Add flake8 Github Action (#331)

* Add flake8 Github Action

* fix PEP8 format

Author: giancastro

.github/workflows/flake8.yml

@@ -0,0 +1,18 @@
+name: flake8 Lint
+
+on: [push, pull_request]
+
+jobs:
+  flake8-lint:
+    runs-on: ubuntu-latest
+    name: Lint with flake8
+    steps:
+      - uses: actions/checkout@v1
+      - uses: ricardochaves/python-lint@v1.3.0
+        with:
+          use-pylint: false
+          use-pycodestyle: false
+          use-flake8: true
+          use-black: false
+          use-mypy: false
+          use-isort: false

docs/source/conf.py

@@ -15,6 +15,10 @@
 import os
 import json
 import sys
+
+import xrspatial
+
+
 sys.path.insert(0, os.path.abspath('../..'))
 
 # -- Project information -----------------------------------------------------
@@ -23,7 +27,6 @@
 copyright = u'2021, makepath'
 author = u'makepath'
 
-import xrspatial
 version = release = xrspatial.__version__
 
 # -- General configuration ---------------------------------------------------

setup.py

@@ -1,14 +1,15 @@
-import os, sys
+import os
+import sys
 import shutil
 from setuptools import setup
-import pkg_resources
 
 # build dependencies
 import pyct.build
 
 # dependencies
 
-# datashader first, then pyct unless pyct version compatible with ds is specified
+# datashader first, then pyct unless pyct version compatible with ds
+# is specified
 # spatialpandas may not be required in final pharmacy_desert version
 # pyct may not be required after pyctdev is released
 install_requires = [
@@ -22,18 +23,18 @@
     'scipy',
     'xarray',
     'pyct <=0.4.6',
-    ]
+]
 
 examples = [
-  'spatialpandas',
+    'spatialpandas',
 ]
 
 # Additional tests dependencies and examples_extra may be needed in the future
 extras_require = {
-  'tests': [
-    'pytest',
-  ],
-  'examples': examples,
+    'tests': [
+        'pytest',
+    ],
+    'examples': examples,
 }
 
 # additional doc dependencies may be needed
@@ -44,37 +45,37 @@
 # metadata for setuptools
 
 setup_args = dict(
-  name='xarray-spatial',
-  use_scm_version={
-    "write_to": "xrspatial/_version.py",
-    "write_to_template": '__version__ = "{version}"',
-    "tag_regex": r"^(?P<prefix>v)?(?P<version>[^\+]+)(?P<suffix>.*)?$",
-  },
-  description='xarray-based spatial analysis tools',
-  install_requires=install_requires,
-  extras_require=extras_require,
-  tests_require=extras_require['tests'],
-  zip_safe=False,
-  classifiers=["Programming Language :: Python :: 3",
-               "License :: OSI Approved :: MIT License",
-               "Operating System :: OS Independent"],
-  packages=['xrspatial',
-            'xrspatial.tests'
-            ],
-  include_package_data=True,
-  entry_points={
-    'console_scripts': [
-      'xrspatial = xrspatial.__main__:main'
-    ]
-  },
+    name='xarray-spatial',
+    use_scm_version={
+        'write_to': 'xrspatial/_version.py',
+        'write_to_template': '__version__ = "{version}"',
+        'tag_regex': r'^(?P<prefix>v)?(?P<version>[^\+]+)(?P<suffix>.*)?$',
+    },
+    description='xarray-based spatial analysis tools',
+    install_requires=install_requires,
+    extras_require=extras_require,
+    tests_require=extras_require['tests'],
+    zip_safe=False,
+    classifiers=['Programming Language :: Python :: 3',
+                 'License :: OSI Approved :: MIT License',
+                 'Operating System :: OS Independent'],
+    packages=['xrspatial',
+              'xrspatial.tests'
+              ],
+    include_package_data=True,
+    entry_points={
+        'console_scripts': [
+            'xrspatial = xrspatial.__main__:main'
+        ]
+    },
 )
 
