def test_out_redirection(self):
import tempfile
py = create_tmp_test(
"""
import sys
import os
sys.stdout.write("stdout")
sys.stderr.write("stderr")
"""
)
file_obj = tempfile.TemporaryFile()
out = python(py.name, _out=file_obj)
self.assertTrue(len(out) == 0)
file_obj.seek(0)
actual_out = file_obj.read()
file_obj.close()
self.assertTrue(len(actual_out) != 0)
# test with tee
file_obj = tempfile.TemporaryFile()
out = python(py.name, _out=file_obj, _tee=True)
self.assertTrue(len(out) != 0)
file_obj.seek(0)
actual_out = file_obj.read()
file_obj.close()
self.assertTrue(len(actual_out) != 0)
def execute_locally(self):
"""Runs the equivalent command locally in a blocking way."""
# Make script file #
self.make_script()
# Do it #
with open(self.kwargs['out_file'], 'w') as handle:
sh.python(self.script_path, _out=handle, _err=handle)
def test_environment(self):
import os
env = {"HERP": "DERP"}
py = create_tmp_test(
"""
import os
osx_cruft = ["__CF_USER_TEXT_ENCODING", "__PYVENV_LAUNCHER__"]
for key in osx_cruft:
try: del os.environ[key]
except: pass
print(os.environ["HERP"] + " " + str(len(os.environ)))
"""
)
out = python(py.name, _env=env).strip()
self.assertEqual(out, "DERP 1")
py = create_tmp_test(
"""
import os, sys
sys.path.insert(0, os.getcwd())
import sh
osx_cruft = ["__CF_USER_TEXT_ENCODING", "__PYVENV_LAUNCHER__"]
for key in osx_cruft:
try: del os.environ[key]
except: pass
print(sh.HERP + " " + str(len(os.environ)))
"""
)
out = python(py.name, _env=env, _cwd=THIS_DIR).strip()
self.assertEqual(out, "DERP 1")
def test_no_err(self):
py = create_tmp_test(
"""
import sys
sys.stdout.write("stdout")
sys.stderr.write("stderr")
"""
)
p = python(py.name, _no_err=True)
self.assertEqual(p.stderr, b"")
self.assertEqual(p.stdout, b"stdout")
self.assertFalse(p.process._pipe_queue.empty())
def callback(line):
pass
p = python(py.name, _err=callback)
self.assertEqual(p.stderr, b"")
self.assertEqual(p.stdout, b"stdout")
self.assertFalse(p.process._pipe_queue.empty())
p = python(py.name)
self.assertEqual(p.stderr, b"stderr")
self.assertEqual(p.stdout, b"stdout")
self.assertFalse(p.process._pipe_queue.empty())
def test_binary_pipe(self):
binary = b"\xec;\xedr\xdbF\x92\xf9\x8d\xa7\x98\x02/\x15\xd2K\xc3\x94d\xc9"
py1 = create_tmp_test(
"""
import sys
import os
sys.stdout = os.fdopen(sys.stdout.fileno(), "wb", 0)
sys.stdout.write(%r)
"""
% binary
)
py2 = create_tmp_test(
"""
import sys
import os
sys.stdin = os.fdopen(sys.stdin.fileno(), "rb", 0)
sys.stdout = os.fdopen(sys.stdout.fileno(), "wb", 0)
sys.stdout.write(sys.stdin.read())
"""
)
out = python(python(py1.name), py2.name)
self.assertEqual(out.stdout, binary)
def test_with_context_args(self):
from sh import whoami
import getpass
py = create_tmp_test("""
import sys
import os
import subprocess
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-o", "--opt", action="store_true", default=False, dest="opt")
options, args = parser.parse_args()
if options.opt:
subprocess.Popen(args[0], shell=False).wait()
""")
with python(py.name, opt=True, _with=True):
out = whoami()
self.assertTrue(getpass.getuser() == out.strip())
with python(py.name, _with=True):
out = whoami()
self.assertTrue(out == "")
def test_err_redirection(self):
import tempfile
py = create_tmp_test(
"""
import sys
import os
sys.stdout.write("stdout")
sys.stderr.write("stderr")
"""
)
file_obj = tempfile.TemporaryFile()
p = python(py.name, _err=file_obj)
file_obj.seek(0)
stderr = file_obj.read().decode()
file_obj.close()
self.assertTrue(p.stdout == b"stdout")
self.assertTrue(stderr == "stderr")
self.assertTrue(len(p.stderr) == 0)
# now with tee
file_obj = tempfile.TemporaryFile()
p = python(py.name, _err=file_obj, _tee="err")
file_obj.seek(0)
stderr = file_obj.read().decode()
file_obj.close()
self.assertTrue(p.stdout == b"stdout")
self.assertTrue(stderr == "stderr")
self.assertTrue(len(p.stderr) != 0)
def run(self, clean):
sh.cd(self.working_dir)
try:
sh.python(self.mainfile, _out=self.print_output, _err=self.print_output).wait()
except Exception:
pass
if clean:
self.clean()
def test_make_migrations(cookies):
"""generated project should be able to generate migrations"""
with bake_in_temp_dir(cookies, extra_context={}) as result:
res = result.project.join('manage.py')
try:
sh.python(res, 'makemigrations')
except sh.ErrorReturnCode as e:
pytest.fail(str(e))
def test_run_tests(cookies):
"""generated project should run tests"""
with bake_in_temp_dir(cookies, extra_context={}) as result:
res = result.project.join('runtests.py')
try:
sh.python(res)
except sh.ErrorReturnCode as e:
pytest.fail(str(e))
def test_list(ts):
n, s = ts
with open("log/%s.log" % n, "w") as f:
for t in s:
dax = "dax/%s" % t
start = time.time()
sh.python("emo4.py", dax)
cost= time.time() - start
print >>f, "%s\t%.2fs" % (dax, cost)
def test_screenly_should_exit_if_no_settings_file_found(self):
new_env = os.environ.copy()
new_env["HOME"] = "/tmp"
project_dir = os.path.dirname(__file__)
with self.assertRaises(sh.ErrorReturnCode_1):
sh.python(project_dir + '/../viewer.py', _env=new_env)
with self.assertRaises(sh.ErrorReturnCode_1):
sh.python(project_dir + '/../server.py', _env=new_env)
def test_long_option(self):
py = create_tmp_test("""
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-l", "--long-option", action="store", default="", dest="long_option")
options, args = parser.parse_args()
print(options.long_option.upper())
""")
self.assertTrue(python(py.name, long_option="testing").strip() == "TESTING")
self.assertTrue(python(py.name).strip() == "")
def test_long_bool_option(self):
py = create_tmp_test("""
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-l", "--long-option", action="store_true", default=False, dest="long_option")
options, args = parser.parse_args()
print(options.long_option)
""")
self.assertTrue(python(py.name, long_option=True).strip() == "True")
self.assertTrue(python(py.name).strip() == "False")
def upload():
if request.method == 'GET':
return render_template("upload.html")
else:
f = request.files['file']
filename = secure_filename(f.filename)
if not os.path.exists('/tmp/polly'):
os.makedirs('/tmp/polly')
f.save(os.path.join('/tmp/polly', filename))
sh.python("/srv/polly/python-client/send_file.py")
