diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 73b146d08919fff25f646dab664ef632e4b24c59..74147a94fe67733d80d4035bbf6c5b4b15670bea 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,6 +4,7 @@ before_script:
test-3.4:
image: mmpe/wetb
script:
- - python3 setup.py test
- - coverage run ./tests/run_pytest.py
- - coverage report -m
\ No newline at end of file
+ #- python3 setup.py test
+ - pip3 install pytest-cov
+ - python3 -m pytest --cov=wetb
+
diff --git a/README.md b/README.md
index b8f2fbbb678a74baacf870f4f16355e27f5c5cc1..f019bc546495292a060e55d267991173a96ff24f 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
+[](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
+[](https://gitlab.windenergy.dtu.dk/toolbox/WindEnergyToolbox/commits/master)
# Introduction
The Wind Energy Toolbox (or ```wetb```, pronounce as wee-tee-bee) is a collection
diff --git a/setup.cfg b/setup.cfg
index d2a646f0bdebeeaa4cde8ce65d6fe06d26160521..6c20abb966dd98029c40dac0f33ffcc90a89b7b6 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -62,6 +62,7 @@ packages =
#addopts =
# --cov wetb --cov-report term-missing
# --verbose
+python_files = WindEnergyToolbox/wetb/*
[aliases]
docs = build_sphinx
diff --git a/wetb/fast/tests/__init__.py b/wetb/fast/tests/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/wetb/fatigue_tools/rainflowcounting/compile.py b/wetb/fatigue_tools/rainflowcounting/compile.py
deleted file mode 100644
index ba4576622a7bb3bfc76fbef7c76379d63cf64ed5..0000000000000000000000000000000000000000
--- a/wetb/fatigue_tools/rainflowcounting/compile.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from __future__ import unicode_literals
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-from future import standard_library
-standard_library.install_aliases()
-from wetb.utils.cython_compile.cython_compile import cython_import
-cython_import('pair_range')
-cython_import('peak_trough')
-cython_import('rainflowcount_astm')
diff --git a/wetb/fatigue_tools/rainflowcounting/rainflowcount.py b/wetb/fatigue_tools/rainflowcounting/rainflowcount.py
index 645da85e332a8cd5296d602e982c46b1cd79c1cf..8d1bdd76e8bb550114bb552e5ae6985a8c9b427b 100644
--- a/wetb/fatigue_tools/rainflowcounting/rainflowcount.py
+++ b/wetb/fatigue_tools/rainflowcounting/rainflowcount.py
@@ -6,7 +6,7 @@ from builtins import str
from future import standard_library
standard_library.install_aliases()
import numpy as np
-from wetb.utils.cython_compile.cython_compile import cython_import
+
def check_signal(signal):
@@ -73,9 +73,6 @@ def rainflow_windap(signal, levels=255., thresshold=(255 / 50)):
# If possible the module is compiled using cython otherwise the python implementation is used
- cython_import('wetb.fatigue_tools.rainflowcounting.peak_trough')
- cython_import('wetb.fatigue_tools.rainflowcounting.pair_range')
-
from wetb.fatigue_tools.rainflowcounting.peak_trough import peak_trough
from wetb.fatigue_tools.rainflowcounting.pair_range import pair_range_amplitude_mean
@@ -129,7 +126,7 @@ def rainflow_astm(signal):
