Merge pull request #51 from neilflood/flake8support

Flake8support

.flake8

@@ -0,0 +1,13 @@
+[flake8]
+exclude = .git,__pycache__,build,dist
+# Error codes we should ignore
+# W291 trailing whitespace
+# W293 blank line contains whitespace
+# W391 blank line at end of file
+# W504 line break after binary operator
+# W605 invalid escape sequence \*    NOTE: This \ is required by readthedocs
+# E128 continuation line under-indented for visual indent
+# E225 missing whitespace around operator
+# E228 missing whitespace around modulo operator
+# E501 line too long (??? > 79 characters)
+ignore = W291,W293,W391,W504,W605,E128,E225,E228,E501

.github/workflows/runflake8.yml

@@ -0,0 +1,16 @@
+name: Flake8 Lint
+
+on: [push, pull_request]
+
+jobs:
+  do-flake8:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+    - name: Setup Python
+      uses: actions/setup-python@v1
+    - name: Lint with flake8
+      uses: py-actions/flake8@v2

doc/source/conf.py

@@ -14,16 +14,15 @@
 # serve to show the default.
 
 import sys
-import os
-import fmask # for version info
-
+import fmask  # for version info
 
 # Set up 'mock' modules, needed to build docs if numpy, gdal etc., aren't installed
 import mock
 import importlib
 
-MOCK_MODULES = ['numpy','scipy','scipy.ndimage','scipy.constants','scipy.stats',
-        'osgeo','gdal','osgeo.gdal','rios','fmask._fillminima','fmask._valueindexes']
+MOCK_MODULES = ['numpy', 'scipy', 'scipy.ndimage', 'scipy.constants',
+    'scipy.stats', 'osgeo', 'gdal', 'osgeo.gdal', 'rios', 'fmask._fillminima',
+    'fmask._valueindexes']
 for mod_name in MOCK_MODULES:
     try:
         importlib.import_module(mod_name)
@@ -32,13 +31,13 @@
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+#  documentation root, use os.path.abspath to make it absolute, like shown here.
+# sys.path.insert(0, os.path.abspath('.'))
 
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -55,7 +54,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -75,41 +74,41 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 exclude_patterns = []
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 
 # -- Options for HTML output ----------------------------------------------
@@ -121,26 +120,26 @@
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
-#html_theme_options = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
@@ -150,48 +149,48 @@
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
 # directly to the root of the documentation.
-#html_extra_path = []
+# html_extra_path = []
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'Fmaskdoc'
@@ -200,43 +199,43 @@
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  ('index', 'fmask.tex', 'PythonFmask Documentation',
-   'Neil Flood, Sam Gillingham', 'manual'),
+    ('index', 'fmask.tex', 'PythonFmask Documentation',
+    'Neil Flood, Sam Gillingham', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True
 
 
 # -- Options for manual page output ---------------------------------------
@@ -249,7 +248,7 @@
 ]
 
 # If true, show URL addresses after external links.
-#man_show_urls = False
+# man_show_urls = False
 
 
 # -- Options for Texinfo output -------------------------------------------
@@ -258,20 +257,20 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  ('index', 'fmask', 'PythonFmask Documentation',
-   'Neil Flood, Sam Gillingham', 'fmask', 'One line description of project.',
-   'Miscellaneous'),
+    ('index', 'fmask', 'PythonFmask Documentation',
+    'Neil Flood, Sam Gillingham', 'fmask', 'One line description of project.',
+    'Miscellaneous'),
 ]
 
 # Documents to append as an appendix to all manuals.
-#texinfo_appendices = []
+# texinfo_appendices = []
 
 # If false, no module index is generated.
-#texinfo_domain_indices = True
+# texinfo_domain_indices = True
 
 # How to display URL addresses: 'footnote', 'no', or 'inline'.
-#texinfo_show_urls = 'footnote'
+# texinfo_show_urls = 'footnote'
 
 # If true, do not generate a @detailmenu in the "Top" node's menu.
-#texinfo_no_detailmenu = False
+# texinfo_no_detailmenu = False
 autodoc_member_order = 'groupwise'

fmask/cmdline/sentinel2Stacked.py

@@ -23,7 +23,6 @@
 import sys
 import os
 import argparse
-import numpy
 import tempfile
 import glob
 import subprocess
@@ -153,7 +152,6 @@ def checkAnglesFile(inputAnglesFile, toafile):
     toaImgInfo = fileinfo.ImageInfo(toafile)
     anglesImgInfo = fileinfo.ImageInfo(inputAnglesFile)
 
-
     outputAnglesFile = inputAnglesFile
     if (toaImgInfo.xRes != anglesImgInfo.xRes) or (toaImgInfo.yRes != anglesImgInfo.yRes):
         (fd, vrtName) = tempfile.mkstemp(prefix='angles', suffix='.vrt')
@@ -211,8 +209,8 @@ def makeStackAndAngles(cmdargs):
         # Now make a resampled copy to the desired pixel size, using the right resample method
         resampleMethod = chooseResampleMethod(cmdargs.pixsize, inBandImg)
         subprocess.check_call([GDALWARPCMD, '-q', '-tr', str(cmdargs.pixsize),
-                str(cmdargs.pixsize), '-co', 'TILED=YES', '-of', 'VRT', '-r',
-                resampleMethod, inBandImg, tmpBand])
+            str(cmdargs.pixsize), '-co', 'TILED=YES', '-of', 'VRT', '-r',
+            resampleMethod, inBandImg, tmpBand])
 
         resampledBands.append(tmpBand)
 
@@ -363,7 +361,7 @@ def mainRoutine(argv=None):
     tempStack = False
     if cmdargs.safedir is not None or cmdargs.granuledir is not None:
         tempStack = True
-        resampledBands = makeStackAndAngles(cmdargs)
+        makeStackAndAngles(cmdargs)
     topMeta = readTopLevelMeta(cmdargs)
 
     anglesfile = checkAnglesFile(cmdargs.anglesfile, cmdargs.toa)

fmask/cmdline/sentinel2makeAnglesImage.py

@@ -41,7 +41,6 @@
 
 import numpy
 from osgeo import gdal
-gdal.UseExceptions()
 from osgeo import osr
 
 from rios import applier
@@ -50,6 +49,8 @@
 
 from fmask import sen2meta
 
+gdal.UseExceptions()
+
 # This scale value will convert between DN and radians in output image file, 
 #    radians = dn * SCALE_TO_RADIANS
 SCALE_TO_RADIANS = 0.01
@@ -115,7 +116,7 @@ def makeAngles(infile, outfile):
 
     lnames = ['SatelliteAzimuth', 'SatelliteZenith', 'SunAzimuth', 'SunZenith']
     for i in range(ds.RasterCount):
-        b = ds.GetRasterBand(i+1)
+        b = ds.GetRasterBand(i + 1)
         b.WriteArray(stackDN[i])
         b.SetNoDataValue(nullValDN)
         b.SetDescription(lnames[i])

fmask/cmdline/usgsLandsatSaturationMask.py

@@ -21,6 +21,7 @@
 from fmask import saturationcheck
 from fmask import config
 
+
 def getCmdargs():
     """
     Get command line arguments