fixed indentation

Author: mengaldo

pyspod/postprocessing.py

@@ -882,10 +882,10 @@ def plot_3D_modes_slice_at_frequency(modes, freq_required, freq, vars_idx=[0], m
 					real_ax.set_aspect('equal')
 					imag_ax.set_aspect('equal')
 				if len(title) > 1:
-	 				fig.suptitle(title + \
+					fig.suptitle(title + \
 						', mode: {}, variable ID: {}'.format(mode_id, var_id))
 				else:
-	 				fig.suptitle('mode: {}, variable ID: {}'.format(mode_id, var_id))
+					fig.suptitle('mode: {}, variable ID: {}'.format(mode_id, var_id))
 				real_ax.set_title('Real part')
 				imag_ax.set_title('Imaginary part')
 			else:
@@ -991,7 +991,7 @@ def plot_mode_tracers(modes, freq_required, freq, coords_list, x=None, vars_idx=
 	# use the data dimensions
 	if not coords_list:
 		print('You must provide coords to `plot_mode_tracers` '
-		      'in the form list(tuple(), tuple(), ...)')
+			  'in the form list(tuple(), tuple(), ...)')
 
 	# check the coord_list is indeed list
 	if not isinstance(coords_list, list):
@@ -1176,7 +1176,7 @@ def plot_data_tracers(X, coords_list, x=None, time_limits=[0,10],
 	# check coord_list has correct shape and type
 	if not coords_list:
 		print('You must provide coords to `plot_mode_tracers` '
-		      'in the form list(tuple(), tuple(), ...)')
+			  'in the form list(tuple(), tuple(), ...)')
 	if not isinstance(coords_list, list):
 		raise TypeError('`coords` must be a list')
 	# get idx variables
@@ -1237,7 +1237,7 @@ def plot_data_tracers(X, coords_list, x=None, time_limits=[0,10],
 def generate_2D_data_video(X, time_limits=[0,10], vars_idx=None, sampling=1,
 	x1=None, x2=None, coastlines='', figsize=(12,8), path='CWD', filename='data_video.mp4'):
 	"""
-        Make movie of 2D data.
+		Make movie of 2D data.
 
 	:param numpy.ndarray X: 2D data to be plotted. \
 		First dimension must be time. Last dimension must be variable.
@@ -1308,7 +1308,7 @@ def generate_2D_data_video(X, time_limits=[0,10], vars_idx=None, sampling=1,
 								vmin=-0.9*vmean,
 								vmax= 0.9*vmean),
 				 plt.scatter(coast['coastlon'],
-				 			 coast['coastlat'],
+							 coast['coastlat'],
 							 marker='.', c='k', s=1)]
 				for state in time_range
 			]

pyspod/spod_low_ram.py

@@ -122,7 +122,7 @@ def fit(self):
 			if n_modes_save == 0:
 				raise ValueError('Memory required for storing at least one mode '
 								 'is equal or larger than available storage memory in your system ...\n'
-							 	 '... aborting computation...')
+								 '... aborting computation...')
 
 		# load FFT blocks from hard drive and save modes on hard drive (for large data)
 		for iFreq in tqdm(range(0,self._n_freq),desc='computing frequencies'):

pyspod/spod_streaming.py

@@ -29,8 +29,8 @@ class SPOD_streaming(SPOD_base):
 	the `SPOD_base` class.
 	"""
 	def __init__(self, X, params, data_handler, variables):
-                """Constructor of SPOD_streaming."""
-	        super().__init__(X, params, data_handler, variables)
+				"""Constructor of SPOD_streaming."""
+			super().__init__(X, params, data_handler, variables)
 
 	def fit(self):
 		"""

pyspod/weights.py

@@ -8,7 +8,7 @@
 def geo_weights_trapz_2D(lat, lon, R, n_vars):
 	'''
 	2D integration weights for geospatial
-        data via trapezoidal rule
+		data via trapezoidal rule
 	'''
 	n_lat = len(lat)
 	n_lon = len(lon)
@@ -40,7 +40,7 @@ def geo_weights_trapz_2D(lat, lon, R, n_vars):
 def geo_weights_trapz_3D(lat, lon, R, z, n_vars):
 	'''
 	3D integration weights for geospatial
-        data via trapezoidal rule
+		data via trapezoidal rule
 	'''
 	n_lat = len(lat)
 	n_lon = len(lon)
@@ -101,7 +101,7 @@ def geo_weights_trapz_3D(lat, lon, R, z, n_vars):
 
 
 def apply_normalization(X, weights, method='variance'):
-        '''Normalization of weights if required.'''
+		'''Normalization of weights if required.'''
 
