apply pylint and refactor accordingly

python/lammps/.pylintrc.toml

@@ -0,0 +1,556 @@
+[tool.pylint.main]
+# Analyse import fallback blocks. This can be used to support both Python 2 and 3
+# compatible code, which means that the block might have code that exists only in
+# one or another interpreter, leading to false positives when analysed.
+# analyse-fallback-blocks =
+
+# Clear in-memory caches upon conclusion of linting. Useful if running pylint in
+# a server-like mode.
+# clear-cache-post-run =
+
+# Always return a 0 (non-error) status code, even if lint errors are found. This
+# is primarily useful in continuous integration scripts.
+# exit-zero =
+
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code.
+# extension-pkg-allow-list =
+
+# A comma-separated list of package or module names from where C extensions may
+# be loaded. Extensions are loading into the active Python interpreter and may
+# run arbitrary code. (This is an alternative name to extension-pkg-allow-list
+# for backward compatibility.)
+# extension-pkg-whitelist =
+
+# Return non-zero exit code if any of these messages/categories are detected,
+# even if score is above --fail-under value. Syntax same as enable. Messages
+# specified are enabled, while categories only check already-enabled messages.
+# fail-on =
+
+# Specify a score threshold under which the program will exit with error.
+fail-under = 10
+
+# Interpret the stdin as a python script, whose filename needs to be passed as
+# the module_or_package argument.
+# from-stdin =
+
+# Files or directories to be skipped. They should be base names, not paths.
+ignore = ["CVS"]
+
+# Add files or directories matching the regular expressions patterns to the
+# ignore-list. The regex matches against paths and can be in Posix or Windows
+# format. Because '\\' represents the directory delimiter on Windows systems, it
+# can't be used as an escape character.
+# ignore-paths =
+
+# Files or directories matching the regular expression patterns are skipped. The
+# regex matches against base names, not paths. The default value ignores Emacs
+# file locks
+ignore-patterns = ["^\\.#"]
+
+# List of module names for which member attributes should not be checked and will
+# not be imported (useful for modules/projects where namespaces are manipulated
+# during runtime and thus existing member attributes cannot be deduced by static
+# analysis). It supports qualified module names, as well as Unix pattern
+# matching.
+# ignored-modules =
+
+# Python code to execute, usually for sys.path manipulation such as
+# pygtk.require().
+# init-hook =
+
+# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
+# number of processors available to use, and will cap the count on Windows to
+# avoid hangs.
+jobs = 1
+
+# Control the amount of potential inferred values when inferring a single object.
+# This can help the performance when dealing with large functions or complex,
+# nested conditions.
+limit-inference-results = 100
+
+# List of plugins (as comma separated values of python module names) to load,
+# usually to register additional checkers.
+# load-plugins =
+
+# Pickle collected data for later comparisons.
+persistent = true
+
+# Resolve imports to .pyi stubs if available. May reduce no-member messages and
+# increase not-an-iterable messages.
+# prefer-stubs =
+
+# Minimum Python version to use for version dependent checks. Will default to the
+# version used to run pylint.
+py-version = "3.13"
+
+# Discover python modules and packages in the file system subtree.
+# recursive =
+
+# Add paths to the list of the source roots. Supports globbing patterns. The
+# source root is an absolute path or a path relative to the current working
+# directory used to determine a package namespace for modules located under the
+# source root.
+# source-roots =
+
+# When enabled, pylint would attempt to guess common misconfiguration and emit
+# user-friendly hints instead of false-positive error messages.
+suggestion-mode = true
+
+# Allow loading of arbitrary C extensions. Extensions are imported into the
+# active Python interpreter and may run arbitrary code.
+# unsafe-load-any-extension =
+
+[tool.pylint.basic]
+# Naming style matching correct argument names.
+argument-naming-style = "snake_case"
+
+# Regular expression matching correct argument names. Overrides argument-naming-
+# style. If left empty, argument names will be checked with the set naming style.
+# argument-rgx =
+
+# Naming style matching correct attribute names.
+attr-naming-style = "snake_case"
+
+# Regular expression matching correct attribute names. Overrides attr-naming-
+# style. If left empty, attribute names will be checked with the set naming
+# style.
+# attr-rgx =
+
+# Bad variable names which should always be refused, separated by a comma.
+bad-names = ["foo", "bar", "baz", "toto", "tutu", "tata"]
+
+# Bad variable names regexes, separated by a comma. If names match any regex,
+# they will always be refused
+# bad-names-rgxs =
+
+# Naming style matching correct class attribute names.
+class-attribute-naming-style = "any"
+
+# Regular expression matching correct class attribute names. Overrides class-
+# attribute-naming-style. If left empty, class attribute names will be checked
+# with the set naming style.
+# class-attribute-rgx =
+
+# Naming style matching correct class constant names.
+class-const-naming-style = "UPPER_CASE"
+
+# Regular expression matching correct class constant names. Overrides class-
