From 4aaf41d205b57f0162b935f54c7991349189ffc5 Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Fri, 28 Jan 2022 14:54:58 +0100
Subject: [PATCH 01/10] lint is flake8

---
 tox.ini | 12 +-----------
 1 file changed, 1 insertion(+), 11 deletions(-)

diff --git a/tox.ini b/tox.ini
index e320750c..de54a3e1 100644
--- a/tox.ini
+++ b/tox.ini
@@ -2,7 +2,6 @@
 envlist = 
     lint, 
     format, 
-    flake8,
     test
 
 [testenv:test]
@@ -13,16 +12,6 @@ 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
@@ -72,6 +61,7 @@ exclude =
     .tox
 max-line-length = 88
 max-complexity = 10
+count=true
 
 [isort]
 profile = black

From a0ac5a8a3eb8614bfb0dff777a559ca54baf4cfe Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Fri, 28 Jan 2022 15:01:13 +0100
Subject: [PATCH 02/10] Remove - in order to not ignore exit code

---
 tox.ini | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tox.ini b/tox.ini
index de54a3e1..ebf74e37 100644
--- a/tox.ini
+++ b/tox.ini
@@ -14,7 +14,7 @@ basepython = python3
 skip_install = true
 deps = flake8
 commands = 
-    - flake8
+    flake8 .
 
 [testenv:format]
 basepython = python3
@@ -23,8 +23,8 @@ deps =
     isort
     black
 commands =
-    - isort .
-    - black .
+    isort .
+    black .
 
 [testenv:build]
 basepython = python3

From 66c831f2ecf1785fec9d4348f9de4c82993af85d Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Fri, 28 Jan 2022 15:08:10 +0100
Subject: [PATCH 03/10] Add extended ignores for flake8

---
 tox.ini | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tox.ini b/tox.ini
index ebf74e37..695465d4 100644
--- a/tox.ini
+++ b/tox.ini
@@ -50,7 +50,12 @@ commands =
 
 [flake8]
 extend-ignore = 
-    E203,
+    E203, # whitespace before ':' 
+    E501, # line too long
+    F401, # imported but unused
+    C901, # is too complex
+    E402, # module level import not at top of file (for docs)
+
 exclude =
     .git,
     __pycache__,

From 731d979249bb0b1eb49ec7299de1d6bc7847e9cc Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Mon, 31 Jan 2022 12:17:34 +0100
Subject: [PATCH 04/10] Rm unused vars

---
 solaris/eval/base.py              | 1 -
 tests/test_eval/evaluator_test.py | 1 -
 2 files changed, 2 deletions(-)

diff --git a/solaris/eval/base.py b/solaris/eval/base.py
index 7bb8806a..0a61a5cb 100644
--- a/solaris/eval/base.py
+++ b/solaris/eval/base.py
@@ -112,7 +112,6 @@ def eval_iou_spacenet_csv(
         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[
diff --git a/tests/test_eval/evaluator_test.py b/tests/test_eval/evaluator_test.py
index 0c52087f..6355cfca 100644
--- a/tests/test_eval/evaluator_test.py
+++ b/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)

From 7b47c20c45eea9516ac489e1911bd72eeceebb00 Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Mon, 31 Jan 2022 12:18:38 +0100
Subject: [PATCH 05/10] Remove extra #

---
 tests/test_data/test_coco.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_data/test_coco.py b/tests/test_data/test_coco.py
index 02494667..f7c91ba9 100644
--- a/tests/test_data/test_coco.py
+++ b/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"]

From b715ecdeb7b8feb37b7bf182e2d41e08039bbcbf Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Mon, 31 Jan 2022 12:19:31 +0100
Subject: [PATCH 06/10] Rm unused var

---
 solaris/eval/base.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/solaris/eval/base.py b/solaris/eval/base.py
index 0a61a5cb..53b08908 100644
--- a/solaris/eval/base.py
+++ b/solaris/eval/base.py
@@ -111,7 +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
 
         for imageID in tqdm(imageIDList):
             self.ground_truth_GDF_Edit = self.ground_truth_GDF[

From 82bc1718f12dbe2263ed04db3b059de9d8b6a9d4 Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Mon, 31 Jan 2022 12:32:16 +0100
Subject: [PATCH 07/10] Add rio-cogeo dependency

