reapply hack around pycodestyle not respecting noqa E241 via autopep8…

… (see PyCQA/pycodestyle#996)

Makefile

@@ -469,12 +469,24 @@ fix-imports-only: mkdir-reports	## apply import code checks corrections
 		isort --recursive $(APP_ROOT) \
 		1> >(tee "$(REPORTS_DIR)/fixed-imports.txt")'
 
+# FIXME: https://github.com/PyCQA/pycodestyle/issues/996
+# Tool "pycodestyle" doesn't respect "# noqa: E241" locally, but "flake8" and other tools do.
+# Because "autopep8" uses "pycodestyle", it is impossible to disable locally extra spaces (as in tests to align values).
+# Override the codes here from "setup.cfg" because "autopep8" also uses the "flake8" config, and we want to preserve
+# global detection of those errors (typos, bad indents), unless explicitly added and excluded for readability purposes.
+# WARNING: this will cause inconsistencies between what 'check-lint' detects and what 'fix-lint' can actually fix
+_DEFAULT_SETUP_ERROR := E126,E226,E402,F401,W503,W504
+_EXTRA_SETUP_ERROR := E241
+
 .PHONY: fix-lint-only
 fix-lint-only: mkdir-reports  ## fix some PEP8 code style problems automatically
 	@echo "Fixing PEP8 code style problems..."
 	@-rm -fr "$(REPORTS_DIR)/fixed-lint.txt"
 	@bash -c '$(CONDA_CMD) \
-		autopep8 -v -j 0 -i -r $(APP_ROOT) \
+		autopep8 \
+		 	--global-config "$(APP_ROOT)/setup.cfg" \
+		 	--ignore "$(_DEFAULT_SETUP_ERROR),$(_EXTRA_SETUP_ERROR)" \
+			-v -j 0 -i -r $(APP_ROOT) \
 		1> >(tee "$(REPORTS_DIR)/fixed-lint.txt")'
 
 # FIXME: move parameters to setup.cfg when implemented (https://github.com/myint/docformatter/issues/10)

setup.cfg

@@ -5,21 +5,21 @@ tag = True
 tag_name = {new_version}
 
 [bumpversion:file:CHANGES.rst]
-search = 
+search =
 	`Unreleased <https://github.com/crim-ca/weaver/tree/master>`_ (latest)
 	========================================================================
-replace = 
+replace =
 	`Unreleased <https://github.com/crim-ca/weaver/tree/master>`_ (latest)
 	========================================================================
-	
+
 	Changes:
 	--------
 	- No change.
-	
+
 	Fixes:
 	------
 	- No change.
-	
+
 	`{new_version} <https://github.com/crim-ca/weaver/tree/{new_version}>`_ ({now:%%Y-%%m-%%d})
 	========================================================================
 
@@ -40,12 +40,12 @@ search = LABEL version="{current_version}"
 replace = LABEL version="{new_version}"
 
 [tool:pytest]
-addopts = 
+addopts =
 	--strict-markers
 	--tb=native
 	weaver/
 python_files = test_*.py
-markers = 
+markers =
 	testbed14: mark test as 'testbed14' validation
 	functional: mark test as functionality validation
 	workflow: mark test as workflow execution (E2E)
@@ -70,9 +70,12 @@ exclude = *.egg-info,build,dist,env,tests,./tests,test_*
 targets = .
 
 [flake8]
+# FIXME: https://github.com/PyCQA/pycodestyle/issues/996
+# see Makefile for some specific overrides to avoid false-positive during 'fix-lint'
+# new codes must be synced between below list and corresponding one in Makefile
 ignore = E126,E226,E402,F401,W503,W504
 max-line-length = 120
-exclude = 
+exclude =
 	src,
 	.git,
 	__pycache__,
@@ -88,18 +91,19 @@ max-line-length = 120
 ignore-path = docs/build,docs/source/autoapi
 
 [pylint]
+# use .pylintrc
 
 [coverage:run]
 branch = true
 source = ./
 include = weaver/*
-omit = 
+omit =
 	setup.py
 	docs/*
 	tests/*
 
 [coverage:report]
-exclude_lines = 
+exclude_lines =
 	pragma: no cover
 	raise AssertionError
 	raise NotImplementedError