+# const-naming-style. If left empty, class constant names will be checked with
+# the set naming style.
+# class-const-rgx =
+
+# Naming style matching correct class names.
+class-naming-style = "PascalCase"
+
+# Regular expression matching correct class names. Overrides class-naming-style.
+# If left empty, class names will be checked with the set naming style.
+# class-rgx =
+
+# Naming style matching correct constant names.
+const-naming-style = "UPPER_CASE"
+
+# Regular expression matching correct constant names. Overrides const-naming-
+# style. If left empty, constant names will be checked with the set naming style.
+# const-rgx =
+
+# Minimum line length for functions/classes that require docstrings, shorter ones
+# are exempt.
+docstring-min-length = -1
+
+# Naming style matching correct function names.
+function-naming-style = "snake_case"
+
+# Regular expression matching correct function names. Overrides function-naming-
+# style. If left empty, function names will be checked with the set naming style.
+# function-rgx =
+
+# Good variable names which should always be accepted, separated by a comma.
+good-names = ["i", "j", "k", "ex", "Run", "_"]
+
+# Good variable names regexes, separated by a comma. If names match any regex,
+# they will always be accepted
+# good-names-rgxs =
+
+# Include a hint for the correct naming format with invalid-name.
+# include-naming-hint =
+
+# Naming style matching correct inline iteration names.
+inlinevar-naming-style = "any"
+
+# Regular expression matching correct inline iteration names. Overrides
+# inlinevar-naming-style. If left empty, inline iteration names will be checked
+# with the set naming style.
+# inlinevar-rgx =
+
+# Naming style matching correct method names.
+method-naming-style = "snake_case"
+
+# Regular expression matching correct method names. Overrides method-naming-
+# style. If left empty, method names will be checked with the set naming style.
+# method-rgx =
+
+# Naming style matching correct module names.
+module-naming-style = "snake_case"
+
+# Regular expression matching correct module names. Overrides module-naming-
+# style. If left empty, module names will be checked with the set naming style.
+# module-rgx =
+
+# Colon-delimited sets of names that determine each other's naming style when the
+# name regexes allow several styles.
+# name-group =
+
+# Regular expression which should only match function or class names that do not
+# require a docstring.
+no-docstring-rgx = "^_"
+
+# List of decorators that produce properties, such as abc.abstractproperty. Add
+# to this list to register other decorators that produce valid properties. These
+# decorators are taken in consideration only for invalid-name.
+property-classes = ["abc.abstractproperty"]
+
+# Regular expression matching correct type alias names. If left empty, type alias
+# names will be checked with the set naming style.
+# typealias-rgx =
+
+# Regular expression matching correct type variable names. If left empty, type
+# variable names will be checked with the set naming style.
+# typevar-rgx =
+
+# Naming style matching correct variable names.
+variable-naming-style = "snake_case"
+
+# Regular expression matching correct variable names. Overrides variable-naming-
+# style. If left empty, variable names will be checked with the set naming style.
+# variable-rgx =
+
+[tool.pylint.classes]
+# Warn about protected attribute access inside special methods
+# check-protected-access-in-special-methods =
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods = ["__init__", "__new__", "setUp", "asyncSetUp", "__post_init__"]
+
+# List of member names, which should be excluded from the protected access
+# warning.
+exclude-protected = ["_asdict", "_fields", "_replace", "_source", "_make", "os._exit"]
+
+# List of valid names for the first argument in a class method.
+valid-classmethod-first-arg = ["cls"]
+
+# List of valid names for the first argument in a metaclass class method.
+valid-metaclass-classmethod-first-arg = ["mcs"]
+
+[tool.pylint.design]
+# List of regular expressions of class ancestor names to ignore when counting
+# public methods (see R0903)
+# exclude-too-few-public-methods =
+
+# List of qualified class names to ignore when counting class parents (see R0901)
+# ignored-parents =
+
+# Maximum number of arguments for function / method.
+max-args = 10
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes = 20
+
+# Maximum number of boolean expressions in an if statement (see R0916).
+max-bool-expr = 5
+
+# Maximum number of branch for function / method body.
+max-branches = 50
+
+# Maximum number of locals for function / method body.
+max-locals = 20
+
+# Maximum number of parents for a class (see R0901).
+max-parents = 7
+
+# Maximum number of positional arguments for function / method.
+max-positional-arguments = 10
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods = 100
+
+# Maximum number of return / yield for function / method body.
+max-returns = 15
+
+# Maximum number of statements in function / method body.
+max-statements = 500
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods = 2
+
+[tool.pylint.exceptions]
+# Exceptions that will emit a warning when caught.
+overgeneral-exceptions = ["builtins.BaseException", "builtins.Exception"]
+
+[tool.pylint.format]
+# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
+# expected-line-ending-format =
+
+# Regexp for a line that is allowed to be longer than the limit.
+ignore-long-lines = "^\\s*(# )?<?https?://\\S+>?$"
+
