Fix flake8

.github/workflows/tests.yml

@@ -47,8 +47,6 @@ jobs:
         run: tox -e lint
       - name: Format with tox
         run: tox -e format
-      - name: Flake8 with tox
-        run: tox -e flake8
       - name: Test with tox
         run: tox -e test
 

docs/conf.py

@@ -14,7 +14,7 @@
 import sys
 
 sys.path.insert(0, os.path.abspath(".."))
-import numpy as np
+import numpy as np  # noqa: F401
 import sphinx_bootstrap_theme
 
 # -- Project information -----------------------------------------------------

setup.py

@@ -52,6 +52,7 @@ def check_output(cmd):
         "pyproj>=2.1",
         "PyYAML>=5.4",
         "rasterio>=1.0.23",
+        "rio-cogeo>=3.0.2",
         "requests==2.22.0",
         "rtree>=0.9.3",
         "scikit-image>=0.16.2",

solaris/__init__.py

@@ -1,4 +1,4 @@
-from . import data, utils, vector
+from . import data, utils, vector  # noqa: F401
 
 #  data, eval, preproc, raster, tile, have gdal in them need to replace with rasterio
 __version__ = "0.0.1"

solaris/eval/__init__.py

@@ -1 +1 @@
-from . import base, iou, pixel, vector
+from . import base, iou, pixel, vector  # noqa: F401

solaris/eval/base.py

@@ -111,8 +111,6 @@ def eval_iou_spacenet_csv(
         scoring_dict_list = []
         self.ground_truth_GDF[iou_field] = 0.0
         iou_index = self.ground_truth_GDF.columns.get_loc(iou_field)
-        id_cols = 2
-        ground_truth_ids = self.ground_truth_GDF.iloc[:, :id_cols]
 
         for imageID in tqdm(imageIDList):
             self.ground_truth_GDF_Edit = self.ground_truth_GDF[

solaris/preproc/__init__.py

@@ -1 +1 @@
-from . import image, label, optical, pipesegment, sar
+from . import image, label, optical, pipesegment, sar  # noqa: F401

solaris/preproc/image.py

@@ -9,7 +9,7 @@
 import pandas as pd
 from osgeo import gdal_array
 
-from .pipesegment import LoadSegment, MergeSegment, PipeSegment
+from .pipesegment import LoadSegment, PipeSegment
 
 
 class Image:

solaris/preproc/label.py

@@ -4,7 +4,7 @@
 import shapely.wkt
 
 from ..vector.polygon import convert_poly_coords
-from .pipesegment import LoadSegment, MergeSegment, PipeSegment
+from .pipesegment import LoadSegment, PipeSegment
 
 
 class LoadString(LoadSegment):

solaris/preproc/optical.py

@@ -2,9 +2,8 @@
 
 import numpy as np
 
-from . import image
 from .image import Image
-from .pipesegment import LoadSegment, MergeSegment, PipeSegment
+from .pipesegment import PipeSegment
 
 
 class RGBToHSL(PipeSegment):

solaris/preproc/pipesegment.py

@@ -412,7 +412,7 @@ def PipeFunction(inner_class=PipeSegment, pin=(), *args, **kwargs):
     and *args and **kwargs are sent to the PipeSegment's constructor.
     """
     psobject = inner_class(*args, **kwargs)
-    if issubclass(self.inner_class, LoadSegment):
+    if issubclass(self.inner_class, LoadSegment):  # noqa: F821
         return psobject()
     else:
         return (pin * psobject)()

solaris/preproc/sar.py

@@ -1,6 +1,5 @@
 import json
 import math
-import os
 import uuid
 import warnings
 import xml.etree.ElementTree as ET
@@ -12,7 +11,7 @@
 
 from . import image
 from .image import Image
-from .pipesegment import LoadSegment, MergeSegment, PipeSegment
+from .pipesegment import PipeSegment
 
 
 class BandMath(PipeSegment):

solaris/raster/__init__.py

@@ -1 +1 @@
-from . import image
+from . import image  # noqa: F401

solaris/raster/image.py

@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 import rasterio
 

solaris/tile/__init__.py

@@ -1 +1 @@
-from . import raster_tile, vector_tile
+from . import raster_tile, vector_tile  # noqa: F401

solaris/tile/raster_tile.py

@@ -5,10 +5,10 @@
 from rasterio.mask import mask as rasterio_mask
 from rasterio.vrt import WarpedVRT
 from rasterio.warp import Resampling, calculate_default_transform
+from rio_cogeo.cogeo import cog_translate  # ,cog_validate
 from shapely.geometry import box
 from tqdm.auto import tqdm
 
