Merge branch 'master' into imp/205-custom-template-index-pattern

.black.cfg

@@ -1,4 +1,4 @@
 [tool.black]
 line-length = 100
-target-version = ['py38']
+target-version = ['py310']
 skip-string-normalization = true

.github/workflows/publish-pypi.yml

@@ -48,7 +48,7 @@ jobs:
 
   publish-cpp:
     needs: tag
-    environment: prod
+    environment: prod-cpp
     runs-on: ubuntu-22.04
     steps:
       - name: Checkout code
@@ -65,7 +65,7 @@ jobs:
 
       - name: Update version
         working-directory: hyperon_das_atomdb_cpp
-        run: sed -i 's/version = ".*"/version = "${{ github.event.inputs.version }}"/' pyproject.toml
+        run: sed -i 's/^version = ".*"/version = "${{ github.event.inputs.version }}"/' pyproject.toml
 
       - name: Build Wheels
         working-directory: hyperon_das_atomdb_cpp

.gitignore

@@ -14,7 +14,7 @@ dist/
 downloads/
 eggs/
 .eggs/
-lib/
+./lib/
 lib64/
 parts/
 sdist/

cpp/Makefile

@@ -0,0 +1,23 @@
+format:
+	@find ./lib/include ./lib/src ./nanobind/include ./nanobind/src \
+		-iname "*.hpp" -o \
+		-iname "*.cpp" -o \
+		-iname "*.hh" -o \
+		-iname "*.cc" -o \
+		-iname "*.h" -o \
+		-iname "*.c" \
+		| xargs clang-format -verbose -style=file -i
+
+packer-images:
+	@./scripts/build_glibc_packer_docker_image.sh
+	@./scripts/build_musl_packer_docker_image.sh
+
+packs: packer-images
+	@./scripts/run_glibc_packer.sh
+	@./scripts/run_musl_packer.sh
+
+install:
+	@./scripts/build_glibc_packer_docker_image.sh
+	@./scripts/run_glibc_packer.sh
+	@pip install ./nanobind/dist/hyperon_das_atomdb_cpp*manylinux*.whl --force-reinstall --no-cache-dir
+

hyperon_das_atomdb_cpp/deps/requirements.txt → cpp/deps/requirements.txt

@@ -2,3 +2,4 @@ wheel>=0.37.1
 nanobind>=2.1.0
 scikit-build-core>=0.10
 auditwheel>=6.1.0
+

hyperon_das_atomdb_cpp/docker/Dockerfile.musl.wheeler → cpp/docker/Dockerfile.common.packer

@@ -1,14 +1,11 @@
-# See https://github.com/pypa/manylinux for more information
-FROM quay.io/pypa/musllinux_1_2_x86_64
-
-ENV MBEDTLS_VERSION=3.6.2
-ENV PYTHON_PATH=/opt/python/cp310-cp310
-ENV PYTHON_EXECUTABLE=${PYTHON_PATH}/bin/python3.10
+ARG BASE_IMAGE="empty"
+FROM ${BASE_IMAGE}
 
 COPY ./deps /tmp/deps
 
+ENV MBEDTLS_VERSION=3.6.2
+
 # Install `mbedtls` from source
-# (there was no pre-built package available in the AlmaLinux repos)
 RUN cd /tmp \
     && tar jxf ./deps/mbedtls-${MBEDTLS_VERSION}.tar.bz2 \
     && cd mbedtls-${MBEDTLS_VERSION} \
@@ -20,10 +17,11 @@ RUN cd /tmp \
     && make install \
     && rm -rf /tmp/mbedtls-${MBEDTLS_VERSION}
 
+ENV PYTHON_PATH=/opt/python/cp310-cp310
+ENV PYTHON_EXECUTABLE=${PYTHON_PATH}/bin/python3.10
+
 RUN ${PYTHON_EXECUTABLE} -m pip install -r /tmp/deps/requirements.txt
 
 RUN rm -rf /tmp/deps
 
 WORKDIR /hyperon_das_atomdb_cpp
-
-CMD ["bash", "-x", "./scripts/_build_musl_wheel.sh"]

cpp/docker/Dockerfile.glibc.packer

@@ -0,0 +1,6 @@
+# See https://github.com/pypa/manylinux for more information
+FROM quay.io/pypa/manylinux_2_28_x86_64
+
+RUN dnf install -y rpm-build
+
+CMD ["bash", "-x", "./scripts/_build_glibc_packs.sh"]

cpp/docker/Dockerfile.musl.packer

@@ -0,0 +1,4 @@
+# See https://github.com/pypa/manylinux for more information
+FROM quay.io/pypa/musllinux_1_2_x86_64
+
+CMD ["bash", "-x", "./scripts/_build_musl_packs.sh"]