+# Number of spaces of indent required inside a hanging or continued line.
+indent-after-paren = 2
+
+# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
+# tab).
+indent-string = "  "
+
+# Maximum number of characters on a single line.
+max-line-length = 160
+
+# Maximum number of lines in a module.
+max-module-lines = 5000
+
+# Allow the body of a class to be on the same line as the declaration if body
+# contains single statement.
+# single-line-class-stmt =
+
+# Allow the body of an if to be on the same line as the test if there is no else.
+# single-line-if-stmt =
+
+[tool.pylint.imports]
+# List of modules that can be imported at any level, not just the top level one.
+# allow-any-import-level =
+
+# Allow explicit reexports by alias from a package __init__.
+# allow-reexport-from-package =
+
+# Allow wildcard imports from modules that define __all__.
+# allow-wildcard-with-all =
+
+# Deprecated modules which should not be used, separated by a comma.
+# deprecated-modules =
+
+# Output a graph (.gv or any supported image format) of external dependencies to
+# the given file (report RP0402 must not be disabled).
+# ext-import-graph =
+
+# Output a graph (.gv or any supported image format) of all (i.e. internal and
+# external) dependencies to the given file (report RP0402 must not be disabled).
+# import-graph =
+
+# Output a graph (.gv or any supported image format) of internal dependencies to
+# the given file (report RP0402 must not be disabled).
+# int-import-graph =
+
+# Force import order to recognize a module as part of the standard compatibility
+# libraries.
+# known-standard-library =
+
+# Force import order to recognize a module as part of a third party library.
+known-third-party = ["enchant"]
+
+# Couples of modules and preferred modules, separated by a comma.
+# preferred-modules =
+
+[tool.pylint.logging]
+# The type of string formatting that logging methods do. `old` means using %
+# formatting, `new` is for `{}` formatting.
+logging-format-style = "old"
+
+# Logging modules to check that the string format arguments are in logging
+# function parameter format.
+logging-modules = ["logging"]
+
+[tool.pylint."messages control"]
+# Only show warnings with the listed confidence levels. Leave empty to show all.
+# Valid levels: HIGH, CONTROL_FLOW, INFERENCE, INFERENCE_FAILURE, UNDEFINED.
+confidence = ["HIGH", "CONTROL_FLOW", "INFERENCE", "INFERENCE_FAILURE", "UNDEFINED"]
+
+# Disable the message, report, category or checker with the given id(s). You can
+# either give multiple identifiers separated by comma (,) or put this option
+# multiple times (only on the command line, not in the configuration file where
+# it should appear only once). You can also use "--disable=all" to disable
+# everything first and then re-enable specific checks. For example, if you want
+# to run only the similarities checker, you can use "--disable=all
+# --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 = ["raw-checker-failed", "bad-inline-option", "locally-disabled", "file-ignored", "suppressed-message", "useless-suppression", "deprecated-pragma", "use-implicit-booleaness-not-comparison-to-string", "use-implicit-booleaness-not-comparison-to-zero", "use-symbolic-message-instead"]
+
+# Enable the message, report, category or checker with the given id(s). You can
+# either give multiple identifier separated by comma (,) or put this option
+# multiple time (only on the command line, not in the configuration file where it
+# should appear only once). See also the "--disable" option for examples.
+# enable =
+
+[tool.pylint.method_args]
+# List of qualified names (i.e., library.method) which require a timeout
+# parameter e.g. 'requests.api.get,requests.api.post'
+timeout-methods = ["requests.api.delete", "requests.api.get", "requests.api.head", "requests.api.options", "requests.api.patch", "requests.api.post", "requests.api.put", "requests.api.request"]
+
+[tool.pylint.miscellaneous]
+# List of note tags to take in consideration, separated by a comma.
+notes = ["FIXME", "XXX", "TODO"]
+
+# Regular expression of note tags to take in consideration.
+# notes-rgx =
+
+[tool.pylint.refactoring]
+# Maximum number of nested blocks for function / method body
+max-nested-blocks = 5
+
+# Complete name of functions that never returns. When checking for inconsistent-
+# return-statements if a never returning function is called then it will be
+# considered as an explicit return statement and no message will be printed.
+never-returning-functions = ["sys.exit", "argparse.parse_error"]
+
+# Let 'consider-using-join' be raised when the separator to join on would be non-
+# empty (resulting in expected fixes of the type: ``"- " + " - ".join(items)``)
+suggest-join-with-non-empty-separator = true
+
+[tool.pylint.reports]
+# Python expression which should return a score less than or equal to 10. You
+# have access to the variables 'fatal', 'error', 'warning', 'refactor',
+# 'convention', and 'info' which contain the number of messages in each category,
+# as well as 'statement' which is the total number of statements analyzed. This
+# score is used by the global evaluation report (RP0004).
+evaluation = "max(0, 0 if fatal else 10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10))"
+
+# Template used to display messages. This is a python new-style format string
+# used to format the message information. See doc for all details.
+# msg-template =
+
+# Set the output format. Available formats are: 'text', 'parseable', 'colorized',
