Restructure and dump cmake.

.clang-format

+BasedOnStyle: Google
+Standard: c++17
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+DerivePointerBinding: false
+TabWidth: 2
+ForEachMacros: ["foreach"]
+SpaceBeforeParens: ControlStatementsExceptForEachMacros
+
+SortIncludes: true
+IncludeBlocks: Regroup
+# Custom order of includes (listed by regex match priority)
+IncludeCategories:
+  # Local libraries
+  - Regex: '".*'
+    Priority: 1
+  # Third party libraries
+  - Regex: '^[<"](relic_sym|relic_asym|relic).*'
+    Priority: 2
+  # C++ STL headers
+  - Regex: "^<[a-z0-9_]+>.*"
+    Priority: 3
+  # System headers
+  - Regex: '^<.*\.h>.*'
+    Priority: 4
+IncludeIsMainRegex: "(_test)?$"

.devcontainer.json

+{
+	"image": "docker.io/dbogatov/docker-images:relic-latest-multi-arch",
+	"customizations": {
+		// Configure properties specific to VS Code.
+		"vscode": {
+			// Add the IDs of extensions you want installed when the container is created.
+			"extensions": [
+				"ms-vscode.cpptools-extension-pack",
+				"streetsidesoftware.code-spell-checker",
+				"cschlosser.doxdocgen",
+				"editorconfig.editorconfig",
+				"eamodio.gitlens",
+				"redhat.vscode-yaml"
+			]
+		}
+	}
+}

.gitignore

-# Github cmake ignores.
-CMakeLists.txt.user
-CMakeCache.txt
-CMakeFiles
-CMakeScripts
-Testing
-Makefile
-cmake_install.cmake
-install_manifest.txt
-compile_commands.json
-CTestTestfile.cmake
-_deps
-
-# CLion ignores.
+*.out
+*.o
+*.dSYM
+*.gcov
+*.gcda
+*.gcno
+*.tmp
+*.bin
+junit-*.xml
+cobertura.xml
+coverage-html/
+docs/
+ipch
+ppann/bin/*
+!ppann/bin/.gitkeep
+ppann/lib/*
+!ppann/lib/.gitkeep
+ppann/results/*
+!ppann/results/.gitkeep
 .idea
-# CMake
-cmake-build-*/
-# File-based project format
-*.iws
\ No newline at end of file

.vscode/launch.json

+{
+	"version": "0.2.0",
+	"configurations": [
+		{
+			"name": "(gdb) Test",
+			"type": "cppdbg",
+			"request": "launch",
+			"program": "${workspaceFolder}/build/tests/test_asym_group",
+			"args": [],
+			"stopAtEntry": false,
+			"cwd": "${workspaceFolder}/build",
+			"environment": [],
+			"externalConsole": false,
+			"MIMode": "gdb",
+			"setupCommands": [
+				{
+					"description": "Enable pretty-printing for gdb",
+					"text": "-enable-pretty-printing",
+					"ignoreFailures": true
+				},
+				{
+					"description": "Set Disassembly Flavor to Intel",
+					"text": "-gdb-set disassembly-flavor intel",
+					"ignoreFailures": true
+				}
+			]
+		}
+	]
+}

CMakeLists.txt

-# Set cmake version.
-cmake_minimum_required(VERSION 3.22)
-
-# Project name and language.
-project(
-        PPANN
-        VERSION 0.1
-        DESCRIPTION "This project implements the inner product revealing encryption."
-        LANGUAGES CXX
-)
-
-# Set standards and include tests.
-if (CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
-    set(CMAKE_CXX_STANDARD 17)
-    set_property(GLOBAL PROPERTY USE_FOLDERS ON)
-    include(CTest)
-endif ()
-
-# Find the relic library.
-find_library(RELIC_LIB_SYM relic_sym)
-find_library(RELIC_LIB_ASYM relic_asym)
-
-# Add desired subdirectories.
-add_subdirectory(src)
-add_subdirectory(apps)
-add_subdirectory(tests)
\ No newline at end of file

