Python Hierarchy Implementation

.gitignore

@@ -130,3 +130,9 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# PyCharm
+.idea/
+
+# 2to3 path
+convert_proto.sh

.gitmodules

@@ -1,9 +1,8 @@
-[submodule "pybmix/src/bayesmix"]
-	path = pybmix/core/pybmixcpp/bayesmix
-	url = https://github.com/bayesmix-dev/bayesmix.git
-	depth = 1
-	update = merge
 [submodule "lib/pybind11"]
 	path = lib/pybind11
 	depth = 1
 	url = https://github.com/pybind/pybind11.git
+[submodule "pybmix/core/pybmixcpp/bayesmix"]
+	path = pybmix/core/pybmixcpp/bayesmix
+	url = https://github.com/bayesmix-dev/bayesmix.git
+	depth = 1

CMakeLists.txt

@@ -1,48 +1,48 @@
 cmake_minimum_required(VERSION 3.13.0)
 project(pybmixcpp)
 
-set (CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
 set(COMPILE_OPTIONS -D_REENTRANT -fPIC)
 set(CMAKE_BUILD_TYPE Release)
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -funroll-loops -ftree-vectorize")
 set(CMAKE_FIND_PACKAGE_PREFER_CONFIG TRUE)
 
 
 SET(SOURCE_DIR "${CMAKE_CURRENT_LIST_DIR}/pybmix/core/pybmixcpp")
-add_subdirectory(${SOURCE_DIR}/bayesmix)
+add_subdirectory(${SOURCE_DIR})
 include_directories(${SOURCE_DIR})
 SET_SOURCE_FILES_PROPERTIES(${PROTO_HEADERS} ${PROTO_SOURCES} PROPERTIES GENERATED TRUE)
 
 # Generate python module
 add_subdirectory(lib/pybind11)
 pybind11_add_module(pybmixcpp ${SOURCES}
-    "${SOURCE_DIR}/module.cpp"
-    "${SOURCE_DIR}/algorithm_wrapper.hpp"
-    "${SOURCE_DIR}/algorithm_wrapper.cpp"
-    "${SOURCE_DIR}/serialized_collector.hpp"
-    "${SOURCE_DIR}/serialized_collector.cpp"
-    ${PROTO_HEADERS} ${PROTO_SOURCES})
+        "${SOURCE_DIR}/module.cpp"
+        "${SOURCE_DIR}/algorithm_wrapper.hpp"
+        "${SOURCE_DIR}/algorithm_wrapper.cpp"
+        "${SOURCE_DIR}/serialized_collector.hpp"
+        "${SOURCE_DIR}/serialized_collector.cpp"
+        ${PROTO_HEADERS} ${PROTO_SOURCES})
 
 # generate Python's proto classes
 set(PY_PROTO_DIR "${CMAKE_CURRENT_LIST_DIR}/pybmix/proto")
 set(PROTO_PYS)
 message("ProtoFiles: ${ProtoFiles}")
-foreach(PROTO_FILE IN LISTS ProtoFiles)
-  get_filename_component(PROTO_DIR ${PROTO_FILE} DIRECTORY)
-  get_filename_component(PROTO_NAME ${PROTO_FILE} NAME_WE)
-  set(PROTO_PY ${PY_PROTO_DIR}/${PROTO_NAME}_pb2.py)
-  message(STATUS "GENERATING PYTHON protoc proto(cc): ${PROTO_FILE} --> ${PROTO_PY}")
-  add_custom_command(
-    OUTPUT ${PROTO_PY}
-    COMMAND protobuf::protoc "--proto_path=${SOURCE_DIR}/bayesmix/src/proto"
-    ${PROTO_DIRS} "--python_out=${PY_PROTO_DIR}" ${PROTO_FILE}
-    DEPENDS ${PROTO_FILE} protobuf::protoc
-    COMMENT "Generate Python protocol buffer for ${PROTO_FILE}"
-    VERBATIM)
+foreach (PROTO_FILE IN LISTS ProtoFiles)
+    get_filename_component(PROTO_DIR ${PROTO_FILE} DIRECTORY)
+    get_filename_component(PROTO_NAME ${PROTO_FILE} NAME_WE)
+    set(PROTO_PY ${PY_PROTO_DIR}/${PROTO_NAME}_pb2.py)
+    message(STATUS "GENERATING PYTHON protoc proto(cc): ${PROTO_FILE} --> ${PROTO_PY}")
+    add_custom_command(
+            OUTPUT ${PROTO_PY}
+            COMMAND protobuf::protoc "--proto_path=${SOURCE_DIR}/bayesmix/src/proto"
+            ${PROTO_DIRS} "--python_out=${PY_PROTO_DIR}" ${PROTO_FILE}
+            DEPENDS ${PROTO_FILE} protobuf::protoc
+            COMMENT "Generate Python protocol buffer for ${PROTO_FILE}"
+            VERBATIM)
     list(APPEND PROTO_PYS ${PROTO_PY})
-endforeach()
+endforeach ()
 
