def run(self):
from pyquickhelper.loghelper import run_cmd
parameters = self.get_parameters()
location = parameters['file_or_folder']
folder = os.path.join(location, "_doc", "notebooks")
if not os.path.exists(folder):
folder = location
cmd = [
"jupyter-notebook",
"--notebook-dir=%s" % folder, "--NotebookApp.token=",
"--NotebookApp.password="******" ".join(cmd), wait=True, fLOG=print, communicate=False)
def plot_pipeline(dot=None, pipeline=None, dataframe=None, name='pipeline'):
dot_file = name + "_graph.dot"
if dot == None:
dot = pipeline2dot(pipeline, dataframe)
with open(dot_file, "w", encoding="utf-8") as f:
f.write(dot)
if sys.platform.startswith("win") and "Graphviz" not in os.environ["PATH"]:
os.environ['PATH'] = os.environ[
'PATH'] + r';C:\Program Files (x86)\Graphviz2.38\bin'
cmd = "dot -G=300 -Tpng {0} -o{0}.png".format(dot_file)
run_cmd(cmd, wait=True, fLOG=print)
def build_machinelearningext(version="Release"):
"Builds the module machinelearningext."
from pyquickhelper.loghelper import run_cmd
env = os.environ.get('DOTNET_CLI_TELEMETRY_OPTOUT', None)
if env is None:
os.environ['DOTNET_CLI_TELEMETRY_OPTOUT'] = '1'
print('[csharpyml.env] DOTNET_CLI_TELEMETRY_OPTOUT={0}'.format(
os.environ['DOTNET_CLI_TELEMETRY_OPTOUT']))
# builds the other libraries
cmds = [
'dotnet restore machinelearningext.sln',
'dotnet build -c %s machinelearningext.sln' % version
]
folder = os.path.abspath("cscode")
folder = os.path.join("machinelearningext", "machinelearningext")
outs = []
for cmd in cmds:
out, err = run_cmd(cmd, fLOG=print, wait=True, change_path=folder)
if len(err) > 0:
raise RuntimeError(
"Unable to compile C# code.\nCMD: {0}\n--ERR--\n{1}".format(
cmd, err))
elif len(out) > 0:
outs.append(out)
print('[csharpyml.dotnet] OUT')
print(out)
# Copy specific files.
copy_assemblies(version=version)
def run_graphviz(filename, image, engine="dot"):
"""
Run :epkg:`GraphViz`.
@param filename filename which contains the graph definition
@param image output image
@param engine *dot* or *neato*
@return output of graphviz
"""
ext = os.path.splitext(image)[-1]
if ext != ".png":
raise Exception("extension should be .png not " + str(ext))
if sys.platform.startswith("win"):
bin_ = os.path.dirname(find_graphviz_dot())
# if bin not in os.environ["PATH"]:
# os.environ["PATH"] = os.environ["PATH"] + ";" + bin
cmd = '"{0}\\{3}" -Tpng "{1}" -o "{2}"'.format(
bin_, filename, image, engine)
else:
cmd = '"{0}" -Tpng "{1}" -o "{2}"'.format(engine, filename, image)
out, err = run_cmd(cmd, wait=True)
if len(err) > 0:
raise Exception(
"unable to run Graphviz\nCMD:\n{0}\nOUT:\n{1}\nERR:\n{2}".format(cmd, out, err))
return out
def test_reap_children(self):
fLOG(__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if sys.platform.startswith("win"):
cmd = "pause"
else:
cmd = 'ls -la | less'
temp = get_temp_folder(__file__, "temp_reap_children")
clog = CustomLog(temp)
proc, _ = run_cmd(cmd, wait=False, fLOG=clog)
self.assertTrue(_ is None)
clog('proc={} pid={}'.format(proc, proc.pid))
ki = reap_children(fLOG=clog, subset={proc.pid})
clog('ki={0}'.format(ki))
if ki is None and not is_travis_or_appveyor(
) and __name__ != '__main__':
warnings.warn(
"reap_children could not be fully tested ki is None.")
return
self.assertTrue(ki is not None)
self.assertEqual(len(ki), 1)
# fLOG(ki)
# To avoid a warning.
proc.returncode = 0
def test_exe(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
command = "dir" if sys.platform.startswith("win32") else "ls"
yml = """
language: python
python:
- {{Python35}}
before_script:
- %s
after_script:
- %s {{PLATFORM}}
script:
- %s
""".replace(" ", "") % (command, command, command)
temp = get_temp_folder(__file__, "temp_yaml_exe")
context = dict(Python34="fake", Python35=os.path.dirname(sys.executable),
Python27=None, Anaconda3=None, Anaconda2=None,
WinPython35=None, project_name="pyquickhelper",
root_path="ROOT", PLATFORM="win32")
obj, name = load_yaml(yml, context=context)
self.assertTrue(name is not None)
res = list(enumerate_convert_yaml_into_instructions(
obj, variables=context))
for r, var in res:
conv = convert_sequence_into_batch_file(r, variables=var)
if ("%s " % command) not in conv:
raise Exception("{0}\n--\n{1}".format(command, conv))
fLOG("####", conv)
ext = "bat" if command == "dir" else "sh"
name = os.path.join(temp, "yml.%s" % ext)
with open(name, "w") as f:
f.write(conv)
if is_travis_or_appveyor() == "__travis":
# linux, unable to test TestYamlExe.test_exe.
pass
else:
if sys.platform.startswith("win"):
cmd = name
else:
cmd = "bash " + name
try:
out, err = run_cmd(cmd, wait=True)
except PermissionError as e:
raise Exception(
"Unable to execute '{0}' which contains\n{1}".format(name, conv)) from e
fLOG("###")
fLOG(out)
if "BEFORE_SCRIPT" not in out:
raise Exception(
"{0}\nERR\n{2}\n#########\n{1}".format(out, conv, err))
if "AFTER_SCRIPT" not in out:
raise Exception(
"{0}\nERR\n{2}\n#########\n{1}".format(out, conv, err))
if "SCRIPT" not in out:
raise Exception(
"{0}\nERR\n{2}\n#########\n{1}".format(out, conv, err))
def convert(pathname, verbose=0):
"""
Converts into ONNX.
"""
# tflite
lite = os.path.join(pathname, 'model.lite')
if False and not os.path.exists(lite):
import tensorflow.lite as tfl
if verbose:
print('[convert] to lite %r.' % pathname)
converter = tfl.TFLiteConverter.from_saved_model(pathname)
try:
tflite_model = converter.convert()
except Exception as e:
print('[convert] lite failed due to %r.' % e)
tflite_model = None
if tflite_model is not None:
if verbose:
print('[convert] save lite %r.' % pathname)
with open(lite, "wb") as f:
f.write(tflite_model)
# node list
if verbose:
res = get_node_list(pathname, verbose=verbose)
print('[convert] node types: %r' % res)
# onnx
output = os.path.join(pathname, "model.onnx")
lastname = pathname.replace("\\", "/").split('/')[-1]
inputs = None
if lastname not in MODELS:
raise ValueError("Unknown model %r." % lastname)
model = MODELS[lastname]
inputs = model['inputs']
outputs = model['outputs']
tag = model['tag']
sig = model['signature_def']
onnx_inputs = model['onnx_inputs']
if inputs is None:
if verbose:
print('[convert] to ONNX %r.' % pathname)
raise NotImplementedError("Unable to convert %r." % lastname)
inputs = ",".join(inputs)
outputs = ",".join(outputs)
if not os.path.exists(output):
def noprint(*args):
pass
cmd = [
"python", "-m", "tf2onnx.convert", "--saved-model", pathname,
"--output", output, "--inputs", inputs, "--outputs", outputs,
'--tag', tag, '--signature_def', sig
]
out, err = run_cmd(" ".join(cmd),
wait=True,
fLOG=print if verbose else noprint,
shell=True)
return pathname, output, inputs, outputs, onnx_inputs
def run_graphviz(filename, image, engine="dot"):
"""
Run :epkg:`GraphViz`.
@param filename filename which contains the graph definition
@param image output image
@param engine *dot* or *neato*
@return output of graphviz
"""
ext = os.path.splitext(image)[-1]
if ext != ".png":
raise Exception("extension should be .png not " + str(ext))
if sys.platform.startswith("win"):
bin_ = os.path.dirname(find_graphviz_dot())
# if bin not in os.environ["PATH"]:
# os.environ["PATH"] = os.environ["PATH"] + ";" + bin
cmd = '"{0}\\{3}" -Tpng "{1}" -o "{2}"'.format(bin_, filename, image,
engine)
else:
cmd = '"{0}" -Tpng "{1}" -o "{2}"'.format(engine, filename, image)
out, err = run_cmd(cmd, wait=True)
if len(err) > 0:
raise Exception(
"Unable to run Graphviz\nCMD:\n{0}\nOUT:\n{1}\nERR:\n{2}".format(
cmd, out, err))
return out
def git_change_remote_origin(local_folder, url_https, user=None, password=None,
add_fetch=False, timeout=10, fLOG=noLOG):
"""
Changes the origin of the repository. The url and the password
refer to the new repository.
@param local_folder local folder
@param url_https url, example ``https://gitlab.server/folder/project_name``
@param user part 1 of the credentials
@param password part 2 of the credentials
@param timeout timeout for the command line
@param add_fetch add instruction ``fetch``
@param fLOG logging function
@return something
The function runs the instruction::
git remote remove origin
git remote add origin url
"""
url_user = git_url_user_password(url_https, user, password)
cmds = """
cd {0}
git remote remove origin
git remote add origin {1}
""".format(local_folder, url_user).replace(" ", "").strip(" \n\r\t")
if add_fetch:
cmds += "\ngit fetch"
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(cmd, sin=sin, wait=True, timeout=timeout, fLOG=fLOG)
git_check_error(out, err, fLOG)
def build_module(version="Release"):
"build the module"
# git submodule add https://github.com/dotnet/machinelearning.git cscode/machinelearning
# We build a dotnet application.
from pyquickhelper.loghelper import run_cmd
env = os.environ.get('DOTNET_CLI_TELEMETRY_OPTOUT', None)
if env is None:
os.environ['DOTNET_CLI_TELEMETRY_OPTOUT'] = '1'
print('[csharpyml.env] DOTNET_CLI_TELEMETRY_OPTOUT={0}'.format(
os.environ['DOTNET_CLI_TELEMETRY_OPTOUT']))
# builds the other libraries
cmds = [
'dotnet restore CSharPyMLExtension_netcore.sln',
'dotnet build -c %s CSharPyMLExtension_netcore.sln' % version
]
folder = os.path.abspath("cscode")
outs = []
for cmd in cmds:
out, err = run_cmd(cmd, fLOG=print, wait=True, change_path=folder)
if len(err) > 0:
raise RuntimeError(
"Unable to compile C# code.\nCMD: {0}\n--ERR--\n{1}".format(
cmd, err))
elif len(out) > 0:
outs.append(out)
print('[csharpyml.dotnet] OUT')
print(out)
# Copy specific files.
copy_assemblies(version=version)
def run_benchmark(runtime, srcdir, logger, skip, white_list=None):
filenames = []
skls = sklearn_operators(extended=True)
skls = [_['name'] for _ in skls]
if white_list:
skls = [_ for _ in skls if _ in white_list]
skls.sort()
pbar = tqdm(skls)
for op in pbar:
if skip is not None and op in skip:
continue
pbar.set_description("[%s]" % (op + " " * (25 - len(op))))
out_raw = os.path.join(srcdir, "bench_raw_%s_%s.csv" % (runtime, op))
out_sum = os.path.join(srcdir, "bench_sum_%s_%s.csv" % (runtime, op))
cmd = ('{0} -m mlprodict validate_runtime --verbose=0 --out_raw={1} --out_summary={2} '
'--benchmark=1 --dump_folder={3} --runtime={4} --models={5}'.format(
get_interpreter_path(), out_raw, out_sum, srcdir, runtime, op))
logger.info("[mlprodict] cmd '{}'.".format(cmd))
out, err = run_cmd(cmd, wait=True, fLOG=None)
if not os.path.exists(out_sum):
logger.warning("[mlprodict] unable to find '{}'.".format(out_sum))
print("[mlprodict-sphinx] cmd '{}'".format(cmd))
print("[mlprodict-sphinx] unable to find '{}'".format(out_sum))
msg = "Unable to find '{}'\n--CMD--\n{}\n--OUT--\n{}\n--ERR--\n{}".format(
out_sum, cmd, out, err)
print(msg)
rows = [{'name': op, 'scenario': 'CRASH',
'ERROR-msg': msg.replace("\n", " -- ")}]
df = DataFrame(rows)
df.to_csv(out_sum, index=False)
filenames.append((out_raw, out_sum))
return filenames
def is_java_installed(fLOG=noLOG):
"""
Checks if :epkg:`java` is installed.