# Import find extremes and rainflow.
# If possible the module is compiled using cython otherwise the python implementation is used
- cython_import('wetb.fatigue_tools.rainflowcounting.rainflowcount_astm')
+
from wetb.fatigue_tools.rainflowcounting.rainflowcount_astm import find_extremes, rainflowcount
# Remove points which is not local minimum/maximum
diff --git a/wetb/gtsdf/__init__.py b/wetb/gtsdf/__init__.py
index 7339aa3425109db20313635013bf75b0e14db84c..364d20a40cbaa101738ccc39ca6e896806f2ab1a 100644
--- a/wetb/gtsdf/__init__.py
+++ b/wetb/gtsdf/__init__.py
@@ -44,12 +44,25 @@ class Dataset(object):
self.time, self.data, self.info = load(filename)
def __call__(self, id):
if isinstance(id, str):
- return self((['Time'] + self.info['attribute_names']).index(id) + 1)
+ if id=="Time":
+ return self.time
+ else:
+ return self(self.info['attribute_names'].index(id) + 2)
if id == 1:
return self.time
else:
return self.data[:, id - 2]
+ def __getattribute__(self, name):
+ try:
+ return object.__getattribute__(self, name)
+
+ except Exception as e:
+ try:
+ return self(name)
+ except:
+ raise e
+
__all__ = sorted([m for m in set(dir()) - set(d)])
diff --git a/wetb/gtsdf/tests/test_gtsdf.py b/wetb/gtsdf/tests/test_gtsdf.py
index 004eed321612f21ae8dd045db9e13f87d7a7fb99..7a5ed608a2918223edfbdda3a010b17798ca8058 100644
--- a/wetb/gtsdf/tests/test_gtsdf.py
+++ b/wetb/gtsdf/tests/test_gtsdf.py
@@ -18,10 +18,10 @@ from wetb import gtsdf
import unittest
import os
-import shutil
tmp_path = os.path.dirname(__file__) + "/tmp/"
-tfp = os.path.dirname(__file__) + "/test_files/"
+tfp = os.path.dirname(os.path.abspath(__file__)) + "/test_files/"
+
class Test_gsdf(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
@@ -230,11 +230,33 @@ class Test_gsdf(unittest.TestCase):
df = gtsdf.load_pandas(fn)
def test_loadtesthdf5(self):
-
time, data, info = gtsdf.load(tfp + 'test.hdf5')
self.assertEqual(time[1], 0.05)
self.assertEqual(data[1, 1], 11.986652374267578)
self.assertEqual(info['attribute_names'][1], "WSP gl. coo.,Vy")
+
+ def test_loadhdf5File(self):
+ f = h5py.File(tfp + 'test.hdf5')
+ time, data, info = gtsdf.load(f)
+
+ self.assertEqual(time[1], 0.05)
+ self.assertEqual(data[1, 1], 11.986652374267578)
+ self.assertEqual(info['attribute_names'][1], "WSP gl. coo.,Vy")
+
+
+ def test_gtsdf_dataset(self):
+ ds = gtsdf.Dataset(tfp+'test.hdf5')
+ self.assertEqual(ds.data.shape, (2440,49))
+ self.assertEqual(ds('Time')[1], 0.05)
+ self.assertEqual(ds.Time[1], 0.05)
+ self.assertRaisesRegex(AttributeError, "'Dataset' object has no attribute 'Time1'", lambda : ds.Time1)
+ self.assertEqual(ds(2)[1], 12.04148006439209)
+ n = ds.info['attribute_names'][2]
+ self.assertEqual(n, "WSP gl. coo.,Vy")
+ self.assertEqual(ds(n)[1], 12.04148006439209)
+
+
+
diff --git a/wetb/gtsdf/tests/test_unix_time.py b/wetb/gtsdf/tests/test_unix_time.py
index 434b7c3d87446840831aadf273943f2476604b07..f976195a1dcedd22b82fc28d35d25e8b2ddf4f87 100644
--- a/wetb/gtsdf/tests/test_unix_time.py
+++ b/wetb/gtsdf/tests/test_unix_time.py
@@ -12,30 +12,33 @@ standard_library.install_aliases()
import unittest
import numpy as np
import datetime
-from wetb.utils.timing import print_time
from wetb.gtsdf.unix_time import to_unix, from_unix
+
class TestUnixTime(unittest.TestCase):
def test_to_unix(self):
+ print (np.array([5]))
self.assertEqual(to_unix(datetime.datetime(2016, 2, 2, 13, 6, 25)), 1454418385)