 	# variable-wise normalization by variance via weight matrix
 	if method.lower() == 'variance':

setup.py

@@ -13,36 +13,36 @@
 VERSION = "0.3"
 KEYWORDS='spectral-proper-orthogonal-decomposition spod'
 REQUIRED = [
-    "numpy",
-    "scipy",
-    "matplotlib",
-    "xarray",
-    "netcdf4",
-    "h5py",
-    "psutil",
-    "tqdm",
-    "Sphinx",
-    "sphinx_rtd_theme",
-    "ecmwf_api_client",
-    "cdsapi",
-    "pyFFTW",
+	"numpy",
+	"scipy",
+	"matplotlib",
+	"xarray",
+	"netcdf4",
+	"h5py",
+	"psutil",
+	"tqdm",
+	"Sphinx",
+	"sphinx_rtd_theme",
+	"ecmwf_api_client",
+	"cdsapi",
+	"pyFFTW",
 	"future",
-    "ffmpeg",
-    "pytest",
+	"ffmpeg",
+	"pytest",
 ]
 EXTRAS = {
-    'docs': ['Sphinx==3.2.1', 'sphinx_rtd_theme'],
+	'docs': ['Sphinx==3.2.1', 'sphinx_rtd_theme'],
 }
 DESCR = (
-    "PySPOD is a Python package that implements the Spectral Proper Orthogonal"
-    " Decomposition (SPOD). SPOD is used to extract perfectly coherent spatio-temporal"
-    " patterns in complex datasets. Original work on this technique dates back"
-    " to (Lumley 1970), with recent development brought forward by (Towne et al. 2017),"
-    " (Schmidt et al. 2018), (Schmidt et al. 2019).\n"
-    "\n"
-    "PySPOD comes with a set of tutorials spanning weather and climate, seismic and "
-    " fluidmechanics applicaitons, and it can be used for both canonical problems "
-    " as well as large datasets. \n"
+	"PySPOD is a Python package that implements the Spectral Proper Orthogonal"
+	" Decomposition (SPOD). SPOD is used to extract perfectly coherent spatio-temporal"
+	" patterns in complex datasets. Original work on this technique dates back"
+	" to (Lumley 1970), with recent development brought forward by (Towne et al. 2017),"
+	" (Schmidt et al. 2018), (Schmidt et al. 2019).\n"
+	"\n"
+	"PySPOD comes with a set of tutorials spanning weather and climate, seismic and "
+	" fluidmechanics applicaitons, and it can be used for both canonical problems "
+	" as well as large datasets. \n"
 )
 CWD = os.path.abspath(os.path.dirname(__file__))
 
@@ -51,78 +51,78 @@
 # COMMANDS
 class UploadCommand(Command):
 
-    description = 'Build and publish the package.'
-    user_options = []
+	description = 'Build and publish the package.'
+	user_options = []
 
-    @staticmethod
-    def status(s):
-        """Prints things in bold."""
-        print('\033[1m{0}\033[0m'.format(s))
+	@staticmethod
+	def status(s):
+		"""Prints things in bold."""
+		print('\033[1m{0}\033[0m'.format(s))
 
-    def initialize_options(self):
-        pass
+	def initialize_options(self):
+		pass
 
-    def finalize_options(self):
-        pass
+	def finalize_options(self):
+		pass
 
-    def run(self):
-        try:
-            self.status('Removing previous builds...')
-            rmtree(os.path.join(CWD, 'dist'))
-        except OSError:
-            pass
+	def run(self):
+		try:
+			self.status('Removing previous builds...')
+			rmtree(os.path.join(CWD, 'dist'))
+		except OSError:
+			pass
 
-        self.status('Building Source and Wheel (universal) distribution...')
-        os.system('{0} setup.py sdist bdist_wheel --universal'.format(sys.executable))
+		self.status('Building Source and Wheel (universal) distribution...')
+		os.system('{0} setup.py sdist bdist_wheel --universal'.format(sys.executable))
 
-        self.status('Uploading the package to PyPI via Twine...')
-        os.system('twine upload dist/*')
+		self.status('Uploading the package to PyPI via Twine...')
+		os.system('twine upload dist/*')
 
-        self.status('Pushing git tags...')
-        os.system('git tag v{0}'.format(VERSION))
-        os.system('git push --tags')
-        sys.exit()
+		self.status('Pushing git tags...')
+		os.system('git tag v{0}'.format(VERSION))
+		os.system('git push --tags')
+		sys.exit()
 
 
 