Dockerfile

-FROM ubuntu:23.10
-
-# Set the relic version number in case we may want to update it.
-ENV VERSION=0.6.0
-
-# Update libraries.
-RUN apt update && apt upgrade -y
-# Install needed libraries.
-RUN apt install -y wget unzip build-essential libgmp-dev libssl-dev cmake
-# Clean up.
-RUN apt clean
-
-# Download library and unzip.
-RUN wget -P /home https://github.com/relic-toolkit/relic/archive/refs/tags/$VERSION.tar.gz &&  \
-    tar -xzf /home/0.6.0.tar.gz -C /home
-
-# Library installation; first install the symmetric curve.
-RUN mkdir -p /home/relic-$VERSION/relic-target-sym
-WORKDIR "/home/relic-$VERSION/relic-target-sym"
-RUN cmake -DLABEL=sym ..
-RUN ../preset/gmp-pbc-ss1536.sh ../
-RUN make
-RUN make install
-
-# Library installation; now install the asymmetric curve.
-RUN mkdir -p /home/relic-$VERSION/relic-target-asym
-WORKDIR "/home/relic-$VERSION/relic-target-asym"
-RUN cmake -DLABEL=asym ..
-RUN ../preset/gmp-pbc-bn254.sh ../
-RUN make
-RUN make install
+FROM dbogatov/docker-images:relic-latest-multi-arch
 
 # Copy the files over to working directory.
 RUN mkdir -p /home/project/build

README.md

 # Privacy-Preserving Approximate Nearest Neighbor
+
 To run the library, one needs to install relic and itialize it with the SS1536 curve. You must also have GMP installed to benefit from the optimizations.

apps/CMakeLists.txt

-# Call this executable app.
-add_executable(app app.cpp)
-target_link_libraries(app PRIVATE ppann_lib)
\ No newline at end of file

apps/app.cpp

-#include <iostream>
-
-using namespace std;
-
-int main() {
-    cout << "Testing in the app." << endl;
-}
\ No newline at end of file

include/asym_field.hpp

-#pragma once
-
-#include <gmp.h>
-
-extern "C" {
-#include "relic_asym/relic.h"
-}
-
-// Set specific asym data types.
-typedef bn_t asymPoint;
-struct asymZp {
-    asymPoint point{};
-    asymPoint modular{};
-};
-
-namespace asym {
-    asymZp rand_zp(asymPoint modular);
-
-    asymZp zp_zero(asymPoint modular);
-
-    asymZp zp_one(asymPoint modular);
-
-    asymZp zp_copy(asymZp x);
-
-    asymZp zp_from_int(int x, asymPoint modular);
-
-    asymZp zp_add(asymZp x, asymZp y);
-
-    asymZp zp_neg(asymZp x);
-
-    asymZp zp_mul(asymZp x, asymZp y);
-
-    asymZp zp_inv(asymZp x);
-
-    int zp_cmp(asymZp x, asymZp y);
-
-    int zp_cmp_int(asymZp x, int y);
-}

include/asym_group.hpp

-#pragma once
-
-#include "asym_field.hpp"
-
-typedef g1_t asymG1;
-typedef g2_t asymG2;
-typedef gt_t asymGt;
-
-namespace asym {
-    void g1_gen(asymG1 x);
-
-    void g2_gen(asymG2 x);
-
-    void g1_mul(asymG1 r, asymG1 x, asymZp y);
-
-    void g2_mul(asymG2 r, asymG2 x, asymZp y);
-
-    void gt_raise(asymGt r, asymGt x, asymZp y);
-
-    void bp_map(asymGt r, asymG1 x, asymG2 y);
-}