+ self.assertEqual(to_unix([datetime.datetime(2016, 2, 2, 13, 6, 25),datetime.datetime(2016, 2, 2, 13, 6, 26)]), [1454418385,1454418386])
self.assertNotEqual(to_unix(datetime.datetime(2016, 2, 2, 13, 6, 26)), 1454418385)
+ self.assertRaises(Exception, to_unix,1)
+
+
+
+
def test_from_unix(self):
self.assertEqual(from_unix(1454418385), datetime.datetime(2016, 2, 2, 13, 6, 25))
self.assertNotEqual(from_unix(1454418385), datetime.datetime(2016, 2, 2, 13, 6, 26))
+
+ self.assertEqual(from_unix(np.nan), datetime.datetime(1970,1,1,0,0))
+ self.assertEqual(from_unix([1454418385,1454418386]), [datetime.datetime(2016, 2, 2, 13, 6, 25),datetime.datetime(2016, 2, 2, 13, 6, 26)])
+
-# @print_time
-# def r(self, dt):
-# return [to_unix(dt) for dt in dt]
-
-# def test_to_unix_time(self):
-# dt = [datetime.datetime(2000, 1, 1, 12, s % 60) for s in np.arange(1000000)]
-# self.r(dt)
-
if __name__ == "__main__":
#import sys;sys.argv = ['', 'Test.testName']
unittest.main()
diff --git a/wetb/gtsdf/unix_time.py b/wetb/gtsdf/unix_time.py
index dfd4bc6ebb2beadd4720cecf292ab84d199855e3..c5ac88c06e9f8978e8415574f5c74f80bff9ccae 100644
--- a/wetb/gtsdf/unix_time.py
+++ b/wetb/gtsdf/unix_time.py
@@ -18,10 +18,10 @@ def to_unix(dateTime):
return [(dt - timestamp0).total_seconds() for dt in dateTime]
raise
-def from_unix_old(sec):
- if np.isnan(sec):
- return datetime.utcfromtimestamp(0)
- return datetime.utcfromtimestamp(sec)
+# def from_unix_old(sec):
+# if np.isnan(sec):
+# return datetime.utcfromtimestamp(0)
+# return datetime.utcfromtimestamp(sec)
day_dict = {}
diff --git a/wetb/hawc2/ascii2bin/Example.py b/wetb/hawc2/ascii2bin/Example.py
index 38785246e1e7a920711ce2ad2fbfdd21ec8378bf..b0afee5e9af2d676c50a77d3618534446f18c337 100644
--- a/wetb/hawc2/ascii2bin/Example.py
+++ b/wetb/hawc2/ascii2bin/Example.py
@@ -11,6 +11,6 @@ from future import standard_library
standard_library.install_aliases()
from wetb.hawc2.ascii2bin.ascii2bin import ascii2bin
-
-ascii2bin(r"tests/hawc2ascii.sel", "temp_hawc2ascii.sel")
+if __name__=="__main__":
+ ascii2bin(r"tests/hawc2ascii.sel", "temp_hawc2ascii.sel")
diff --git a/wetb/hawc2/ascii2bin/make_exe.py b/wetb/hawc2/ascii2bin/make_exe.py
index 7e31b83af2c8607331179e01e6b267da5b002daa..8b1e848075529830a94f1595d1fb5fb2332061a3 100644
--- a/wetb/hawc2/ascii2bin/make_exe.py
+++ b/wetb/hawc2/ascii2bin/make_exe.py
@@ -6,11 +6,9 @@ Created on 06/09/2013
from __future__ import division, print_function, absolute_import, unicode_literals
from future import standard_library
standard_library.install_aliases()
-from build_exe.cx.build_cx_exe import NUMPY
-try: range = xrange; xrange = None
-except NameError: pass
-try: str = unicode; unicode = None
-except NameError: pass
-from build_exe.cx import build_cx_exe
-build_cx_exe.build_exe("ascii2bin.py", version="3.0.1", includes=["'pandas'"], modules=['email', NUMPY])
+
+if __name__=="__main__":
+ from build_exe.cx.build_cx_exe import NUMPY
+ from build_exe.cx import build_cx_exe
+ build_cx_exe.build_exe("ascii2bin.py", version="3.0.1", includes=["'pandas'"], modules=['email', NUMPY])
diff --git a/wetb/hawc2/simulation.py b/wetb/hawc2/simulation.py
index 4de23bab686aa8cf30b68baeae3266dfabbee2b6..01ae9412adf0d6484edc853c88a334f862abaf83 100755
--- a/wetb/hawc2/simulation.py
+++ b/wetb/hawc2/simulation.py
@@ -458,11 +458,7 @@ class SimulationThread(Thread):