---
 setup.py                    | 1 +
 solaris/tile/raster_tile.py | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 33bd7914..3de8cd71 100644
--- a/setup.py
+++ b/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",
diff --git a/solaris/tile/raster_tile.py b/solaris/tile/raster_tile.py
index 841c79b8..d74db78d 100644
--- a/solaris/tile/raster_tile.py
+++ b/solaris/tile/raster_tile.py
@@ -8,7 +8,7 @@
 from shapely.geometry import box
 from tqdm.auto import tqdm
 
-# from rio_cogeo.cogeo import cog_validate, cog_translate
+from rio_cogeo.cogeo import cog_translate  # ,cog_validate
 from ..utils.core import _check_crs, _check_rasterio_im_load
 
 # removing the following until COG functionality is implemented

From fc819996ffc5af1a7dc82882f31110e8351194b0 Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Mon, 31 Jan 2022 12:35:58 +0100
Subject: [PATCH 08/10] Fix undefined variable, ignore ambigous name

---
 solaris/preproc/pipesegment.py | 2 +-
 tox.ini                        | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/solaris/preproc/pipesegment.py b/solaris/preproc/pipesegment.py
index 00c335c6..d0a88f98 100644
--- a/solaris/preproc/pipesegment.py
+++ b/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)()
diff --git a/tox.ini b/tox.ini
index 695465d4..256a464c 100644
--- a/tox.ini
+++ b/tox.ini
@@ -55,6 +55,7 @@ extend-ignore =
     F401, # imported but unused
     C901, # is too complex
     E402, # module level import not at top of file (for docs)
+    E741, # ambiguous variable name
 
 exclude =
     .git,

From 9b648dd64606ae1aabc66031af3a40ea2a67f69d Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Mon, 31 Jan 2022 12:39:06 +0100
Subject: [PATCH 09/10] Rm flake8

---
 .github/workflows/tests.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index f37f10e1..a6262baf 100644
--- a/.github/workflows/tests.yml
+++ b/.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
 

From 63fbce32e180f130907b840908b5f2599566076c Mon Sep 17 00:00:00 2001
From: Rodrigo Almeida <rodrigo@developmentseed.org>
Date: Tue, 1 Feb 2022 13:28:01 +0100
Subject: [PATCH 10/10] Fix unused imports F401

---
 docs/conf.py                    | 2 +-
 solaris/__init__.py             | 2 +-
 solaris/eval/__init__.py        | 2 +-
 solaris/preproc/__init__.py     | 2 +-
 solaris/preproc/image.py        | 2 +-
 solaris/preproc/label.py        | 2 +-
 solaris/preproc/optical.py      | 3 +--
 solaris/preproc/sar.py          | 3 +--
 solaris/raster/__init__.py      | 2 +-
 solaris/raster/image.py         | 2 --
 solaris/tile/__init__.py        | 2 +-
 solaris/tile/raster_tile.py     | 2 +-
 solaris/utils/__init__.py       | 2 +-
 solaris/utils/tile.py           | 6 ------
 solaris/vector/__init__.py      | 2 +-
 tests/test_cli/test_cli.py      | 2 --
 tests/test_imports.py           | 1 +
 tests/test_raster/test_image.py | 5 +----
 tox.ini                         | 1 -
 19 files changed, 15 insertions(+), 30 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index f0eeee2a..48a37a50 100644
--- a/docs/conf.py
+++ b/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 -----------------------------------------------------
diff --git a/solaris/__init__.py b/solaris/__init__.py
index e8e0fc12..cb4bdf79 100644
--- a/solaris/__init__.py
+++ b/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"
diff --git a/solaris/eval/__init__.py b/solaris/eval/__init__.py
index f62093a2..dc24d18b 100644
--- a/solaris/eval/__init__.py
+++ b/solaris/eval/__init__.py
@@ -1 +1 @@
-from . import base, iou, pixel, vector
+from . import base, iou, pixel, vector  # noqa: F401
diff --git a/solaris/preproc/__init__.py b/solaris/preproc/__init__.py
index b3ce3174..bd0a804c 100644
--- a/solaris/preproc/__init__.py
+++ b/solaris/preproc/__init__.py
@@ -1 +1 @@
-from . import image, label, optical, pipesegment, sar
+from . import image, label, optical, pipesegment, sar  # noqa: F401
diff --git a/solaris/preproc/image.py b/solaris/preproc/image.py
index f358493b..47bf4463 100644
--- a/solaris/preproc/image.py
+++ b/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:
diff --git a/solaris/preproc/label.py b/solaris/preproc/label.py
index 1fe510a2..012f15c8 100644
--- a/solaris/preproc/label.py
+++ b/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):
diff --git a/solaris/preproc/optical.py b/solaris/preproc/optical.py
index f26bd352..44007483 100644
--- a/solaris/preproc/optical.py
+++ b/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):
diff --git a/solaris/preproc/sar.py b/solaris/preproc/sar.py
index 23932bf3..a46add22 100644
--- a/solaris/preproc/sar.py
+++ b/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):
diff --git a/solaris/raster/__init__.py b/solaris/raster/__init__.py
index e82a84ad..be5d49c7 100644
--- a/solaris/raster/__init__.py
+++ b/solaris/raster/__init__.py
@@ -1 +1 @@
-from . import image
+from . import image  # noqa: F401
diff --git a/solaris/raster/image.py b/solaris/raster/image.py
index 49237e26..cc751dc3 100644
--- a/solaris/raster/image.py
+++ b/solaris/raster/image.py
@@ -1,5 +1,3 @@
-import os
-
 import numpy as np
 import rasterio
 