@return boolean
"""
if sys.platform.startswith("win"):
cmd = get_java_cmd() + " -showversion"
out, err = run_cmd(cmd, wait=True, log_error=False)
fLOG("OUT:\n", out)
fLOG("ERR:\n", err)
return "Java(TM)" in err
else:
cmd = get_java_cmd() + " -showversion"
out, err = run_cmd(cmd, wait=True, log_error=False)
fLOG("OUT:\n", out)
fLOG("ERR:\n", err)
return "OpenJDK Runtime Environment" in err
def test_notebook_runner_ml_huge(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if is_travis_or_appveyor() == "appveyor":
# pytables has an issue
# return
pass
if sys.platform.startswith("win"):
import numpy
import tables
foldn = os.path.abspath(os.path.dirname(numpy.__file__))
foldt = os.path.normpath(os.path.dirname(tables.__file__))
rootn = os.path.dirname(foldn)
roott = os.path.dirname(foldt)
if rootn != roott:
pp = os.environ.get('PYTHONPATH', '')
if "SECONDTRY" in pp:
raise Exception(
"Infinite loog\n{0}\n{1}\n**EXE\n{2}\n**PP\n{3}\n****".format(rootn, roott, sys.executable, pp))
# We need to run this file with the main python.
# Otherwise it fails for tables: DLL load failed.
exe = os.path.normpath(os.path.join(
rootn, "..", "..", "python.exe"))
cmd = '"{0}" -u "{1}"'.format(exe, os.path.abspath(__file__))
import pyquickhelper
import pyensae
import jyquickhelper
import src.ensae_teaching_cs
import mlstatpy
import pymyinstall
add = ["SECONDTRY"]
for mod in [pyquickhelper, pyensae, jyquickhelper, src.ensae_teaching_cs, mlstatpy, pymyinstall]:
add.append(os.path.normpath(os.path.join(
os.path.dirname(mod.__file__), "..")))
fLOG("set PYTHONPATH={0}".format(";".join(add)))
os.environ['PYTHONPATH'] = ";".join(add)
out, err = run_cmd(cmd, wait=True, fLOG=fLOG)
if len(err) > 0:
lines = err.split("\n")
lines = [_ for _ in lines if _[0] != " "]
lines = [_ for _ in lines if "warning" not in _.lower()]
if len(lines) > 0:
raise Exception("--CMD:\n{0}\n--OUT:\n{1}\n--ERR\n{2}\n--ERR2\n{3}\n--PP\n{4}".format(
cmd, out, err, "\n".join(lines), pp))
return
import tables
assert tables is not None
this = os.path.abspath(os.path.dirname(tables.__file__))
self.a_test_notebook_runner(
"ml_huge", "expose", additional_path=[this])
def is_java_installed(fLOG=noLOG):
"""
this function checks if java is installed
@return boolean
"""
cmd = get_java_cmd() + " -showversion"
out, err = run_cmd(cmd, wait=True, log_error=False)
fLOG("OUT:\n", out)
fLOG("ERR:\n", err)
return "Java(TM)" in err
def test_notebook_runner_ml_huge(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if sys.platform.startswith("win"):
import numpy
import tables # pylint: disable=E0401
foldn = os.path.abspath(os.path.dirname(numpy.__file__))
foldt = os.path.normpath(os.path.dirname(tables.__file__))
rootn = os.path.dirname(foldn)
roott = os.path.dirname(foldt)
if rootn != roott:
pp = os.environ.get('PYTHONPATH', '')
if "SECONDTRY" in pp:
raise Exception(
"Infinite loog\n{0}\n{1}\n**EXE\n{2}\n**PP\n{3}\n****".format(rootn, roott, sys.executable, pp))
# We need to run this file with the main python.
# Otherwise it fails for tables: DLL load failed.
exe = os.path.normpath(os.path.join(
rootn, "..", "..", "python.exe"))
cmd = '"{0}" -u "{1}"'.format(exe, os.path.abspath(__file__))
import pyquickhelper
import pyensae
import jyquickhelper
import ensae_teaching_cs
import mlstatpy
import pymyinstall
add = ["SECONDTRY"]
for mod in [pyquickhelper, pyensae, jyquickhelper, ensae_teaching_cs,
mlstatpy, pymyinstall]:
add.append(os.path.normpath(os.path.join(
os.path.dirname(mod.__file__), "..")))
fLOG("set PYTHONPATH={0}".format(";".join(add)))
os.environ['PYTHONPATH'] = ";".join(add)
out, err = run_cmd(cmd, wait=True, fLOG=fLOG)
if len(err) > 0:
lines = err.split("\n")
lines = [_ for _ in lines if _[0] != " "]
lines = [_ for _ in lines if "warning" not in _.lower()]
if len(lines) > 0:
raise Exception("--CMD:\n{0}\n--OUT:\n{1}\n--ERR\n{2}\n--ERR2\n{3}\n--PP\n{4}".format(
cmd, out, err, "\n".join(lines), pp))
return
import tables # pylint: disable=E0401
assert tables is not None
this = os.path.abspath(os.path.dirname(tables.__file__))
self.a_test_notebook_runner(
"ml_huge", "expose", additional_path=[this])
def runpy(self, line, cell=None):
"""
Defines command ``%%runpy``.
.. nbref::
:title: runpy
``%%runpy`` runs a python script which accepts
standards input and produces standard outputs,
a timeout is set up at 10s. It is almost equivalent to::
from pyquickhelper.loghelper import run_cmd
import sys
cmd = sys.executable.replace(
"pythonw",
"python") + " " + filename + " " + args
out, err = run_cmd(
cmd, wait=True, sin=cell, communicate=True, timeout=10, shell=False)
.. versionadded:: 1.1
"""
parser = self.get_parser(MagicFile.runpy_parser, "runpy")
args = self.get_args(line, parser)
if args is not None:
filename = args.file
if len(filename) == 0:
self.runpy("")
else:
args = args.args
cmd = sys.executable.replace("pythonw", "python")
cmd += " " + filename + " "
cmd += " ".join(
'"{0}"'.format(_)
for _ in args) if isinstance(args, list) else args
tosend = cell
out, err = run_cmd(cmd,
wait=True,
sin=tosend,
communicate=True,
timeout=10,
shell=False)
if len(err) > 0:
return HTML(
'<font color="#DD0000">Error</font><br /><pre>\n%s\n</pre>'
% err)
else:
return HTML('<pre>\n%s\n</pre>' % out)
return None
def test_notebook_svg(self):
"""
If the test fails, look into issue
`216 <https://github.com/sdpython/pyquickhelper/issues/216>`_.
Avoid nbconvert==5.4.0,==5.4.1.
"""
fLOG(__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
path = os.path.abspath(os.path.split(__file__)[0])
fold = os.path.normpath(os.path.join(path, "notebooks_svg"))
nbs = [
os.path.join(fold, _) for _ in os.listdir(fold) if ".ipynb" in _
]
formats = ["latex", "pdf"]
temp = os.path.join(path, "temp_nb_bug_svg")
if not os.path.exists(temp):
os.mkdir(temp)
for file in os.listdir(temp):
os.remove(os.path.join(temp, file))
if is_travis_or_appveyor() in ('travis', 'appveyor', 'azurepipe',
'circleci'):
return
setup_environment_for_help()
obj = SVG2PDFPreprocessor()
self.assertIn('inkscape', obj.inkscape)
cmd = '%s --version' % obj.inkscape
out, err = run_cmd(cmd, wait=True, shell=False)
self.assertIn('inkscape', out.lower())
vers = obj.inkscape_version
self.assertIn('inkscape', out.lower())
res = process_notebooks(nbs, temp, temp, formats=formats)
for _ in res:
fLOG(_)
self.assertExists(_[0])
with open(os.path.join(temp,
"seance4_projection_population_correction.tex"),
"r",
encoding="utf8") as f:
content = f.read()
exp = "seance4_projection_population_correction_50_0.pdf"
if exp not in content:
raise Exception(content)
def test_py3to2(self):
fLOG(__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
temp = get_temp_folder(__file__, "temp_py3to2")
root = os.path.abspath(os.path.dirname(__file__))
root = os.path.normpath(os.path.join(root, "..", ".."))
conv = py3to2_convert_tree(root, temp, fLOG=fLOG)
if len(conv) < 20:
raise Exception("not enough copied files")
script = """
import sys
sys.path = [p for p in sys.path if "src" not in p and "ut_" not in p]
sys.path.append(r"{0}")
print ""
for k in sys.path:
print k
import pyquickhelper
""".replace(" ", "")
script = script.format(os.path.join(temp, "src"))
to = os.path.join(temp, "simpletry.py")
with open(to, "w", encoding="utf8") as f:
f.write(script)
pyexe2 = None
for location in [
r"C:\Anaconda2",
r"C:\Anaconda",
r"C:\WinPython-64bit-2.7.9.3\python-2.7.9.amd64",
]:
exe = os.path.join(location, "python.exe")
if os.path.exists(exe):
pyexe2 = exe
break
if pyexe2 is not None:
cmd = "{0} {1}".format(pyexe2, to)
out, err = run_cmd(cmd, wait=True)
if len(err) > 0:
raise Exception(
"conversion did not work:\nOUT\n:{0}\nERR:\n{1}".format(
out, err))
else:
fLOG("python 2.7 was not found")
def test_script_pig(self):
fLOG(__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
data = os.path.join(os.path.abspath(os.path.split(__file__)[0]),
"data")
pyth = """
import sys, datetime
cols = [ _ for _ in sys.argv if ".py" not in _ ]
for row in sys.stdin:
js = eval(row)
for station in js:
vals = [ station[c] for c in cols ]
sys.stdout.write(",".join(vals))
sys.stdout.write("\\n")
sys.stdout.flush()
""".replace(" ", "")
fold = os.path.join(data, "..", "temp_pypig_out")
if not os.path.exists(fold):
os.mkdir(fold)
pyfile = os.path.join(fold, "pystream.py")
with open(pyfile, "w", encoding="utf8") as f:
f.write(pyth)
tosend = """[{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - """ + \
"""75010 PARIS", 'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), """ + \
"""'lng': 2.348395236282807, 'contract_name': """ + \
"""'Paris', 'name': '10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': """ + \
"""48.87242006305313, 'bonus': 0, 'status': 'OPEN', 'available_bikes': 32, """ + \
"""'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), """ + \
"""'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33}]"""
cmd = sys.executable.replace("pythonw",
"python") + " " + pyfile + " name"
out, err = run_cmd(cmd,
wait=True,
sin=tosend,
communicate=True,
timeout=3,
shell=False)
fLOG("OUT\n", out)
fLOG("ERR\n", err)
assert len(out) > 0
def run_dot(dot_file, outimg):
"""
calls graphivz on a dot file and produces an image
@param dot_file file, format `DOT <http://www.graphviz.org/doc/info/lang.html>`_
@param outimg output image
@return out, err (stdout, stderr from graphviz)
.. versionadded:: 1.1
"""
ext = os.path.splitext(outimg)[-1].strip(".")
exe = dot_exe()
cmd = "\"{0}\" -T{1} -o{2} {3}".format(exe, ext, outimg, dot_file)
out, err = run_cmd(cmd, wait=True)
if len(err) > 0:
raise Exception("unable to run graphviz on {0}.\nCMD:\n{1}\nOUT:\n{2}\nERR:\n{3}".format(
dot_file, cmd, out, err))
return out, err
def run_jython(pyfile,
argv=None,
jython_path=None,
sin=None,
timeout=None,
fLOG=noLOG):
"""
runs a jython script and returns the standard output and error
@param pyfile jython file
@param argv arguments to sned to the command line
@param jython_path path to jython standalone
@param sin data to send to the standard input
@param timeout timeout
@param fLOG logging function
@return out, err
If *jython_path* is None, the function looks into this directory.
"""
if jython_path is None:
jython_path = get_jython_jar()
def clean(i, p):
"local function"
if i == 0:
return p
if '"' in p:
p = p.replace('"', '\\"')
if " " in p:
p = '"{0}"'.format(p)
return p
cmd = [get_java_cmd(), "-jar", jython_path, pyfile]
if argv is not None:
cmd.extend(argv)
cmd = " ".join(clean(i, _) for i, _ in enumerate(cmd))
out, err = run_cmd(cmd,
wait=True,
sin=sin,
communicate=True,
timeout=timeout,
shell=False)
return out, err
def git_commit_all(local_folder,
url_https,
message,
user=None,
password=None,
timeout=300,
fLOG=noLOG):
"""
from a git repository,
it requires `GIT <http://git-scm.com/>`_ to be installed
and uses the command line.