 # SETUP
 setup(
-    name=NAME,
-    version=VERSION,
-    description="Python Spectral Proper Orthogonal Decomposition",
-    long_description=DESCR,
-    author=AUTHOR,
-    author_email=EMAIL,
+	name=NAME,
+	version=VERSION,
+	description="Python Spectral Proper Orthogonal Decomposition",
+	long_description=DESCR,
+	author=AUTHOR,
+	author_email=EMAIL,
 	classifiers=[
-        'License :: OSI Approved :: MIT License',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.6',
-        'Programming Language :: Python :: 3.7',
-        'Programming Language :: Python :: 3.8',
-        'Intended Audience :: Science/Research',
-        'Topic :: Scientific/Engineering :: Mathematics'
+		'License :: OSI Approved :: MIT License',
+		'Programming Language :: Python :: 3',
+		'Programming Language :: Python :: 3.6',
+		'Programming Language :: Python :: 3.7',
+		'Programming Language :: Python :: 3.8',
+		'Intended Audience :: Science/Research',
+		'Topic :: Scientific/Engineering :: Mathematics'
 	],
 	keywords=KEYWORDS,
 	url=URL,
 	license='MIT',
 	# packages=[NAME],
-    packages=find_packages(),
-    package_data={'': [
-        'plotting_support/coast.mat',
-        'plotting_support/coast_centred.mat'
-    ]},
-    data_files=[
-        ('pyspod',['pyspod/plotting_support/coast.mat']),
-        ('pyspod',['pyspod/plotting_support/coast_centred.mat'])],
-    # package_dir={NAME: NAME},
-    # package_data={NAME: [
-    #     'pyspod/plotting_support/*.mat',
-    # ]},
-    install_requires=REQUIRED,
-    extras_require=EXTRAS,
+	packages=find_packages(),
+	package_data={'': [
+		'plotting_support/coast.mat',
+		'plotting_support/coast_centred.mat'
+	]},
+	data_files=[
+		('pyspod',['pyspod/plotting_support/coast.mat']),
+		('pyspod',['pyspod/plotting_support/coast_centred.mat'])],
+	# package_dir={NAME: NAME},
+	# package_data={NAME: [
+	#     'pyspod/plotting_support/*.mat',
+	# ]},
+	install_requires=REQUIRED,
+	extras_require=EXTRAS,
 	include_package_data=True,
 	zip_safe=False,
 
-    cmdclass={
-        'upload': UploadCommand,
-    },)
+	cmdclass={
+		'upload': UploadCommand,
+	},)

tests/test_basic.py

@@ -166,9 +166,9 @@ def test_basic_spod_streaming():
 
 	# clean up results
 	try:
-	    shutil.rmtree(os.path.join(CWD,'results'))
+		shutil.rmtree(os.path.join(CWD,'results'))
 	except OSError as e:
-	    print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
+		print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
 
 
 

tests/test_basic_file.py

@@ -218,13 +218,13 @@ def test_basic_file_spod_streaming():
 	# 	   (np.max(np.abs(modes_at_freq))   > 0.029917334301665384 -tol))
 
 	try:
-	    shutil.rmtree(os.path.join(CWD,'results'))
+		shutil.rmtree(os.path.join(CWD,'results'))
 	except OSError as e:
-	    print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
+		print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
 	try:
-	    os.remove(os.path.join(CWD,'data.nc'))
+		os.remove(os.path.join(CWD,'data.nc'))
 	except OSError as e:
-	    print("Error: %s : %s" % (os.path.join(CWD,'data.nc'), e.strerror))
+		print("Error: %s : %s" % (os.path.join(CWD,'data.nc'), e.strerror))
 
 
 

tests/test_earthquakes.py

@@ -258,9 +258,9 @@ def test_spod_low_storage_savefft():
 
 	# clean up results
 	try:
-	    shutil.rmtree(os.path.join(CWD,'results'))
+		shutil.rmtree(os.path.join(CWD,'results'))
 	except OSError as e:
-	    print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
+		print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
 
 
 
@@ -316,9 +316,9 @@ def test_spod_low_ram_savefft():
 
 	# clean up results
 	try:
-	    shutil.rmtree(os.path.join(CWD,'results'))
+		shutil.rmtree(os.path.join(CWD,'results'))
 	except OSError as e:
-	    print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
+		print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
 
 
 
@@ -379,13 +379,13 @@ def test_postprocessing():
 
 	# clean up results
 	try:
-	    shutil.rmtree(os.path.join(CWD,'results'))
+		shutil.rmtree(os.path.join(CWD,'results'))
 	except OSError as e:
-	    print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
+		print("Error: %s : %s" % (os.path.join(CWD,'results'), e.strerror))
 	try:
-	    shutil.rmtree(os.path.join(CFD,'__pycache__'))
+		shutil.rmtree(os.path.join(CFD,'__pycache__'))
 	except OSError as e:
-	    print("Error: %s : %s" % (os.path.join(CFD,'__pycache__'), e.strerror))
+		print("Error: %s : %s" % (os.path.join(CFD,'__pycache__'), e.strerror))