 if __name__ == '__main__':
-  example_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), 
-                                              'xarray-spatial', 'examples')
-  if 'develop' not in sys.argv:
-    pyct.build.examples(example_path, __file__, force=True)
-  setup(**setup_args)
-  
-  if os.path.isdir(example_path):
-    shutil.rmtree(example_path)
+    example_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
+                                'xarray-spatial', 'examples')
+    if 'develop' not in sys.argv:
+        pyct.build.examples(example_path, __file__, force=True)
+    setup(**setup_args)
+
+    if os.path.isdir(example_path):
+        shutil.rmtree(example_path)

test_examples_cli.py

@@ -5,17 +5,18 @@
 
 # test_args include copy-examples, fetch-data, or examples (does both)
 def run_examples_cmds(*cli_cmds):
-    
     """
+    Run conda package cli commands to download examples and fetch data
+    for notebooks.
 
-    Run conda package cli commands to download examples and fetch data for notebooks
     Parameters: 'copy-examples', 'fetch-data', 'examples'
-    Output: downloads examples and data to new xrspatial-examples directory in xarray-spatial
-
+    Output: downloads examples and data to new xrspatial-examples
+    directory in xarray-spatialx
     """
 
     for arg in cli_cmds:
         with patch.object(sys, 'argv', ['xrspatial', arg]):
             m.main()
 
+
 run_examples_cmds('examples')

xrspatial/__main__.py

@@ -1,5 +1,3 @@
-import os
-
 def main(args=None):
     try:
         import pyct.cmd
@@ -8,7 +6,8 @@ def main(args=None):
         from . import _missing_cmd
         print(_missing_cmd())
         sys.exit(1)
-    return pyct.cmd.substitute_main('xrspatial',args=args)
+    return pyct.cmd.substitute_main('xrspatial', args=args)
+
 
 if __name__ == "__main__":
-    main()
+    main()

xrspatial/aspect.py

@@ -179,10 +179,9 @@ def aspect(agg: xr.DataArray,
     Notes:
     ----------
     Algorithm References:
-        - http://desktop.arcgis.com/en/arcmap/10.3/tools/spatial-analyst-toolbox/how-aspect-works.htm#ESRI_SECTION1_4198691F8852475A9F4BC71246579FAA
-        - Burrough, P. A., and McDonell, R. A., 1998.
-          Principles of Geographical Information Systems
-          (Oxford University Press, New York), pp 406
+    - http://desktop.arcgis.com/en/arcmap/10.3/tools/spatial-analyst-toolbox/how-aspect-works.htm#ESRI_SECTION1_4198691F8852475A9F4BC71246579FAA # noqa
+    - Burrough, P. A., and McDonell, R. A., 1998. Principles of Geographical
+    Information Systems (Oxford University Press, New York), pp 406
 
     Examples:
     ----------
@@ -217,7 +216,8 @@ def aspect(agg: xr.DataArray,
     * lon      (lon) float64 0.0 1.0 2.0 3.0
     * lat      (lat) float64 0.0 1.0 2.0 3.0 4.0
 
-    Terrain Example: https://makepath.github.io/xarray-spatial/assets/examples/user-guide.html
+    Terrain Example:
+    - https://makepath.github.io/xarray-spatial/assets/examples/user-guide.html
     """
 
     # numpy case

xrspatial/bump.py

@@ -118,7 +118,7 @@ def bump(width: int, height: int, count: Optional[int] = None,
         res:      1
 
     Terrrain Example:
-        - https://makepath.github.io/xarray-spatial/assets/examples/user-guide.html
+        - https://makepath.github.io/xarray-spatial/assets/examples/user-guide.html # noqa
     """
 
     linx = range(width)
@@ -128,7 +128,7 @@ def bump(width: int, height: int, count: Optional[int] = None,
         count = width * height // 10
 
     if height_func is None:
-        height_func = lambda bumps: np.ones(len(bumps))
+        height_func = lambda bumps: np.ones(len(bumps)) # noqa
 