+# 'json2' (improved json format), 'json' (old json format), msvs (visual studio)
+# and 'github' (GitHub actions). You can also give a reporter class, e.g.
+# mypackage.mymodule.MyReporterClass.
+# output-format =
+
+# Tells whether to display a full report or only the messages.
+# reports =
+
+# Activate the evaluation score.
+score = true
+
+[tool.pylint.similarities]
+# Comments are removed from the similarity computation
+ignore-comments = true
+
+# Docstrings are removed from the similarity computation
+ignore-docstrings = true
+
+# Imports are removed from the similarity computation
+ignore-imports = true
+
+# Signatures are removed from the similarity computation
+ignore-signatures = true
+
+# Minimum lines number of a similarity.
+min-similarity-lines = 4
+
+[tool.pylint.spelling]
+# Limits count of emitted suggestions for spelling mistakes.
+max-spelling-suggestions = 4
+
+# Spelling dictionary name. Available dictionaries: en_AG (hunspell), en_AU
+# (hunspell), en_BS (hunspell), en_BW (hunspell), en_BZ (hunspell), en_CA
+# (hunspell), en_DK (hunspell), en_GB (hunspell), en_GH (hunspell), en_HK
+# (hunspell), en_IE (hunspell), en_IN (hunspell), en_JM (hunspell), en_MW
+# (hunspell), en_NA (hunspell), en_NG (hunspell), en_NZ (hunspell), en_PH
+# (hunspell), en_SG (hunspell), en_TT (hunspell), en_US (hunspell), en_ZA
+# (hunspell), en_ZM (hunspell), en_ZW (hunspell).
+# spelling-dict =
+
+# List of comma separated words that should be considered directives if they
+# appear at the beginning of a comment and should not be checked.
+spelling-ignore-comment-directives = "fmt: on,fmt: off,noqa:,noqa,nosec,isort:skip,mypy:"
+
+# List of comma separated words that should not be checked.
+# spelling-ignore-words =
+
+# A path to a file that contains the private dictionary; one word per line.
+# spelling-private-dict-file =
+
+# Tells whether to store unknown words to the private dictionary (see the
+# --spelling-private-dict-file option) instead of raising a message.
+# spelling-store-unknown-words =
+
+[tool.pylint.typecheck]
+# List of decorators that produce context managers, such as
+# contextlib.contextmanager. Add to this list to register other decorators that
+# produce valid context managers.
+contextmanager-decorators = ["contextlib.contextmanager"]
+
+# List of members which are set dynamically and missed by pylint inference
+# system, and so shouldn't trigger E1101 when accessed. Python regular
+# expressions are accepted.
+# generated-members =
+
+# Tells whether missing members accessed in mixin class should be ignored. A
+# class is considered mixin if its name matches the mixin-class-rgx option.
+# Tells whether to warn about missing members when the owner of the attribute is
+# inferred to be None.
+ignore-none = true
+
+# This flag controls whether pylint should warn about no-member and similar
+# checks whenever an opaque object is returned when inferring. The inference can
+# return multiple potential results while evaluating a Python object, but some
+# branches might not be evaluated, which results in partial inference. In that
+# case, it might be useful to still emit no-member and other checks for the rest
+# of the inferred objects.
+ignore-on-opaque-inference = true
+
+# List of symbolic message names to ignore for Mixin members.
+ignored-checks-for-mixins = ["no-member", "not-async-context-manager", "not-context-manager", "attribute-defined-outside-init"]
+
+# List of class names for which member attributes should not be checked (useful
+# for classes with dynamically set attributes). This supports the use of
+# qualified names.
+ignored-classes = ["optparse.Values", "thread._local", "_thread._local", "argparse.Namespace"]
+
+# Show a hint with possible names when a member name was not found. The aspect of
+# finding the hint is based on edit distance.
+missing-member-hint = true
+
+# The maximum edit distance a name should have in order to be considered a
+# similar match for a missing member name.
+missing-member-hint-distance = 1
+
+# The total number of similar names that should be taken in consideration when
+# showing a hint for a missing member.
+missing-member-max-choices = 1
+
+# Regex pattern to define which classes are considered mixins.
+mixin-class-rgx = ".*[Mm]ixin"
+
+# List of decorators that change the signature of a decorated function.
+# signature-mutators =
+
+[tool.pylint.variables]
+# List of additional names supposed to be defined in builtins. Remember that you
+# should avoid defining new builtins when possible.
+# additional-builtins =
+
+# Tells whether unused global variables should be treated as a violation.
+allow-global-unused-variables = true
+
+# List of names allowed to shadow builtins
+# allowed-redefined-builtins =
+
+# List of strings which can identify a callback function by name. A callback name
+# must start or end with one of those strings.
+callbacks = ["cb_", "_cb"]
+
+# A regular expression matching the name of dummy variables (i.e. expected to not
+# be used).
+dummy-variables-rgx = "_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_"
+
+# Argument names that match this expression will be ignored.
+ignored-argument-names = "_.*|^ignored_|^unused_"
+
+# Tells whether we should check for unused import in __init__ files.
+# init-import =
+
+# List of qualified module names which can have objects that can redefine
+# builtins.
+redefining-builtins-modules = ["six.moves", "past.builtins", "future.builtins", "builtins", "io"]
+
+

