fix-clang-db.py

# fix clang compilation database in the cases where one compiler uses another host compiler
# e.g. nvcc/icc using gcc headers
from subprocess import Popen, PIPE
from typing import List
import re, json
startRe = re.compile(r"#include [\"<][.]{3}[\">] search starts here:")
endRe = re.compile(r"^End of search list.$")

def getDefaultIncludes():
    p1 = Popen(["echo", ""], stdout=PIPE)
    p2 = Popen(["/uufs/chpc.utah.edu/sys/installdir/gcc/9.2.0/bin/g++", "-", "-E", "-v"], stdin=p1.stdout, stdout=PIPE, stderr=PIPE)
    p1.stdout.close()  # Allow p1 to receive a SIGPIPE if p2 exits.
    out = p2.communicate()[1]
    start = False
    includes = []
    for line in out.decode().split('\n'):
        if endRe.match(line):
            break
        if startRe.match(line):
            start = True
            continue
        if start:
            includes.append(line.strip())
    return (includes)

commands = json.load(open('compile_commands.json'))
additionToCommandLine = "".join([" -I " + x for x in getDefaultIncludes()])
for target in commands:
    target['command'] = target['command'] + additionToCommandLine

with open('compile_commands.json', 'w') as json_file:
    json.dump(commands, json_file, indent=' ')