V2 wip

.github/cpp.yml

@@ -0,0 +1,45 @@
+name: C++ test
+
+on:
+  workflow_dispatch:
+  push:
+    branches: ["v2_wip"]
+    paths:
+      - ".github/workflows/cpp.yml"
+  pull_request:
+    branches: ["v2_wip"]
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-latest, ubuntu-latest]
+        python-version: ["3.10", "3.11"]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Add requirements
+      run: python -m pip install --upgrade wheel setuptools numpy gsd networkx biopython matplotlib
+
+    - name: build and install python module
+      run: pip install --verbose .
+
+    - name: build cpp tests
+      run: |
+        cmake -S tests/cpp -B build/ -DpatchyAnalysisTools_ROOT=$(python -m patchyAnalysisTools --cmakefiles)
+        cmake --build build/
+
+    - name: run cpp tests
+      run: |
+        cd build/
+        ctest

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/pip.yml

@@ -0,0 +1,40 @@
+name: Pip
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - v2_wip
+    paths:
+      - ".github/workflows/pip.yml"
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-latest, ubuntu-latest]
+        python-version: ["3.11"]
+
+    runs-on: ${{ matrix.platform }}
+
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Add requirements
+      run: python -m pip install --upgrade wheel setuptools numpy gsd networkx biopython matplotlib
+
+    - name: Build and install
+      run: pip install --verbose .[test]
+
+    - name: Test
+      run: |
+        cd tests
+        python -m pytest

.gitignore

@@ -6,3 +6,6 @@ eggs/
 build/
 dist/
 */__pycache__/
+_skbuild
+.pytest_cache
+*/*.egg-info

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "pybind11"]
+    path = pybind11
+    url = https://github.com/pybind/pybind11.git
+    branch = master

.vscode/settings.json

@@ -0,0 +1,95 @@
+{
+    "files.associations": {
+        "array": "cpp",
+        "atomic": "cpp",
+        "bit": "cpp",
+        "*.tcc": "cpp",
+        "cctype": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "compare": "cpp",
+        "concepts": "cpp",
+        "cstdarg": "cpp",
+        "cstddef": "cpp",
+        "cstdint": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "deque": "cpp",
+        "string": "cpp",
+        "unordered_map": "cpp",
+        "vector": "cpp",
+        "exception": "cpp",
+        "algorithm": "cpp",
+        "functional": "cpp",
+        "iterator": "cpp",
+        "memory": "cpp",
+        "memory_resource": "cpp",
+        "numeric": "cpp",
+        "random": "cpp",
+        "string_view": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "utility": "cpp",
+        "fstream": "cpp",
+        "initializer_list": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "new": "cpp",
+        "numbers": "cpp",
+        "ostream": "cpp",
+        "sstream": "cpp",
+        "stdexcept": "cpp",
+        "streambuf": "cpp",
+        "typeinfo": "cpp",
+        "__bit_reference": "cpp",
+        "__bits": "cpp",
+        "__config": "cpp",
+        "__debug": "cpp",
+        "__errc": "cpp",
+        "__hash_table": "cpp",
+        "__locale": "cpp",
+        "__mutex_base": "cpp",
+        "__node_handle": "cpp",
+        "__split_buffer": "cpp",
+        "__threading_support": "cpp",
+        "__tree": "cpp",
+        "__tuple": "cpp",
+        "__verbose_abort": "cpp",
+        "bitset": "cpp",
+        "charconv": "cpp",
+        "codecvt": "cpp",
+        "complex": "cpp",
+        "condition_variable": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "format": "cpp",
+        "forward_list": "cpp",
+        "iomanip": "cpp",
+        "ios": "cpp",
+        "list": "cpp",
+        "locale": "cpp",
+        "map": "cpp",
+        "mutex": "cpp",
+        "optional": "cpp",
+        "queue": "cpp",
+        "ratio": "cpp",
+        "semaphore": "cpp",
+        "set": "cpp",
+        "span": "cpp",
+        "stack": "cpp",
+        "thread": "cpp",
+        "typeindex": "cpp",
+        "unordered_set": "cpp",
+        "valarray": "cpp",
+        "variant": "cpp",
+        "__nullptr": "cpp",
+        "__string": "cpp",
+        "chrono": "cpp"
+    },
+    "cmake.configureOnOpen": true
+}