python/lammps/__init__.py

@@ -15,12 +15,13 @@ from .pylammps import *                 # lgtm [py/polluting-import]
 
 # convert installed module string version to numeric version
 def get_version_number():
+  # pylint: disable=C0415
   import time
-    from os.path import join
+  from os import path
   from sys import version_info
 
   # must report 0 when inside LAMMPS source tree
-    if __file__.find(join('python', 'lammps', '__init__.py')) > 0:
+  if __file__.find(path.join('python', 'lammps', '__init__.py')) > 0:
     return 0
 
   if version_info.major < 3 or (version_info.major == 3 and version_info.minor < 6):

python/lammps/core.py

@@ -12,11 +12,10 @@
 # -------------------------------------------------------------------------
 # Python wrapper for the LAMMPS library via ctypes
 
-# for python2/3 compatibility
-
-from __future__ import print_function
-
+# avoid pylint warnings about naming conventions
+# pylint: disable=C0103
 import os
+import platform
 from ctypes import CDLL, POINTER, RTLD_GLOBAL, CFUNCTYPE, py_object, byref, cast, sizeof, \
   create_string_buffer, c_int, c_int32, c_int64, c_double, c_void_p, c_char_p, c_char,    \
   pythonapi
@@ -58,15 +57,11 @@ class ExceptionCheck:
 
 # -------------------------------------------------------------------------
 
-class command_wrapper(object):
+class command_wrapper:
   def __init__(self, lmp):
     self.lmp = lmp
     self.auto_flush = False
 
-  def lmp_print(self, s):
-    """ needed for Python2 compatibility, since print is a reserved keyword """
-    return self.__getattr__("print")(s)
-
   def __dir__(self):
     return sorted(set(['angle_coeff', 'angle_style', 'atom_modify', 'atom_style', 'atom_style',
     'bond_coeff', 'bond_style', 'boundary', 'change_box', 'communicate', 'compute',
@@ -82,6 +77,7 @@ class command_wrapper(object):
 
   def _wrap_args(self, x):
     if callable(x):
+      # pylint: disable=C0415
       import hashlib
       import __main__
       sha = hashlib.sha256()
@@ -94,6 +90,7 @@ class command_wrapper(object):
         setattr(__main__, func_name, handler)
         return func_name
       return x
+    return None
 
   def __getattr__(self, name):
     """
@@ -114,12 +111,12 @@ class command_wrapper(object):
       cmd_args = [name] + [str(self._wrap_args(x)) for x in args]
 