return redirect('/upload')
def import_data(json_name, package_dir):
json_path = os.path.join(get_json_dir(), json_name)
if os.path.exists(json_path):
print('loading %s' % json_name)
sh.cd(package_dir)
if IS_PY2:
sh.python('manage.py', 'loaddata', json_path)
else:
sh.python3('manage.py', 'loaddata', json_path)
else:
log('%s does not exist' % json_path)
def test_exit_code_from_exception(self):
from sh import ErrorReturnCode
py = create_tmp_test("""
exit(3)
""")
self.assertRaises(ErrorReturnCode, python, py.name)
try:
python(py.name)
except Exception as e:
self.assertEqual(e.exit_code, 3)
def test_multiple_args_long_option(self):
py = create_tmp_test("""
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-l", "--long-option", dest="long_option")
options, args = parser.parse_args()
print(len(options.long_option.split()))
""")
num_args = int(python(py.name, long_option="one two three"))
self.assertEqual(num_args, 3)
num_args = int(python(py.name, "--long-option", "one's two's three's"))
self.assertEqual(num_args, 3)
def gen_model_code(model_codegen_dir,
platform,
model_file_path,
weight_file_path,
model_sha256_checksum,
weight_sha256_checksum,
input_nodes,
output_nodes,
runtime,
model_tag,
input_shapes,
dsp_mode,
embed_model_data,
winograd,
quantize,
quantize_range_file,
obfuscate,
model_graph_format,
data_type,
graph_optimize_options):
bazel_build_common("//mace/python/tools:converter")
if os.path.exists(model_codegen_dir):
sh.rm("-rf", model_codegen_dir)
sh.mkdir("-p", model_codegen_dir)
sh.python("bazel-bin/mace/python/tools/converter",
"-u",
"--platform=%s" % platform,
"--model_file=%s" % model_file_path,
"--weight_file=%s" % weight_file_path,
"--model_checksum=%s" % model_sha256_checksum,
"--weight_checksum=%s" % weight_sha256_checksum,
"--input_node=%s" % input_nodes,
"--output_node=%s" % output_nodes,
"--runtime=%s" % runtime,
"--template=%s" % "mace/python/tools",
"--model_tag=%s" % model_tag,
"--input_shape=%s" % input_shapes,
"--dsp_mode=%s" % dsp_mode,
"--embed_model_data=%s" % embed_model_data,
"--winograd=%s" % winograd,
"--quantize=%s" % quantize,
"--quantize_range_file=%s" % quantize_range_file,
"--obfuscate=%s" % obfuscate,
"--output_dir=%s" % model_codegen_dir,
"--model_graph_format=%s" % model_graph_format,
"--data_type=%s" % data_type,
"--graph_optimize_options=%s" % graph_optimize_options,
_fg=True)
def build_sigar_python(target):
target.pushd(os.path.join(target.dirname, target.buildpath))
target.pushd('bindings')
target.pushd('python')
tmpenv = os.environ.copy()
if "Darwin" in sh.uname('-a'):
tmpenv['CPPFLAGS'] = '-Qunused-arguments'
tmpenv['CFLAGS'] = '-Qunused-arguments'
try:
tmpenv['LDFLAGS'] = '-L' + target.prefix + '/lib -L' + target.prefix + '/lib64'
sh.python("setup.py", "--with-sigar="+target.prefix, "install", "--prefix="+target.prefix, _env=tmpenv)
except sh.ErrorReturnCode,ex:
print "Unable to build SIGAR python extensions: %s" % ex.stderr
raise ex
def test_files(self):
tpl_filename = self.tempfile('test.txt.tpl')
txt_filename = self.tempfile('test.txt')
with open(tpl_filename, 'wt') as f:
f.write('hello {{FOO}}')
sh.python(
self.envtpl(), tpl_filename,
_env={'FOO': 'world'},
)
self.assertFalse(os.path.exists(tpl_filename))
self.assertTrue(os.path.exists(txt_filename))
with open(txt_filename, 'r') as f:
self.assertEquals('hello world', f.read())
def extract_config():
def git_sha(base=''):
try:
return str(sh.git('rev-parse', 'HEAD', _cwd=base)).strip()
except Exception:
return 'NA'
config = c = {}
versions = v = {}
v['bloscpack'] = bp.__version__
v['blosc'] = blosc.__version__
v['numpy'] = np.__version__
v['joblib'] = jb.__version__
v['tables'] = tables.__version__
v['conda'] = str(sh.conda('--version', _tty_in=True)).strip()
v['python'] = str(sh.python('--version', _tty_in=True)).strip()
hashes = h = {}
h['bloscpack'] = git_sha(os.path.dirname(bp.__file__))
h['joblib'] = git_sha(jb.__path__[0])
h['blosc'] = git_sha(blosc.__path__[0])
h['numpy'] = git_sha(np.__path__[0])
h['tables'] = git_sha(tables.__path__[0])
h['benchmark'] = git_sha()
c['uname'] = str(sh.uname('-a')).strip()
c['hostname'] = str(sh.hostname()).strip()
c['whoami'] = str(sh.whoami()).strip()
c['date'] = str(sh.date()).strip()
c['versions'] = versions
c['hashes'] = hashes
return config
def CustomPythonCmakeArgs():
# The CMake 'FindPythonLibs' Module does not work properly.
# So we are forced to do its job for it.
python_prefix = sh.python_config( '--prefix' ).strip()
if p.isfile( p.join( python_prefix, '/Python' ) ):
python_library = p.join( python_prefix, '/Python' )
python_include = p.join( python_prefix, '/Headers' )
else:
which_python = sh.python(
'-c',
'import sys;i=sys.version_info;print "python%d.%d" % (i[0], i[1])'
).strip()
lib_python = '{0}/lib/lib{1}'.format( python_prefix, which_python ).strip()
if p.isfile( '{0}.a'.format( lib_python ) ):
python_library = '{0}.a'.format( lib_python )
# This check is for CYGWIN
elif p.isfile( '{0}.dll.a'.format( lib_python ) ):
python_library = '{0}.dll.a'.format( lib_python )
else:
python_library = '{0}.dylib'.format( lib_python )
python_include = '{0}/include/{1}'.format( python_prefix, which_python )
return [
'-DPYTHON_LIBRARY={0}'.format( python_library ),
'-DPYTHON_INCLUDE_DIR={0}'.format( python_include )
]
def test_stdout_callback_no_wait(self):
import time
py = create_tmp_test(
"""
import sys
import os
import time
for i in range(5):
print(i)
time.sleep(.5)
"""
)
stdout = []
def agg(line):
stdout.append(line)
p = python(py.name, _out=agg, u=True)
# we give a little pause to make sure that the NamedTemporaryFile
# exists when the python process actually starts
time.sleep(0.5)
self.assertTrue(len(stdout) != 5)
def test_stdout_callback_kill(self):
import signal
py = create_tmp_test("""
import sys
import os
import time
for i in range(5):
print(i)
time.sleep(.5)
""")
stdout = []
def agg(line, stdin, process):
line = line.strip()
stdout.append(line)
if line == "3":
process.kill()
return True
p = python(py.name, _out=agg, u=True)
p.wait()
self.assertEqual(p.process.exit_code, -signal.SIGKILL)
self.assertTrue("4" not in p)
self.assertTrue("4" not in stdout)
def minify():
proj()
print(". minifying ...")