stdout = self.sim.stdout_filename
if not os.path.isdir(os.path.dirname(self.modelpath + self.sim.stdout_filename)):
os.makedirs(os.path.dirname(self.modelpath + self.sim.stdout_filename))
- #if os.name == "nt":
- # self.process = subprocess.Popen('"%s" %s 1> %s 2>&1' % (hawc2exe, htcfile, stdout), stdout=None, stderr=None, shell=True, cwd=modelpath) #, creationflags=CREATE_NO_WINDOW)
- #else:
- # self.process = subprocess.Popen('wine "%s" %s 1> %s 2>&1' % (hawc2exe, htcfile, stdout), stdout=None, stderr=None, shell=True, cwd=modelpath)
-
+
with open (os.path.join(self.modelpath, stdout), 'wb') as stdout:
if isinstance(hawc2exe, tuple):
wine, hawc2exe = hawc2exe
@@ -471,15 +467,6 @@ class SimulationThread(Thread):
self.process = subprocess.Popen([hawc2exe, htcfile], stdout=stdout, stderr=STDOUT, shell=False, cwd=modelpath) #, creationflags=CREATE_NO_WINDOW)
self.process.communicate()
-
-# if isinstance(hawc2exe, tuple):
-# self.process = subprocess.Popen('%s "%s" %s 1> %s 2>&1' % (hawc2exe + (htcfile, stdout)), stdout=None, stderr=None, shell=False, cwd=modelpath)
-# else:
-# self.process = subprocess.Popen('"%s" %s 1> %s 2>&1' % (hawc2exe, htcfile, stdout), stdout=None, stderr=None, shell=False, cwd=modelpath) #, creationflags=CREATE_NO_WINDOW)
-# with open("cmd.txt", 'w') as fid:
-# fid.write("cd %s\n" % modelpath)
-# fid.write('"%s" %s 1> %s 2>&1' % (hawc2exe, htcfile, stdout))
-
import psutil
try:
self.sim.host.resource.process_name = psutil.Process(self.process.pid).name()
diff --git a/wetb/prepost/Simulations.py b/wetb/prepost/Simulations.py
index b2ccffdf089f4f1d5b38d1a53c5dd08c33129159..5bcfe6302f160d9a207359193e96bda7e526fb41 100755
--- a/wetb/prepost/Simulations.py
+++ b/wetb/prepost/Simulations.py
@@ -1455,7 +1455,7 @@ class HtcMaster(object):
for root, dirs, files in os.walk(os.path.join(plocal, path)):
for file_name in files:
src = os.path.join(root, file_name)
- dst = root.replace(os.path.abspath(plocal),
+ dst = os.path.abspath(root).replace(os.path.abspath(plocal),
os.path.abspath(prun))
if not os.path.exists(dst):
os.makedirs(dst)
diff --git a/wetb/utils/caching.py b/wetb/utils/caching.py
index 84a38a69b5a171244a2aadc4519cbacb3415646a..1ca38d4bf4d77251898cfdd9921fbdb3c5828702 100644
--- a/wetb/utils/caching.py
+++ b/wetb/utils/caching.py
@@ -35,6 +35,8 @@ def set_cache_property(obj, name, get_func, set_func=None):
>>> e = Example()
>>> e.test # Call, store and return result of e.slow_function
>>> e.test # Return stored result of e.slow_function
+ >>> e._test = None # clear cache result
+ >>> e.test # Call, store and return result of e.slow_function
"""
_name = "_" + name
setattr(obj, _name, None)
diff --git a/wetb/utils/cython_compile/__init__.py b/wetb/utils/cython_compile/__init__.py
deleted file mode 100644
index 7db504d7fb31152836d8c88fcbc87882dff54f60..0000000000000000000000000000000000000000
--- a/wetb/utils/cython_compile/__init__.py
+++ /dev/null
@@ -1,11 +0,0 @@
-from __future__ import unicode_literals
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-from future import standard_library
-standard_library.install_aliases()
-d = None;d = dir()
-
-from .cython_compile import cython_compile, cython_import, cython_compile_autodeclare, is_compiled
-
-__all__ = [m for m in set(dir()) - set(d)]
\ No newline at end of file
diff --git a/wetb/utils/cython_compile/cython_compile.py b/wetb/utils/cython_compile/cython_compile.py