include/helper.h

-#pragma once
-
-#include <cstdio>
-#include <cstring>
-#include <sys/stat.h>
-#include "hnsw.h"
-#include "ipre.hpp"
-
-float *fvecs_read(const char *file_path, size_t *d_out, size_t *n_out);
-
-int *ivecs_read(const char *file_path, size_t *d_out, size_t *n_out);
-
-int *float_to_int(const float *data, size_t size);
-
-Item *encrypt_data(const int *data, Key key, size_t d, size_t n);
\ No newline at end of file

include/hnsw.h

-#pragma once
-
-#include <set>
-#include <random>
-#include <vector>
-#include <algorithm>
-#include <unordered_map>
-#include <unordered_set>
-#include "ipre.hpp"
-
-using namespace std;
-
-
-struct Item {
-    // The ciphertext as value.
-    Ct value;
-
-    // Compute distance between item with something else.
-    int dist(Item &other, Key key, int size, int bound) const;
-};
-
-
-struct HNSWGraph {
-    // Constructor.
-    HNSWGraph(int NN, int MN, int MNZ, int SN, int ML, Key key, int size, int bound);
-
-    /* HNSW related settings. */
-    // Number of neighbors.
-    int NN;
-    // Max number of neighbors in layers >= 1.
-    int MN;
-    // Max number of neighbors in layers 0.
-    int MNZ;
-    // search numbers in construction (efConstruction).
-    int SN;
-    // Max number of layers.
-    int ML;
-    // number of items
-    int numItem;
-    // enter node id
-    int enterNode{};
-    // actual vector of the items
-    vector<Item> items;
-    // adjacent edge lists in each layer
-    vector<unordered_map<int, vector<int>>> layerEdgeLists;
-    // The default generator.
-    default_random_engine generator;
-
-    /* For the IPRE scheme. */
-    Key key;
-    int size;
-    int bound;
-
-    /* Methods. */
-    void insert(Item &q);
-
-    void addEdge(int st, int ed, int lc);
-
-    vector<int> search(Item &q, int K);
-
-    vector<int> searchLayer(Item &q, int ep, int ef, int lc);
-};

include/ipre.hpp

-#pragma once
-
-#include "sym_vector.hpp"
-#include "sym_matrix.hpp"
-
-const int B_SIZE = 6;
-
-struct Key {
-    symZpMat A;
-    symZpMat B;
-    symZpMat Bi;
-    symG base;
-    symGt t_base;
-    bn_t modular;
-};
-
-struct Ct {
-    symGVec ctx;
-    symGVec ctk;
-    symGVec ctc;
-};
-
-Key setup(int size);
-
-Ct enc(Key key, const int *message, int size);
-
-int eval(Key key, Ct x, Ct y, int size, int bound);
\ No newline at end of file

include/sym_field.hpp

-#pragma once
-
-#include <gmp.h>
-
-extern "C" {
-#include "relic_sym/relic.h"
-}
-
-// Set specific sym data types.
-typedef bn_t symPoint;
-struct symZp {
-    symPoint point{};
-    symPoint modular{};
-};
-
-namespace sym {
-    symZp zp_rand(symPoint modular);
-
-    symZp zp_zero(symPoint modular);
-
-    symZp zp_one(symPoint modular);
-
-    symZp zp_copy(symZp x);
-
-    symZp zp_from_int(int x, symPoint modular);
-
-    symZp zp_add(symZp x, symZp y);
-
-    symZp zp_neg(symZp x);
-
-    symZp zp_mul(symZp x, symZp y);
-
-    symZp zp_inv(symZp x);
-
-    int zp_cmp(symZp x, symZp y);
-
-    int zp_cmp_int(symZp x, int y);
-}

include/sym_group.hpp

-#pragma once
-
-#include "sym_field.hpp"
-
-typedef g1_t symG;
-typedef gt_t symGt;
-
-namespace sym {
-    void g_gen(symG x);
-
-    void g_mul(symG r, symG x, symZp y);
-
-    void gt_raise(symGt r, symGt x, symZp y);
-
-    void bp_map(symGt r, symG a, symG b);
-}
-