sources = dict(js=[], css=[])
for user in ["./frame", "."]:
for min_id, asset_list in dict(js="scripts", css="styles").items():
asset_list = os.path.join(user, asset_list+".txt")
if os.path.exists(asset_list):
[
sources[min_id].append(asset)
for asset
in [x.strip() for x in open(asset_list).read().split("\n")]
if asset
and not asset.startswith("#")
and asset not in sources[min_id]
]
cfg = open("setup.cfg", "w")
cfg.writelines([
CFG_TEMPLATE % {"src": src, "assets": " ".join(assets)}
for src, assets in sources.items()
])
print ".. writing out production setup.cfg"
cfg.close()
[
pprint(sh.python("setup.py", "minify_" + src, verbose=True))
for src in sources
]
def test_general_signal(self):
import signal
from signal import SIGINT
py = create_tmp_test("""
import sys
import os
import time
import signal
def sig_handler(sig, frame):
print(10)
exit(0)
signal.signal(signal.SIGINT, sig_handler)
for i in range(5):
print(i)
sys.stdout.flush()
time.sleep(0.5)
""")
stdout = []
def agg(line, stdin, process):
line = line.strip()
stdout.append(line)
if line == "3":
process.signal(SIGINT)
return True
p = python(py.name, _out=agg)
p.wait()
self.assertEqual(p.process.exit_code, 0)
self.assertEqual(p, "0\n1\n2\n3\n10\n")
def test_mods_parameter_id_lines(self):
log = pd.read_csv(self.testlog, sep='\t', comment='#')
cmd = '{script} {xml} {trees} {log}'.format(
script=join(dirname(THIS),'bio_pieces','beast_checkpoint.py'),
xml=self.testxml, trees=self.testtrees, log=self.testlog
)
ac = log.tail(1)['ac'].values[0]
freqs = log.tail(1)[
['frequencies1','frequencies2','frequencies3','frequencies4']
]
freqs = [str(v.values[0]) for k,v in freqs.iteritems()]
freqs = ' '.join(freqs)
# These all need to exist in output
find_in_lines = [
'<parameter id="frequencies" value="0.225554'.format(freqs),
'<parameter id="ac" value="{0}" lower="0.0" upper="Infinity"/>'.format(ac),
]
not_find_in_lines = [
'<parameter id="treeModel.rootHeight" value=',
]
found = []
def find_lines(line):
''' look for required lines in output '''
for l in find_in_lines + not_find_in_lines:
if l in line:
found.append(l)
out = sh.python(cmd.split(), _out=find_lines, _err=find_lines)
print("Looking for lines {0}".format(find_in_lines))
print("Found {0}".format(found))
self.assertEqual(sorted(find_in_lines), sorted(found))
def _():
cmd = sh.python('pocha/cli.py',
'--reporter', 'xunit',
'test/input/mixed_its.py',
_ok_code=[1],
_tty_out=False)
stdout = cmd.stdout.decode('utf-8')
expect(stdout).to.have.xpath('./testsuite[' +
'@name="Pocha Tests" and ' +
'@tests="3" and ' +
'@errors="0" and ' +
'@failures="1" and ' +
'@skip="0"]')
expect(stdout).to.have.xpath('./testsuite/testcase[' +
'@name="can run a passing it" and ' +
'@classname=""]')
# XXX: should find a way to validate the stacktrace
expect(stdout).to.have.xpath('./testsuite/testcase[' +
'@name="can runa a failing it" and ' +
'@classname=""]/error')
expect(stdout).to.have.xpath('./testsuite/testcase[' +
'@name="can run another passing it" and ' +
'@classname=""]')
def _():
cmd = sh.python('pocha/cli.py',
'test/input/skip_its.py',
'--reporter', 'xunit',
_tty_out=False)
stdout = cmd.stdout.decode('utf-8')
expect(stdout).to.have.xpath('./testsuite[' +
'@name="Pocha Tests" and ' +
'@tests="3" and ' +
'@errors="0" and ' +
'@failures="0" and ' +
'@skip="2"]')
expect(stdout).to.have.xpath('./testsuite/testcase[' +
'@name="first it" and ' +
'@classname="" and ' +
'@time="0.000"]/skipped')
expect(stdout).to.have.xpath('./testsuite/testcase[' +
'@name="second it" and ' +
'@classname="" and ' +
'@time="0.000"]')
expect(stdout).to.have.xpath('./testsuite/testcase[' +
'@name="third it" and ' +
'@classname="" and ' +
'@time="0.000"]/skipped')
def predict(sentences, gold_file, output_file):
with open(output_file, "w") as f:
result = parser.Predict(sentences)
for i in result:
f.write(i.to_string())
eval_script = os.path.join(
current_path, "utils/evaluation_script/conll17_ud_eval.py")
weight_file = os.path.join(current_path,
"utils/evaluation_script/weights.clas")
eval_process = sh.python(eval_script,
"-v",
"-w",
weight_file,
gold_file,
output_file,
_out=output_file + '.txt')
eval_process.wait()
sh.cat(output_file + '.txt', _out=sys.stdout)
print('Finished predicting {}'.format(gold_file))
def test_dry_run(runner):
with runner.isolated_filesystem():
with open("train.py", "w") as f:
f.write(train_py)
os.environ["WANDB_MODE"] = "dryrun"
os.environ["WANDB_TEST"] = "true"
try:
res = sh.python("train.py")
run_dir = glob.glob(os.path.join("wandb", "dry*"))[0]
meta = json.loads(
open(os.path.join(run_dir, "wandb-metadata.json")).read())
assert meta["state"] == "finished"
assert meta["program"] == "train.py"
assert meta["exitcode"] == 0
assert os.path.exists(os.path.join(run_dir, "output.log"))
assert "loss:" in open(os.path.join(run_dir, "output.log")).read()
assert os.path.exists(os.path.join(run_dir, "wandb-history.jsonl"))
assert os.path.exists(os.path.join(run_dir, "wandb-events.jsonl"))
assert os.path.exists(os.path.join(run_dir, "wandb-summary.json"))
finally:
del os.environ["WANDB_MODE"]
del os.environ["WANDB_TEST"]
def test_dry_run_kill(runner):
with runner.isolated_filesystem():
with open("train.py", "w") as f:
f.write(train_py.replace("#os.kill", "os.kill"))
environ = {
"WANDB_MODE": "dryrun",
"WANDB_TEST": "true",
}
res = sh.python("train.py", epochs=10, _bg=True, _env=environ)
try:
res.wait()
print(res)
except sh.ErrorReturnCode:
pass
dirs = glob.glob(os.path.join("wandb", "dry*"))
print(dirs)
run_dir = dirs[0]
meta = json.loads(
open(os.path.join(run_dir, "wandb-metadata.json")).read())
assert meta["state"] == "killed"
assert meta["exitcode"] == 255
assert meta["args"] == ["--epochs=10"]
def test_multiple_pipes(self):
from sh import tr, python
import time
py = create_tmp_test("""
import sys
import os
import time
for l in "andrew":
print(l)
time.sleep(.2)
""")
class Derp(object):
def __init__(self):
self.times = []
self.stdout = []
self.last_received = None
def agg(self, line):
self.stdout.append(line.strip())
now = time.time()
if self.last_received: self.times.append(now - self.last_received)
self.last_received = now
derp = Derp()
p = tr(
tr(
tr(
python(py.name, _piped=True),
"aw", "wa", _piped=True),
"ne", "en", _piped=True),
"dr", "rd", _out=derp.agg)
p.wait()
self.assertEqual("".join(derp.stdout), "werdna")
self.assertTrue(all([t > .15 for t in derp.times]))
def _():
cmd = sh.python('pocha/cli.py',
'--reporter',
'xunit',
'test/input/describe_with_multiple_failing_it.py',
_ok_code=[1],
_tty_out=False)
stdout = cmd.stdout.decode('utf-8')
expect(stdout).to.have.xpath('./testsuite[' +
'@name="Pocha Tests" and ' +
'@tests="1" and ' +
'@errors="0" and ' +
'@failures="2" and ' + '@skip="0"]')
