[CI] Revise R tests. (#8430)
- Use the standard package check (check on the tarball instead of the source tree). - Run commands in parallel. - Cleanup dependencies installation. - Replace makefile. - Documentation. - Test using the image from rhub.
This commit is contained in:
Jiaming Yuan
GitHub
@@ -1,95 +1,315 @@
|
||||
"""Utilities for packaging R code and running tests."""
|
||||
import argparse
|
||||
import os
|
||||
import shutil
|
||||
import subprocess
|
||||
from time import time
|
||||
from pathlib import Path
|
||||
from platform import system
|
||||
|
||||
from test_utils import DirectoryExcursion
|
||||
from test_utils import DirectoryExcursion, cd, print_time, record_time
|
||||
|
||||
ROOT = os.path.normpath(
|
||||
os.path.join(os.path.dirname(os.path.abspath(__file__)), os.path.pardir,
|
||||
os.path.pardir))
|
||||
r_package = os.path.join(ROOT, 'R-package')
|
||||
os.path.join(
|
||||
os.path.dirname(os.path.abspath(__file__)), os.path.pardir, os.path.pardir
|
||||
)
|
||||
)
|
||||
r_package = os.path.join(ROOT, "R-package")
|
||||
|
||||
|
||||
def get_mingw_bin():
|
||||
return os.path.join('c:/rtools40/mingw64/', 'bin')
|
||||
def get_mingw_bin() -> str:
|
||||
return os.path.join("c:/rtools40/mingw64/", "bin")
|
||||
|
||||
|
||||
def test_with_autotools(args):
|
||||
with DirectoryExcursion(r_package):
|
||||
@cd(ROOT)
|
||||
@record_time
|
||||
def pack_rpackage() -> Path:
|
||||
"""Compose the directory used for creating R package tar ball."""
|
||||
dest = Path("xgboost")
|
||||
|
||||
def pkgroot(path: str) -> None:
|
||||
"""Change makefiles according to the package layout."""
|
||||
with open(Path("R-package") / "src" / path, "r") as fd:
|
||||
makefile = fd.read()
|
||||
makefile = makefile.replace("PKGROOT=../../", "PKGROOT=.", 1)
|
||||
with open(dest / "src" / path, "w") as fd:
|
||||
fd.write(makefile)
|
||||
|
||||
output = subprocess.run(["git", "clean", "-xdf", "--dry-run"], capture_output=True)
|
||||
if output.returncode != 0:
|
||||
raise ValueError("Failed to check git repository status.", output)
|
||||
would_remove = output.stdout.decode("utf-8").strip().split("\n")
|
||||
|
||||
if would_remove and not all(f.find("tests/ci_build") != -1 for f in would_remove):
|
||||
raise ValueError(
|
||||
"\n".join(would_remove) + "\nPlease cleanup the working git repository."
|
||||
)
|
||||
|
||||
shutil.copytree("R-package", dest)
|
||||
os.remove(dest / "demo" / "runall.R")
|
||||
# core
|
||||
shutil.copytree("src", dest / "src" / "src")
|
||||
shutil.copytree("include", dest / "src" / "include")
|
||||
shutil.copytree("amalgamation", dest / "src" / "amalgamation")
|
||||
# rabit
|
||||
rabit = Path("rabit")
|
||||
os.mkdir(dest / "src" / rabit)
|
||||
shutil.copytree(rabit / "src", dest / "src" / "rabit" / "src")
|
||||
shutil.copytree(rabit / "include", dest / "src" / "rabit" / "include")
|
||||
# dmlc-core
|
||||
dmlc_core = Path("dmlc-core")
|
||||
os.mkdir(dest / "src" / dmlc_core)
|
||||
shutil.copytree(dmlc_core / "include", dest / "src" / "dmlc-core" / "include")
|
||||
shutil.copytree(dmlc_core / "src", dest / "src" / "dmlc-core" / "src")
|
||||
# makefile & license
|
||||
shutil.copyfile("LICENSE", dest / "LICENSE")
|
||||
osxmakef = dest / "src" / "Makevars.win-e"
|
||||
if os.path.exists(osxmakef):
|
||||
os.remove(osxmakef)
|
||||
pkgroot("Makevars.in")
|
||||
pkgroot("Makevars.win")
|
||||
# misc
|
||||
rwsp = Path("R-package") / "remove_warning_suppression_pragma.sh"
|
||||
if system() != "Windows":
|
||||
subprocess.check_call(rwsp)
|
||||
rwsp = dest / "remove_warning_suppression_pragma.sh"
|
||||
if system() != "Windows":
|
||||
subprocess.check_call(rwsp)
|
||||
os.remove(rwsp)
|
||||
os.remove(dest / "CMakeLists.txt")
|
||||
shutil.rmtree(dest / "tests" / "helper_scripts")
|
||||
return dest
|
||||
|
||||
|
||||
@cd(ROOT)
|
||||
@record_time
|
||||
def build_rpackage(path: str) -> str:
|
||||
def find_tarball() -> str:
|
||||
found = []
|
||||
for root, subdir, files in os.walk("."):
|
||||
for f in files:
|
||||
if f.endswith(".tar.gz") and f.startswith("xgboost"):
|
||||
found.append(os.path.join(root, f))
|
||||
if not found:
|
||||
raise ValueError("Failed to find output tar ball.")