diff --git a/solaris/tile/__init__.py b/solaris/tile/__init__.py
index 08743baa..bfedeece 100644
--- a/solaris/tile/__init__.py
+++ b/solaris/tile/__init__.py
@@ -1 +1 @@
-from . import raster_tile, vector_tile
+from . import raster_tile, vector_tile  # noqa: F401
diff --git a/solaris/tile/raster_tile.py b/solaris/tile/raster_tile.py
index d74db78d..ea7a3dd2 100644
--- a/solaris/tile/raster_tile.py
+++ b/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_translate  # ,cog_validate
 from ..utils.core import _check_crs, _check_rasterio_im_load
 
 # removing the following until COG functionality is implemented
diff --git a/solaris/utils/__init__.py b/solaris/utils/__init__.py
index 1f7ae20a..49f839f8 100644
--- a/solaris/utils/__init__.py
+++ b/solaris/utils/__init__.py
@@ -1 +1 @@
-from . import cli, core, data, geo, io, tile
+from . import cli, core, data, geo, io, tile  # noqa: F401
diff --git a/solaris/utils/tile.py b/solaris/utils/tile.py
index 06932eb3..3b34229e 100644
--- a/solaris/utils/tile.py
+++ b/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
diff --git a/solaris/vector/__init__.py b/solaris/vector/__init__.py
index 4323d396..9a4f4ccf 100644
--- a/solaris/vector/__init__.py
+++ b/solaris/vector/__init__.py
@@ -1 +1 @@
-from . import graph, mask, polygon
+from . import graph, mask, polygon  # noqa: F401
diff --git a/tests/test_cli/test_cli.py b/tests/test_cli/test_cli.py
index ff74fddd..94f35cd9 100644
--- a/tests/test_cli/test_cli.py
+++ b/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
 
diff --git a/tests/test_imports.py b/tests/test_imports.py
index 72e52305..144606cf 100644
--- a/tests/test_imports.py
+++ b/tests/test_imports.py
@@ -1,3 +1,4 @@
+# flake8: noqa: F401
 class TestImports(object):
     def test_imports(self):
         import solaris
diff --git a/tests/test_raster/test_image.py b/tests/test_raster/test_image.py
index 02527d9a..4b4e0a64 100644
--- a/tests/test_raster/test_image.py
+++ b/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/"))
 
diff --git a/tox.ini b/tox.ini
index 256a464c..72f30073 100644
--- a/tox.ini
+++ b/tox.ini
@@ -52,7 +52,6 @@ commands =
 extend-ignore = 
     E203, # whitespace before ':' 
     E501, # line too long
-    F401, # imported but unused
     C901, # is too complex
     E402, # module level import not at top of file (for docs)
     E741, # ambiguous variable name