@param local_folder local folder of the project
@param url_https url, example ``https://gitlab.server/folder/project_name``
@param message message for the commit
@param user part 1 of the credentials
@param password part 2 of the credentials
@param timeout timeout for the command line
@param fLOG logging function
@return None
If the reposity has already been cloned, it does not do it again.
We assume that git can be run without giving its full location.
The function executes the following commands::
cd [folder]
git add -A
git commit -m "[message]"
git push -u origin master
"""
cmds = """
cd {0}
git add -A
git commit -m "{1}"
git push -u origin master
""".format(local_folder, message).replace(" ",
"").strip(" \n\r\t")
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(cmd, sin=sin, wait=True, timeout=timeout, fLOG=fLOG)
git_check_error(out, err, fLOG)
def run_dot(dot_file, outimg):
"""
calls graphivz on a dot file and produces an image
@param dot_file file, format `DOT <http://www.graphviz.org/doc/info/lang.html>`_
@param outimg output image
@return out, err (stdout, stderr from graphviz)
.. versionadded:: 1.1
"""
ext = os.path.splitext(outimg)[-1].strip(".")
exe = dot_exe()
cmd = "\"{0}\" -T{1} -o{2} {3}".format(exe, ext, outimg, dot_file)
out, err = run_cmd(cmd, wait=True)
if len(err) > 0:
raise Exception(
"unable to run graphviz on {0}.\nCMD:\n{1}\nOUT:\n{2}\nERR:\n{3}".
format(dot_file, cmd, out, err))
return out, err
def runpy(self, line, cell=None):
"""
Defines command ``%%runpy``.
.. nbref::
:title: runpy
``%%runpy`` runs a python script which accepts
standards input and produces standard outputs,
a timeout is set up at 10s. It is almost equivalent to::
from pyquickhelper.loghelper import run_cmd
import sys
cmd = sys.executable.replace(
"pythonw",
"python") + " " + filename + " " + args
out, err = run_cmd(
cmd, wait=True, sin=cell, communicate=True, timeout=10, shell=False)
.. versionadded:: 1.1
"""
parser = self.get_parser(MagicFile.runpy_parser, "runpy")
args = self.get_args(line, parser)
if args is not None:
filename = args.file
if len(filename) == 0:
self.runpy("")
else:
args = args.args
cmd = sys.executable.replace("pythonw", "python")
cmd += " " + filename + " "
cmd += " ".join('"{0}"'.format(_)
for _ in args) if isinstance(args, list) else args
tosend = cell
out, err = run_cmd(
cmd, wait=True, sin=tosend, communicate=True, timeout=10, shell=False)
if len(err) > 0:
return HTML(
'<font color="#DD0000">Error</font><br /><pre>\n%s\n</pre>' % err)
else:
return HTML('<pre>\n%s\n</pre>' % out)
return None
def git_commit_all(
local_folder,
url_https,
message,
user=None,
password=None,
timeout=300,
fLOG=noLOG):
"""
from a git repository,
it requires `GIT <http://git-scm.com/>`_ to be installed
and uses the command line.
@param local_folder local folder of the project
@param url_https url, example ``https://gitlab.server/folder/project_name``
@param message message for the commit
@param user part 1 of the credentials
@param password part 2 of the credentials
@param timeout timeout for the command line
@param fLOG logging function
@return None
If the reposity has already been cloned, it does not do it again.
We assume that git can be run without giving its full location.
The function executes the following commands::
cd [folder]
git add -A
git commit -m "[message]"
git push -u origin master
"""
cmds = """
cd {0}
git add -A
git commit -m "{1}"
git push -u origin master
""".format(local_folder, message).replace(" ", "").strip(" \n\r\t")
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(cmd, sin=sin, wait=True, timeout=timeout, fLOG=fLOG)
git_check_error(out, err, fLOG)
def build_machinelearning(version="Release"):
"Builds machinelearning (ml.net)."
from pyquickhelper.loghelper import run_cmd
print('[csharpyml.machinelearning]')
this = os.path.abspath(os.path.dirname(__file__))
folder = os.path.join(this, 'cscode', 'machinelearning')
cmd = "build{0}"
if sys.platform.startswith("win"):
cmd = cmd.format('.cmd')
else:
cmd = cmd.format('.sh')
full = os.path.join(folder, cmd)
if not os.path.exists(full):
existing = os.listdir(folder)
raise FileNotFoundError(
"Unable to find '{0}', build failed. Found:\n{1}".format(
full, "\n".join(existing)))
if not sys.platform.startswith("win"):
cmd = "bash --verbose " + cmd
cmd += ' -' + version
out, err = run_cmd(cmd, wait=True, change_path=folder)
if len(err) > 0:
# Filter out small errors.
errs = []
lines = err.split('\n')
for line in lines:
if 'ILAsmVersion.txt: No such file or directory' in line:
continue
errs.append(line)
err = "\n".join(errs)
if len(err) > 0:
raise RuntimeError(
"Unable to build machinelearning code.\nCMD: {0}\n--ERR--\n{1}".
format(cmd, err))
elif len(out) > 0:
print('[csharpyml.machinelearning] OUT')
print(out)
bin = os.path.join(folder, "bin")
if not os.path.exists(bin):
existing = os.listdir(folder)
raise FileNotFoundError(
"Unable to find '{0}', build failed. Found:\n{1}".format(
bin, "\n".join(existing)))
def test_script_pig(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
data = os.path.join(
os.path.abspath(
os.path.split(__file__)[0]),
"data")
pyth = """
import sys, datetime
cols = [ _ for _ in sys.argv if ".py" not in _ ]
for row in sys.stdin:
js = eval(row)
for station in js:
vals = [ station[c] for c in cols ]
sys.stdout.write(",".join(vals))
sys.stdout.write("\\n")
sys.stdout.flush()
""".replace(" ", "")
fold = os.path.join(data, "..", "temp_pypig_out")
if not os.path.exists(fold):
os.mkdir(fold)
pyfile = os.path.join(fold, "pystream.py")
with open(pyfile, "w", encoding="utf8") as f:
f.write(pyth)
tosend = """[{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - 75010 PARIS", 'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), 'lng': 2.348395236282807, 'contract_name': """ + \
"""'Paris', 'name': '10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, 'bonus': 0, 'status': 'OPEN', 'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), """ + \
"""'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33}]"""
cmd = sys.executable.replace(
"pythonw",
"python") + " " + pyfile + " name"
out, err = run_cmd(cmd, wait=True, sin=tosend,
communicate=True, timeout=3, shell=False)
fLOG("OUT\n", out)
fLOG("ERR\n", err)
assert len(out) > 0
def git_change_remote_origin(local_folder,
url_https,
user=None,
password=None,
add_fetch=False,
timeout=10,
fLOG=noLOG):
"""
Change the origin of the repository. The url and the password
refer to the new repository.
@param local_folder local folder
@param url_https url, example ``https://gitlab.server/folder/project_name``
@param user part 1 of the credentials
@param password part 2 of the credentials
@param timeout timeout for the command line
@param add_fetch add instruction ``fetch``
@param fLOG logging function
@return something
The function runs the instruction::
git remote remove origin
git remote add origin url
"""
url_user = git_url_user_password(url_https, user, password)
cmds = """
cd {0}
git remote remove origin
git remote add origin {1}
""".format(local_folder, url_user).replace(" ",
"").strip(" \n\r\t")
if add_fetch:
cmds += "\ngit fetch"
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(cmd, sin=sin, wait=True, timeout=timeout, fLOG=fLOG)
git_check_error(out, err, fLOG)
def run_jython(pyfile,
argv=None,
jython_path=None,
sin=None,
timeout=None,
fLOG=noLOG):
"""
runs a jython script and returns the standard output and error
@param pyfile jython file
@param argv arguments to sned to the command line
@param jython_path path to jython standalone
@param sin data to send to the standard input
@param timeout timeout
@param fLOG logging function
@return out, err
If *jython_path* is None, the function looks into this directory.
"""
if jython_path is None:
jython_path = get_jython_jar()
def clean(i, p):
if i == 0:
return p
if '"' in p:
p = p.replace('"', '\\"')
if " " in p:
p = '"{0}"'.format(p)
return p
cmd = [get_java_cmd(), "-jar", jython_path, pyfile]
if argv is not None:
cmd.extend(argv)
cmd = " ".join(clean(i, _) for i, _ in enumerate(cmd))
out, err = run_cmd(
cmd, wait=True, sin=sin, communicate=True, timeout=timeout, shell=False)
return out, err
def git_clone(local_folder, url_https, user=None, password=None, timeout=60,
init=True, fLOG=noLOG):
"""
Clones a project from a git repository in a non empty local folder,
it requires `GIT <http://git-scm.com/>`_ to be installed
and uses the command line.
@param local_folder local folder of the project
@param url_https url, example ``https://gitlab.server/folder/project_name``
@param user part 1 of the credentials
@param password part 2 of the credentials
@param timeout timeout for the command line
@param init see below (True, use fetch, False, use clone)
@param fLOG logging function
@return local_folder
If the reposity has already been cloned, it does not do it again.
We assume that git can be run without giving its full location.
The function executes the following commands (if init is True)::
cd [folder]
git init
git remote add origin [https://user.password@server/project.git]
git fetch
Otherwise, it does::
cd [folder]
git clone origin [https://user.password@server/project.git]
git fetch
A folder will be created.
.. exref::
:tag: Automation
:title: Clone many folders in one row
::
eleves = "project1;project2;..."
root = r"destination"
for el in eleves.split(";"):
cl = el.lower().replace(".","-")
fold = os.path.join(root, el)
if not os.path.exists(fold):
print("clone", el)
url = "https://<gitlab>/<group>/{0}.git".format(cl)
git_clone( fold, url,user=user,password=password, init=False,fLOG=print)
"""
url_user = git_url_user_password(url_https, user, password)
timeout = 60
local_folder = os.path.normpath(os.path.abspath(local_folder))
if init:
if not os.path.exists(local_folder):
fLOG("creating folder", local_folder)
os.mkdir(local_folder)
hg = os.path.join(local_folder, ".git")
if os.path.exists(hg):
raise Exception("folder {0} should not exist".format(local_folder))
if not os.path.exists(hg):
cmds = """
cd {0}
git init
git remote add origin {1}
git fetch
""".format(local_folder, url_user).replace(" ", "").strip(" \n\r\t")
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(
cmd, sin=sin, wait=True, timeout=timeout, fLOG=fLOG)
git_check_error(out, err, fLOG)
return local_folder
else:
if not os.path.exists(local_folder):
fLOG("creating folder", local_folder)
os.mkdir(local_folder)
hg = os.path.join(local_folder, ".git")
if os.path.exists(hg):
raise Exception("folder {0} should not exist".format(local_folder))
final = os.path.split(url_user)[-1].replace(".git", "")
locf = os.path.join(local_folder, final)
if os.path.exists(locf):
raise Exception(
"folder {0} should not exists before cloning".format(locf))
cmds = """
cd {0}
git clone {1} .
