
         submodules: 'recursive'
 
-    - name: Install system dependencies (Ubuntu)
-      if: runner.os == 'Linux'
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y cmake build-essential ninja-build libboost-all-dev
-
-    - name: Install system dependencies (macOS)
-      if: runner.os == 'macOS'
+    - name: upgrade g++ compiler on ubuntu
       run: |
-        brew install cmake ninja boost
+        sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-9 10
+        sudo update-alternatives --set g++ /usr/bin/g++-9
+      if: runner.os == 'Linux'
 
     - name: make build directory
       run: cmake -E make_directory ${{runner.workspace}}/build
 
     - name: configure cmake
       shell: bash
       working-directory: ${{runner.workspace}}/build
-      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DBUILD_DOCS=OFF -DBUILD_PYTHON_BINDINGS=OFF
+      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Debug -DBUILD_DOCS=OFF
 
     - name: build
       shell: bash
@@ -56,26 +52,30 @@ jobs:
 
 
   coverage-test:
-    name: C++ Coverage Testing
-    runs-on: ubuntu-latest
+    name: Coverage Testing
+    runs-on: ubuntu-18.04
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v2
       with:
         submodules: 'recursive'
 
-    - name: Install dependencies
+    - name: Install LCov
+      run: |
+        sudo apt-get install -y lcov
+
+    - name: upgrade g++ compiler on ubuntu
       run: |
-        sudo apt-get update
-        sudo apt-get install -y lcov cmake build-essential ninja-build libboost-all-dev
+        sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-9 10
+        sudo update-alternatives --set g++ /usr/bin/g++-9
 
     - name: make build directory
       run: cmake -E make_directory ${{runner.workspace}}/build
 
     - name: configure cmake
       shell: bash
       working-directory: ${{runner.workspace}}/build
-      run: cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="--coverage" -DBUILD_DOCS=OFF -DBUILD_PYTHON_BINDINGS=OFF
+      run: cmake $GITHUB_WORKSPACE -DCMAKE_CXX_FLAGS="--coverage" -DBUILD_DOCS=OFF
 
     - name: build
       shell: bash

.github/workflows/sonarcloud.yml

@@ -18,7 +18,7 @@ jobs:
     name: SonarCloud
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
           submodules: 'recursive'

.gitignore

@@ -1,75 +1,24 @@
-# Python build artifacts
-__pycache__/
-*.py[cod]
-*$py.class
-*.so
-*.egg-info/
-dist/
-build/
-.eggs/
-*.egg
-
-# LaTeX build artifacts
 *.aux
 *.log
 *.out
 *.synctex.gz
 *.toc
 *.pyc
+*.so
+*.egg-info/
 
-# CMake build artifacts
-CMakeCache.txt
-CMakeFiles/
-cmake_install.cmake
-Makefile
-install_manifest.txt
-*.cmake
-!*Config.cmake.in
-*-prefix/
-*-build/
-
-# Compiled extensions
-*.dll
-*.dylib
-*.pyd
-
-# IDE files
-.vscode/
-.idea/
-*.swp
-*.swo
-
-# OS files
-.DS_Store
-Thumbs.db
-
-# Testing
-.pytest_cache/
-.coverage
-htmlcov/
-
-# Virtual environments
-venv/
-env/
-.env
-
-# Temporary files
-*.tmp
-*.bak
-*~
-
-# Build directories
-build/
-install/
-cmake_install/
-ODEVisualizationLib.egg-info/
-
-# Documentation source (keep only specific files)
 doc/source/*
 !doc/source/figures/
 !doc/source/report.tex
 !doc/source/references.bib
 
+build/
+install/
+.vscode/
+.idea/
+__pychache__/
+ODEVisualizationLib.egg-info/
+
 examples/applications/c++/*
 !examples/applications/c++/CMakeLists.txt
 !examples/applications/c++/include
@@ -107,3 +56,6 @@ examples/further_systems/FourPointSystem/*
 !examples/further_systems/FourPointSystem/src
 
 config.h
+odevis/cmake_install/
+
+examples/flow_equations/Betafunctionsyukawa/

.readthedocs.yml

@@ -1,7 +1,7 @@
 version: 2
 
 sphinx:
-  configuration: odevis/doc/conf.py
+  configuration: doc/conf.py
 
 formats: all
 
@@ -11,4 +11,4 @@ submodules:
 
 python:
   install:
-    - requirements: odevis/doc/requirements-rtd.txt
+    - requirements: doc/requirements-rtd.txt

