From 57d6316aa76bdabcc51e6b69a063191fc72772b5 Mon Sep 17 00:00:00 2001
From: perry0513 <perrypeiweichen@gmail.com>
Date: Wed, 19 Oct 2022 02:32:36 -0700
Subject: [PATCH] Update Makefile and Z3 auto-compilation

---
 .gitignore              |  1 +
 .gitmodules             |  3 +++
 recognizer/Makefile     | 29 +++++++++++++++++++++++++
 recognizer/src/test.cpp | 48 -----------------------------------------
 recognizer/z3           |  1 +
 5 files changed, 34 insertions(+), 48 deletions(-)
 create mode 100644 .gitmodules
 create mode 100755 recognizer/Makefile
 delete mode 100755 recognizer/src/test.cpp
 create mode 160000 recognizer/z3

diff --git a/.gitignore b/.gitignore
index bb5ae8149..004a42139 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,7 @@
 __pycache__/
 g.smt2
 *.smt2
+*.o
 slides/
 **/prev/
 multiseq_alignment/original_betterconcat.fasta
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 000000000..fc8be3185
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "recognizer/z3"]
+	path = recognizer/z3
+	url = https://github.com/Z3Prover/z3
diff --git a/recognizer/Makefile b/recognizer/Makefile
new file mode 100755
index 000000000..cdf256cf9
--- /dev/null
+++ b/recognizer/Makefile
@@ -0,0 +1,29 @@
+CXX = g++
+CFLAGS = -std=c++17 -lstdc++fs -pthread -O3
+SRCDIR = ./src
+Z3DIR = ./z3
+SRC = $(shell find $(SRCDIR) -name '*.cpp')
+OBJ = $(SRC:%.cpp=%.o)
+STATIC_LIB = $(Z3DIR)/lib/libz3.a
+INCLUDE=-I $(Z3DIR)/include/
+EXE = recognizer
+
+.PHONY: z3 clean
+
+$(EXE): $(OBJ)
+	@echo "> Compiling $(EXE)"
+	@$(CXX) $^ -o $(EXE) $(CFLAGS) $(STATIC_LIB) $(INCLUDE) -w
+	@mkdir -p ../bin; cp $(EXE) ../bin
+	@echo $(EXE) copied to ../bin
+
+%.o: %.cpp
+	@echo "> Compiling $^"
+	@$(CXX) $(CFLAGS) -c $(INCLUDE) $< -o $@
+
+z3:
+	@cd $(Z3DIR); python3 scripts/mk_make.py -p ../ --staticlib
+	@cd $(Z3DIR)/build; make -j4; sudo make install
+
+clean:
+	@rm $(EXE) $(OBJ)
+
diff --git a/recognizer/src/test.cpp b/recognizer/src/test.cpp
deleted file mode 100755
index 36b65a91c..000000000
--- a/recognizer/src/test.cpp
+++ /dev/null
@@ -1,48 +0,0 @@
-// #define DEBUGPRINT
-
-#include <iostream>
-#include <fstream>
-#include <filesystem>
-#include <string>
-#include <vector>
-#include <regex>
-#include <map>
-#include <unordered_map>
-#include <set>
-#include <new>
-#include <chrono>
-#include <numeric>
-
-#include "GArgs.h"
-#include "edge.hpp"
-#include "graph.hpp"
-
-#define VERSION "0.1.0"
-#define USAGE "  usage:\n\n\
-\trecognizer_p <in.dot> [--version] [-h / --help] [-v / --verbose] [-i / --print_invalid] [-a / --all_valid_WG]\n\n"
-
-using namespace std;
-
-// bool valid_wg=true;
-// bool debugMode=false;
-// bool verbose=false;
-// bool print_invalid=false;
-// bool all_valid_WG = false;
-// chrono::high_resolution_clock::time_point c_start;
-// chrono::high_resolution_clock::time_point c_end;
-
-// void processOptions(GArgs& args);
-
-int main(int argc, char* argv[]) {
-    // vector<int> vect{ 10, 20, 30 };
-    // vector<int> a{1, 10, 11, 13, 19, 23, 37, 40, 44};
-    // vector<int> b{2};
-    // bool res = a < b;
-    // cout << res << endl;
-    string a = "SASQ!";
-    int new_a = std::stoi( a );
-    cout << new_a << endl;
-
-    return 0;
-}
-
diff --git a/recognizer/z3 b/recognizer/z3
new file mode 160000
index 000000000..77cbd8942
--- /dev/null
+++ b/recognizer/z3
@@ -0,0 +1 @@
+Subproject commit 77cbd89420b08db8fb4a276d584c682b6dc7935f