include/sym_matrix.hpp

-#pragma once
-
-#include "sym_field.hpp"
-
-typedef symZp *symZpMat;
-
-namespace sym {
-    symZpMat matrix_zp_from_int(const int *int_mat, int row, int col, symPoint modular);
-
-    symZpMat matrix_zp_rand(int row, int col, symPoint modular);
-
-    symZpMat matrix_identity(int size, symPoint modular);
-
-    int matrix_is_identity(symZpMat x, int size);
-
-    symZpMat matrix_transpose(symZpMat x, int row, int col);
-
-    symZpMat matrix_merge(symZpMat x, symZpMat y, int row, int col_x, int col_y);
-
-    symZpMat matrix_multiply(symZpMat x, symZpMat y, int row_x, int row_y, int col_y, symPoint modular);
-
-    symZpMat matrix_inverse(symZpMat x, int size, symPoint modular);
-}

include/sym_vector.hpp

-#pragma once
-
-#include "sym_field.hpp"
-#include "sym_group.hpp"
-
-typedef symZp *symZpVec;
-typedef symG *symGVec;
-
-namespace sym {
-    symZpVec vector_zp_from_int(const int *int_vec, int size, symPoint modular);
-
-    symZpVec vector_zp_rand(int size, symPoint modular);
-
-    symZpVec vector_merge(symZpVec a, symZpVec b, int size_a, int size_b);
-
-    symZpVec vector_add(symZpVec a, symZpVec b, int size);
-
-    symGVec vector_raise(symG base, symZpVec x, int size);
-
-    void inner_product(symGt r, symGVec a, symGVec b, int size);
-}