expect(stdout).to.have.xpath('./testsuite/testcase[' +
'@name="can run a failing it" and ' +
'@classname=""]/error')
expect(stdout).to.have.xpath(
'./testsuite/testcase[' +
'@name="can run another failing it" and ' +
'@classname=""]/error')
def _():
cmd = sh.python(
'pocha/cli.py',
'test/input/multiple_its_in_a_describe_with_after_failure.py',
_ok_code=[1],
_tty_out=False)
stdout = cmd.stdout.decode('utf-8')
expect(stdout).to.match(u'''
a describe
✓ can run a passing it
✓ can run another passing it
1\) "after all" hook
2 passing \(\d+ms\)
1 failing
1\) "after all" hook:
Exception: doing it on purpose
File "test/input/multiple_its_in_a_describe_with_after_failure.py", line 8, in teardown
raise Exception\('doing it on purpose'\)
''')
def test_dry_run_kill(runner):
with runner.isolated_filesystem():
with open("train.py", "w") as f:
f.write(train_py.replace("#os.kill", "os.kill"))
os.environ["WANDB_MODE"] = "dryrun"
os.environ["WANDB_TEST"] = "true"
try:
res = sh.python("train.py", epochs=10, _bg=True)
try:
res.wait()
print(res)
except sh.ErrorReturnCode:
pass
dirs = glob.glob("wandb/dry*")
print(dirs)
run_dir = dirs[0]
meta = json.loads(open(run_dir + "/wandb-metadata.json").read())
assert meta["state"] == "killed"
assert meta["exitcode"] == 255
assert meta["args"] == ["--epochs=10"]
finally:
del os.environ["WANDB_MODE"]
del os.environ["WANDB_TEST"]
def test_decode_error_handling(self):
from functools import partial
py = create_tmp_test("""
# -*- coding: utf8 -*-
import sys
import os
sys.stdout = os.fdopen(sys.stdout.fileno(), 'wb')
IS_PY3 = sys.version_info[0] == 3
if IS_PY3:
sys.stdout.write(bytes("te漢字st", "utf8"))
else:
sys.stdout.write("te漢字st")
""")
fn = partial(python, py.name, _encoding="ascii")
def s(fn):
str(fn())
self.assertRaises(UnicodeDecodeError, s, fn)
p = python(py.name, _encoding="ascii", _decode_errors="ignore")
self.assertEqual(p, "test")
def build(target_python, requirements):
"""
Builds an APK given a target Python and a set of requirements.
"""
if not requirements:
return
testapp = 'setup_testapp_python2.py'
android_sdk_home = os.environ['ANDROID_SDK_HOME']
android_ndk_home = os.environ['ANDROID_NDK_HOME']
if target_python == TargetPython.python3:
testapp = 'setup_testapp_python3.py'
requirements.add(target_python.name)
requirements = ','.join(requirements)
print('requirements:', requirements)
with current_directory('testapps/'):
try:
for line in sh.python(
testapp, 'apk', '--sdk-dir', android_sdk_home,
'--ndk-dir', android_ndk_home, '--bootstrap', 'sdl2', '--requirements',
requirements, _err_to_out=True, _iter=True):
print(line)
except sh.ErrorReturnCode as e:
raise
def test_stdout_callback_no_wait(self):
import time
py = create_tmp_test("""
import sys
import os
import time
for i in range(5):
print(i)
time.sleep(.5)
""")
stdout = []
def agg(line): stdout.append(line)
p = python(py.name, _out=agg, u=True)
# we give a little pause to make sure that the NamedTemporaryFile
# exists when the python process actually starts
time.sleep(.5)
self.assertTrue(len(stdout) != 5)
def sign_file(self, work_dir, from_, cert_type, signing_formats, to=None):
if to is None:
to = from_
token = os.path.join(work_dir, "token")
nonce = os.path.join(work_dir, "nonce")
self.get_token(token, cert_type, signing_formats)
signtool = os.path.join(self.tools_checkout,
"release/signing/signtool.py")
cmd = [signtool, "-n", nonce, "-t", token, "-c", self.cert]
for s in self.get_suitable_signing_servers(cert_type, signing_formats):
cmd.extend(["-H", s.server])
for f in signing_formats:
cmd.extend(["-f", f])
cmd.extend(["-o", to, from_])
log.debug("Running python %s", " ".join(cmd))
out = sh.python(*cmd, _err_to_out=True, _cwd=work_dir)
log.debug("COMMAND OUTPUT: %s", out)
abs_to = os.path.join(work_dir, to)
log.info("SHA512SUM: %s SIGNED_FILE: %s",
get_hash(abs_to, "sha512"), to)
log.info("SHA1SUM: %s SIGNED_FILE: %s",
get_hash(abs_to, "sha1"), to)
log.debug("Finished signing")
def test_general_signal(self):
import signal
from signal import SIGINT
py = create_tmp_test("""
import sys
import os
import time
import signal
def sig_handler(sig, frame):
print(10)
exit(0)
signal.signal(signal.SIGINT, sig_handler)
for i in range(5):
print(i)
sys.stdout.flush()
time.sleep(0.5)
""")
stdout = []
def agg(line, stdin, process):
line = line.strip()
stdout.append(line)
if line == "3":
process.signal(SIGINT)
return True
p = python(py.name, _out=agg)
p.wait()
self.assertEqual(p.process.exit_code, 0)
self.assertEqual(p, "0\n1\n2\n3\n10\n")
def test_auto_change_buffering(self):
binary = b'\xec;\xedr\xdbF\x92\xf9\x8d\xa7\x98\x02/\x15\xd2K\xc3\x94d\xc9'
py1 = create_tmp_test("""
import sys
import os
import time
sys.stdout = os.fdopen(sys.stdout.fileno(), "wb", 0)
sys.stdout.write(b"testing")
sys.stdout.flush()
# to ensure that sh's select loop picks up the write before we write again
time.sleep(0.5)
sys.stdout.write(b"again\\n")
sys.stdout.flush()
time.sleep(0.5)
sys.stdout.write(%r)
sys.stdout.flush()
""" % binary)
out = python(py1.name, _out_bufsize=1)
self.assertTrue(
out.stdout ==
b'testingagain\n\xec;\xedr\xdbF\x92\xf9\x8d\xa7\x98\x02/\x15\xd2K\xc3\x94d\xc9'
)
def _():
cmd = sh.python('pocha/cli.py',
'test/input/multiple_its_with_before_each_failure.py',
_ok_code=[1],
_tty_out=False)
stdout = cmd.stdout.decode('utf-8')
expect(stdout).to.match(u'''
1\) "before each" hook for "can run a passing it"
2\) "before each" hook for "can run another passing it"
0 passing \(\d+ms\)
2 failing
1\) "before each" hook for "can run a passing it":
Exception: doing it on purpose
File "test/input/multiple_its_with_before_each_failure.py", line 6, in setup
raise Exception\('doing it on purpose'\)
2\) "before each" hook for "can run another passing it":
Exception: doing it on purpose
File "test/input/multiple_its_with_before_each_failure.py", line 6, in setup
raise Exception\('doing it on purpose'\)
''')
def test_quote_escaping(self):
py = create_tmp_test("""
from optparse import OptionParser
parser = OptionParser()
options, args = parser.parse_args()
print(args)
""")
out = python(py.name, "one two three").strip()
self.assertEqual(out, "['one two three']")
out = python(py.name, "one \"two three").strip()
self.assertEqual(out, "['one \"two three']")
out = python(py.name, "one", "two three").strip()
self.assertEqual(out, "['one', 'two three']")
out = python(py.name, "one", "two \"haha\" three").strip()
self.assertEqual(out, "['one', 'two \"haha\" three']")
out = python(py.name, "one two's three").strip()
self.assertEqual(out, "[\"one two's three\"]")
out = python(py.name, 'one two\'s three').strip()
self.assertEqual(out, "[\"one two's three\"]")
def main(args):
if not os.path.exists('services.json'):
print('Must run this script from Data/Site')
