update flake8 >= 3.0 and code format accordingly

Author: wjlei1990

.gitignore

@@ -66,3 +66,6 @@ target/
 
 # temp files
 *.sw*
+
+# hdf5 file
+*.h5

pypaw/bins/count_overall_windows.py

@@ -7,7 +7,7 @@
 each category have and the number will then be used in the weighting
 stage.
 If "weight_output_file" is in the path file, then a default weight param
-file will also be genrated. Be sure to modify some values and then it can
+file will also be generated. Be sure to modify some values and then it can
 be used in the weighting stage.
 """
 from __future__ import print_function, division, absolute_import

pypaw/convert.py

@@ -73,8 +73,8 @@ def add_stationxml_to_asdf(ds, staxml_filelist, event=None,
         for tag, value in sta_dict.iteritems():
             count += 1
             inv = create_simple_inventory(
-                    value[0], value[1], latitude=value[2], longitude=value[3],
-                    elevation=value[4], depth=value[5], start_date=start_date)
+                value[0], value[1], latitude=value[2], longitude=value[3],
+                elevation=value[4], depth=value[5], start_date=start_date)
             ds.add_stationxml(inv)
             if status_bar > 0:
                 drawProgressBar((count)/nstaxml,

pypaw/window_weights.py

@@ -153,8 +153,8 @@ def extract_source_location(input_info):
     event_base = asdf_events[asdf_events.keys()[0]]
     origin = event_base.preferred_origin()
     src_info = {
-         "latitude": origin.latitude, "longitude": origin.longitude,
-         "depth_in_m": origin.depth}
+        "latitude": origin.latitude, "longitude": origin.longitude,
+        "depth_in_m": origin.depth}
 
     return src_info
 

setup.py

@@ -68,8 +68,8 @@ def run_tests(self):
         "seismology", "tomography", "adjoint", "signal", "inversion", "window"
     ],
     install_requires=[
-        "numpy", "obspy>=1.0.0", "flake8", "pytest", "nose", "future>=0.14.1",
-        "pytomo3d", "pyasdf"
+        "numpy", "obspy>=1.0.0", "flake8>=3.0", "pytest", "nose",
+        "future>=0.14.1", "pytomo3d", "pyasdf"
     ],
     entry_points={
         'console_scripts': consoles

tests/test_code_formatting.py

@@ -10,9 +10,7 @@
     GNU General Public License, Version 3
     (http://www.gnu.org/copyleft/gpl.html)
 """
-import flake8
-import flake8.engine
-import flake8.main
+from flake8.api import legacy as flake8
 import inspect
 import os
 
@@ -46,16 +44,11 @@ def test_flake8():
             full_path = os.path.join(dirpath, py_file)
             files.append(full_path)
 
-    # Get the style checker with the default style.
-    flake8_style = flake8.engine.get_style_guide(
-        parse_argv=False, config_file=flake8.main.DEFAULT_CONFIG)
+    style_guide = flake8.get_style_guide(ignore=['E24', 'W503', 'E226'])
+    report = style_guide.check_files(files)
+    assert report.get_statistics('E') == [], 'Flake8 found violations'
+    assert report.total_errors == 0
 
-    report = flake8_style.check_files(files)
-
-    # Make sure at least 10 files are tested.
-    assert report.counters["files"] > 10
-    # And no errors occured.
-    assert report.get_count() == 0
 
 if __name__ == "__main__":
     test_flake8()