CMakeLists.txt

@@ -33,7 +33,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 # Setup install directories for the external projects
-set(SUPERBUILD_INSTALL_DIR ${CMAKE_BINARY_DIR}/installed)
+set(SUPERBUILD_INSTALL_DIR ${CMAKE_BINARY_DIR}/installed CACHE PATH "Directory where superbuild dependencies are installed")
 set(CMAKE_PREFIX_PATH ${SUPERBUILD_INSTALL_DIR} ${CMAKE_PREFIX_PATH})
 
 # Find Boost (required)
@@ -53,6 +53,10 @@ FetchContent_MakeAvailable(nlohmann_json)
 # Store the nlohmann/json path to pass to dependencies
 get_target_property(JSON_INCLUDE_DIR nlohmann_json::nlohmann_json INTERFACE_INCLUDE_DIRECTORIES)
 
+# Copy nlohmann/json headers to superbuild directory immediately for examples to use
+file(COPY ${nlohmann_json_SOURCE_DIR}/include/nlohmann 
+     DESTINATION ${SUPERBUILD_INSTALL_DIR}/include)
+
 # 1. devdat library
 if(USE_SYSTEM_DEVDAT)
     find_package(devdat REQUIRED)

MANIFEST.in

@@ -7,19 +7,17 @@ include pyproject.toml
 recursive-include . CMakeLists.txt
 recursive-include cmake *.cmake.in
 recursive-include cmake *.cmake
-recursive-include odevis/cmake *.cmake.in
-recursive-include odevis/cmake *.cmake
 
 # Include all source files
-recursive-include odevis/src *.cpp *.cu *.hpp *.h
-recursive-include odevis/include *.hpp *.h
-recursive-include odevis/python *.cpp *.cu *.hpp *.h *.py
+recursive-include src *.cpp *.cu *.hpp *.h
+recursive-include include *.hpp *.h
+recursive-include python *.cpp *.cu *.hpp *.h *.py
 
 # Include flow equation wrapper
-graft odevis/python/flow_equation_wrapper/
+graft python/flow_equation_wrapper/
 
 # Include test files
-recursive-include odevis/tests *.py *.cpp *.cu *.hpp *.h
+recursive-include tests *.py *.cpp *.cu *.hpp *.h
 
 # Exclude build artifacts and temporary files
 global-exclude *.pyc
@@ -34,4 +32,4 @@ global-exclude build/*
 global-exclude *.egg-info/*
 
 # Include package data files
-recursive-include odevis/python *.json *.yaml *.yml
+recursive-include python *.json *.yaml *.yml

README.md

@@ -128,8 +128,8 @@ If you use ODEVisualization in your research, please cite:
 
 ```bibtex
 @software{odevisualization,
-  title={ODEVisualization: GPU-Accelerated Analysis of Ordinary Differential Equations},
-  author={Kades, Lukas},
+  title={ODE Visualization: GPU-Accelerated Analysis of Ordinary Differential Equations for the Functional Renormalization Group},
+  author={Kades, Lukas; Sadlo, Filip; Pawlowski, Jan M.}
   url={https://github.com/statphysandml/ODEVisualization},
   version={1.0.0},
   year={2025}

examples/applications/python/evolution_t.py

@@ -1,4 +1,4 @@
-from lorentzattractor.lorentz_attractor import LorentzAttractor
+from lorentz_attractor import LorentzAttractor
 
 # from odesolver.observers import TrajectoryObserver, IntersectionObserver
 

examples/applications/python/experiments.py

@@ -1,7 +1,7 @@
 import numpy as np
 from odesolver.coordinates import Coordinates
 
-from lorentzattractor.lorentz_attractor import LorentzAttractor
+from lorentz_attractor import LorentzAttractor
 
 from odesolver.recursive_search import RecursiveSearch