return -1
tmpfile = tempfile.mktemp(suffix='.txt')
print(tmpfile)
sh.python('../../Scripts/serviceMap.py', '-s', tmpfile)
service_map = get_service_map(tmpfile)
exts = ['json', 'yml', 'yaml']
for ext in exts:
contents = get_contents('services.%s' % ext)
if contents:
contents = process_services(service_map, contents)
if contents:
store_contents('services.%s' % ext, contents)
if os.path.exists('services') and os.path.isdir('services'):
for root, dirs, files in os.walk('services'):
for f in files:
file_name = os.path.join(root, f)
contents = get_contents(file_name)
if contents:
contents = process_services(service_map, contents)
if contents:
store_contents(file_name, contents)
if os.path.exists('../Cloud') and os.path.isdir('../Cloud'):
file_types = ['ccp', 'rcp', 'scp']
for root, dirs, files in os.walk('../Cloud'):
for f in files:
for ft in file_types:
if f.startswith(ft):
file_name = os.path.join(root, f)
contents = get_contents(file_name)
if contents:
contents = process_control_plane(
service_map, contents)
if contents:
store_contents(file_name, contents)
if os.path.exists('../Cloud') and os.path.isdir('../Cloud'):
for root, dirs, files in os.walk('../Cloud'):
for f in files:
if f.find('cloudConfig') != -1 or f.find('CloudConfig') != -1:
file_name = os.path.join(root, f)
contents = get_contents(file_name)
if contents:
contents = process_cloud_config(service_map, contents)
if contents:
store_contents(file_name, contents)
# if os.path.exists('../Cloud') and os.path.isdir('../Cloud'):
# for root, dirs, files in os.walk('../Cloud'):
# for f in files:
# if (f.find('networkConfig') != -1 or
# f.find('NetworkConfig') != -1):
# file_name = os.path.join(root, f)
# contents = get_contents(file_name)
# if contents:
# contents = process_network_config(
# service_map, contents)
# if contents:
# store_contents(file_name, contents)
# if os.path.exists('../Cloud') and os.path.isdir('../Cloud'):
# for root, dirs, files in os.walk('../Cloud'):
# for f in files:
# if (f.find('environmentConfig') != -1 or
# f.find('EnvironmentConfig') != -1):
# file_name = os.path.join(root, f)
# contents = get_contents(file_name)
# if contents:
# contents = process_environment_config(
# service_map, contents)
# if contents:
# store_contents(file_name, contents)
# if os.path.exists('../Cloud') and os.path.isdir('../Cloud'):
# for root, dirs, files in os.walk('../Cloud'):
# for f in files:
# if (f.find('serverConfig') != -1 or
# f.find('ServerConfig') != -1):
# file_name = os.path.join(root, f)
# contents = get_contents(file_name)
# if contents:
# contents = process_server_config(
# service_map, contents)
# if contents:
# store_contents(file_name, contents)
# exts = ['json', 'yml', 'yaml']
# for ext in exts:
# contents = get_contents('network_traffic.%s' % ext)
# if contents:
# contents = process_network_traffic(
# service_map, contents)
# if contents:
# store_contents('network_traffic.%s' % ext, contents)
#
# if os.path.exists('network_traffic') and os.path.isdir('network_traffic'):
# for root, dirs, files in os.walk('network_traffic'):
# for f in files:
# file_name = os.path.join(root, f)
# contents = get_contents(file_name)
# if contents:
# contents = process_network_traffic(
# service_map, contents)
# if contents:
# store_contents(file_name, contents)
os.remove(tmpfile)
def grade_q2a(uniqname):
try:
repo, path = clone('q2a', uniqname, 'csprag-git-conflict1')
except sh.ErrorReturnCode as e:
text = '''
<p><strong>Error! Failed to clone {}</strong></p>
<p>Ran command: <tt>{}</tt></p>
<p>stdout:</p>
<pre>
{}
</pre></p>
<p>stderr:</p>
<pre>
{}
</pre>
'''.format('csprag-git-conflict1', e.full_cmd, e.stdout.decode('utf8'),
e.stderr.decode('utf8'))
return 0, text
with sh.pushd(path):
golden = '''\
Welcome to the simple test program
According to current estimates, the diag construction will be done:
Summer 2017.
'''
test_golden = '''\
Success
'''
text = ''
grade = 0
text += '<dd><strong>Merge content conflict [base 1.0]</strong></dd>\n'
grade += 1.0
if not os.path.exists('main.py'):
text += '<dd>No <tt>main.py</tt> in repository [-1.0]</dd>'
grade -= 1.0
elif not os.path.exists('test.sh'):
text += '<dd>No <tt>test.sh</tt> in repository [-1.0]</dd>'
grade -= 1.0
else:
mainpy = open('main.py').read()
testsh = open('test.sh').read()
if ('>>>>' in mainpy) or ('<<<<' in mainpy):
text += '<dd>Unresolved conflict in <tt>main.py</tt>. Contents:<pre>{}</pre></dd>'.format(
mainpy)
grade -= 1.0
elif ('>>>>' in testsh) or ('<<<<' in testsh):
text += '<dd>Unresolved conflict in <tt>test.sh</tt>. Contents:<pre>{}</pre></dd>'.format(
testsh)
grade -= 1.0
else:
try:
out = sh.python('main.py')
test_out = sh.bash('test.sh')
if ('diag construction' not in out) or ('Summer 2017'
not in out):
text += '<dd><tt>main.py</tt> content not merged, missing diag construction or completion date [-1.0]. Output of main.py:<pre>{}</pre></dd>'.format(
out)
grade -= 1.0
else:
# fuzz is a fuzzy string matching library that should
# allow for modest formatting or text differences
if fuzz.ratio(out, golden) < 75:
text += '<dd>Output of main.py seems to be a merge, but not quite correct [-0.4]. Expected <pre>{}</pre>, student main.py output <pre>{}</pre>'.format(
golden, out)
grade -= 0.4
if fuzz.ratio(test_out, test_golden) < 75:
text += '<dd><tt>test.sh</tt> does not report success [-0.4]. Output of test.sh:<pre>{}</pre></dd>'.format(
test_out)
grade -= 0.4
except sh.ErrorReturnCode as e:
text += '<dd><tt>main.py</tt> or <tt>test.sh</tt> does not run [-1.0]. Output <pre>Ran {}\n\nStdout\n{}Stderr\n{}</pre></dd>'.format(
e.full_cmd, e.stdout.decode('utf8'),
e.stderr.decode('utf8'))
grade -= 1.0
if grade == 1.0:
text += '<dd>All correct!</dd>'
q2a_entry = '''
<dt>Question 2a</dt>
<dd>{:1.1f}/1.0</dd>
<dl>
{}</dl>
'''.format(grade, text)
return grade, text
commit_count = sh.git('rev-list', ['--all']).count('\n')
with open('setup.py') as f:
setup = f.read()
setup = re.sub("MICRO_VERSION = '[0-9]+'",
"MICRO_VERSION = '{}'".format(commit_count), setup)
major = re.search("MAJOR_VERSION = '([0-9]+)'", setup).groups()[0]
minor = re.search("MINOR_VERSION = '([0-9]+)'", setup).groups()[0]
micro = re.search("MICRO_VERSION = '([0-9]+)'", setup).groups()[0]
version = '{}.{}.{}'.format(major, minor, micro)
with open('setup.py', 'w') as f:
f.write(setup)
with open('whereami/__init__.py') as f:
init = f.read()
with open('whereami/__init__.py', 'w') as f:
f.write(
re.sub('__version__ = "[0-9.]+"', '__version__ = "{}"'.format(version),
init))
print(sh.python('setup.py', ['sdist', 'bdist_wheel', 'upload']))
sh.cd('../')
sh.pip3('install', ['-U', 'whereami'])
for new_config in tests:
with open(config_file, "r+") as f:
d = f.readlines()
f.seek(0)
