Move some files around (#14)

* Update CMakeLists.txt

* Move examples to a new folder.
Change the location of some installation headers

* Update CI

* Update READMEs

* Update README

.github/workflows/ci.yml

@@ -50,6 +50,13 @@ jobs:
         mkdir build && cd build
         cmake -DCMAKE_VERBOSE_MAKEFILE=yes -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX ..
         make -j3 all install
+
+    - name: Compile examples
+      run: |
+        micromamba activate libmobility
+        mkdir examples/cpp/build && cd examples/cpp/build
+        cmake -DCMAKE_VERBOSE_MAKEFILE=yes -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX ..
+        make -j3
         
     - name: Try to import libMobility
       run: |

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "third_party/uammd"]
-	path = third_party/uammd
+	path = include/third_party/uammd
 	url = https://github.com/raulppelaez/uammd
 [submodule "third_party/LanczosAlgorithm"]
-	path = third_party/LanczosAlgorithm
+	path = include/third_party/LanczosAlgorithm
 	url = https://github.com/Raulppelaez/LanczosAlgorithm

CMakeLists.txt

@@ -1,18 +1,20 @@
-cmake_minimum_required(VERSION 3.22)
+cmake_minimum_required(VERSION 3.24)
 project(libMobility)
 enable_language(CUDA)
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/" "$ENV{CONDA_PREFIX}/share/cmake/Modules")
 set(CMAKE_BUILD_TYPE Release)
 
-#add_compile_definitions(PUBLIC MAXLOGLEVEL=15)
+add_compile_definitions(PUBLIC MAXLOGLEVEL=3)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CUDA_STANDARD 14)
 set(CMAKE_CUDA_STANDARD_REQUIRED ON)
 set(CMAKE_CUDA_SEPARABLE_COMPILATION OFF)
+# Set CUDA archs so all supported GPUs are covered
+set(CMAKE_CUDA_ARCHITECTURES "all")
 
 #add_compile_definitions(PUBLIC DOUBLE_PRECISION)
-set(UAMMD_INCLUDE third_party/uammd/src third_party/uammd/src/third_party)
+set(UAMMD_INCLUDE include/third_party/uammd/src include/third_party/uammd/src/third_party)
 # When UAMMD is available in conda-forge, use the following lines to find it instead of the above
 # find_package(UAMMD REQUIRED)
 # set(UAMMD_INCLUDE ${UAMMD_INCLUDE_DIR})
@@ -57,7 +59,7 @@ endif()
 find_package(Python3 REQUIRED COMPONENTS Interpreter Development)
 include_directories(${Python3_INCLUDE_DIRS})
 include_directories(${UAMMD_INCLUDE} ${BLAS_INCLUDE_DIRS} ${LAPACKE_INCLUDE_DIRS})
-include_directories(third_party/LanczosAlgorithm/include)
+include_directories(include/third_party/LanczosAlgorithm/include)
 include_directories(include)
 link_libraries(${CUDA_LIBRARY})
 if(CMAKE_CUDA_COMPILER_ID STREQUAL "NVIDIA")
@@ -81,6 +83,6 @@ IF (CMAKE_BUILD_TYPE MATCHES "Debug")
 ENDIF()
 
 # Install headers under include/ to the CMAKE_INSTALL_PREFIX include directory
-install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
-install(DIRECTORY third_party/LanczosAlgorithm/include/ DESTINATION ${CMAKE_INSTALL_PREFIX}/include/MobilityInterface)
-install(DIRECTORY third_party/uammd/src/ DESTINATION ${CMAKE_INSTALL_PREFIX}/include/uammd/src)
+install(DIRECTORY include/MobilityInterface DESTINATION ${CMAKE_INSTALL_PREFIX}/include/)
+install(DIRECTORY include/third_party/LanczosAlgorithm/include/ DESTINATION ${CMAKE_INSTALL_PREFIX}/include/MobilityInterface/)
+install(DIRECTORY include/third_party/uammd/src/ DESTINATION ${CMAKE_INSTALL_PREFIX}/include/uammd/src)

README.md

@@ -15,14 +15,24 @@ For each solver, a python and a C++ interface are provided. All solvers have the
 
 Some of the solvers have different functionalities than the others. For instance, some modules accept torques while others don't. The documentation for a particular solver must be visited to know more.  
 