cpp/lib/.gitignore

@@ -0,0 +1,3 @@
+build/
+dist/
+

cpp/lib/CMakeLists.txt

@@ -0,0 +1,83 @@
+cmake_minimum_required(VERSION 3.15...3.30)
+
+if(DEFINED CMAKE_PROJECT_VERSION AND NOT "${CMAKE_PROJECT_VERSION}" STREQUAL "")
+  set(LIB_VERSION ${CMAKE_PROJECT_VERSION})
+else()
+  message(FATAL_ERROR "CMAKE_PROJECT_VERSION is not defined or is empty")
+endif()
+
+if(NOT DEFINED TARGET_TYPE OR "${TARGET_TYPE}" STREQUAL "")
+  message(FATAL_ERROR "TARGET_TYPE is not defined or is empty")
+endif()
+
+set(namespace "atomdb")
+project(
+  "hyperon_das_atomdb_cpp"
+  VERSION ${LIB_VERSION}
+  DESCRIPTION "Atom Space DB for Hyperon DAS"
+)
+
+set(CPACK_PACKAGE_NAME "${PROJECT_NAME}-dev")
+
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -Ofast")
+set(CMAKE_VERBOSE_MAKEFILE ON)
+
+add_library(${PROJECT_NAME} STATIC)
+
+# Detect the installed mbedtls static library and import it into hyperon_das_atomdb_cpp
+if(EXISTS /usr/local/lib/libmbedcrypto.a)
+  set(LIBMBCRYPTO_PATH /usr/local/lib/libmbedcrypto.a)
+elseif(EXISTS /usr/local/lib64/libmbedcrypto.a)
+  set(LIBMBCRYPTO_PATH /usr/local/lib64/libmbedcrypto.a)
+else()
+  message(FATAL_ERROR "libmbedcrypto.a not found in /usr/local/lib or /usr/local/lib64")
+endif()
+
+# This step is required to embed the `mbedtls` library into the `hyperon_das_atomdb_cpp` static
+# library. This is done to avoid the need to install the `mbedtls` library on the target system.
+# Teoretically, it would be possible to do the same with just `CMAKE_CXX_ARCHIVE_CREATE`, but it
+# does not work as expected due to some limitations related to the number of files that can be
+# passed as objects.
+set(MBCRYPTO_SYMBOLS_PATH ${CMAKE_BINARY_DIR}/mbedcrypto_symbols)
+make_directory(${MBCRYPTO_SYMBOLS_PATH})
+execute_process(COMMAND ar x ${LIBMBCRYPTO_PATH} --output=${MBCRYPTO_SYMBOLS_PATH})
+file(GLOB mbedcrypto_symbols ${MBCRYPTO_SYMBOLS_PATH}/*.o)
+set(CREATE_STATIC_LIB_SCRIPT ${PROJECT_SOURCE_DIR}/scripts/_create_static_library.sh)
+set(CMAKE_CXX_CREATE_STATIC_LIBRARY
+  "${CREATE_STATIC_LIB_SCRIPT} <TARGET> <OBJECTS> ${MBCRYPTO_SYMBOLS_PATH}/*o")
+
+file(GLOB_RECURSE sources
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/*.c
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/*.cc
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/*.cpp)
+file(GLOB_RECURSE headers
+  ${CMAKE_CURRENT_SOURCE_DIR}/include/*.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/include/*.hh
+  ${CMAKE_CURRENT_SOURCE_DIR}/include/*.hpp)
+
+target_sources(${PROJECT_NAME} PRIVATE ${sources} ${headers})
+
+target_include_directories(${PROJECT_NAME}
+  PRIVATE
+  # where the library itself will look for its internal headers
+  ${CMAKE_CURRENT_SOURCE_DIR}/src
+  PUBLIC
+  # where top-level project will look for the library's public headers
+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+  # where external projects will look for the library's public headers
+  $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+)
+
+# without it public headers won't get installed
+set(public_headers ${headers})
+
+target_compile_options(${PROJECT_NAME} PRIVATE -Werror)
+
+# where to find our CMake modules
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")
+include(Installing)
+include(Packing)
+
+

cpp/lib/Config.cmake.in

@@ -0,0 +1,5 @@
+@PACKAGE_INIT@
+
+include("${CMAKE_CURRENT_LIST_DIR}/@[email protected]")
+
+check_required_components(@PROJECT_NAME@)

cpp/lib/LICENSE

@@ -0,0 +1,20 @@
+The MIT License (MIT)
+
+Copyright (c) 2024 SingularityNET
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