for i in d:
print(f"{i}")
if i.find("link_data_rate_megabit_per_s") != -1:
network_bw = i.split("=")[1].strip("\n") + "Mbits"
if i.find("num_of_active_bursts") == -1:
f.write(i)
else:
f.write(f"num_of_active_bursts={new_config}")
f.truncate()
sh.cp(
"/mnt/raid10/hanjing/thesis/ns3/ns3-basic-sim/simulator/run.sh",
"/mnt/raid10/hanjing/thesis/ns3/ns3-basic-sim/simulator/run.sh.bak"
)
# sh.sed( "-i", f"s/program/{main_program}/g", "/mnt/raid10/hanjing/thesis/ns3/ns3-basic-sim/simulator/run.sh.bak", _err="sed_err_log", _out="sed_out_log")
sh.sed(
"-i", f"s/program/{main_program}/g",
"/mnt/raid10/hanjing/thesis/ns3/ns3-basic-sim/simulator/run.sh.bak"
)
new_log_dir = f"logs_ns3_{network_bw}_ActiveBurstsCt_{new_config}"
print(f"new_log_dir: {new_log_dir}")
sh.bash(
"/mnt/raid10/hanjing/thesis/ns3/ns3-basic-sim/simulator/run.sh.bak"
)
sh.python(
"/mnt/raid10/hanjing/thesis/ns3/ns3-basic-sim/simulator/src/basic-apps/helper/horovod_worker_plot.py",
f"{log_dir}/{horovod_prg}")
# sh.cp("-r",f"{log_dir}", f"{run_dir}/{new_log_dir}")
#Testing shell commands from Python by Zwaan / refactor by Bragatte#
<https://blog.esciencecenter.nl/testing-shell-commands-from-python-2a2ec87ebf71>
import sh
sh.python(['setup.py', 'install'])
import pytest
import os
import sh
def test_install(cookies):
# generate a temporary project using the cookiecutter
# cookies fixture
project = cookies.bake()
# remember the directory where tests should be run from
cwd = os.getcwd()
# change directories to the generated project directory
# (the installation command must be run from here)
os.chdir(str(project.project))
try:
# run the shell command
sh.python(['setup.py', 'install'])
except sh.ErrorReturnCode as e:
# print the error, so we know what went wrong
print(e)
# make sure the test fails
pytest.fail(e)
finally:
# always change directories to the test directory
os.chdir(cwd)
def main(name):
base, cmtfiles, ref, output, database = get_paths(name)
to_run_pyname = join(current_file_dir, "forward_structure_base.py")
sh.python(to_run_pyname, "--base", base, "--cmtfiles",
cmtfiles, "--ref", ref, "--output", output, "--database", database)
argparser = ArgumentParser()
argparser.add_argument('logfile')
argparser.add_argument('--random', action='store_true')
argparser.add_argument('--metric', default='cosine')
argparser.add_argument('--type', default='similarity')
return argparser.parse_args()
if __name__ == "__main__":
args = parse_args()
for num_centers in [10, 20, 50, 100, 1000, 2000, 4000, 8000]:
if num_centers < 100:
increment = int(num_centers / 10)
else:
increment = int(num_centers / 100)
for top_centers in range(increment, num_centers + increment,
increment):
print("Running with parameters: %u / %u" %
(top_centers, num_centers))
python(
cmd, **{
"num_centers": num_centers,
"top_centers": top_centers,
"logfile": args.logfile,
"random": args.random,
"metric": args.metric,
"type": args.type,
"_long_sep": " "
})
def python_job_func(job_file_name):
print "python %s " % job_file_name
sh.python(job_file_name)
def test_valid():
try:
sh.python(["-m", "zuul_lint", "tests/data/zuul-config-valid.yaml"])
except sh.ErrorReturnCode as e:
pytest.fail(e)
def gen_model_code(model_codegen_dir,
platform,
model_file_path,
weight_file_path,
model_sha256_checksum,
weight_sha256_checksum,
input_nodes,
input_data_formats,
output_nodes,
output_data_formats,
check_nodes,
runtime,
model_tag,
input_shapes,
input_ranges,
output_shapes,
check_shapes,
dsp_mode,
embed_model_data,
winograd,
quantize,
quantize_range_file,
change_concat_ranges,
obfuscate,
model_graph_format,
data_type,
cl_mem_type,
graph_optimize_options):
bazel_build_common("//mace/python/tools:converter")
if os.path.exists(model_codegen_dir):
sh.rm("-rf", model_codegen_dir)
sh.mkdir("-p", model_codegen_dir)
sh.python("bazel-bin/mace/python/tools/converter",
"-u",
"--platform=%s" % platform,
"--model_file=%s" % model_file_path,
"--weight_file=%s" % weight_file_path,
"--model_checksum=%s" % model_sha256_checksum,
"--weight_checksum=%s" % weight_sha256_checksum,
"--input_node=%s" % input_nodes,
"--input_data_formats=%s" % input_data_formats,
"--output_node=%s" % output_nodes,
"--output_data_formats=%s" % output_data_formats,
"--check_node=%s" % check_nodes,
"--runtime=%s" % runtime,
"--template=%s" % "mace/python/tools",
"--model_tag=%s" % model_tag,
"--input_shape=%s" % input_shapes,
"--input_range=%s" % input_ranges,
"--output_shape=%s" % output_shapes,
"--check_shape=%s" % check_shapes,
"--dsp_mode=%s" % dsp_mode,
"--embed_model_data=%s" % embed_model_data,
"--winograd=%s" % winograd,
"--quantize=%s" % quantize,
"--quantize_range_file=%s" % quantize_range_file,
"--change_concat_ranges=%s" % change_concat_ranges,
"--obfuscate=%s" % obfuscate,
"--output_dir=%s" % model_codegen_dir,
"--model_graph_format=%s" % model_graph_format,
"--data_type=%s" % data_type,
"--graph_optimize_options=%s" % graph_optimize_options,
"--cl_mem_type=%s" % cl_mem_type,
_fg=True)
import os
import sys
import glob
import pdb
import nlp_ml
from nlp_ml import CustomPipeline, spacy_tokenizer, cleaner
import numpy as np
from sqlitedict import SqliteDict
try:
import sh
except ImportError:
# fallback: emulate the sh API with pbs
import pbs
class Sh(object):
def __getattr__(self, attr):
return pbs.Command(attr)
sh = Sh()
train = './spam_data/SMSSpamCollectionMini_train.csv'
test = './spam_data/SMSSpamCollectionMini_test.csv'
iters = 2
path_to_db = './output.db'
sh.python('nlp_ml.py', train, test, iters, path_to_db)
def main():
try:
prog = "pypi-up"
desc = "%s %s" % (__title__, __version__)
desc += " - pypi-up a simple command line tool to increase version number of package" \
"and release on Pypi. Also Git Tag/Push the release"
parser = argparse.ArgumentParser(prog=prog, description=desc)
parser.add_argument("--setup",
help="Setup PYPI-REL",
action="store_true")
parser.add_argument("-v",
"--version",
help="Show the current version",
action="store_true")
parser.add_argument("-p",
"--patch",
help="Increment PATCH version",
action="store_true")
parser.add_argument("-m",
"--minor",
help="Increment MINOR version and reset patch",
action="store_true")
parser.add_argument(
"-j",
"--major",
help="Increment MAJOR version and reset minor and patch",
action="store_true")
parser.add_argument("-e",
"--edit",
help="Manually enter the version number to bump",
action="store")
parser.add_argument(
"--dry",
help=
"DRY RUN. To test the release, but it will not make any changes",
action="store_true")
parser.add_argument("-x",
"--skip-prompt",
help="Skip prompt",
action="store_true")
arg = parser.parse_args()
config = ConfigParser.ConfigParser()
print("-" * 80)
print("=== PYPI Up ===")
print("")
if arg.setup:
print("Setting up...")