""".format(local_folder, url_user).replace(" ", "").strip(" \n\r\t")
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(cmd, sin=sin, wait=True, timeout=timeout, fLOG=fLOG)
git_check_error(out, err, fLOG)
return locf
def test_compile_module(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
temp = get_temp_folder(__file__, "temp_compile_module")
source = os.path.join(temp, "cdemo.cpp")
init = os.path.join(temp, "__init__.py")
setup = os.path.join(temp, "setup.py")
with open(source, "w") as f:
f.write(TestModuleC.content_c)
with open(init, "w") as f:
pass
setup_content = dedent("""
from distutils.core import setup, Extension
module1 = Extension('stdchelper_demo', sources=['{0}'])
setup (name = 'ccdemo', version = '1.0',
description = 'This is a demo package.',
ext_modules = [module1])
""".format(source.replace("\\", "/")))
with open(setup, "w") as f:
f.write(setup_content)
cmd = "{0} {1} build_ext --inplace".format(sys.executable, setup)
out, err = run_cmd(cmd, wait=True, fLOG=fLOG, change_path=temp)
if "error" in out or "error" in err:
out_ = out.replace("-Werror=format-security", "")
if "error" in out_:
raise Exception(
"Unable to compile\n--OUT--\n{0}\n--ERR--\n{1}".format(out, err))
if sys.platform == "win32":
name = "stdchelper_demo.cp%d%d-win_amd64.pyd" % sys.version_info[:2]
elif sys.platform == "darwin":
if sys.version_info[:2] <= (3, 7):
name = "stdchelper_demo.cpython-%d%dm-darwin.so" % sys.version_info[:2]
else:
name = "stdchelper_demo.cpython-%d%d-darwin.so" % sys.version_info[:2]
else:
if sys.version_info[:2] <= (3, 7):
name = "stdchelper_demo.cpython-%d%dm-x86_64-linux-gnu.so" % sys.version_info[:2]
else:
name = "stdchelper_demo.cpython-%d%d-x86_64-linux-gnu.so" % sys.version_info[:2]
fullname = os.path.join(temp, name)
if not os.path.exists(fullname):
files = os.listdir(os.path.dirname(fullname))
raise FileNotFoundError(
"Unable to find '{0}' (platform '{1}')\nFound:\n{2}".format(
fullname, sys.platform, "\n".join(files)))
mo = import_module(None, fullname, fLOG,
additional_sys_path=None, first_try=True)
self.assertIsInstance(mo, tuple)
self.assertEqual(len(mo), 2)
self.assertTrue(hasattr(mo[0], '__doc__'))
if 'stdchelper_demo' in sys.modules:
del sys.modules['stdchelper_demo']
temp2 = get_temp_folder(__file__, "temp_compile_module2")
store_obj = {}
actions = copy_source_files(temp, temp2, fLOG=fLOG)
store_obj = {}
indexes = {}
add_file_rst(temp2, store_obj, actions, fLOG=fLOG,
rootrep=("stdchelper_demo.", ""), indexes=indexes)
if sys.platform == "darwin":
warnings.warn(
"add_file_rst does not work yet on MacOSX for C++ modules.")
return
self.assertNotEmpty(store_obj)
self.assertEqual(len(store_obj), 1)
if len(actions) not in (3, 4):
raise Exception("{0}\n{1}".format(
len(actions), "\n".join(str(_) for _ in actions)))
self.assertEqual(len(indexes), 1)
def test_script_pig(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if self.client is None:
return
data = os.path.join(
os.path.abspath(
os.path.split(__file__)[0]),
"data")
fold = os.path.join(data, "..", "temp_pypig_az")
if not os.path.exists(fold):
os.mkdir(fold)
# python script
pyth = """
import sys, datetime
cols = [ _ for _ in sys.argv if ".py" not in _ ]
for row in sys.stdin:
row = row.strip()
if len(row) == 0 :
continue
js = eval(row)
for station in js:
vals = [ str(station[c]).strip() for c in cols ]
sys.stdout.write(",".join(vals))
sys.stdout.write("\\n")
sys.stdout.flush()
""".replace(" ", "")
pyfile = os.path.join(fold, "pystream.py")
with open(pyfile, "w", encoding="utf8") as f:
f.write(pyth)
tosend = """[{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - 75010 PARIS", 'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), """ + \
"""'lng': 2.348395236282807, 'contract_name': 'Paris', 'name': '10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, 'bonus': 0, 'status': """ + \
"""'OPEN', 'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), 'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33},""" + \
"""{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - 75010 PARIS", 'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), """ + \
"""'lng': 2.348395236282807, 'contract_name': 'Paris', 'name': '10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, 'bonus': 0, 'status': """ + \
"""'OPEN', 'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), 'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33}]"""
cmd = sys.executable.replace(
"pythonw",
"python") + " " + pyfile + " name"
out, err = run_cmd(
cmd, wait=True, sin=tosend, communicate=True, timeout=3, shell=False)
out = out.strip("\n\r ")
spl = out.split("\n")
if len(spl) != 2:
raise Exception(
"len:{2}\nOUT:\n{0}\nERR:\n{1}".format(
out,
err,
len(out)))
# PIG script
pig = """
DEFINE pystream `python pystream.py bonus available_bike_stands available_bikes lat lng name status`
SHIP ('pystream.py')
INPUT(stdin USING PigStreaming(',')) OUTPUT (stdout USING PigStreaming(','));
jspy = LOAD '$CONTAINER/$UTT/*.txt' USING PigStorage('\t') AS (arow:chararray);
--DUMP jspy ;
matrice = STREAM jspy THROUGH pystream AS
( bonus:chararray,
available_bike_stands:double,
available_bikes:double,
lat:double,
lng:double,
name:chararray,
status:chararray) ;
DUMP matrice ;
DESCRIBE jspy ;
DESCRIBE matrice ;
STORE matrice INTO '$CONTAINER/$PSEUDO/unittest2/results.txt' USING PigStorage('\t') ;
""".replace(" ", "")
pigfile = os.path.join(fold, "pystream.pig")
with open(pigfile, "w", encoding="utf8") as f:
f.write(pig)
# we upload some files
files = os.listdir(data)
files = [os.path.join(data, _) for _ in files]
files = [_ for _ in files if os.path.isfile(_) and "paris" in _]
import azure.common
try:
content = self.client.ls(
self.blob_serv, self.container, "unittest2")
except azure.common.AzureException as e:
warnings.warn(
"Unable to test azure, storage is still up?\n" + str(e))
return
if len(content) == 0:
self.client.upload(
self.blob_serv,
self.container,
"unittest2",
files)
if self.client.exists(
self.blob_serv, self.container, "unittest2/results.txt"):
self.client.delete_folder(
self.blob_serv,
self.container,
"unittest2/results.txt")
# we submit the job
recall = None
if recall is None:
try:
job = self.client.pig_submit(self.blob_serv, self.container,
pigfile, dependencies=[pyfile],
params=dict(UTT="unittest2"))
except (ConnectionError, NewConnectionError):
# the cluster is probably not set up
warnings.warn("hadoop cluster is not set up")
return
job_id = job["id"]
else:
job_id = recall
status = self.client.wait_job(job_id, fLOG=fLOG)
out, err = self.client.standard_outputs(
status, self.blob_serv, self.container, fold)
if "Total records written : 4" not in err:
raise Exception("OUT:\n{0}\nERR:\n{1}".format(out, err))
dest = os.path.join(fold, "out_merged.txt")
fLOG("dest=", dest)
if os.path.exists(dest):
os.remove(dest)
self.client.download_merge(
self.blob_serv,
self.container,
"$PSEUDO/unittest2/results.txt",
dest)
if not os.path.exists(dest):
raise FileNotFoundError(dest)
with open(dest, "r", encoding="utf8") as f:
content = f.read()
fLOG("-----\n", content)
assert len(content.strip(" \n\r\t")) > 0
df = self.client.df_head(self.blob_serv, self.container,
"$PSEUDO/unittest2/results.txt", sep=",", merge=True)
fLOG(df)
assert len(df) > 0
return df
#########################
# Clones skl2onnx
# +++++++++++++++
this = os.path.abspath(os.path.dirname(__file__))
skl = os.path.join(this, "sklearn-onnx")
if os.path.exists(skl):
pth = skl
cmd = "git pull"
else:
pth = None
cmd = "git clone https://github.com/onnx/sklearn-onnx.git " + skl
run_cmd(cmd, wait=True, change_path=pth, fLOG=print)
#########################
# Runs the benchmark
# ++++++++++++++++++
folder = os.path.join(this, 'onnxruntime-skl2onnx')
location = os.path.join(this, 'sklearn-onnx', "tests")
filename = os.path.splitext(os.path.split(__file__)[-1])[0]
full_filename = filename + ".perf.csv"
if not os.path.exists(full_filename):
with sklearn.config_context(assume_finite=True):
df = run_all_tests(location, folder, verbose=True)
print("[benchmark] saves into '{}'.".format(full_filename))
df.to_csv(full_filename, index=False)
else:
def convert_short_latex_into_png(
latex,
temp_folder=".",
fLOG=print,
miktex=r"C:\Program Files\MiKTeX 2.9\miktex\bin\x64",
final_name=None):
"""
Convert a short latex script into an image.
@param latex latex equation
@param temp_folder temp_folder (where temporary files will be placed)
@param fLOG logging function
@param miktex miktex location
@param final_name if not None, copy the image at this location using this name
@return a location to the image (it should be copied), and its size
You should not call the function twice at the same in the same folder.
@warning The function ends the program if there was a failure. Something is missing on the command line.
"""
if not os.path.exists(miktex):
raise FileNotFoundError("unable to find miktex")
if sys.platform.startswith("win"):
htlatex = os.path.join(miktex, "htlatex.exe")
if not os.path.exists(htlatex):
raise FileNotFoundError("unable to find htlatex")
else:
htlatex = os.path.join(miktex, "htlatex")
if not os.path.exists(temp_folder):
os.makedirs(temp_folder)
eq = os.path.join(temp_folder, "eq.tex")
with open(eq, "w") as f:
f.write(r"""\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
%s
$$
\end{document}""".replace(" ", "") %
latex.strip("\n\r "))
cmd = '"' + htlatex + '" eq.tex "html, graphics-300" "" "" "--interaction=nonstopmode"'
cwd = os.getcwd()
os.chdir(temp_folder)
out, err = run_cmd(cmd, wait=True)
os.chdir(cwd)
if "FAILED" in err:
raise Exception("it failed\n-----\n{0}\n----------\n{1}".format(
out, err))
img = os.path.join(temp_folder, "eq0x.png")
if not os.path.exists(img):
with open(os.path.join(temp_folder, "eq.log"), "r") as f:
log = f.read()
raise FileNotFoundError("the compilation did not work\n" + log)
if final_name is not None:
# size reduction
im = Image.open(img)
shutil.copy(img, final_name)
return final_name, im.size
else:
im = Image.open(img)
return img, im.size
def git_clone(local_folder,
url_https,
user=None,
password=None,
timeout=60,
init=True,
fLOG=noLOG):
"""
clone a project from a git repository in a non empty local folder,
it requires `GIT <http://git-scm.com/>`_ to be installed
and uses the command line.
@param local_folder local folder of the project
@param url_https url, example ``https://gitlab.server/folder/project_name``
@param user part 1 of the credentials
@param password part 2 of the credentials
@param timeout timeout for the command line
@param init see below (True, use fetch, False, use clone)
@param fLOG logging function
@return local_folder
If the reposity has already been cloned, it does not do it again.
We assume that git can be run without giving its full location.
The function executes the following commands (if init is True)::
cd [folder]
git init
git remote add origin [https://user.password@server/project.git]
git fetch
Otherwise, it does::
cd [folder]
git clone origin [https://user.password@server/project.git]
git fetch
A folder will be created.
.. exref::
:tag: Automation
:title: Clone many folders in one row
::
eleves = "project1;project2;..."
root = r"destination"
for el in eleves.split(";"):
cl = el.lower().replace(".","-")
fold = os.path.join(root, el)
if not os.path.exists(fold):
print("clone", el)
url = "https://<gitlab>/<group>/{0}.git".format(cl)
git_clone( fold, url,user=user,password=password, init=False,fLOG=print)
"""
url_user = git_url_user_password(url_https, user, password)
timeout = 60
local_folder = os.path.normpath(os.path.abspath(local_folder))
if init:
if not os.path.exists(local_folder):
fLOG("creating folder", local_folder)
os.mkdir(local_folder)
hg = os.path.join(local_folder, ".git")
if os.path.exists(hg):
raise Exception("folder {0} should not exist".format(local_folder))
if not os.path.exists(hg):
cmds = """
cd {0}
git init
git remote add origin {1}
git fetch
""".format(local_folder,
url_user).replace(" ",
"").strip(" \n\r\t")
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(cmd,
sin=sin,
wait=True,
timeout=timeout,
fLOG=fLOG)
git_check_error(out, err, fLOG)
return local_folder
else:
if not os.path.exists(local_folder):
fLOG("creating folder", local_folder)
os.mkdir(local_folder)
hg = os.path.join(local_folder, ".git")
if os.path.exists(hg):
raise Exception("folder {0} should not exist".format(local_folder))
final = os.path.split(url_user)[-1].replace(".git", "")
locf = os.path.join(local_folder, final)
if os.path.exists(locf):
raise Exception(
"folder {0} should not exists before cloning".format(locf))
cmds = """
cd {0}
git clone {1} .
""".format(local_folder,
url_user).replace(" ",
"").strip(" \n\r\t")
cmd = cmds.replace("\n", "&")
sin = "" # "{0}\n".format(password)
out, err = run_cmd(cmd, sin=sin, wait=True, timeout=timeout, fLOG=fLOG)
git_check_error(out, err, fLOG)
return locf
def compile_cython_single_script(script, skip_warn=True, fLOG=noLOG):
"""
This function considers a script ``.pyx``, writes
the proper setup file, and compiles it.
@param script filename
@param skip_warn skip warnings
@param fLOG logging function
The function applies the steps described in the basic tutorial
`The Basics of Cython <http://docs.cython.org/src/tutorial/cython_tutorial.html>`_.
