RF: Run linting check over whole source tree, use setup.cfg to configure flake8 (closer aligns to pep8speaks bot behavior)

Author: Jacob Roberts

doc/source/dicom/derivations/spm_dicom_orient.py

@@ -46,7 +46,7 @@ def numbered_vector(nrows, symbol_prefix):
 R = zeros(4, 2)
 R[:3, :] = R3
 
-# The following is specific to the SPM algorithm. 
+# The following is specific to the SPM algorithm.
 x1 = ones(4, 1)
 y1 = ones(4, 1)
 y1[:3, :] = pos_pat_0

doc/source/scripts/make_coord_examples.py

@@ -68,6 +68,7 @@
 x, y = 0, 1
 # Make a rectangular box with these sides
 
+
 def make_ortho_box(bl, x_len, y_len):
     """ Make a box with sides parallel to the axes
     """
@@ -76,6 +77,7 @@ def make_ortho_box(bl, x_len, y_len):
                      [bl[x], bl[y] + y_len],
                      [bl[x] + x_len, bl[y] + y_len]))
 
+
 orth_epi_box = make_ortho_box(epi_bl, epi_x_len, epi_y_len)
 
 # Structural bounding box
@@ -126,6 +128,7 @@ def plot_localizer():
 def save_plot():
     # Plot using global variables
     plot_localizer()
+
     def vx2mm(pts):
         return pts - iso_center
     plot_box(vx2mm(rot_box), label='EPI bounding box')

doc/tools/build_modref_templates.py

@@ -37,7 +37,7 @@ def abort(error):
 
     try:
         __import__(package)
-    except ImportError as e:
+    except ImportError:
         abort("Can not import " + package)
 
     module = sys.modules[package]
@@ -73,7 +73,7 @@ def abort(error):
     if source_version != installed_version:
         abort(
             "Installed version does not match source version. "
-            "source_version=" +  str(source_version) + 
+            "source_version=" + str(source_version) +
             "installed_version=" + str(installed_version)
         )
 

setup.cfg

@@ -96,10 +96,17 @@ nibabel =
 max-line-length = 100
 ignore = D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D208,D209,D210,D300,D301,D400,D401,D403,E24,E121,E123,E126,E226,E266,E402,E704,E731,F821,I100,I101,I201,N802,N803,N804,N806,W503,W504,W605
 exclude =
+    venv
+    build
     *test*
     *sphinx*
     nibabel/externals/*
     */__init__.py
+    # temporary -- should be removed in another PR
+    ./doc/source/conf.py
+    ./doc/tools/apigen.py
+    ./nisext
+    ./tools
 
 [versioneer]
 VCS = git

tools/ci/check.sh

@@ -14,8 +14,7 @@ set -x
 export NIBABEL_DATA_DIR="$PWD/nibabel-data"
 
 if [ "${CHECK_TYPE}" == "style" ]; then
-    # Run styles only on core nibabel code.
-    flake8 nibabel
+    flake8
 elif [ "${CHECK_TYPE}" == "doc" ]; then
     cd doc
     make html && make doctest