deleted file mode 100644
index 1e17e16f68208962ccf5a20e72efe528e29c178b..0000000000000000000000000000000000000000
--- a/wetb/utils/cython_compile/cython_compile.py
+++ /dev/null
@@ -1,392 +0,0 @@
-'''
-Created on 10/07/2013
-
-@author: Mads M. Pedersen (mmpe@dtu.dk)
-
-
-Wrapper functions and decorators for compiling functions using Cython
-
-'''
-from __future__ import print_function
-from __future__ import unicode_literals
-from __future__ import division
-from __future__ import absolute_import
-from builtins import dict
-from io import open
-from builtins import zip
-from builtins import str
-from future import standard_library
-standard_library.install_aliases()
-import inspect
-import os
-import re
-import shutil
-import subprocess
-import sys
-import numpy as np
-import warnings
-import imp
-
-
-
-def wrap(f, autodeclare, *args, **kwargs):
- """
- Wrapper function returned by the cython_compile and cython_compile_autodeclare decorators
-
- :param f: Function to compile
- :type f: function
- :param py2pyx_func: py2pyx or py2pyx_autodeclare
- :type py2pyx_func: function
- """
-
- # Generate name: "c:\documents\project\mymodule.py" -> mymodule_myfunction
- # When called from ipython notebooks, filename is an object e.g: "<ipython-input-12-e897f9fefc0c>"
- # therefore <,>,- is removed to make it a legal python module name
- name = os.path.relpath(inspect.getabsfile(f), str(os.getcwd())).replace(".py", "")
- name = name.replace("<", "").replace(">", "").replace("-", "")
- name = "%s_%s" % (name, f.__name__)
- if name.startswith(".."):
- rel_dir = os.path.dirname(name) + os.path.sep
- sys.path.append(rel_dir)
- name = name[len(rel_dir):]
- pass
-
- module_name = name.replace(os.path.sep, ".")
-
- # import compiled module_name if exists, otherwise compile and import
- try:
- cmodule = __import__(module_name, fromlist="*")
- if cmodule.__name__ != module_name or not hasattr(cmodule, f.__name__):
- raise ImportError()
- except ImportError:
- # Generate pyrex code lines
- if autodeclare:
- pyx_lines = py2pyx_autodeclare(f, args, kwargs.copy())
- else:
- # source lines except '@cython_compile'
- source_lines = inspect.getsourcelines(f)[0][1:]
- indent = source_lines[0].index("def")
- pyx_lines = py2pyx([l[indent:] for l in source_lines])
-
- # Write pyrex code lines to .pyx file
- pyx_filename = name.replace("\\", "/") + ".pyx"
- with open(pyx_filename, 'w', encoding='utf-8') as fid:
- fid.writelines(pyx_lines)
-
- # compile, import compiled module_name and delete temporary files
- cmodule = compile_and_cleanup(module_name, pyx_filename, module_name)
- try:
- cf = getattr(cmodule, f.__name__)
- if kwargs == {}:
- return cf(*args)
- else:
- return cf(*args, **kwargs)
- except AttributeError:
- warnings.warn(
- "Compilation or import of %s failed. Python function used instead" %
- f)
- return f(*args, **kwargs)
-
-
-def cython_compile(f):
- """Decorator for compilation, import and execution of the function, f.
- Variables can be declared using Pure or cdef syntax, see module description
- Example:
- @cython_compile
- def my_func(p):
- pass
- """
- w = lambda *args, **kwargs: wrap(f, False, *args, **kwargs)
- w.__name__ = f.__name__
- return w
-
-
-def cython_compile_autodeclare(f):
- """Decorator for autodeclaring, compilation, import and execution of the function, f.