The function creates a ``setup.py``
in the same location and compiles it.
The compilation requires a compiler
(not `MinGW <http://www.mingw.org/>`_ or
`Visual Studio (Community Edition) <https://www.microsoft.com/france/visual-studio/produits/community/Default.aspx>`_).
If none was found, Python usually displays an error message like::
Unable to find vcvarsall.bat
You can also read this old blog post:
`Build a Python 64 bit extension on Windows <http://www.xavierdupre.fr/blog/2013-07-07_nojs.html>`_
about this file:: ``C:\\Python35_x64\\lib\\distutils\\msvc9compiler.py``.
.. faqref::
:tag: cython
:title: Compiler une function Cython ?
Cette fonction compile un script
`Cython <http://cython.org/>`_.
Cette extension permet d'implémenter des fonctions Python dans un
pseudo-langage proche du `C <https://en.wikipedia.org/wiki/C_(programming_language)>`_.
Il faut suivre les instructions décrite dans le tutorial
`The Basics of Cython <http://docs.cython.org/src/tutorial/cython_tutorial.html>`_
pour réussir à utiliser une fonction codée en Cython.
C'est ce que fait la fonction :func:`compile_cython_single_script`.
Etant donné que la partie en pseudo C est compilée afin de la rendre beaucoup
plus rapide, la partie la plus difficile est généralement celle qui consiste à faire
en sorte que l'interpréteur Python trouve le <b>bon</b> compilateur.
Ce compilateur est nécessairement le même que celui utilisé pour compiler
Python et celui-ci change à chaque version.
Voir
`Compiling Python on Windows <https://docs.python.org/3/using/windows.html?highlight=visual%20studio#compiling-python-on-windows>`_
et faire attention à la version de Python que vous utilisez.
"""
ext = os.path.splitext(script)[-1]
if ext != ".pyx":
raise ValueError("no extension .pyx: " + script)
if not os.path.exists(script):
raise FileNotFoundError(script)
name = os.path.split(script)[-1]
namen = os.path.splitext(name)[0]
setup_script = """
from distutils.core import setup
from Cython.Build import cythonize
setup(
name='{1}',
ext_modules=cythonize("{0}")
)
""".replace(" ", "").format(name, namen)
current, name = os.path.split(script)
filename = os.path.join(os.path.dirname(script), name + ".setup.py")
with open(filename, "w") as f:
f.write(setup_script)
cmd = sys.executable + " -u {0} build_ext --inplace".format(filename)
out, err = run_cmd(cmd, wait=True, fLOG=fLOG, change_path=current)
if len(err) > 0:
if skip_warn:
do_raise = False
lines = err.split("\n")
for line in lines:
if len(line) > 0 and not line.startswith(" "):
if "UserWarning" not in line:
do_raise = True
break
else:
do_raise = True
if do_raise:
with open(script, "r", encoding="utf-8") as f:
content = f.read()
raise CustomCythonError(
"CMD:\n{0}\nOUT:\n{1}ERR:\n{2}\nSCRIPT:\n{3}".format(cmd, out, err, content))
else:
warnings.warn(
"[compile_cython_single_script] CMD:\n{0}\nOUT:\n{1}ERR:\n{2}".format(cmd, out, err))
return out
def execute_python_scripts(root, df, col_names=None, url=None, eol="/", fLOG=noLOG, gen_mail=None):
"""
retrieve all python scripts and run them
@param root main folder
@param df dataframe
@param col_names dictionary for columns:
folder, mail, program, out, err, url, cmp, url_content, key, time
@param eol if not None, replaces end of lines by *eof*
@param gen_mail generator of mails
@param fLOG logging function
@return dataframe
"""
if gen_mail is None:
def iter_mail(mail):
yield mail
yield mail.lower()
gen_mail = iter_mail
def post_process(out, eol):
out = out.strip("\r\t\n").rstrip().replace(
"\r", "").replace("\t", " ")
if eol:
out = out.replace("\n", eol)
return out
downloads = {}
res = []
for name, mail in zip(df[col_names.get("folder", "folder")], df[col_names.get("mail", "mail")]):
row = {col_names.get("folder", "folder"): name}
fLOG("[execute_python_script], look into '{0}'".format(name))
subf = os.path.join(root, name)
col_find = col_names.get("exists", "exists")
if not os.path.exists(subf):
subf = os.path.join(root, name.replace("-", "."))
if not os.path.exists(subf):
row[col_find] = False
res.append(row)
else:
row[col_find] = True
store = []
for py in explore_folder_iterfile(subf, ".*[.]py$"):
store.append(py)
fLOG(" -", len(store), "programs found")
col_out = col_names.get("out", "out")
col_err = col_names.get("err", "err")
col_prog = col_names.get("program", "program")
col_time = col_names.get("time", "time")
col_key = col_names.get("key", "key")
col_size = col_names.get("size", "size")
col_url = col_names.get("url", "url")
col_ind = col_names.get("pattern_id", "pattern_id")
if len(store) == 0:
for mm in sorted(gen_mail(mail.strip())):
mailid = _get_code(mm.encode("utf-8"))
r = row.copy()
loc = url.format(mailid)
ind = {col_key: mm, col_ind: mailid, col_url: loc}
r.update(ind)
res.append(r)
continue
# test all programs
outs = []
for py in sorted(store):
cmd = '"{0}" "{1}"'.format(sys.executable, py)
t1 = time.clock()
try:
out, err = run_cmd(cmd, wait=True)
except Exception as e:
out = None
err = str(e)
out = post_process(out, eol)
t2 = time.clock()
outs.append({col_out: out, col_err: post_process(err, eol),
col_prog: os.path.split(py)[-1], col_time: t2 - t1,
col_size: os.stat(py).st_size})
if url is None:
for o in outs:
r = row.copy()
r.update(o)
res.append(r)
elif url is not None:
col_cmp = col_names.get("cmp", "cmp")
col_in = col_names.get(
"sortie_dans_motif", "sortie_dans_motif")
col_in2 = col_names.get(
"motif_dans_sortie", "motif_dans_sortie")
col_dist = col_names.get("dist", "dist")
col_content = col_names.get("content", "content")
if out is None:
for ii, mm in gen_mail(mail.strip()):
mailid = _get_code(mm.encode("utf-8"))
ind = {col_ind: mailid}
for o in outs:
r = row.copy()
r.update(o)
r.update(ind)
res.append(r)
else:
for mm in sorted(gen_mail(mail.strip())):
mailid = _get_code(mm.encode("utf-8"))
loc = url.format(mailid)
ind = {col_key: mm, col_ind: mailid, col_url: loc}
if loc not in downloads:
downloads[loc] = get_url_content_timeout(
loc).strip("\n\r\t ")
content = post_process(downloads[loc], eol)
ind[col_content] = content
for o in outs:
r = row.copy()
r.update(o)
r.update(ind)
out = r[col_out]
r[col_cmp] = out == content or out.strip(
) == content.strip()
r[col_in] = out in content
r[col_in2] = content in out
r[col_dist] = (edit_distance(out, content)[0]) if (
len(content) > len(out) // 2) else abs(len(content) - len(out))
res.append(r)
return pandas.DataFrame(res)
def build_grammar(g4, version="4.7.1", fLOG=noLOG):
"""
Compiles the grammar for a specific file.
@param g4 grammar format antlr4
@param version version of *antlr4* to use, 4.7
@param fLOG logging function
@return list of files
The compilation must be done with `antlr4 <http://www.antlr.org/>`_.
It generates a lexer and a parser which can be imported in Python.
The options for the command line are described at:
`antlr4 options <https://theantlrguy.atlassian.net/wiki/display/ANTLR4/Options>`_.
.. exref::
:title: Builds a Antlr4 grammar
See `grammars-v4 <https://github.com/antlr/grammars-v4>`_
::
build_grammar("R.g4")
"""
if not g4.endswith(".g4"):
fold = os.path.abspath(os.path.dirname(__file__))
g4 = os.path.join(fold, g4 + ".g4")
url = "http://www.antlr.org/download/antlr-{0}-complete.jar".format(
version)
spl = url.split("/")
domain, name = "/".join(spl[:-1]) + "/", spl[-1]
folder = os.path.abspath(os.path.dirname(__file__))
final = os.path.join(folder, name)
if not os.path.exists(final):
from ..datasource.http_retrieve import download_data
name = download_data(name, website=domain, whereTo=folder)
if not os.path.exists(name):
raise FileNotFoundError("unable to download: " + url)
path = os.environ.get("CLASSPATH", "")
if name not in path:
path = ".;{0}\\antlr-{1}-complete.jar".format(folder, version)
else:
path = ".;{0}\\antlr-{1}-complete.jar;{2}".format(
folder,
version,
os.environ["CLASSPATH"])
os.environ["CLASSPATH"] = path
fLOG("CLASSPATH", os.environ["CLASSPATH"])
# we remove -rc...
version = version.split("-")[0]
cmd = "org.antlr.v4.Tool "
if "Lexer" not in g4:
cmd += "-Dlanguage=Python3 "
cmd += g4
from pyquickhelper.loghelper import run_cmd
out, err = run_cmd("java " + cmd, wait=True, fLOG=fLOG)
def compiled():
if "Lexer" in g4:
lexer = g4.replace(".g4", ".tokens")
else:
lexer = g4.replace(".g4", ".py")
return os.path.exists(lexer)
if not compiled() or (len(err) > 0 and "error" in err):
javapath = r'C:\Program Files\Java\jre7\bin\java.exe'
os.environ["PATH"] = os.environ["PATH"] + ";" + javapath
if sys.platform.startswith("win") and os.path.exists(javapath):
out, err = run_cmd(
'"' + javapath + '" ' + cmd, wait=True, fLOG=fLOG)
if not compiled() or (len(err) > 0 and "error" in err):
raise Exception(
"unable to compile: " +
final +
"\nCLASSPATH:\n" +
os.environ["CLASSPATH"] +
"\nERR:\n" +
err +
"\nCMD:\njava " +
cmd +
"\nYou should do it manually.")
elif err:
err_lines = err.split(err)
err_lines = [_ for _ in err_lines if not _.startswith("warning(")]
err2 = "\n".join(err_lines).strip("\n ")
if len(err2) > 0:
raise Exception(
"unable to compile: " +
final +
"\nCLASSPATH:\n" +
os.environ["CLASSPATH"] +
"\nERR:\n" +
err +
"\nCMD:\njava " +
cmd)
if os.environ.get("USERNAME", os.environ.get("USER", "")) in g4:
dest = os.path.dirname(g4)
for name in os.listdir(dest):
if "Parser" not in name and "Lexer" not in name and \
"Token" not in name and "Listener" not in name:
continue
full = os.path.join(dest, name)
with open(full, "r", encoding="utf-8") as f:
content = f.read()
content1 = content.replace(dest, "")
if content1 != content:
fLOG("[build_grammar] modified", name)
with open(full, "w", encoding="utf-8") as f:
f.write(content1)
return out + "\n---ERR---\n" + err
def test_matplotlib_example(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
progs = ["ffmpeg"]
if not sys.platform.startswith("win"):
progs.append("avconv")
errs = []
prog = None
for prog in progs:
out, err = run_cmd(prog, wait=True, fLOG=fLOG)
exps = "usage:"
if (exps not in out and exps not in err) or err is None or len(err) == 0:
errs.append((prog, err))
else:
break
if len(errs) >= len(progs):
if sys.platform.startswith("win"):
fLOG("download ffmpeg")
add_missing_development_version(
["pyensae"], __file__, hide=True)
from pyensae.datasource import download_data
download_data("ffmpeg.zip", website="xd")
else:
raise FileNotFoundError(
"Unable to find '{1}'.\nPATH='{0}'\n--------\n[OUT]\n{2}\n[ERR]\n{3}".format(
os.environ["PATH"], prog, out,
"\n----\n".join("{0}:\n{1}".format(*_) for _ in errs)))
temp = get_temp_folder(__file__, "temp_example_example")
fix_tkinter_issues_virtualenv()
# update a distribution based on new data.
import numpy as np
import matplotlib.pyplot as plt
import scipy.stats as ss
from matplotlib.animation import FuncAnimation, writers
# To get the list of available writers
if not writers.is_available(prog):
writers.register(prog)
fLOG(writers.list())
class UpdateDist:
def __init__(self, ax, prob=0.5):
self.success = 0
self.prob = prob
self.line, = ax.plot([], [], 'k-')
self.x = np.linspace(0, 1, 200)
self.ax = ax
# Set up plot parameters
self.ax.set_xlim(0, 1)
self.ax.set_ylim(0, 15)
self.ax.grid(True)