if not os.path.isfile(about_file):
with open(about_file, "w+") as f:
f.write(about_file_content)
if not os.path.isfile(setup_cfg):
config.add_section(conf_section_name)
config.set(conf_section_name, "version-file", "__about__.py")
config.set(conf_section_name, "auto-increment", "patch")
with open(setup_cfg, "w+") as f:
config.write(f)
print("Done!")
print("-" * 80)
exit()
with sh.pushd(CWD):
if sh.git("status", "--porcelain").strip():
raise Exception("Repository is UNCLEAN. Commit your changes")
config.read(setup_cfg)
version_file = config.get(conf_section_name, "version-file")
version_file = os.path.join(CWD, version_file)
if not os.path.isfile(version_file):
raise Exception("version-file '%s' is required" % version_file)
auto_inc = ""
if config.has_option(conf_section_name, "auto-increment"):
auto_inc = config.get(conf_section_name,
"auto-increment").strip()
rvnup = Reversionup(file=setup_cfg)
old_version = rvnup.version
def test_auto_inc(auto_inc_):
return auto_inc == auto_inc_ and (
not arg.patch and not arg.minor and not arg.major
and not arg.version and not arg.edit)
if arg.edit:
rvnup.version = arg.edit
elif arg.patch or test_auto_inc("patch"):
rvnup.inc_patch()
elif arg.minor or test_auto_inc("minor"):
rvnup.inc_minor()
elif arg.major or test_auto_inc("major"):
rvnup.inc_major()
elif arg.version:
print("Current version: %s" % rvnup.version)
print("-" * 80)
exit()
if arg.dry:
print("** DRY RUNNING **")
print("")
print("* New version: %s " % rvnup.version)
print("Old version: %s" % old_version)
print("")
if not arg.skip_prompt \
and raw_input("Continue with the release? (y | n) ").strip() == "n":
print("** Release Aborted")
print("-" * 80)
exit()
skip_tag = not arg.skip_prompt \
and raw_input("Git Tag/Push release version? (y | n) ").strip().lower() == "n"
skip_pypi = not arg.skip_prompt \
and raw_input("Release to PYPI? (y | n) ").strip().lower() == "n"
print("")
if not arg.dry:
rvnup.write()
replace_file_version(version_file, rvnup.version)
if arg.dry or skip_tag:
print("- Git Tag/Push release: skipped")
else:
tag_name = "v%s" % rvnup.version
print("+ Git Tag release version: %s " % tag_name)
sh.git("add", ".")
sh.git("commit", "-m", "Tagged release: %s" % tag_name)
sh.git("tag", "-a", tag_name, "-m", tag_name)
print("+ Git Push release to repo ...")
sh.git("push", "origin", "master")
sh.git("push", "--tags")
if arg.dry or skip_pypi:
print("- Release to Pypi: skipped")
else:
print("+ Releasing to PYPI ...")
sh.python("setup.py", "register", "-r", "pypi")
sh.python("setup.py", "sdist", "upload", "-r", "pypi")
print("-" * 80)
print("")
except Exception as ex:
print("Error: %s" % ex.message)
exit(1)
arg_list = [
filename_arg, path, ss_symex_opt, PC, rep_opt, rep, struct_opt,
struct
]
else:
run_description = '-- running ss-concrete --\n'
arg_list = [filename_arg, path, ss_opt]
print run_description
f.append_data(run_summary_log, run_description)
while (not done) and (not exceeded_num_runs):
print 'RUN', test_ctr, ':',
#sh.python(prog_name, benchmark_path, _out=output_log, _err=process_stderr)
# ./secam.py --filename ./examples/heater/heater.tst --ss-symex klee
sh.python(prog_name,
*arg_list,
_out=process_stdout,
_err=process_stderr)
f.append_data(output_log, STDOUT_DATA)
STDOUT_DATA = ''
test_ctr = test_ctr + 1 if LAST_RESULT else test_ctr
done = NUM_TESTS == test_ctr
exceeded_num_runs = test_ctr > MAX_TESTS
avg_time_str = 'average time = {}\n'.format(T / NUM_TESTS)
success_str = 'successfull runs = {}\n'.format(SUCC_CTR)
fail_str = 'failures = {}\n'.format(FAIL_CTR)
# time_summary = ''.join(time_spent_list) \
time_summary = \
'total_time_taken = {}\n'.format(T) \
+ avg_time_str \
def render_paraview_scene(pvd_file,
outfile=None,
field_name='m',
timesteps=None,
camera_position=[0, -200, +200],
camera_focal_point=[0, 0, 0],
camera_view_up=[0, 0, 1],
view_size=(800, 600),
magnification=1,
fit_view_to_scene=True,
color_by_axis=0,
colormap='coolwarm',
rescale_colormap_to_data_range=True,
show_colorbar=True,
colorbar_label_format='%-#5.2g',
add_glyphs=True,
glyph_type='cones',
glyph_scale_factor=1.0,
glyph_random_mode=True,
glyph_mask_points=True,
glyph_max_number_of_points=10000,
show_orientation_axes=False,
show_center_axes=False,
representation="Surface With Edges",
palette='screen',
use_parallel_projection=False,
trim_border=True,
rescale=None,
diffuse_color=None,
debug=False,
use_display=None):
# Convert color_by_axis to integer and store the name separately
try:
color_by_axis = _axes[color_by_axis.lower()]
except AttributeError:
if not color_by_axis in [0, 1, 2, -1]:
raise ValueError("color_by_axis must have one of the values "
"[0, 1, 2, -1] or ['x', 'y', 'z', 'magnitude']. "
"Got: {}".format(color_by_axis))
# Use absolute path for filenames because the script will be
# written to a temporary directory in a different location.
pvd_file = os.path.abspath(pvd_file)
if outfile is None:
_, outfile = tempfile.mkstemp(suffix='.png')
outfile_is_temporary = True
else:
outfile_is_temporary = False
outfile = os.path.abspath(outfile)
outdir = os.path.dirname(outfile)
if not os.path.exists(outdir):
logger.debug(
"Creating non-existing directory component '{}' of output filename."
