chore: Enable pylint on project (#2326)

Previously, this repo did not do any linting. The linting that is enabled
is basic, as this commit disables all of what pylint was complaining about.

Co-authored-by: Jacob Fuss <jfuss@users.noreply.github.com>

.pylintrc

@@ -9,16 +9,21 @@
 
 # Add files or directories to the ignore list. They should be base names, not
 # paths.
-ignore=compat.py
+ignore=compat.py, __main__.py
 
 # Pickle collected data for later comparisons.
 persistent=yes
 
 # List of plugins (as comma separated values of python modules names) to load,
 # usually to register additional checkers.
 load-plugins=
+    pylint.extensions.check_elif, # Else If Used checker
+    pylint.extensions.emptystring, # compare to empty string
+    pylint.extensions.comparetozero, # compare to 0
+    pylint.extensions.docparams, # Parameter documentation checker
 
 # Use multiple processes to speed up Pylint.
+# Pylint has a bug on multitread, turn it off.
 jobs=1
 
 # Allow loading of arbitrary C extensions. Extensions are imported into the
@@ -59,7 +64,103 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=R0201,W0613,I0021,I0020,W1618,W1619,R0902,R0903,W0231,W0611,R0913,W0703,C0330,R0204,I0011,R0904
+disable=
+    W0613, # Unused argument %r
+    W0640, # Cell variable %s defined in loop A variable used in a closure is defined in a loop
+    R0902, # Too many instance attributes (%s/%s)
+    R0903, # Too few public methods (%s/%s)
+    R0913, # Too many arguments (%s/%s)
+    W0703, # Catching too general exception %s
+    R0904, # Too many public methods (%s/%s)
+    R0914, # Too many local variables (%s/%s)
+    R0915, # Too many statements
+    C0415, # Import outside toplevel (%s) Used when an import statement is used anywhere other than the module toplevel. Move this import to the top of the file.
+    C0115, # missing-class-docstring
+    # below are docstring lint rules, in order to incrementally improve our docstring while
+    # without introduce too much effort at a time, we exclude most of the docstring lint rules.
+    # We will remove them one by one.
+    # W9005, # "%s" has constructor parameters documented in class and __init__
+    W9006, # "%s" not documented as being raised
+    # W9008, # Redundant returns documentation
+    # W9010, # Redundant yields documentation
+    W9011, # Missing return documentation
+    W9012, # Missing return type documentation
+    # W9013, # Missing yield documentation
+    # W9014, # Missing yield type documentation
+    # W9015, # "%s" missing in parameter documentation
+    W9016, # "%s" missing in parameter type documentation
+    # W9017, # "%s" differing in parameter documentation
+    # W9018, # "%s" differing in parameter type documentation
+    # W9019, # "%s" useless ignored parameter documentation
+    # W9020, # "%s" useless ignored parameter type documentation
+    # Constant name style warnings. We will remove them one by one.
+    C0103, # Class constant name "%s" doesn't conform to UPPER_CASE naming style ('([^\\W\\da-z][^\\Wa-z]*|__.*__)$' pattern) (invalid-name)
+    # New recommendations, disable for now to avoid introducing behaviour changes.
+    R1729, # Use a generator instead '%s' (use-a-generator)
+    R1732, # Consider using 'with' for resource-allocating operations (consider-using-with)
+    # This applies to CPython only.
+    I1101, # Module 'math' has no 'pow' member, but source is unavailable. Consider adding this module to extension-pkg-allow-list if you want to perform analysis based on run-time introspection of living objects. (c-extension-no-member)    
+    # Added to allow linting. Need to work on removing over time
+    R0801, # dupilcated code
+    R0401, # Cyclic import
+    C0411, # import ordering
+    W9015, # missing parameter in doc strings
+    W0612, # unused variable
+    R0205, # useless-object-inheritanc
+    C0301, # line to long
+    R0201, # no self use, method could be a function
+    C0114, # missing-module-docstring
+    W1202, # Use lazy % formatting in logging functions (logging-format-interpolation)
+    E1101, # No member 
+    W0622, # Redefining built-in 'property' (redefined-builtin)
+    W0611, # unused imports
+    W0231, # super not called
+    W0212, # protected-access
+    W0201, # attribute-defined-outside-init
+    R1725, # Consider using Python 3 style super() without arguments (super-with-arguments)
+    C2001, # Avoid comparisons to zero (compare-to-zero)
+    R0912, # too many branches
+    W0235, # Useless super delegation in method '__init__' (useless-super-delegation)
+    C0412, # Imports from package samtranslator are not grouped (ungrouped-imports)
+    W0223, # abstract-method
+    W0107, # unnecessary-pass
+    W0707, # raise-missing-from
+    R1720, # no-else-raise
+    W0621, # redefined-outer-name
+    E0203, # access-member-before-definition
+    W0221, # arguments-differ
+    R1710, # inconsistent-return-statements
+    R1702, # too-many-nested-blocks
+    C0123, # Use isinstance() rather than type() for a typecheck. (unidiomatic-typecheck)
+    W0105, # String statement has no effect (pointless-string-statement)
+    C0206, # Consider iterating with .items() (consider-using-dict-items)
+    W9008, # Redundant returns documentation (redundant-returns-doc)
+    E0602, # undefined-variable
+    C0112, # empty-docstring
+    C0116, # missing-function-docstring
+    C0200, # consider-using-enumerate
+    R5501, # Consider using "elif" instead of "else if" (else-if-used)
+    W9017, # differing-param-doc
+    W9018, # differing-type-doc
+    W0511, # fixme
+    C0325, # superfluous-parens
+    R1701, # consider-merging-isinstance
+    C0302, # too-many-lines
+    C0303, # trailing-whitespace
+    R1721, # unnecessary-comprehension
+    C0121, # singleton-comparison
+    E1305, # too-many-format-args
+    R1724, # no-else-continue
+    E0611, # no-name-in-module
+    W9013, # missing-yield-doc
+    W9014, # missing-yield-type-doc
+    C0201, # consider-iterating-dictionary
+    W0237, # arguments-renamed
+    R1718, # consider-using-set-comprehension
+    R1723, # no-else-break
+    E1133, # not-an-iterable
+    E1135, # unsupported-membership-test
+    R1705, # no-else-return
 