-# from rio_cogeo.cogeo import cog_validate, cog_translate
 from ..utils.core import _check_crs, _check_rasterio_im_load
 
 # removing the following until COG functionality is implemented

solaris/utils/__init__.py

@@ -1 +1 @@
-from . import cli, core, data, geo, io, tile
+from . import cli, core, data, geo, io, tile  # noqa: F401

solaris/utils/tile.py

@@ -1,11 +1,5 @@
 import json
 
-import geopandas as gpd
-from affine import Affine
-from rasterio.enums import Resampling
-from rasterio.vrt import WarpedVRT
-from rasterio.windows import Window
-
 from .core import _check_crs
 
 # temporarily removing the below until I can get COG functionality implemented

solaris/vector/__init__.py

@@ -1 +1 @@
-from . import graph, mask, polygon
+from . import graph, mask, polygon  # noqa: F401

tests/test_cli/test_cli.py

@@ -1,8 +1,6 @@
 import os
-import pickle
 import subprocess
 
-import networkx as nx
 import numpy as np
 import skimage.io
 

tests/test_data/test_coco.py

@@ -23,7 +23,7 @@ def test_multiclass_single_geojson(self):
             expected_dict = json.load(f)
         with open(os.path.join(data_dir, "tmp_coco.json"), "r") as f:
             saved_result = json.load(f)
-        ## Simplified test due to rounding errors- JSS
+        # Simplified test due to rounding errors- JSS
         assert (
             coco_dict["annotations"][0]["bbox"]
             == expected_dict["annotations"][0]["bbox"]
@@ -62,7 +62,7 @@ def test_singleclass_multi_geojson(self):
 
         with open(os.path.join(data_dir, "coco_sample_1.json"), "r") as f:
             expected_dict = json.load(f)
-        ## Simplified test due to rounding errors- JSS
+        # Simplified test due to rounding errors- JSS
         assert (
             expected_dict["annotations"][0]["bbox"]
             == coco_dict["annotations"][0]["bbox"]

tests/test_eval/evaluator_test.py

@@ -86,7 +86,6 @@ def test_iou_by_building(self):
         path_truth = os.path.join(data_folder, "SN2_sample_truth.csv")
         path_pred = os.path.join(data_folder, "SN2_sample_preds.csv")
         path_ious = os.path.join(data_folder, "SN2_sample_iou_by_building.csv")
-        path_temp = "./temp.pd"
         eb = Evaluator(path_truth)
         eb.load_proposal(path_pred, conf_field_list=["Confidence"], proposalCSV=True)
         eb.eval_iou_spacenet_csv(miniou=0.5, imageIDField="ImageId", min_area=20)

tests/test_imports.py

@@ -1,3 +1,4 @@
+# flake8: noqa: F401
 class TestImports(object):
     def test_imports(self):
         import solaris

tests/test_raster/test_image.py

@@ -1,12 +1,9 @@
 import os
 
-import numpy as np
-import skimage.io
 from affine import Affine
 
-import solaris as sol
 from solaris.data import sample_load_rasterio
-from solaris.raster.image import get_geo_transform, stitch_images
+from solaris.raster.image import get_geo_transform
 
 data_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "../data/"))
 

tox.ini

@@ -2,7 +2,6 @@
 envlist = 
     lint, 
     format, 
-    flake8,
     test
 
 [testenv:test]
@@ -13,19 +12,9 @@ commands =
 [testenv:lint]
 basepython = python3
 skip_install = true
-deps = 
-    isort
-    black
-commands =
-    - isort --check-only --df .
-    - black --check --diff --color .
-
-[testenv:flake8]
-basepython = python3
-skip_install = true
 deps = flake8
 commands = 
-    - flake8
+    flake8 .
 
 [testenv:format]
 basepython = python3
@@ -34,8 +23,8 @@ deps =
     isort
     black
 commands =
-    - isort .
-    - black .
+    isort .
+    black .
 
 [testenv:build]
 basepython = python3
@@ -61,7 +50,12 @@ commands =
 
 [flake8]
 extend-ignore = 
-    E203,
+    E203, # whitespace before ':' 
+    E501, # line too long
+    C901, # is too complex
+    E402, # module level import not at top of file (for docs)
+    E741, # ambiguous variable name
+
 exclude =
     .git,
     __pycache__,
@@ -72,6 +66,7 @@ exclude =
     .tox
 max-line-length = 88
 max-complexity = 10
+count=true
 
 [isort]
 profile = black