cpp/lib/cmake/Installing.cmake

@@ -0,0 +1,50 @@
+# for CMAKE_INSTALL_LIBDIR, CMAKE_INSTALL_BINDIR, CMAKE_INSTALL_INCLUDEDIR and others
+include(GNUInstallDirs)
+
+# note that ${public_headers} should be in quotes
+set_target_properties(${PROJECT_NAME} PROPERTIES PUBLIC_HEADER "${public_headers}")
+
+set_target_properties(${PROJECT_NAME} PROPERTIES DEBUG_POSTFIX "d")
+
+# install the target and create export-set
+install(
+  TARGETS ${PROJECT_NAME}
+  EXPORT "${PROJECT_NAME}-targets"
+  COMPONENT ${PROJECT_NAME} # must be here, not any line lower
+  PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/${PROJECT_NAME} # include/hyperon_das_atomdb_cpp
+  INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} # include
+)
+
+set(CMAKE_INSTALL_DESTINATION "cmake/${PROJECT_NAME}")
+
+# generate and install export file
+install(
+  EXPORT "${PROJECT_NAME}-targets"
+  FILE "${PROJECT_NAME}-targets.cmake"
+  NAMESPACE ${namespace}::
+  DESTINATION ${CMAKE_INSTALL_DESTINATION}
+  COMPONENT ${PROJECT_NAME}
+)
+
+include(CMakePackageConfigHelpers)
+
+# generate the version file for the config file
+write_basic_package_version_file(
+  "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake"
+  COMPATIBILITY AnyNewerVersion
+)
+# create config file
+configure_package_config_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/Config.cmake.in
+  "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config.cmake"
+  INSTALL_DESTINATION ${CMAKE_INSTALL_DESTINATION}
+)
+# install config files
+install(
+  FILES
+  "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config.cmake"
+  "${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}-config-version.cmake"
+  DESTINATION ${CMAKE_INSTALL_DESTINATION}
+  COMPONENT ${PROJECT_NAME}
+)
+

cpp/lib/cmake/Packing.cmake

@@ -0,0 +1,43 @@
+set(CPACK_PACKAGE_NAME ${PROJECT_NAME} CACHE STRING "hyperon_das_atomdb_cpp")
+set(
+  CPACK_PACKAGE_DESCRIPTION_SUMMARY "Atom Space DB for Hyperon DAS"
+  CACHE STRING "Atom Space DB for Hyperon DAS is a C++ library for managing Atom databases."
+)
+set(CPACK_PACKAGE_VENDOR "SingularityNET")
+
+set(CPACK_VERBATIM_VARIABLES YES)
+
+set(CPACK_PACKAGE_INSTALL_DIRECTORY ${CPACK_PACKAGE_NAME})
+set(CPACK_OUTPUT_FILE_PREFIX "${CMAKE_SOURCE_DIR}/dist")
+set(CPACK_STRIP_FILES YES)
+
+set(
+  CPACK_INSTALL_DEFAULT_DIRECTORY_PERMISSIONS
+  OWNER_READ OWNER_WRITE OWNER_EXECUTE
+  GROUP_READ GROUP_EXECUTE
+  WORLD_READ WORLD_EXECUTE
+)
+
+set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local")
+
+set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
+set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
+set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
+
+set(CPACK_PACKAGE_CONTACT "[email protected]")
+set(CPACK_DEBIAN_PACKAGE_MAINTAINER "Andre Senna <${CPACK_PACKAGE_CONTACT}>")
+
+set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENSE")
+set(CPACK_RESOURCE_FILE_README "${CMAKE_CURRENT_SOURCE_DIR}/README.md")
+
+set(CPACK_PACKAGE_ARCHITECTURE "amd64")
+set(CPACK_DEBIAN_PACKAGE_ARCHITECTURE ${CPACK_PACKAGE_ARCHITECTURE})
+set(CPACK_PACKAGE_VERSION
+  "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+set(CPACK_PACKAGE_FILE_NAME
+  "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_PACKAGE_ARCHITECTURE}-${TARGET_TYPE}")
+set(CPACK_COMPONENTS_GROUPING ALL_COMPONENTS_IN_ONE)
+set(CPACK_DEB_COMPONENT_INSTALL YES)
+
+include(CPack)
+

hyperon_das_atomdb_cpp/src/constants.h → cpp/lib/include/constants.h

@@ -1,7 +1,7 @@
 #pragma once
 
+#include "expression_hasher.h"
 #include "type_aliases.h"
-#include "utils/expression_hasher.h"
 
 using namespace std;
 

hyperon_das_atomdb_cpp/src/database.h → cpp/lib/include/database.h

@@ -33,8 +33,8 @@
 #include "constants.h"
 #include "document_types.h"
 #include "exceptions.h"
+#include "expression_hasher.h"
 #include "type_aliases.h"
-#include "utils/expression_hasher.h"
 
 using namespace std;