- Declared variables using cdef syntax overrides autodeclaration, see module description
- Example:
- @cython_compile_autocompile
- def my_func(p):
- pass
- """
- w = lambda *args, **kwargs: wrap(f, True, *args, **kwargs)
- w.__name__ = f.__name__
- return w
-
-
-def cython_import(import_module_name, compiler=None):
- """Compiles and imports a module. Use it similar to the normal import
- Example (import my_func from my_module):
-
- from wetb.utils.cython_compile import cython_import
- cython_import('my_module')
- import my_module # import must be after cython_import statement
- my_module.my_func()
-
- """
- module_name = import_module_name.split(".")[-1]
- globals()[module_name] = __import__(import_module_name, fromlist=module_name)
-
- pyd_module = eval(module_name)
- if not is_compiled(pyd_module):
-
- # Read py-module
- file_name = import_module_name.replace(".", "/") + ".py"
- for p in ["."] + sys.path:
- if os.path.isfile(os.path.join(p, file_name)):
- file_path = os.path.join(p, file_name).replace("\\", "/")
- break
- else:
- raise IOError("Module %s cannot be found" % file_name)
-
- fid = open(file_path)
- pylines = fid.readlines()
- fid.close()
-
- # write pyrex file
- pyx_filename = file_path.replace('.py', '.pyx')
- fid = open(pyx_filename, 'w')
- pyxlines = py2pyx(pylines)
- fid.writelines(pyxlines)
- fid.close()
-
- # compile, import compiled module and delete temporary files
- module_relname = eval(module_name).__package__ + "." + module_name #"os.path.relpath(eval(module_name).__file__, str(os.getcwd())).replace(os.path.sep, ".")[:-3]
- return compile_and_cleanup(import_module_name, pyx_filename, module_relname, compiler)
- return eval(module_name)
-
-
-def compile_and_cleanup(module, pyx_filename, module_relname, compiler=None):
- """compile, import compiled module and delete temporary files"""
-
- # Generate setup.py script
- fid = open('setup.py', 'w')
- setup_str = """from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Distutils import build_ext
-import numpy
-
-ext_modules = [Extension("%s", ["%s"], include_dirs = [numpy.get_include()])]
-
-setup(
-name = 'name',
-cmdclass = {'build_ext': build_ext},
-ext_modules = ext_modules
-)""" % (module_relname, pyx_filename)
- fid.write(setup_str)
- fid.close()
- if hasattr(sys, 'frozen'):
- raise Exception ("Trying to compile %s in frozen application" % str(module))
- # create compile command
- import platform
- if compiler is not None:
- compiler_str = "--compiler=%s" % compiler
- elif platform.architecture()[0] == "32bit" and os.name == 'nt' and "mingw" in os.environ['path'].lower():
- compiler_str = "--compiler=mingw32"
- else:
- compiler_str = ""
-
-
-
- bin_python = sys.executable
- cmd = "%s setup.py build_ext --inplace %s" % (bin_python, compiler_str)
-
- # compile
- print ("compiling %s: %s" % (module, cmd))
- proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True)
- (out, err) = proc.communicate()
-
- # Reload and check that module is compiled
- try:
- try:
- del sys.modules[module]
- except KeyError:
- pass
- cmodule = __import__(module, fromlist=module.split(".")[-1])
- imp.reload(cmodule)
-
- except ImportError:
- cmodule = None
-
- if cmodule is None or is_compiled(cmodule) == False:
- line = '\n' + '=' * 79 + '\n'
- sys.stderr.write("%s was not compiled correctly. It may result in slower execution" % module)
- sys.stderr.write('%sstdout:\n%s' % (line, out.decode()))
- sys.stderr.write('%sstderr:%s%s' % (line, line, err))
-
- else:
- print ("Compiling succeeded")
- for f in ['setup.py', pyx_filename, pyx_filename.replace(".pyx", '.c')]:
- if os.path.isfile(f):
- os.remove(f)
-
- # Clean up. Remove temporary files and folders
- if os.path.isdir("build"):
- try:
- shutil.rmtree("build")
- except:
- pass
-
- return cmodule
-
-
-def py2pyx_autodeclare(f, args, kwargs):
- """Generate pyrex code of function f and its input arguments
- This function invokes py2pyx and extends with autodeclarations:
- - arguments: input arguments are declared based their values in args and kwargs
- - cdef: Variables declared by cdef, overrides autodeclaration, e.g:
- "def func(a): #cpdef func(int a):" -> "cpdef func(int a):" (independent of type of a)
- "#cdef int a" - "cdef int a" (independent of type of a)
- - assignment: Variables assigned in function, e.g.