|
||||
if len(found) > 1:
|
||||
raise ValueError("Found more than one packages:", found)
|
||||
return found[0]
|
||||
|
||||
env = os.environ.copy()
|
||||
print("Ncpus:", f"{os.cpu_count()}")
|
||||
env.update({"MAKEFLAGS": f"-j{os.cpu_count()}"})
|
||||
subprocess.check_call([R, "CMD", "build", path], env=env)
|
||||
|
||||
tarball = find_tarball()
|
||||
return tarball
|
||||
|
||||
|
||||
@cd(ROOT)
|
||||
@record_time
|
||||
def check_rpackage(path: str) -> None:
|
||||
env = os.environ.copy()
|
||||
print("Ncpus:", f"{os.cpu_count()}")
|
||||
env.update(
|
||||
{
|
||||
"MAKEFLAGS": f"-j{os.cpu_count()}",
|
||||
# cran specific environment variables
|
||||
"_R_CHECK_EXAMPLE_TIMING_CPU_TO_ELAPSED_THRESHOLD_": str(2.5),
|
||||
}
|
||||
)
|
||||
|
||||
# Actually we don't run this check on windows due to dependency issue.
|
||||
if system() == "Windows":
|
||||
# make sure compiler from rtools is used.
|
||||
mingw_bin = get_mingw_bin()
|
||||
CXX = os.path.join(mingw_bin, 'g++.exe')
|
||||
CC = os.path.join(mingw_bin, 'gcc.exe')
|
||||
cmd = ['R.exe', 'CMD', 'INSTALL', str(os.path.curdir)]
|
||||
env = os.environ.copy()
|
||||
env.update({'CC': CC, 'CXX': CXX, "MAKE": "make -j$(nproc)"})
|
||||
subprocess.check_call(cmd, env=env)
|
||||
subprocess.check_call([
|
||||
'R.exe', '-q', '-e',
|
||||
"library(testthat); setwd('tests'); source('testthat.R')"
|
||||
])
|
||||
subprocess.check_call([
|
||||
'R.exe', '-q', '-e',
|
||||
"demo(runall, package = 'xgboost')"
|
||||
])
|
||||
CXX = os.path.join(mingw_bin, "g++.exe")
|
||||
CC = os.path.join(mingw_bin, "gcc.exe")
|
||||
env.update({"CC": CC, "CXX": CXX})
|
||||
|
||||
status = subprocess.run([R, "CMD", "check", "--as-cran", path], env=env)
|
||||
with open(Path("xgboost.Rcheck") / "00check.log", "r") as fd:
|
||||
check_log = fd.read()
|
||||
|
||||
with open(Path("xgboost.Rcheck") / "00install.out", "r") as fd:
|
||||
install_log = fd.read()
|
||||
|
||||
msg = f"""
|
||||
----------------------- Install ----------------------
|
||||
{install_log}
|
||||
|
||||
----------------------- Check -----------------------
|
||||
{check_log}
|
||||
|
||||
"""
|
||||
|
||||
if status.returncode != 0:
|
||||
print(msg)
|
||||
raise ValueError("Failed r package check.")
|
||||
|
||||
if check_log.find("WARNING") != -1:
|
||||
print(msg)
|
||||
raise ValueError("Has unresolved warnings.")
|
||||
if check_log.find("Examples with CPU time") != -1:
|
||||
print(msg)
|
||||
raise ValueError("Suspicious NOTE.")