# This vertical line represents the theoretical value, to
# which the plotted distribution should converge.
self.ax.axvline(prob, linestyle='--', color='black')
def init(self):
self.success = 0
self.line.set_data([], [])
return self.line,
def __call__(self, i):
# This way the plot can continuously run and we just keep
# watching new realizations of the process
if i == 0:
return self.init()
# Choose success based on exceed a threshold with a uniform
# pick
if np.random.rand(1,) < self.prob: # pylint: disable=W0143
self.success += 1
y = ss.beta.pdf(self.x, self.success + 1,
(i - self.success) + 1)
self.line.set_data(self.x, y)
return self.line,
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ud = UpdateDist(ax, prob=0.7)
anim = FuncAnimation(fig, ud, frames=np.arange(100), init_func=ud.init,
interval=100, blit=True)
try:
Writer = writers[prog]
except KeyError as e:
if prog == "avconv":
from matplotlib.animation import AVConvWriter
Writer = AVConvWriter
else:
raise e
writer = Writer(fps=15, metadata=dict(artist='Me'), bitrate=1800)
anim.save(os.path.join(temp, 'lines2.mp4'), writer=writer)
plt.close('all')
fLOG("end")
def test_script_pig(self):
fLOG(__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if self.client is None:
return
data = os.path.join(os.path.abspath(os.path.split(__file__)[0]),
"data")
fold = os.path.join(data, "..", "temp_pypig_az")
if not os.path.exists(fold):
os.mkdir(fold)
# python script
pyth = """
import sys, datetime
cols = [ _ for _ in sys.argv if ".py" not in _ ]
for row in sys.stdin:
row = row.strip()
if len(row) == 0 :
continue
js = eval(row)
for station in js:
vals = [ str(station[c]).strip() for c in cols ]
sys.stdout.write(",".join(vals))
sys.stdout.write("\\n")
sys.stdout.flush()
""".replace(" ", "")
pyfile = os.path.join(fold, "pystream.py")
with open(pyfile, "w", encoding="utf8") as f:
f.write(pyth)
tosend = """[{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - 75010 PARIS", """ + \
"""'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), """ + \
"""'lng': 2.348395236282807, 'contract_name': 'Paris', 'name': '10042 - POISSONNIÈRE - """ + \
"""ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, 'bonus': 0, 'status': """ + \
"""'OPEN', 'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), """ + \
"""'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33},""" + \
"""{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - 75010 PARIS", """ + \
"""'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), """ + \
"""'lng': 2.348395236282807, 'contract_name': 'Paris', 'name': '10042 - POISSONNIÈRE - """ + \
"""ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, 'bonus': 0, 'status': """ + \
"""'OPEN', 'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), """ + \
"""'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33}]"""
cmd = sys.executable.replace("pythonw",
"python") + " " + pyfile + " name"
out, err = run_cmd(cmd,
wait=True,
sin=tosend,
communicate=True,
timeout=3,
shell=False)
out = out.strip("\n\r ")
spl = out.split("\n")
if len(spl) != 2:
raise Exception("len:{2}\nOUT:\n{0}\nERR:\n{1}".format(
out, err, len(out)))
# PIG script
pig = """
DEFINE pystream `python pystream.py bonus available_bike_stands available_bikes lat lng name status`
SHIP ('pystream.py')
INPUT(stdin USING PigStreaming(',')) OUTPUT (stdout USING PigStreaming(','));
jspy = LOAD '$CONTAINER/$UTT/*.txt' USING PigStorage('\t') AS (arow:chararray);
--DUMP jspy ;
matrice = STREAM jspy THROUGH pystream AS
( bonus:chararray,
available_bike_stands:double,
available_bikes:double,
lat:double,
lng:double,
name:chararray,
status:chararray) ;
DUMP matrice ;
DESCRIBE jspy ;
DESCRIBE matrice ;
STORE matrice INTO '$CONTAINER/$PSEUDO/unittest2/results.txt' USING PigStorage('\t') ;
""".replace(" ", "")
pigfile = os.path.join(fold, "pystream.pig")
with open(pigfile, "w", encoding="utf8") as f:
f.write(pig)
# we upload some files
files = os.listdir(data)
files = [os.path.join(data, _) for _ in files]
files = [_ for _ in files if os.path.isfile(_) and "paris" in _]
import azure.common # pylint: disable=C0415
try:
content = self.client.ls(self.blob_serv, self.container,
"unittest2")
except azure.common.AzureException as e:
warnings.warn("Unable to test azure, storage is still up?\n" +
str(e))
return
if len(content) == 0:
self.client.upload(self.blob_serv, self.container, "unittest2",
files)
if self.client.exists(self.blob_serv, self.container,
"unittest2/results.txt"):
self.client.delete_folder(self.blob_serv, self.container,
"unittest2/results.txt")
# we submit the job
recall = None
if recall is None:
try:
job = self.client.pig_submit(self.blob_serv,
self.container,
pigfile,
dependencies=[pyfile],
params=dict(UTT="unittest2"))
except (ConnectionError, NewConnectionError):
# the cluster is probably not set up
warnings.warn("hadoop cluster is not set up")
return
job_id = job["id"]
else:
job_id = recall
status = self.client.wait_job(job_id, fLOG=fLOG)
out, err = self.client.standard_outputs(status, self.blob_serv,
self.container, fold)
if "Total records written : 4" not in err:
raise Exception("OUT:\n{0}\nERR:\n{1}".format(out, err))
dest = os.path.join(fold, "out_merged.txt")
fLOG("dest=", dest)
if os.path.exists(dest):
os.remove(dest)
self.client.download_merge(self.blob_serv, self.container,
"$PSEUDO/unittest2/results.txt", dest)
if not os.path.exists(dest):
raise FileNotFoundError(dest)
with open(dest, "r", encoding="utf8") as f:
content = f.read()
fLOG("-----\n", content)
assert len(content.strip(" \n\r\t")) > 0
df = self.client.df_head(self.blob_serv,
self.container,
"$PSEUDO/unittest2/results.txt",
sep=",",
merge=True)
fLOG(df)
assert len(df) > 0
def test_script_pig(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if self.client is None:
return
data = os.path.join(
os.path.abspath(
os.path.split(__file__)[0]),
"data")
fLOG("AA")
# python script
pyth = """
import sys, datetime
cols = [ _ for _ in sys.argv if ".py" not in _ ]
for row in sys.stdin:
row = row.strip()
if len(row) == 0 :
continue
js = eval(row)
for station in js:
vals = [ str(station[c]).strip() for c in cols ]
sys.stdout.write(",".join(vals))
sys.stdout.write("\\n")
sys.stdout.flush()
""".replace(" ", "")
fold = os.path.join(data, "..", "temp_pypig")
if not os.path.exists(fold):
os.mkdir(fold)
fLOG("BB")
pyfile = os.path.join(fold, "pystream.py")
with open(pyfile, "w", encoding="utf8") as f:
f.write(pyth)
tosend = """[{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - 75010 PARIS", 'collect_date': """ + \
"""datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), 'lng': 2.348395236282807, 'contract_name': 'Paris', 'name': """ + \
"""'10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, 'bonus': 0, 'status': 'OPEN', """ + \
"""'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), 'number': 10042, """ + \
"""'available_bike_stands': 1, 'bike_stands': 33},{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - """ + \
"""75010 PARIS", 'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), 'lng': 2.348395236282807, """ + \
"""'contract_name': 'Paris', 'name': '10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, """ + \
"""'bonus': 0, 'status': 'OPEN', 'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), """ + \
"""'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33}]"""
cmd = sys.executable.replace(
"pythonw",
"python") + " " + pyfile + " name"
out, err = run_cmd(
cmd, wait=True, sin=tosend, communicate=True, timeout=3, shell=False)
out = out.strip("\n\r ")
spl = out.split("\n")
if len(spl) != 2:
raise Exception(
"len:{2}\nOUT:\n{0}\nERR:\n{1}".format(
out,
err,
len(out)))
fLOG("CC")
# PIG script
pig = """
DEFINE pystream `python pystream.py bonus available_bike_stands available_bikes lat lng name status`
SHIP ('pystream.py')
INPUT(stdin USING PigStreaming(',')) OUTPUT (stdout USING PigStreaming(','));
jspy = LOAD '$UTT/*.txt' USING PigStorage('\t') AS (arow:chararray);
--DUMP jspy ;
matrice = STREAM jspy THROUGH pystream AS
( bonus:chararray,
available_bike_stands:double,
available_bikes:double,
lat:double,
lng:double,
name:chararray,
status:chararray) ;
DUMP matrice ;
DESCRIBE jspy ;
DESCRIBE matrice ;
STORE matrice INTO 'unittest2/results.txt' USING PigStorage('\t') ;
""".replace(" ", "")
fLOG(self.client.username)
hive_sql = """
DROP TABLE IF EXISTS bikes20;
CREATE TABLE bikes20 (sjson STRING);
LOAD DATA INPATH "/user/__USERNAME__/unittest2/paris*.txt"
INTO TABLE bikes20;
SELECT * FROM bikes20 LIMIT 10;
""".replace("__USERNAME__", self.client.username.decode("ascii"))
fLOG(hive_sql)
#${hiveconf:UTT}
pigfile = os.path.join(fold, "pystream.pig")
with open(pigfile, "w", encoding="utf8") as f:
f.write(pig)
fLOG("DD upload")
# we upload some files
files = os.listdir(data)
files = [os.path.join(data, _) for _ in files]
files = [_ for _ in files if os.path.isfile(_) and "paris" in _]
if not self.client.dfs_exists("unittest2"):
self.client.dfs_mkdir("unittest2")
content = self.client.dfs_ls("unittest2")
if len(content) == 0:
self.client.upload_cluster(files, "unittest2")
if self.client.dfs_exists("unittest2/results.txt"):
self.client.dfs_rm("unittest2/results.txt", True)
fLOG("FF")
# we test the syntax
out, err = self.client.pig_submit(pigfile, dependencies=[pyfile], check=True,
no_exception=True,
params=dict(UTT="unittest2"),
fLOG=fLOG)
if "pystream.pig syntax OK" not in err:
raise Exception("OUT:\n{0}\nERR:\n{1}".format(out, err))
fLOG("II")
# we submit the job
out, err = self.client.pig_submit(pigfile, dependencies=[pyfile],
stop_on_failure=True, no_exception=True,
redirection=None,
params=dict(UTT="unittest2"))
fLOG("JJ")
if "Total records written : 4" not in err:
raise Exception("PIG OUT:\n{0}\nPIG ERR:\n{1}".format(out, err))
dest = os.path.join(fold, "out_merged.txt")
fLOG("dest=", dest)
if os.path.exists(dest):
os.remove(dest)
fLOG("KK")
self.client.download_cluster("unittest2/results.txt", dest, merge=True)
assert os.path.exists(dest)
with open(dest, "r", encoding="utf8") as f:
content = f.read()
fLOG("-----\n", content)
assert len(content.strip(" \n\r\t")) > 0
fLOG("LL")
# we submit the job
# disable HIVE for the time being (broken)
warnings.warn("hive not being tested")
return
out, err = self.client.hive_submit(hive_sql,
redirection=None,
params=dict(UTT="unittest2"),
fLOG=fLOG)
fLOG("HIVE OUT")
fLOG(out)
fLOG("HIVE ERR")
fLOG(err)
#assert "(0,1.0,32.0,48.8724200631,2.34839523628,10042" in out
fLOG("END")
def compile_cython_single_script(script, skip_warn=True, fLOG=noLOG):
"""
This function considers a script ``.pyx``, writes
a the proper setup file, and compiles it.
@param script filename
@param skip_warn skip warnings
@param fLOG logging function
The function applies the steps described in the basic tutorial
`The Basics of Cython <http://docs.cython.org/src/tutorial/cython_tutorial.html>`_.
The function creates a ``setup.py``
in the same location and compiles it.
The compilation requires a compiler
(not `MinGW <http://www.mingw.org/>`_ or
`Visual Studio (Community Edition) <https://www.microsoft.com/france/visual-studio/produits/community/Default.aspx>`_).
If none was found, Python usually displays an error message like::
Unable to find vcvarsall.bat
You can also read this old blog post:
`Build a Python 64 bit extension on Windows <http://www.xavierdupre.fr/blog/2013-07-07_nojs.html>`_
about this file:: ``C:\\Python35_x64\\lib\\distutils\\msvc9compiler.py``.
.. faqref::
:tag: cython
:title: Compiler une function Cython ?
Cette fonction compile un script
`Cython <http://cython.org/>`_.
Cette extension permet d'implémenter des fonctions Python dans un
pseudo-langage proche du `C <https://en.wikipedia.org/wiki/C_(programming_language)>`_.