ppann/Makefile

+# definitions
+
+SDIR=src
+TDIR=test
+HDIR=benchmark
+IDIR=include
+ODIR=obj
+LDIR=lib
+BDIR=bin
+
+LDFLAGS=-L $(LDIR)
+LDLIBS=-l relic_sym -l relic_asym # libs for main code
+LDTESTLIBS=-l gtest -l benchmark # libs for tests and benchmarks
+INCLUDES=-I $(IDIR) -I $(LDIR)/include
+CPPFLAGS= --std=c++20 -Wall -Wno-unknown-pragmas -fPIC -O3
+CC=g++
+RM=rm -rf
+
+LIBNAME=ppann
+
+# if you follow the convention that for each class CLASS you have a header in
+# $(IDIR)/CLASS.hpp, a code in $(SDIR)/CLASS.cpp and a test in $(TDIR)/test-CLASS.cpp,
+# then the rest will magically work - it will compile each class and test and will run the tests.
+# CLASS does not even have to be a class in C++.
+ENTITIES = asym-field asym-group helper hnsw ipre sym-field sym-group sym-matrix sym-vector
+
+# dependencies - definitions plus header files
+_DEPS = $(addsuffix .hpp, $(ENTITIES))
+DEPS = $(patsubst %, $(IDIR)/%, $(_DEPS))
+
+_OBJ = $(addsuffix .o, $(ENTITIES))
+OBJ = $(patsubst %, $(ODIR)/%, $(_OBJ))
+
+# TODO: here will go executables (what used to be "app")
+TARGETS = 
+TARGETBIN = $(addprefix $(BDIR)/, $(TARGETS))
+
+# Kudos for having a test for every entity!
+TESTS = $(ENTITIES)
+TESTBIN = $(addprefix $(BDIR)/test-, $(TESTS))
+JUNITS= $(foreach test, $(TESTS), bin/test-$(test)?--gtest_output=xml:junit-$(test).xml)
+
+BENCHMARKS =
+BENCHMARKSBIN = $(addprefix $(BDIR)/benchmark-, $(BENCHMARKS))
+
+INTEGRATION =
+INTEGRATIONBIN = $(addprefix $(BDIR)/test-, $(INTEGRATION))
+
+ENTRYPOINTCC = $(CC) -o $@ $^ $(CPPFLAGS) $(INCLUDES) $(LDFLAGS) $(LDLIBS)
+
+# flags-setting commands
+
+all: shared docs
+
+binaries: LDLIBS += $(LDTESTLIBS)
+binaries: $(TARGETBIN) $(TESTBIN) $(INTEGRATIONBIN) $(BENCHMARKSBIN)
+cleandebug: clean debug
+
+debug: CPPFLAGS += -g -DTESTING
+debug: CPPFLAGS := $(filter-out -O3,$(CPPFLAGS))
+debug: binaries
+
+profile: CPPFLAGS += -fprofile-arcs -ftest-coverage -fPIC -O0
+profile: clean run-tests-junit
+
+# executables
+
+.SECONDEXPANSION:
+$(TARGETBIN): $(OBJ) $$(subst $$(BDIR), $(SDIR), $$@).cpp
+	$(ENTRYPOINTCC)
+
+.SECONDEXPANSION:
+$(TESTBIN): $(OBJ) $$(subst $$(BDIR), $(TDIR), $$@).cpp
+	$(ENTRYPOINTCC)
+
+.SECONDEXPANSION:
+$(BENCHMARKSBIN): $(OBJ) $$(subst $$(BDIR), $(HDIR), $$@).cpp
+	$(ENTRYPOINTCC)
+
+.SECONDEXPANSION:
+$(INTEGRATIONBIN): $(OBJ) $$(subst $$(BDIR), $(TDIR), $$@).cpp
+	$(ENTRYPOINTCC)
+
+shared: CPPFLAGS += -DSHARED
+shared: $(OBJ)
+	$(CC) -shared $(LDLIBS) $(LDFLAGS) -o $(BDIR)/lib$(LIBNAME).so $(OBJ)
+
+# programs
+
+# # TODO: 
+# main: bin/main
+
+version:
+	$(CC) -v
+
+# objects
+
+$(ODIR)/%.o: $(SDIR)/%.cpp $(DEPS)
+	$(CC) -c -o $@ $< $(CPPFLAGS) $(INCLUDES)
+
+# commands
+
+run-tests-junit: CPPFLAGS += -DTESTING
+run-tests-junit: $(TESTBIN)
+	$(subst ?, ,$(addsuffix &&, $(JUNITS))) echo Tests passed!
+
+run-tests: CPPFLAGS += -DTESTING
+run-tests: LDLIBS += $(LDTESTLIBS)
+run-tests: $(TESTBIN)
+	$(addsuffix &&, $(TESTBIN)) echo Tests passed!
+
+run-benchmarks: $(BENCHMARKSBIN)
+	$(addsuffix &&, $(BENCHMARKSBIN)) echo Benchmarks completed!
+
+run-integration: CPPFLAGS += -DTESTING
+run-integration: $(INTEGRATIONBIN)
+	$(addsuffix &&, $(INTEGRATIONBIN)) echo Tests passed!
+
+coverage: profile
+	gcovr -r . $(addprefix -f $(SDIR)/, $(addsuffix .cpp, $(ENTITIES))) --exclude-unreachable-branches
+	mkdir -p coverage-html/
+	gcovr -r . --html --html-details -o coverage-html/index.html
+	gcovr -r . -x -o cobertura.xml
+
+docs: clean-docs
+	doxygen ../doxyfile
+
+clean: clean-docs clean-binaries
+	$(RM) $(ODIR)/* *~ *.dSYM *.gcov *.gcda *.gcno *.bin coverage-html junit-*.xml cobertura.xml
+
+clean-docs:
+	$(RM) ../docs
+
+clean-binaries:
+	$(RM) $(BDIR)/*
+
+# phony
+
+.PHONY: docs clean clean-docs clean-binaries coverage
+.PHONY: profile debug cleandebug
+.PHONY: binaries all shared
+.PHONY: run-tests run-integration run-benchmarks run-shared-lib run-tests-junit