-find_package (TBB EXACT PATHS ${TBB_ROOT})
+find_package(TBB EXACT PATHS ${TBB_ROOT})
 find_package(OpenMP REQUIRED)
 
 message("INCLUDE_PATHS" ${INCLUDE_PATHS})
@@ -52,4 +52,5 @@ target_compile_definitions(pybmixcpp PRIVATE VERSION_INFO=${EXAMPLE_VERSION_INFO
 target_link_libraries(pybmixcpp PUBLIC bayesmixlib ${BAYESMIX_LINK_LIBRARIES})
 target_compile_options(pybmixcpp PUBLIC ${BAYESMIX_COMPILE_OPTIONS})
 
-add_custom_target(genterate_protos ALL DEPENDS ${PROTO_PYS})
+add_custom_target(generate_protos ALL DEPENDS ${PROTO_PYS})
+add_custom_target(two_to_three ALL COMMAND ${CMAKE_CURRENT_LIST_DIR}/convert_proto.sh DEPENDS generate_protos)

README.md

@@ -5,20 +5,31 @@ A Python interface to [bayesmix](https://github.com/bayesmix-dev/bayesmix/)
 
 ## Installation
 
-First, clone this repository with its submodules
-```shell
-git clone --recurse-submodule [email protected]:bayesmix-dev/pybmix.git
+1. install ```cmake>=3.21.0``` from source following the official documentation
+2. install ```libtbb-dev=2020.1-2``` (e.g. for Linux ```sudo apt install libtbb-dev=2020.1-2```)
+
+3. clone the repository
 ```
-Ideally things should work by simply typing
-```shell
-pip3 install -e .
+git clone --recurse-submodules [email protected]:bayesmix-dev/pybmix.git
 ```
-from the root folder of this repo.
 
-## Getting Started
+4. setup a python environment with ```python=3.9``` and install the following packages with ```pip```
+```
+pip3 install numpy==1.22.4 scipy==1.7.3 matplotlib==3.5.2 2to3==1.0
+```
 
-See our [tutorials](https://pybmix.readthedocs.io/en/docs/)!
+5. install ```protobuf==3.14.0``` and ```libprotobuf=3.14.0``` (e.g. ```conda install protobuf==3.14.0``` will install both)
 
-## Contributing
 
-Just get in touch with us (email in setup.cfg), open a PR or an Issue! 
+6. add the path for ```2to3``` to the ```PATH``` environment variable, e.g.
+```
+export PYTHONPATH="path/to/2to3/"
+```
+
+7. finally, to build the library
+```
+./build_pybmix.sh build
+```
+
+Note that, the argument ```build``` substitutes ```mkdir build```, thus you can skip it in subsequent builds if only the
+new changes need to be compiled.

build_pybmix.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+
+if [ -z "$1" ]; then
+  cd build/ || exit
+  cmake .. -DDISABLE_DOCS=ON -DDISABLE_BENCHMARKS=ON -DDISABLE_TESTS=ON -DDISABLE_EXAMPLES=ON
+  make pybmixcpp
+  make generate_protos
+  make two_to_three
+else
+  if [[ $1 == build ]]; then
+    rm -rf $1
+    mkdir $1
+    cd $1 || exit
+    cmake .. -DDISABLE_DOCS=ON -DDISABLE_BENCHMARKS=ON -DDISABLE_TESTS=ON -DDISABLE_EXAMPLES=ON
+    make pybmixcpp
+    make generate_protos
+    make two_to_three
+  else
+    echo "wrong argument, pass build"
+  fi
+fi

convert_proto.sh

@@ -0,0 +1,4 @@
+SCRIPT_DIR=$(pwd)/..
+
+# 2to3 must be in the path (e.g. export PYTHONPATH="path/to/2to3/")
+2to3 --output-dir=$SCRIPT_DIR/pybmix/proto -W -n $SCRIPT_DIR/pybmix/proto

docs/conf.py

@@ -12,12 +12,11 @@
 #
 import os
 import sys
+
 sys.path.insert(0, os.path.abspath('.'))
 sys.path.insert(0, os.path.abspath('../'))
 sys.path.insert(0, os.path.join(os.path.abspath('../'),
-                                "pybmix/core/pybmixcpp/bayesmix"))
-
-
+                                "pybmix/core/pybmixcpp/bayesmix_"))
 
 # -- Project information -----------------------------------------------------
 
@@ -28,7 +27,6 @@
 # The full version, including alpha/beta/rc tags
 release = '0.0.1'
 
-
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
@@ -53,7 +51,7 @@
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
-    '_build', 'Thumbs.db', '.DS_Store', '../lib', 
+    '_build', 'Thumbs.db', '.DS_Store', '../lib',
     '../pybmix/core/pybmixcpp']
 
 # html_extra_path = ["protos.html"]