-## How this repository is organized
+## Repository Structure  
 
-The directory **solvers** contains a subfolder for each module. The folder for each solver the implementation of the libMobility interface for that solver.  
-The directory **python** contains the file libMobility.py, which can be imported giving access to all the compiled modules.  
-The directory **cpp** contains an example usage of the C++ interface to the modules.  
-The directory **include** contains the C++ base class and utilities used to construct the modules.  
+This repository is organized into the following directories:  
+
+- **solvers/**: This directory hosts a subfolder for each solver module. Each subfolder contains the implementation of the `libMobility` interface specific to that solver.  
+
+- **examples/**: Contains examples on how to use the library from Python and C++.  
+
+- **include/**: Includes the essential C++ base classes and utility files needed to construct the modules.  
+
+- **conda/**: Contains a meta.yaml file to build a conda package for libMobility using conda-build.  
+
+- **docs/**: Contains the source files for the documentation.  
+
+- **tests/**: Contains the tests for the library.  
 
 ## The libMobility interface
+
 Each solver is encased in a single class which is default constructible (no arguments required for its constructor).  
 Each solver provides the following set of functions (called the same in C++ and python and described here in a kind of language agnostic way):  
   * **[Constructor] (configuration)**: The solver constructors must be provided with a series of system-related parameters (see below).  

conda/README.md

@@ -0,0 +1,13 @@
+## Conda package
+
+Create a conda package for libMobility with the following steps:
+
+1. Install conda-build and conda-verify:
+```bash
+conda install conda-build
+```
+
+2. Build the package:
+```bash
+conda build .
+```

cpp/CMakeLists.txt → examples/cpp/CMakeLists.txt

@@ -8,7 +8,7 @@ set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CUDA_STANDARD 14)
 set(CMAKE_CUDA_STANDARD_REQUIRED ON)
 set(CMAKE_CUDA_SEPARABLE_COMPILATION OFF)
-set(UAMMD_INCLUDE third_party/uammd/src third_party/uammd/src/third_party)
+set(UAMMD_INCLUDE include/third_party/uammd/src include/third_party/uammd/src/third_party)
 set(BLA_STATIC OFF)
 set(BLA_VENDOR Intel10_64lp)
 find_package(BLAS)

cpp/README.md → examples/cpp/README.md

@@ -4,10 +4,16 @@ The code example.cpp showcases how a solver can be included and used with libMob
 
 
 ### Compilation
-In order to succesfully compile example.cpp, ensure the Makefile in the root directory of the repo has generated the libraries for all the modules used (in this case ../solvers/NBody/mobility.so and ../solvers/PSE/mobility.so).  
 
-It is required to compile using the same precision as the libraries, so modify the Makefile if necessary (single precision is the default).  
-Running the Makefile at the root folder, instead of the one directly in this folder, will take care of that.
+After [installing libMobility](https://libmobility.readthedocs.io) you can use CMake to compile this file:
+
+```bash
+	mkdir build
+	cd build
+	cmake ..
+	make
+```
+
 
 ### Running
 A valid CUDA environment and a GPU are needed to run the example.  

cpp/example.cpp → examples/cpp/example.cpp

@@ -2,9 +2,9 @@
  All available solvers are used in a similar way, providing, in each case, the required parameters.
  For instance, a triply periodic algorithm will need at least a box size.
  */
-#include "MobilityInterface/MobilityInterface.h"
-#include"../solvers/NBody/mobility.h"
-#include"../solvers/PSE/mobility.h"
+#include"MobilityInterface/MobilityInterface.h"
+#include"libMobility/solvers/NBody/mobility.h"
+#include"libMobility/solvers/PSE/mobility.h"
 #include <type_traits>
 #include<vector>
 #include<random>