- "a = xxx"
- are declared based on the type of eval(xxx)
- - in: variables returned by iterators, e.g:
- "for a in range(5)",
- "for a,b in [(1,.2)]:"
- are declared base on the type of the first element in eval(iterator), e.g. "type(eval(range(5)[0]))"
- """
-
- arg_names, _, _, defaults = inspect.getargspec(f)
-
- # update kwargs with defaults
- if defaults:
- for k, v in zip(arg_names[::-1], defaults[::-1]):
- if k not in kwargs:
- kwargs[k] = v
- kwargs.update(dict(zip(arg_names, args)))
-
- # get pyx code lines using py2pyx
- lines = inspect.getsourcelines(f)[0]
- if lines[0].strip() == "@cython_compile_autodeclare":
- lines = lines[1:]
- lines = py2pyx(lines)
-
- # prepare regular expressions
- var_name = "(?:_*[a-zA-Z][a-zA-Z0-9_]*)" # optional "_" + one alpha + [0..n] x alphanum. "?:" = no group
- reg_args = re.compile("[ \t]*def +(?:%s) *\(([^:]*)\) *:" % (var_name))
- reg_import = re.compile("[ \t]*c?import *(%s)(?: +as +(%s))?" % (var_name, var_name))
- reg_cdef = re.compile("[ \t]*cdef +(?:(?:signed|unsigned|int|long|float|double|np\.ndarray\[.*\]) *)*(%s)" % var_name)
- reg_assign = re.compile('[ \t]*(%s) *=(.*)' % var_name)
- reg_in = re.compile('[ \t]*for +(%s(?:, *%s)*) +in +(.*):' % (var_name, var_name))
-
-
- def declare_str(var_name, var_value):
- """Generate declaration string '<type(var_value)> <var_name>' e.g:
- declare_str('a',1) -> "long a"
- """
- if isinstance(var_value, (int)):
- return "long long %s" % var_name
- if isinstance(var_value, float):
- return "double %s" % var_name
- elif isinstance(var_value, np.ndarray):
- return "np.ndarray[np.%s_t,ndim=%d] %s" % (var_value.dtype, len(var_value.shape), var_name)
- else:
- raise NotImplementedError(type(var_value))
-
- defs = {} # dict for known local variables
- def_line = None # line nr of "def func():". Autodeclaration of local field inserted below this line
- for i, line in enumerate(lines):
- if def_line is None and 'def' in line:
- # first line containing "def" = function declaration line
- def_line = i
- match = reg_args.match(line)
- if match is not None:
- args = match.group(1).strip() # line=" def func(xxx):#comment" -> args='xxx'
- arg_strs = []
- if args != "":
- for arg in args.split(','):
- arg_name = arg.split('=')[0].strip()
- arg_value = kwargs[arg_name]
- try:
- arg_strs.append(arg.strip().replace(arg_name, declare_str(arg_name, arg_value), 1))
- except NotImplementedError:
- arg_strs.append(arg)
- # replace function declaration line
- lines[i] = '%scpdef %s(%s):\n' % (" " * line.index('def'), f.__name__, ", ".join(arg_strs))
- else:
- #Import: import x as y
- match = reg_import.match(line)
- if match is not None:
- # add imported moduled to kwargs -> enable evaluation of variables
- import_module = match.group(1)
- if match.group(2) is None:
- kwargs[import_module] = __import__(import_module)
- else:
- # import xxx as y
- kwargs[match.group(2)] = __import__(import_module)
- continue
- #Cdef: cdef int x
- match = reg_cdef.match(line)
- if match is not None:
- # line contains a 'cdef' declaration.
- # Add to defs to avoid redeclaration
- var_name = match.group(1)
- if var_name not in defs:
- defs[var_name] = None
- continue
- #Assignment: x = y
- match = reg_assign.match(line)
- if match is not None:
- # line contains an assignment, e.g. a = xxx.
- # Try to evaluate xxx and declare a as type of eval(xxx)
- try:
- var_name = match.group(1)
- if var_name not in defs:
- var_value = eval(match.group(2), globals(), kwargs)
- defs[var_name] = declare_str(
- var_name.strip(), var_value)
- kwargs[var_name] = var_value
- except NotImplementedError:
- pass
- continue
- #In: For x in y
- match = reg_in.match(line)
- if match is not None:
- # line contains 'for xxx in yyy:'.