CMakeLists.txt

@@ -0,0 +1,84 @@
+cmake_minimum_required(VERSION 3.15..3.26)
+
+set(CMAKE_CXX_STANDARD 20)
+
+
+project(
+    patchyAnalysisTools
+    VERSION "2.0.0"
+    LANGUAGES CXX)
+
+include(GNUInstallDirs)
+
+file (GLOB SOURCE_FILES "${PROJECT_SOURCE_DIR}/src/*.cpp")
+
+
+# define the C++ library "patchyAnalysisTools"
+add_library(patchyAnalysisTools SHARED ${SOURCE_FILES})
+
+target_include_directories(
+    patchyAnalysisTools PUBLIC $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
+                 $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+
+install(DIRECTORY "${PROJECT_SOURCE_DIR}/include/"
+        DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+
+install(
+  TARGETS patchyAnalysisTools
+  EXPORT patchyAnalysisToolsTargets
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+
+set(PATCHYANALYSISTOOLS_CMAKE_PACKAGE_INSTALL_SUBDIR "share/patchyAnalysisTools/cmake")
+
+install(
+  EXPORT patchyAnalysisToolsTargets
+  DESTINATION ${PATCHYANALYSISTOOLS_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+include(CMakePackageConfigHelpers)
+
+write_basic_package_version_file(
+  patchyAnalysisToolsConfigVersion.cmake
+  VERSION ${PROJECT_VERSION}
+  COMPATIBILITY SameMinorVersion)
+
+configure_package_config_file(
+  "${PROJECT_SOURCE_DIR}/cmake/patchyAnalysisToolsConfig.cmake.in" patchyAnalysisToolsConfig.cmake
+  INSTALL_DESTINATION ${PATCHYANALYSISTOOLS_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+install(FILES "${PROJECT_BINARY_DIR}/patchyAnalysisToolsConfig.cmake"
+              "${PROJECT_BINARY_DIR}/patchyAnalysisToolsConfigVersion.cmake"
+        DESTINATION ${PATCHYANALYSISTOOLS_CMAKE_PACKAGE_INSTALL_SUBDIR})
+
+# if called by scikit-build
+if(DEFINED SKBUILD)
+
+  # call pybind11-config to obtain the root of the cmake package
+  execute_process(COMMAND ${PYTHON_EXECUTABLE} -m pybind11 --cmakedir
+                  OUTPUT_VARIABLE pybind11_ROOT_RAW)
+  string(STRIP ${pybind11_ROOT_RAW} pybind11_ROOT)
+  find_package(pybind11)
+
+  pybind11_add_module(_patchyAnalysisTools MODULE
+                      "${PROJECT_SOURCE_DIR}/src/patchyAnalysisTools/patchyAnalysisTools_py.cpp")
+
+  target_link_libraries(_patchyAnalysisTools PRIVATE patchyAnalysisTools)
+
+  # Installing the extension module to the root of the package
+  install(TARGETS _patchyAnalysisTools DESTINATION .)
+
+  configure_file("${PROJECT_SOURCE_DIR}/src/patchyAnalysisTools/__main__.py.in"
+                 "${PROJECT_BINARY_DIR}/src/patchyAnalysisTools/__main__.py")
+
+  install(FILES "${PROJECT_BINARY_DIR}/src/patchyAnalysisTools/__main__.py" DESTINATION .)
+
+
+  if(APPLE)
+    set_target_properties(
+        _patchyAnalysisTools PROPERTIES INSTALL_RPATH "@loader_path/${CMAKE_INSTALL_LIBDIR}")
+  else()
+    set_target_properties(_patchyAnalysisTools PROPERTIES INSTALL_RPATH
+                                            "$ORIGIN/${CMAKE_INSTALL_LIBDIR}")
+  endif()
+
+endif()

README.md

@@ -1,78 +1,9 @@
 # patchyAnalysisTools
 
-A set of tools to analyze the output of patchy particle simulations. Works with a very specific format of trajectory files, but the I/O methods can be extended for the analysis tools to work on arbitrary trajectory file formats. See examples for details.
+(In the process of rewriting the whole thing in C++, with python bindings, to support efficient calculation of various trajectory-wide quantities).
 
-## Installation
-
-	git clone https://github.com/sodiumnitrate/patchyAnalysisTools.git
-	cd patchyAnalysisTools
-	python setup.py install
-
-## Examples
-
-(See the `examples` folder for more details.)
-
-### Loading the module
-
-You can load the module as 
-
-	import patchyAnalysisTools.trajectory as trj
-
-The following examples all use the alias `trj` for the module.
-
-### Loading trajectories
-
-To load a trajectory:
-
-	traj = trj.trajectory(file_name="traj.conf")
-
-where `traj.conf` is a trajectory file with specific formatting requirements (see examples). Patch information is then read from a file and set for the `traj` object by
-
-	traj.set_patch_info("patches.dat")
-
-where `patches.dat` is again a special file (see examples). _Some_ analysis can be done without reading and setting patch information, but most require this for determining bonds, etc.
-
-### Selecting frames or subtrajectories
-
-To select the last frame:
-
-	last_frame = traj.get_last_frame()
-
-To select an arbitrary frame:
-
-	frame = traj.get_frame(10)
-
-To select a range of frames:
-
-	subtraj = traj.get_frame(10,20)
-
-### Bonding and cluster info
-
-Determination of bonding and cluster information requires the patches to have been set in the trajectory before a frame is selected (see above).
-
-First, we determine bonds:
-
-	frame.get_list_of_interacting_pairs()
-
-If the trajectory file has the number of bonds per particle written, we can double check the calculated bonds against these values:
-
-	frame.check_calculated_bonds_against_bond_numbers()
-
-We then determine the clusters by
-
-	frame.set_cluster_info()
-
-To find the percolating clusters:
-
-	frame.find_percolating_clusters()
-
-To check if system is percolated:
-
-	frame.is_system_percolated()
-
-which returns a boolean.
-
-## What's missing
-The main thing that is incomplete in this package is support for the output of Gibbs-Ensemble simulations (which contain two boxes). Some of the tools in this package support it, some don't. I may complete it at one point, but for now, everything is only tested for regular simulation outputs.
-
-It is also important to note that not all the tools in this package are thoroughly tested for simulation output with non-cubic boxes.
+## TODO:
+1. GSD C API. Handling things on the python side for now.
+2. Proper error handling from the C++ side, visible to python as well. Using `throw`s for now.
+3. ~~C++-level tests. Sticking to `pytest` for now.~~
+4. Libraries for rotations.

cmake/patchyAnalysisToolsConfig.cmake.in

@@ -0,0 +1,3 @@
+@PACKAGE_INIT@
+
+include("${CMAKE_CURRENT_LIST_DIR}/patchyAnalysisToolsTargets.cmake")