Il faut suivre les instructions décrite dans le tutorial
`The Basics of Cython <http://docs.cython.org/src/tutorial/cython_tutorial.html>`_
pour réussir à utiliser une fonction codée en Cython.
C'est ce que fait la fonction :func:`compile_cython_single_script`.
Etant donné que la partie en pseudo C est compilée afin de la rendre beaucoup
plus rapide, la partie la plus difficile est généralement celle qui consiste à faire
en sorte que l'interpréteur Python trouve le <b>bon</b> compilateur.
Ce compilateur est nécessairement le même que celui utilisé pour compiler
Python et celui-ci change à chaque version.
Voir
`Compiling Python on Windows <https://docs.python.org/3/using/windows.html?highlight=visual%20studio#compiling-python-on-windows>`_
et faire attention à la version de Python que vous utilisez.
"""
ext = os.path.splitext(script)[-1]
if ext != ".pyx":
raise ValueError("no extension .pyx: " + script)
if not os.path.exists(script):
raise FileNotFoundError(script)
name = os.path.split(script)[-1]
namen = os.path.splitext(name)[0]
setup_script = """
from distutils.core import setup
from Cython.Build import cythonize
setup(
name='{1}',
ext_modules=cythonize("{0}")
)
""".replace(" ", "").format(name, namen)
current, name = os.path.split(script)
filename = os.path.join(os.path.dirname(script), name + ".setup.py")
with open(filename, "w") as f:
f.write(setup_script)
cmd = sys.executable + " -u {0} build_ext --inplace".format(filename)
out, err = run_cmd(cmd, wait=True, fLOG=fLOG, change_path=current)
if len(err) > 0:
if skip_warn:
do_raise = False
lines = err.split("\n")
for line in lines:
if len(line) > 0 and not line.startswith(" "):
if "UserWarning" not in line:
do_raise = True
break
if do_raise:
with open(script, "r", encoding="utf-8") as f:
content = f.read()
raise CustomCythonError(
"CMD:\n{0}\nOUT:\n{1}ERR:\n{2}\nSCRIPT:\n{3}".format(cmd, out, err, content))
else:
warnings.warn(
"CMD:\n{0}\nOUT:\n{1}ERR:\n{2}".format(cmd, out, err))
return out
def build_grammar(g4, version="4.6", fLOG=noLOG):
"""
compile the grammar for a specific file
@param g4 grammar format antlr4
@param version version of *antlr4* to use, 4.4, 4.5-rc-2
@param fLOG logging function
@return list of files
The compilation must be done with `antlr4 <http://www.antlr.org/>`_.
It generates a lexer and a parser which can be imported in Python.
The options for the command line are described at: `antlr4 options <https://theantlrguy.atlassian.net/wiki/display/ANTLR4/Options>`_.
.. exref::
:title: Build a Antlr4 grammer
See `grammars-v4 <https://github.com/antlr/grammars-v4>`_
::
build_grammar("R.g4")
"""
if not g4.endswith(".g4"):
fold = os.path.abspath(os.path.dirname(__file__))
g4 = os.path.join(fold, g4 + ".g4")
url = "http://www.antlr.org/download/antlr-{0}-complete.jar".format(
version)
spl = url.split("/")
domain, name = "/".join(spl[:-1]) + "/", spl[-1]
folder = os.path.abspath(os.path.dirname(__file__))
final = os.path.join(folder, name)
if not os.path.exists(final):
from ..datasource.http_retrieve import download_data
name = download_data(name, website=domain, whereTo=folder)
if not os.path.exists(name):
raise FileNotFoundError("unable to download: " + url)
path = os.environ.get("CLASSPATH", "")
if name not in path:
path = ".;{0}\\antlr-{1}-complete.jar".format(folder, version)
else:
path = ".;{0}\\antlr-{1}-complete.jar;{2}".format(
folder,
version,
os.environ["CLASSPATH"])
os.environ["CLASSPATH"] = path
fLOG("CLASSPATH", os.environ["CLASSPATH"])
# we remove -rc...
version = version.split("-")[0]
cmd = "org.antlr.v4.Tool -Dlanguage=Python3 " + g4
from pyquickhelper.loghelper import run_cmd
out, err = run_cmd("java " + cmd, wait=True, fLOG=fLOG)
def compiled():
lexer = g4.replace(".g4", "Lexer.py")
return os.path.exists(lexer)
if not compiled() or (len(err) > 0 and "error" in err):
javapath = r'C:\Program Files\Java\jre7\bin\java.exe'
os.environ["PATH"] = os.environ["PATH"] + ";" + javapath
if sys.platform.startswith("win") and os.path.exists(javapath):
out, err = run_cmd(
'"' + javapath + '" ' + cmd, wait=True, fLOG=fLOG)
if not compiled() or (len(err) > 0 and "error" in err):
raise Exception(
"unable to compile: " +
final +
"\nCLASSPATH:\n" +
os.environ["CLASSPATH"] +
"\nERR:\n" +
err +
"\nCMD:\njava " +
cmd +
"\nYou should do it manually.")
else:
raise Exception(
"unable to compile: " +
final +
"\nCLASSPATH:\n" +
os.environ["CLASSPATH"] +
"\nERR:\n" +
err +
"\nCMD:\njava " +
cmd)
return out + "\nERR:\n" + err
def test_compile_module(self):
fLOG(
__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
temp = get_temp_folder(__file__, "temp_compile_module")
source = os.path.join(temp, "cdemo.cpp")
init = os.path.join(temp, "__init__.py")
setup = os.path.join(temp, "setup.py")
with open(source, "w") as f:
f.write(TestModuleC.content_c)
with open(init, "w") as f:
pass
setup_content = dedent("""
from distutils.core import setup, Extension
module1 = Extension('stdchelper_demo', sources=['{0}'])
setup (name = 'ccdemo', version = '1.0',
description = 'This is a demo package.',
ext_modules = [module1])
""".format(source.replace("\\", "/")))
with open(setup, "w") as f:
f.write(setup_content)
cmd = "{0} {1} build_ext --inplace".format(sys.executable, setup)
out, err = run_cmd(cmd, wait=True, fLOG=fLOG, change_path=temp)
if "error" in out or "error" in err:
out_ = out.replace("-Werror=format-security", "")
if "error" in out_:
raise Exception(
"Unable to compile\n--OUT--\n{0}\n--ERR--\n{1}".format(out, err))
if sys.platform == "win32":
name = "stdchelper_demo.cp%d%d-win_amd64.pyd" % sys.version_info[:2]
elif sys.platform == "darwin":
name = "stdchelper_demo.cpython-%d%dm-darwin.so" % sys.version_info[:2]
else:
name = "stdchelper_demo.cpython-%d%dm-x86_64-linux-gnu.so" % sys.version_info[:2]
fullname = os.path.join(temp, name)
if not os.path.exists(fullname):
files = os.listdir(os.path.dirname(fullname))
raise FileNotFoundError(
"Unable to find '{0}' (platform '{1}')\nFound:\n{2}".format(
fullname, sys.platform, "\n".join(files)))
mo = import_module(None, fullname, fLOG,
additional_sys_path=None, first_try=True)
self.assertIsInstance(mo, tuple)
self.assertEqual(len(mo), 2)
self.assertTrue(hasattr(mo[0], '__doc__'))
if 'stdchelper_demo' in sys.modules:
del sys.modules['stdchelper_demo']
temp2 = get_temp_folder(__file__, "temp_compile_module2")
store_obj = {}
actions = copy_source_files(temp, temp2, fLOG=fLOG)
store_obj = {}
indexes = {}
add_file_rst(temp2, store_obj, actions, fLOG=fLOG,
rootrep=("stdchelper_demo.", ""), indexes=indexes)
if sys.platform == "darwin":
warnings.warn(
"add_file_rst does not work yet on MacOSX for C++ modules.")
return
self.assertNotEmpty(store_obj)
self.assertEqual(len(store_obj), 1)
if len(actions) not in (3, 4):
raise Exception("{0}\n{1}".format(
len(actions), "\n".join(str(_) for _ in actions)))
self.assertEqual(len(indexes), 1)
def test_script_pig(self):
fLOG(__file__,
self._testMethodName,
OutputPrint=__name__ == "__main__")
if self.client is None:
return
data = os.path.join(os.path.abspath(os.path.split(__file__)[0]),
"data")
fLOG("AA")
# python script
pyth = """
import sys, datetime
cols = [ _ for _ in sys.argv if ".py" not in _ ]
for row in sys.stdin:
row = row.strip()
if len(row) == 0 :
continue
js = eval(row)
for station in js:
vals = [ str(station[c]).strip() for c in cols ]
sys.stdout.write(",".join(vals))
sys.stdout.write("\\n")
sys.stdout.flush()
""".replace(" ", "")
fold = os.path.join(data, "..", "temp_pypig")
if not os.path.exists(fold):
os.mkdir(fold)
fLOG("BB")
pyfile = os.path.join(fold, "pystream.py")
with open(pyfile, "w", encoding="utf8") as f:
f.write(pyth)
tosend = """[{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - 75010 PARIS", 'collect_date': """ + \
"""datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), 'lng': 2.348395236282807, 'contract_name': 'Paris', 'name': """ + \
"""'10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, 'bonus': 0, 'status': 'OPEN', """ + \
"""'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), 'number': 10042, """ + \
"""'available_bike_stands': 1, 'bike_stands': 33},{'address': "52 RUE D'ENGHIEN / ANGLE RUE DU FAUBOURG POISSONIERE - """ + \
"""75010 PARIS", 'collect_date': datetime.datetime(2014, 11, 11, 22, 1, 18, 331070), 'lng': 2.348395236282807, """ + \
"""'contract_name': 'Paris', 'name': '10042 - POISSONNIÈRE - ENGHIEN', 'banking': 0, 'lat': 48.87242006305313, """ + \
"""'bonus': 0, 'status': 'OPEN', 'available_bikes': 32, 'last_update': datetime.datetime(2014, 11, 11, 21, 59, 5), """ + \
"""'number': 10042, 'available_bike_stands': 1, 'bike_stands': 33}]"""
cmd = sys.executable.replace("pythonw",
"python") + " " + pyfile + " name"
out, err = run_cmd(cmd,
wait=True,
sin=tosend,
communicate=True,
timeout=3,
shell=False)
out = out.strip("\n\r ")
spl = out.split("\n")
if len(spl) != 2:
raise Exception("len:{2}\nOUT:\n{0}\nERR:\n{1}".format(
out, err, len(out)))
fLOG("CC")
# PIG script
pig = """
DEFINE pystream `python pystream.py bonus available_bike_stands available_bikes lat lng name status`
SHIP ('pystream.py')
INPUT(stdin USING PigStreaming(',')) OUTPUT (stdout USING PigStreaming(','));
jspy = LOAD '$UTT/*.txt' USING PigStorage('\t') AS (arow:chararray);
--DUMP jspy ;
matrice = STREAM jspy THROUGH pystream AS
( bonus:chararray,
available_bike_stands:double,
available_bikes:double,
lat:double,
lng:double,
name:chararray,
status:chararray) ;
DUMP matrice ;
DESCRIBE jspy ;
DESCRIBE matrice ;
STORE matrice INTO 'unittest2/results.txt' USING PigStorage('\t') ;
""".replace(" ", "")
fLOG(self.client.username)
hive_sql = """
DROP TABLE IF EXISTS bikes20;
CREATE TABLE bikes20 (sjson STRING);
LOAD DATA INPATH "/user/__USERNAME__/unittest2/paris*.txt"
INTO TABLE bikes20;
SELECT * FROM bikes20 LIMIT 10;
""".replace("__USERNAME__", self.client.username.decode("ascii"))
fLOG(hive_sql)
# ${hiveconf:UTT}
pigfile = os.path.join(fold, "pystream.pig")
with open(pigfile, "w", encoding="utf8") as f:
f.write(pig)
fLOG("DD upload")
# we upload some files
files = os.listdir(data)
files = [os.path.join(data, _) for _ in files]
files = [_ for _ in files if os.path.isfile(_) and "paris" in _]
if not self.client.dfs_exists("unittest2"):
self.client.dfs_mkdir("unittest2")
content = self.client.dfs_ls("unittest2")
if len(content) == 0:
self.client.upload_cluster(files, "unittest2")
if self.client.dfs_exists("unittest2/results.txt"):
self.client.dfs_rm("unittest2/results.txt", True)
fLOG("FF")
# we test the syntax
out, err = self.client.pig_submit(pigfile,
dependencies=[pyfile],
check=True,
no_exception=True,
params=dict(UTT="unittest2"),
fLOG=fLOG)
if "pystream.pig syntax OK" not in err:
raise Exception("OUT:\n{0}\nERR:\n{1}".format(out, err))
fLOG("II")
# we submit the job
out, err = self.client.pig_submit(pigfile,
dependencies=[pyfile],
stop_on_failure=True,
no_exception=True,
redirection=None,
params=dict(UTT="unittest2"))
fLOG("JJ")
if "Total records written : 4" not in err:
raise Exception("PIG OUT:\n{0}\nPIG ERR:\n{1}".format(out, err))
dest = os.path.join(fold, "out_merged.txt")
fLOG("dest=", dest)
if os.path.exists(dest):
os.remove(dest)
fLOG("KK")
self.client.download_cluster("unittest2/results.txt", dest, merge=True)
assert os.path.exists(dest)
with open(dest, "r", encoding="utf8") as f:
content = f.read()
fLOG("-----\n", content)
assert len(content.strip(" \n\r\t")) > 0
fLOG("LL")
# we submit the job
# disable HIVE for the time being (broken)
warnings.warn("hive not being tested")
out, err = self.client.hive_submit(hive_sql,
redirection=None,
params=dict(UTT="unittest2"),
fLOG=fLOG)
fLOG("HIVE OUT")
fLOG(out)
fLOG("HIVE ERR")
fLOG(err)
#assert "(0,1.0,32.0,48.8724200631,2.34839523628,10042" in out
fLOG("END")
def execute_python_scripts(root,
df,
col_names=None,
url=None,
eol="/",
fLOG=noLOG,
gen_mail=None):
"""
Retrieves all :epkg:`python` scripts and run them.