|
||||
|
||||
|
||||
def test_with_cmake(args):
|
||||
os.mkdir('build')
|
||||
with DirectoryExcursion('build'):
|
||||
if args.compiler == 'mingw':
|
||||
@cd(r_package)
|
||||
@record_time
|
||||
def check_rmarkdown() -> None:
|
||||
assert system() != "Windows", "Document test doesn't support Windows."
|
||||
env = os.environ.copy()
|
||||
env.update({"MAKEFLAGS": f"-j{os.cpu_count()}"})
|
||||
print("Checking R document with devtools.")
|
||||
bin_dir = os.path.dirname(R)
|
||||
rscript = os.path.join(bin_dir, "Rscript")
|
||||
subprocess.check_call([rscript, "-e", "devtools::document()"], env=env)
|
||||
output = subprocess.run(["git", "diff", "--name-only"], capture_output=True)
|
||||
if len(output.stdout.decode("utf-8").strip()) != 0:
|
||||
raise ValueError("Please run `devtools::document()`.")
|
||||
|
||||
|
||||
@cd(r_package)
|
||||
@record_time
|
||||
def test_with_autotools() -> None:
|
||||
"""Windows only test. No `--as-cran` check, only unittests. We don't want to manage
|
||||
the dependencies on Windows machine.
|
||||
|
||||
"""
|
||||
assert system() == "Windows"
|
||||
mingw_bin = get_mingw_bin()
|
||||
CXX = os.path.join(mingw_bin, "g++.exe")
|
||||
CC = os.path.join(mingw_bin, "gcc.exe")
|
||||
cmd = [R, "CMD", "INSTALL", str(os.path.curdir)]
|
||||
env = os.environ.copy()
|
||||
env.update({"CC": CC, "CXX": CXX, "MAKEFLAGS": f"-j{os.cpu_count()}"})
|
||||
subprocess.check_call(cmd, env=env)
|
||||
subprocess.check_call(
|
||||
["R.exe", "-q", "-e", "library(testthat); setwd('tests'); source('testthat.R')"]
|
||||
)
|
||||
subprocess.check_call(["R.exe", "-q", "-e", "demo(runall, package = 'xgboost')"])
|
||||
|
||||
|
||||
@record_time
|
||||
def test_with_cmake(args: argparse.Namespace) -> None:
|
||||
os.mkdir("build")
|
||||
with DirectoryExcursion("build"):
|
||||
if args.compiler == "mingw":
|
||||
mingw_bin = get_mingw_bin()
|
||||
CXX = os.path.join(mingw_bin, 'g++.exe')
|
||||
CC = os.path.join(mingw_bin, 'gcc.exe')
|
||||
CXX = os.path.join(mingw_bin, "g++.exe")
|
||||
CC = os.path.join(mingw_bin, "gcc.exe")
|
||||
env = os.environ.copy()
|
||||
env.update({'CC': CC, 'CXX': CXX})
|
||||
subprocess.check_call([
|
||||
'cmake', os.path.pardir, '-DUSE_OPENMP=ON', '-DR_LIB=ON',
|
||||
'-DCMAKE_CONFIGURATION_TYPES=Release', '-G', 'Unix Makefiles',
|
||||
],
|
||||
env=env)
|
||||
subprocess.check_call(['make', '-j', 'install'])
|
||||
elif args.compiler == 'msvc':
|
||||
subprocess.check_call([
|
||||
'cmake', os.path.pardir, '-DUSE_OPENMP=ON', '-DR_LIB=ON',
|
||||
'-DCMAKE_CONFIGURATION_TYPES=Release', '-A', 'x64'
|
||||
])
|
||||
subprocess.check_call([
|
||||
'cmake', '--build', os.path.curdir, '--target', 'install',
|
||||
'--config', 'Release'
|
||||
])
|
||||
env.update({"CC": CC, "CXX": CXX})
|
||||
subprocess.check_call(
|
||||
[
|
||||
"cmake",
|
||||
os.path.pardir,
|
||||
"-DUSE_OPENMP=ON",
|
||||
"-DR_LIB=ON",
|
||||
"-DCMAKE_CONFIGURATION_TYPES=Release",
|
||||
"-G",
|
||||
"Unix Makefiles",
|
||||
],
|
||||
env=env,
|
||||
)
|
||||
subprocess.check_call(["make", "-j", "install"])
|
||||
elif args.compiler == "msvc":
|
||||
subprocess.check_call(
|
||||
[
|
||||
"cmake",
|
||||
os.path.pardir,
|
||||
"-DUSE_OPENMP=ON",
|
||||
"-DR_LIB=ON",
|
||||
"-DCMAKE_CONFIGURATION_TYPES=Release",