 
 [REPORTS]
@@ -162,18 +263,20 @@ module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
 module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
 
 # Regular expression matching correct method names
-method-rgx=[a-z_][a-z0-9_]{2,30}$
+method-rgx=[a-z_][a-z0-9_]{2,50}$
 
 # Naming hint for method names
 method-name-hint=[a-z_][a-z0-9_]{2,30}$
 
 # Regular expression which should only match function or class names that do
 # not require a docstring.
-no-docstring-rgx=.*
+no-docstring-rgx=^_
 
 # Minimum line length for functions/classes that require docstrings, shorter
 # ones are exempt.
-docstring-min-length=-1
+# To improve our docstring without spending too much effort at a time,
+# here set it to 30 and decrease it gradually in the future.
+docstring-min-length=30
 
 
 [FORMAT]
@@ -221,16 +324,16 @@ notes=FIXME,XXX
 [SIMILARITIES]
 
 # Minimum lines number of a similarity.
-min-similarity-lines=5
+min-similarity-lines=12
 
 # Ignore comments when computing similarities.
-ignore-comments=no
+ignore-comments=yes
 
 # Ignore docstrings when computing similarities.
-ignore-docstrings=no
+ignore-docstrings=yes
 
 # Ignore imports when computing similarities.
-ignore-imports=no
+ignore-imports=yes
 
 
 [SPELLING]
@@ -315,7 +418,7 @@ max-args=5
 ignored-argument-names=_.*
 
 # Maximum number of locals for function / method body
-max-locals=15
+max-locals=17
 
 # Maximum number of return / yield for function / method body
 max-returns=6

Makefile

@@ -20,11 +20,15 @@ black:
 black-check:
 	black --check setup.py samtranslator/* tests/* integration/* bin/*.py
 
+lint:
+	# Linter performs static analysis to catch latent bugs
+	pylint --rcfile .pylintrc samtranslator
+
 # Command to run everytime you make changes to verify everything works
 dev: test
 
 # Verifications to run before sending a pull request
-pr: black-check init dev
+pr: black-check lint init dev
 
 define HELP_MESSAGE
 

requirements/dev.txt

@@ -4,7 +4,7 @@ tox~=3.24
 pytest-cov~=2.10.1
 pytest-xdist~=2.5
 pytest-env~=0.6.2
-pylint>=1.7.2,<2.0
+pylint~=2.9.0
 pyyaml~=5.4
 
 # Test requirements