- # Try to evaluate yyy and declare xxx as type of first element
- # of eval(yyy)
- var_names = [v.strip() for v in match.group(1).split(",")]
- var_values = eval(match.group(2), globals(), kwargs)[0]
- if not isinstance(var_values, (list, tuple)):
- var_values = (var_values,)
- for var_name, var_value in zip(var_names, var_values):
- try:
- if var_name not in defs:
- defs[var_name] = declare_str(var_name, var_value)
- kwargs[var_name] = var_value
- except NotImplementedError:
- pass
- indent = lines[def_line + 1].replace(lines[def_line + 1].lstrip(), "")
-
- # Insert declaration of local fields ordered by name just below function
- # declaration
- for key in sorted(defs.keys(), reverse=True):
- if defs[key] is not None:
- lines.insert(def_line + 1, "%scdef %s\n" % (indent, defs[key]))
-
- return lines
-
-
-def py2pyx(pylines):
- """Generate pyrex code lines from python code lines
- - Adds import of cython and numpy
- - searches every line for "#c". If found text before "#c" is replaced with text after "#c", e.g:
- "def func(a): #cpdef func(int a):" -> "cpdef func(int a):
- "#cdef int b" -> "cdef int b"
- """
- pyxlines = ['import cython\n', 'import numpy as np\n', 'cimport numpy as np\n']
- for l in pylines:
-
- if "#c" in l:
- indent = l[:len(l) - len(l.lstrip())]
- cdef = l[l.index("#c") + 1:]
- l = indent + cdef
- if "__future__" in l:
- pyxlines.insert(0, l) # from __future__ import ... must be first
- else:
- pyxlines.append(l)
- return pyxlines
-
-
-def is_compiled(module):
- return module.__file__.lower()[-4:] == ".pyd" or module.__file__.lower()[-3:] == ".so"
diff --git a/wetb/utils/cython_compile/examples/__init__.py b/wetb/utils/cython_compile/examples/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/wetb/utils/cython_compile/examples/cycheck.py b/wetb/utils/cython_compile/examples/cycheck.py
deleted file mode 100644
index 602cbf3521261a1565a51dc443890686665cb60c..0000000000000000000000000000000000000000
--- a/wetb/utils/cython_compile/examples/cycheck.py
+++ /dev/null
@@ -1,41 +0,0 @@
-'''
-Created on 29/03/2013
-
-@author: Mads
-'''
-from __future__ import unicode_literals
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
-from builtins import range
-from builtins import int
-from future import standard_library
-standard_library.install_aliases()
-import cython
-import math
-
-
-def cycheck(p):
- for i in range(10):
- for y in range(2, int(math.sqrt(p)) + 1):
- if p % y == 0:
- return False
- return True
-
-@cython.ccall
-@cython.locals(y=cython.int, p=cython.ulonglong)
-def cycheck_pure(p):
- for i in range(10):
- for y in range(2, int(math.sqrt(p)) + 1):
- if p % y == 0:
- return False
- return True
-
-
-def cycheck_cdef(p): #cpdef cycheck_cdef(unsigned long long p):
- #cdef int y
- for i in range(10):
- for y in range(2, int(math.sqrt(p)) + 1):
- if p % y == 0:
- return False
- return True
diff --git a/wetb/utils/cython_compile/examples/examples.py b/wetb/utils/cython_compile/examples/examples.py
deleted file mode 100644
index 14f794fe31c4866f8f8597e2ace752e2322c8c74..0000000000000000000000000000000000000000
--- a/wetb/utils/cython_compile/examples/examples.py
+++ /dev/null
@@ -1,62 +0,0 @@
-'''
-Created on 11/07/2013
-
-@author: Mads M. Pedersen (mmpe@dtu.dk)
-'''
-from __future__ import print_function
-from __future__ import unicode_literals
-from __future__ import division
-from __future__ import absolute_import
-from builtins import range
-from builtins import int
-from future import standard_library
-standard_library.install_aliases()
-import math
-
-from wetb.utils.cython_compile.cython_compile import cython_compile, \
- cython_compile_autodeclare, cython_import
-from wetb.utils.cython_compile.examples import cycheck
-
-
-def pycheck(p):
- for i in range(10):
- for y in range(2, int(math.sqrt(p)) + 1):
- if p % y == 0:
- return False
- return True
-
-
-@cython_compile
-def cycheck_compile(p):
- import math
- for i in range(10):
- for y in range(2, int(math.sqrt(p)) + 1):
- if p % y == 0:
- return False
- return True
-
-
-@cython_compile_autodeclare
-def cycheck_compile_autodeclare(p):
- import math
- for i in range(10):
- for y in range(2, int(math.sqrt(p)) + 1):
- if p % y == 0:
- return False
- return True
-
-if __name__ == "__main__":
- p = 17
-
- print (pycheck(p))
-
- cython_import('cycheck')
- print (cycheck.cycheck(p))
- print (cycheck.cycheck_pure(p))
- print (cycheck.cycheck_cdef(p))
-
- print (cycheck_compile(p))
-
- print (cycheck_compile_autodeclare(p))
-
-