.format(outdir))
os.makedirs(outdir)
logger.debug("Done.")
#
# Create the temporary script. The string 'script_string' will
# contain a call to the function in 'visualization_impl.py' which
# has all the parameter values filled in correctly.
#
tmpdir = tempfile.mkdtemp()
scriptfile = os.path.join(tmpdir, 'render_scene.py')
script_string = textwrap.dedent("""
from visualization_impl import render_paraview_scene, find_valid_X_display
import os
if not os.environ.has_key('DISPLAY'):
display = find_valid_X_display()
if display is None:
raise RuntimeError("Could not render Paraview scene as no valid X display was found.")
else:
os.environ['DISPLAY'] = ':' + str(display)
render_paraview_scene(
'{}', '{}', {}, {},
{}, {}, {},
{}, {}, {}, {},
'{}', {}, {},
'{}', {}, '{}',
{}, {}, {},
{}, {},
{}, '{}', '{}', {},
{}, {}, {})
""".format(pvd_file, outfile, repr(field_name),
re.sub('\n', '', repr(timesteps)), camera_position,
camera_focal_point, camera_view_up, view_size,
magnification, fit_view_to_scene, color_by_axis,
colormap, rescale_colormap_to_data_range,
show_colorbar, colorbar_label_format, add_glyphs,
glyph_type, glyph_scale_factor, glyph_random_mode,
glyph_mask_points, glyph_max_number_of_points,
show_orientation_axes, show_center_axes,
representation, palette, use_parallel_projection,
trim_border, rescale, diffuse_color))
with open(scriptfile, 'w') as f:
f.write(script_string)
vis_impl_script = os.path.join(os.path.dirname(__file__),
'./visualization_impl.py')
if not os.path.exists(vis_impl_script):
vis_impl_script = os.path.join(os.path.dirname(__file__),
'./visualization_impl.so')
if not os.path.exists(vis_impl_script):
raise RuntimeError(
"Cannot use Paraview visualisation. This should not happen.")
shutil.copy(vis_impl_script, tmpdir)
# Execute the script in a separate process
curdir_bak = os.getcwd()
xpra_display = None
use_xpra = configuration.get_config_option("visualization", "use_xpra",
"True")
try:
display_bak = os.environ['DISPLAY']
except KeyError:
display_bak = None
try:
os.chdir(tmpdir)
if use_display is None:
use_display = configuration.get_config_option(
"visualization", "use_display", None)
if use_display == 'None':
use_display = None
if use_display is None and use_xpra.lower() != "false":
# Try to create a display using 'xpra'
try:
# Check whether 'xpra' is installed
sh.xpra('--version')
xpra_display = find_unused_X_display(xrange(10, 100))
sh.xpra('start', ':{}'.format(xpra_display))
use_display = xpra_display
logger.debug(
"Rendering Paraview scene on display :{} using xpra.".
format(xpra_display))
except sh.CommandNotFound:
logger.warning(
"Could not find the 'xpra' executable. You may want to "
"install it to avoid annoying pop-up windows from "
"Paraview. Under Debian/Ubuntu you can install it via "
"'sudo apt-get install xpra'.")
xpra_display = None
if use_display is not None:
os.environ['DISPLAY'] = ':{}'.format(use_display)
script_stdout = StringIO.StringIO()
script_stderr = StringIO.StringIO()
sh.python('render_scene.py', _out=script_stdout, _err=script_stderr)
except sh.ErrorReturnCode as ex:
logger.error(
"Could not render Paraview scene. Stdout and stderr of the script: "
"'{}', '{}'".format(script_stdout.getvalue(),
script_stderr.getvalue()))
# raise
finally:
if debug == True:
logger.debug("Temporary directory '{}' kept for debugging. You "
"can try to run 'render_script.py' manually "
"there.".format(tmpdir))
else:
shutil.rmtree(tmpdir)
os.chdir(curdir_bak) # change back into the original directory
if xpra_display is not None:
# XXX TODO: It may be nice to keep the xpra display open
# until Finmag exits, because we are likely to
# render more than one snapshot.
sh.xpra('stop', ':{}'.format(xpra_display))
if display_bak is not None:
os.environ['DISPLAY'] = display_bak
else:
os.environ.pop('DISPLAY', None)
try:
image = IPython.core.display.Image(filename=outfile)
except IOError:
# Something went wrong (missing X display?); let's not choke but return
# None instead.
image = None
if outfile_is_temporary:
# Clean up temporary file
os.remove(outfile)
return image
def release():
"""Release/publish the documentation to the webpage.
"""
# Save the current state.
branch = git('rev-parse', '--abbrev-ref', 'HEAD').stdout.rstrip()
git.stash('save', "Work in progress while updating gh-pages branch")
# Check out the gh-pages branch.
try:
git.checkout('gh-pages')
except ErrorReturnCode_128: # Create the branch if necessary.
git.checkout('-b', 'gh-pages')
# Remove the existing files in the base folder.
extensions = ['*.html', '*.inv']
fnames = util.multiglob('..', extensions)
for fname in fnames:
os.remove(fname)
# Copy the new files to the base folder.
fnames = util.multiglob(BUILD_DIR, extensions)
for fname in fnames:
shutil.copy(fname, '..')
# Track the new files.
fnames = util.multiglob('..', extensions)
git.add(*fnames)
# Copy but rename the folders referenced in the HTML files.
# Github only recognizes images, stylesheets, and javascripts as folders.
folders = [
('_images', 'images'),
('_static', 'javascripts'),
]
for (src, dst) in folders:
dst = os.path.join('..', dst)
# Remove the existing folder.
shutil.rmtree(dst, ignore_errors=True)
# Copy the new folder.
shutil.copytree(os.path.join(BUILD_DIR, src), dst)
# Track the new folder.
git.add(dst)
# Update the HTML files to reference the new folder names.
html_fnames = glob(os.path.join('..', '*.html'))
util.replace(html_fnames, folders)
# Copy and rename the examples folder.
src = os.path.join(BUILD_DIR, 'examples')
dst = '../examples2'
# Remove the existing folder.
shutil.rmtree(dst, ignore_errors=True)
# Copy the new files.
os.mkdir(dst)
for fname in os.listdir(src):
shutil.copy(os.path.join(src, fname), os.path.join(dst, fname))
# Track the new folder.
git.add(dst)
# Update the HTML files to reference the new folder names.
util.replace(html_fnames, [(r'"\./examples/', r'"./examples2/')])
# Update the sitemap.
print((python('sitemap_gen.py', config="sitemap_conf.xml")))
# Commit the changes.
try:
git.commit('-a', m="Rebuilt documentation")
except ErrorReturnCode_1:
pass # No changes to commit
# If desired, rebase and push the changes to origin.
print("The gh-pages branch has been updated and is currently checked out.")
if util.yes("Do you want to rebase it and push the changes to "
"origin (y/n)?"):
git.rebase('-i', 'origin/gh-pages')
git.push.origin('gh-pages')
# Return to the original state.
git.checkout(branch)
try:
git.stash.pop()
except ErrorReturnCode_1:
pass # No stash was necessary in the first place.
print(("Now back on " + branch))