@param root main folder
@param df dataframe
@param col_names dictionary for columns:
folder, mail, program, out, err, url, cmp, url_content, key, time
@param eol if not None, replaces end of lines by *eof*
@param gen_mail generator of mails
@param fLOG logging function
@return dataframe
"""
if gen_mail is None:
def iter_mail(mail):
yield mail
yield mail.lower()
gen_mail = iter_mail
def post_process(out, eol):
out = out.strip("\r\t\n").rstrip().replace("\r",
"").replace("\t", " ")
if eol:
out = out.replace("\n", eol)
return out
downloads = {}
res = []
for name, mail in zip(df[col_names.get("folder", "folder")],
df[col_names.get("mail", "mail")]):
row = {col_names.get("folder", "folder"): name}
fLOG("[execute_python_script], look into '{0}'".format(name))
subf = os.path.join(root, name)
col_find = col_names.get("exists", "exists")
if not os.path.exists(subf):
subf = os.path.join(root, name.replace("-", "."))
if not os.path.exists(subf):
row[col_find] = False
res.append(row)
else:
row[col_find] = True
store = []
for py in explore_folder_iterfile(subf, ".*[.]py$"):
store.append(py)
fLOG(" -", len(store), "programs found")
col_out = col_names.get("out", "out")
col_err = col_names.get("err", "err")
col_prog = col_names.get("program", "program")
col_time = col_names.get("time", "time")
col_key = col_names.get("key", "key")
col_size = col_names.get("size", "size")
col_url = col_names.get("url", "url")
col_ind = col_names.get("pattern_id", "pattern_id")
if len(store) == 0:
for mm in sorted(gen_mail(mail.strip())):
mailid = _get_code(mm.encode("utf-8"))
r = row.copy()
loc = url.format(mailid)
ind = {col_key: mm, col_ind: mailid, col_url: loc}
r.update(ind)
res.append(r)
continue
# test all programs
outs = []
for py in sorted(store):
cmd = '"{0}" "{1}"'.format(sys.executable, py)
t1 = time.clock()
try:
out, err = run_cmd(cmd, wait=True)
except Exception as e:
out = None
err = str(e)
out = post_process(out, eol)
t2 = time.clock()
outs.append({
col_out: out,
col_err: post_process(err, eol),
col_prog: os.path.split(py)[-1],
col_time: t2 - t1,
col_size: os.stat(py).st_size
})
if url is None:
for o in outs:
r = row.copy()
r.update(o)
res.append(r)
elif url is not None:
col_cmp = col_names.get("cmp", "cmp")
col_in = col_names.get("sortie_dans_motif",
"sortie_dans_motif")
col_in2 = col_names.get("motif_dans_sortie",
"motif_dans_sortie")
col_dist = col_names.get("dist", "dist")
col_content = col_names.get("content", "content")
if out is None:
for _, mm in gen_mail(mail.strip()):
mailid = _get_code(mm.encode("utf-8"))
ind = {col_ind: mailid}
for o in outs:
r = row.copy()
r.update(o)
r.update(ind)
res.append(r)
else:
for mm in sorted(gen_mail(mail.strip())):
mailid = _get_code(mm.encode("utf-8"))
loc = url.format(mailid)
ind = {col_key: mm, col_ind: mailid, col_url: loc}
if loc not in downloads:
downloads[loc] = get_url_content_timeout(
loc).strip("\n\r\t ")
content = post_process(downloads[loc], eol)
ind[col_content] = content
for o in outs:
r = row.copy()
r.update(o)
r.update(ind)
out = r[col_out]
r[col_cmp] = out == content or out.strip(
) == content.strip()
r[col_in] = out in content
r[col_in2] = content in out
r[col_dist] = (edit_distance(out, content)[0]) if (
len(content) > len(out) //
2) else abs(len(content) - len(out))
res.append(r)
return pandas.DataFrame(res)
def convert_short_latex_into_png(latex, temp_folder=".", fLOG=print,
miktex=r"C:\Program Files\MiKTeX 2.9\miktex\bin\x64",
final_name=None):
"""
Convert a short latex script into an image.
@param latex latex equation
@param temp_folder temp_folder (where temporary files will be placed)
@param fLOG logging function
@param miktex miktex location
@param final_name if not None, copy the image at this location using this name
@return a location to the image (it should be copied), and its size
You should not call the function twice at the same in the same folder.
@warning The function ends the program if there was a failure. Something is missing on the command line.
"""
if not os.path.exists(miktex):
raise FileNotFoundError("unable to find miktex")
if sys.platform.startswith("win"):
htlatex = os.path.join(miktex, "htlatex.exe")
if not os.path.exists(htlatex):
raise FileNotFoundError("unable to find htlatex")
else:
htlatex = os.path.join(miktex, "htlatex")
if not os.path.exists(temp_folder):
os.makedirs(temp_folder)
eq = os.path.join(temp_folder, "eq.tex")
with open(eq, "w") as f:
f.write(r"""\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
%s
$$
\end{document}""".replace(" ", "") % latex.strip("\n\r "))
cmd = '"' + htlatex + '" eq.tex "html, graphics-300" "" "" "--interaction=nonstopmode"'
cwd = os.getcwd()
os.chdir(temp_folder)
out, err = run_cmd(cmd, wait=True)
os.chdir(cwd)
if "FAILED" in err:
raise Exception(
"it failed\n-----\n{0}\n----------\n{1}".format(out, err))
img = os.path.join(temp_folder, "eq0x.png")
if not os.path.exists(img):
with open(os.path.join(temp_folder, "eq.log"), "r") as f:
log = f.read()
raise FileNotFoundError("the compilation did not work\n" + log)
if final_name is not None:
# size reduction
im = Image.open(img)
shutil.copy(img, final_name)
return final_name, im.size
else:
im = Image.open(img)
return img, im.size
docpath = os.path.normpath(
os.path.join(thispath, "_doc", "presentation" + suffix))
os.chdir(docpath)
lay = "html"
build = "build"
over = ""
sconf = ""
import_pyquickhelper()
from pyquickhelper.helpgen import process_sphinx_cmd
cmd_file = os.path.abspath(process_sphinx_cmd.__file__)
cmd = '"{4}" "{5}" -b {1} -d {0}/doctrees{2}{3} source {0}/{1}'.format(
build, lay, over, sconf, sys.executable, cmd_file)
from pyquickhelper.loghelper import run_cmd
out, err = run_cmd(cmd, wait=True, fLOG=print)
print(out)
print(err)
if sys.platform.startswith("win"):
os.chdir(pa)
else:
# builds the setup
from pyquickhelper.pycode import clean_readme
long_description = clean_readme(long_description)
setup(
name=project_var_name,
version='%s%s' % (sversion, subversion),
def run_pig(pigfile,
argv=None,
pig_path=None,
hadoop_path=None,
jython_path=None,
timeout=None,
logpath="logs",
pig_version="0.15.0",
hadoop_version="2.7.2",
fLOG=noLOG):
"""
runs a pig script and returns the standard output and error
@param pigfile pig file
@param argv arguments to sned to the command line
@param pig_path path to pig 0.XX.0
@param hadoop_path path to hadoop
@param timeout timeout
@param logpath path to the logs
@param pig_version PIG version (if *pig_path* is not defined)
@param hadoop_version Hadoop version (if *hadoop_path* is not defined)
@param fLOG logging function
@return out, err
If *pig_path* is None, the function looks into this directory.
"""
if pig_path is None:
pig_path = os.path.join(get_pig_path(), "pig-%s" % pig_version)
if hadoop_path is None:
hadoop_path = get_hadoop_path()
java = get_java_path()
if "JAVA_HOME" not in os.environ:
os.environ["JAVA_HOME"] = java
if "PIG_CONF_DIR" not in os.environ:
os.environ["PIG_CONF_DIR"] = os.path.normpath(
os.path.join(
pig_path,
"conf"))
if not os.path.exists(os.environ["PIG_CONF_DIR"]):
raise FileNotFoundError(os.environ["PIG_CONF_DIR"])
if "HADOOP_HOME" not in os.environ:
os.environ["HADOOP_HOME"] = hadoop_path
if not os.path.exists(os.environ["HADOOP_HOME"]):
raise FileNotFoundError(os.environ["HADOOP_HOME"])
if "HADOOP_CLIENT_OPTS" not in os.environ:
os.environ["HADOOP_CLIENT_OPTS"] = "-Xmx1024m"
fLOG("PIG_CONF_DIR=", os.environ["PIG_CONF_DIR"])
def clean(i, p):
if i == 0:
return p
if '"' in p:
p = p.replace('"', '\\"')
if " " in p:
p = '"{0}"'.format(p)
return p
full = False
jars = []
if full:
jars.extend(get_pig_jars()) # + get_hadoop_jars()
folds = set(os.path.split(j)[0] for j in jars)
jars = [os.path.join(f, "*.jar") for f in folds]
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"common",
"lib",
"*.jar"))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"hdfs",
"lib",
"*.jar"))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"mapreduce",
"lib",
"*.jar"))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"httpfs",
"tomcat",
"lib",
"*.jar"))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"tools",
"lib",
"*.jar"))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"yarn",
"lib",
"*.jar"))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"common",
"hadoop-common-%s.jar" % hadoop_version))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"common",
"hadoop-nfs-%s" % hadoop_version))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"hdfs",
"hadoop-hdfs-%s.jar" % hadoop_version))
jars.append(
os.path.join(
hadoop_path,
"hadoop-2.5.2",
"share",
"hadoop",
"hdfs",
"hadoop-hdfs-nfs-%s.jar" % hadoop_version))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"mapreduce",
"*.jar"))
jars.append(
os.path.join(
hadoop_path,
"hadoop-%s" % hadoop_version,
"share",
"hadoop",
"yarn",
"*.jar"))
jars.append(os.path.join(pig_path, "pig-%s-core-h1.jar" % pig_version))
else:
jars.append(
os.path.join(
pig_path,
"pig-%s" % pig_version,
"legacy",
"pig-%s-withouthadoop-h2.jar" % pig_version))
jarsall = []
for j in jars:
r = glob.glob(j)
jarsall.extend(r)
jarsall.sort()
for j in jarsall:
fLOG(j)
jars = ";".join(jars)
fLOG("jars", jars)
cmd = [get_java_cmd(), "-Xmx1024m",
"-classpath", jars,
"-Dpig.log.dir=" + logpath,
"-Dhadoop.log.dir=" + logpath,
"-Dhadoop.tmp.dir=" + logpath,
"-Dpig.log.file=pid.log",
"-Djava.io.tmpdir=" + logpath,
"-Dpig.home.dir=" + pig_path,
#"-Dpig.schematuple=true",
#"-Dpig.schematuple.local.dir=" + logpath,
"org.apache.pig.Main",
"-x", "local", pigfile,
"-stop_on_failure"
]
cmd = " ".join(clean(i, _) for i, _ in enumerate(cmd))
out, err = run_cmd(
cmd, wait=True, sin=None, communicate=True, timeout=timeout, shell=False)
return out, err