|
||||
"-A",
|
||||
"x64",
|
||||
]
|
||||
)
|
||||
subprocess.check_call(
|
||||
[
|
||||
"cmake",
|
||||
"--build",
|
||||
os.path.curdir,
|
||||
"--target",
|
||||
"install",
|
||||
"--config",
|
||||
"Release",
|
||||
]
|
||||
)
|
||||
else:
|
||||
raise ValueError('Wrong compiler')
|
||||
raise ValueError("Wrong compiler")
|
||||
with DirectoryExcursion(r_package):
|
||||
subprocess.check_call([
|
||||
'R.exe', '-q', '-e',
|
||||
"library(testthat); setwd('tests'); source('testthat.R')"
|
||||
])
|
||||
subprocess.check_call([
|
||||
'R.exe', '-q', '-e',
|
||||
"demo(runall, package = 'xgboost')"
|
||||
])
|
||||
subprocess.check_call(
|
||||
[
|
||||
R,
|
||||
"-q",
|
||||
"-e",
|
||||
"library(testthat); setwd('tests'); source('testthat.R')",
|
||||
]
|
||||
)
|
||||
subprocess.check_call([R, "-q", "-e", "demo(runall, package = 'xgboost')"])
|
||||
|
||||
|
||||
@record_time
|
||||
def main(args: argparse.Namespace) -> None:
|
||||
start = time()
|
||||
if args.build_tool == 'autotools':
|
||||
test_with_autotools(args)
|
||||
if args.task == "build":
|
||||
src_dir = pack_rpackage()
|
||||
build_rpackage(src_dir)
|
||||
elif args.task == "doc":
|
||||
check_rmarkdown()
|
||||
elif args.task == "check":
|
||||
if args.build_tool == "autotools" and system() != "Windows":
|
||||
src_dir = pack_rpackage()
|
||||
tarball = build_rpackage(src_dir)
|
||||
check_rpackage(tarball)
|
||||
elif args.build_tool == "autotools":
|
||||
test_with_autotools()
|
||||
else:
|
||||
test_with_cmake(args)
|
||||
else:
|
||||
test_with_cmake(args)
|
||||
print("Duration:", time() - start)
|
||||
raise ValueError("Unexpected task.")
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument('--compiler',
|
||||
type=str,
|
||||
choices=['mingw', 'msvc'],
|
||||
help='Compiler used for compiling CXX code.')
|
||||
if __name__ == "__main__":
|
||||
parser = argparse.ArgumentParser(
|
||||
description=(
|
||||
"Helper script for making R package and running R tests on CI. There are"
|
||||
" also other helper scripts in the R tests directory for installing"
|
||||
" dependencies and running linter."
|
||||
)
|
||||
)
|
||||
parser.add_argument(
|
||||
'--build-tool',
|
||||
"--task",
|
||||
type=str,
|
||||
choices=['cmake', 'autotools'],
|
||||
help='Build tool for compiling CXX code and install R package.')
|
||||
choices=["build", "check", "doc"],
|
||||
default="check",
|
||||
required=False,
|
||||
)
|
||||
parser.add_argument(
|
||||
"--compiler",
|
||||
type=str,
|
||||
choices=["mingw", "msvc"],
|
||||
help="Compiler used for compiling CXX code. Only relevant for windows build",
|
||||
default="mingw",
|
||||
required=False,
|
||||
)
|
||||
parser.add_argument(
|
||||
"--build-tool",
|
||||
type=str,
|
||||
choices=["cmake", "autotools"],
|
||||
help="Build tool for compiling CXX code and install R package.",
|
||||
default="autotools",
|
||||
required=False,
|
||||
)
|
||||
parser.add_argument(
|
||||
"--r",
|
||||
type=str,
|
||||
default="R" if system() != "Windows" else "R.exe",
|
||||
help="Path to the R executable.",
|
||||
)
|
||||
args = parser.parse_args()
|
||||
main(args)
|
||||
R = args.r
|
||||
|
||||
try:
|
||||
main(args)
|
||||
finally:
|
||||
print_time()
|
||||
|
||||
Reference in New Issue
Block a user