     # create 2d array of random x, y for bump locations
     locs = np.empty((count, 2), dtype=np.uint16)

xrspatial/classify.py

@@ -358,23 +358,23 @@ def quantile(agg: xr.DataArray,
         Number of quantiles to be produced, default = 4.
     name: str, optional (default = "quantile")
         Name of the output aggregate array.
-        
+
     Returns:
     ----------
     xarray.DataArray, quantiled aggregate
         2D array, of the same type as the input, of quantile allocations.
         All other input attributes are preserved.
-        
+
     Notes:
     ----------
     Adapted from PySAL:
-        - https://pysal.org/mapclassify/_modules/mapclassify/classifiers.html#Quantiles
+    - https://pysal.org/mapclassify/_modules/mapclassify/classifiers.html#Quantiles # noqa
 
     Note that dask's percentile algorithm is approximate,
     while numpy's is exact. This may cause some differences
     between results of vanilla numpy and dask version of the input agg.
-        - https://github.com/dask/dask/issues/3099
-        
+    - https://github.com/dask/dask/issues/3099
+
     Examples:
     ----------
         Imports
@@ -455,7 +455,7 @@ def _run_numpy_jenks_matrices(data, n_classes):
     nl = data.shape[0] + 1
     variance = 0.0
 
-    for l in range(2, nl):
+    for l in range(2, nl): # noqa
         sum = 0.0
         sum_squares = 0.0
         w = 0.0
@@ -573,7 +573,7 @@ def _run_cupy_jenks_matrices(data, n_classes):
     nl = data.shape[0] + 1
     variance = 0.0
 
-    for l in range(2, nl):
+    for l in range(2, nl): # noqa
         sum = 0.0
         sum_squares = 0.0
         w = 0.0
@@ -709,9 +709,9 @@ def natural_breaks(agg: xr.DataArray,
 
     Algorithm References:
     ----------
-    Map Classify
-        - https://pysal.org/mapclassify/_modules/mapclassify/classifiers.html#NaturalBreaks
-    perrygeo
+    Map Classify:
+    - https://pysal.org/mapclassify/_modules/mapclassify/classifiers.html#NaturalBreaks # noqa
+    perrygeo:
     - https://github.com/perrygeo/jenks/blob/master/jenks.pyx
 
     Examples:
@@ -850,8 +850,10 @@ def equal_interval(agg: xr.DataArray,
 
     Algorithm References:
     ----------
-    PySal: https://pysal.org/mapclassify/_modules/mapclassify/classifiers.html#EqualInterval
-    SciKit: https://scikit-learn.org/stable/auto_examples/classification/plot_classifier_comparison.html#sphx-glr-auto-examples-classification-plot-classifier-comparison-py
+    PySal:
+    - https://pysal.org/mapclassify/_modules/mapclassify/classifiers.html#EqualInterval # noqa
+    SciKit:
+    - https://scikit-learn.org/stable/auto_examples/classification/plot_classifier_comparison.html#sphx-glr-auto-examples-classification-plot-classifier-comparison-py # noqa
 
     Examples:
     ----------

xrspatial/convolution.py

@@ -35,7 +35,7 @@ def convolve_2d(image: xr.DataArray,
     convolve_agg: xarray.DataArray
         2D array representation of the impulse function.
         All other input attributes are preserverd.
-    
+
     Examples:
     ----------
     Imports
@@ -163,7 +163,7 @@ def _convolve_2d_cuda(result, kernel, image):
     # with k and l going through the whole kernel array:
     s = 0
     for k in range(kernel.shape[0]):
-        for l in range(kernel.shape[1]):
+        for l in range(kernel.shape[1]): # noqa
             i_k = i - k + delta_rows
             j_l = j - l + delta_cols
             # (-4-) Check if (i_k, j_k)

xrspatial/curvature.py

@@ -127,7 +127,7 @@ def curvature(agg: xr.DataArray,
     Notes:
     ----------
     Algorithm References:
-        - https://pro.arcgis.com/en/pro-app/latest/tool-reference/spatial-analyst/how-curvature-works.htm
+    - https://pro.arcgis.com/en/pro-app/latest/tool-reference/spatial-analyst/how-curvature-works.htm # noqa
 
     Examples:
     ----------