       # Python 3.6+ maintains ordering of kwarg keys
-      for k in kwargs.keys():
-          cmd_args.append(k)
-          if type(kwargs[k]) == bool:
-              cmd_args.append("true" if kwargs[k] else "false")
+      for kw, arg in kwargs.items():
+        cmd_args.append(kw)
+        if isinstance(arg,bool):
+          cmd_args.append("true" if arg else "false")
         else:
-              cmd_args.append(str(self._wrap_args(kwargs[k])))
+          cmd_args.append(str(self._wrap_args(arg)))
 
       cmd = ' '.join(cmd_args)
       self.lmp.command(cmd)
@@ -129,7 +126,7 @@ class command_wrapper(object):
 
 # -------------------------------------------------------------------------
 
-class lammps(object):
+class lammps:
   """Create an instance of the LAMMPS Python class.
 
   .. _mpi4py_docs: https://mpi4py.readthedocs.io/
@@ -169,7 +166,7 @@ class lammps(object):
     # for windows installers the shared library is in a different folder
     winpath = abspath(os.path.join(modpath,'..','..','bin'))
     # allow override for running tests on Windows
-    if (os.environ.get("LAMMPSDLLPATH")):
+    if os.environ.get("LAMMPSDLLPATH"):
       winpath = os.environ.get("LAMMPSDLLPATH")
     self.lib = None
     self.lmp = None
@@ -183,7 +180,8 @@ class lammps(object):
     # load a shared object.
 
     try:
-      if ptr is not None: self.lib = CDLL("",RTLD_GLOBAL)
+      if ptr is not None:
+        self.lib = CDLL("",RTLD_GLOBAL)
     except OSError:
       self.lib = None
 
@@ -196,21 +194,17 @@ class lammps(object):
     #   typically requires LD_LIBRARY_PATH to be set appropriately
     # guess shared library extension based on OS, if not inferred from actual file
 
-    if any([f.startswith('liblammps') and f.endswith('.dylib')
-            for f in os.listdir(modpath)]):
+    if any(f.startswith('liblammps') and f.endswith('.dylib') for f in os.listdir(modpath)):
       lib_ext = ".dylib"
-    elif any([f.startswith('liblammps') and f.endswith('.dll')
-              for f in os.listdir(modpath)]):
+    elif any(f.startswith('liblammps') and f.endswith('.dll') for f in os.listdir(modpath)):
       lib_ext = ".dll"
-    elif os.path.exists(winpath) and any([f.startswith('liblammps') and f.endswith('.dll')
-                  for f in os.listdir(winpath)]):
+    elif os.path.exists(winpath) and \
+         any(f.startswith('liblammps') and f.endswith('.dll') for f in os.listdir(winpath)):
       lib_ext = ".dll"
       modpath = winpath
-    elif any([f.startswith('liblammps') and f.endswith('.so')
-              for f in os.listdir(modpath)]):
+    elif any(f.startswith('liblammps') and f.endswith('.so') for f in os.listdir(modpath)):
       lib_ext = ".so"
     else:
-      import platform
       if platform.system() == "Darwin":
         lib_ext = ".dylib"
       elif platform.system() == "Windows":
@@ -220,14 +214,14 @@ class lammps(object):
 
     if not self.lib:
       if name:
-        libpath = join(modpath,"liblammps_%s" % name + lib_ext)
+        libpath = join(modpath,f'liblammps_{name + lib_ext}')
       else:
-        libpath = join(modpath,"liblammps" + lib_ext)
+        libpath = join(modpath,'liblammps' + lib_ext)
       if not os.path.isfile(libpath):
         if name:
-          libpath = "liblammps_%s" % name + lib_ext
+          libpath = f'liblammps_{name + lib_ext}'
         else:
-          libpath = "liblammps" + lib_ext
+          libpath = 'liblammps' + lib_ext
       self.lib = CDLL(libpath,RTLD_GLOBAL)
 
     # declare all argument and return types for all library methods here.
@@ -442,10 +436,11 @@ class lammps(object):
     # only needed if LAMMPS has been compiled with MPI support.
     self.has_mpi4py = False
     if self.has_mpi_support:
+      # pylint: disable=C0415
       try:
         from mpi4py import __version__ as mpi4py_version
         # tested to work with mpi4py versions 2, 3, and 4
-        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3','4']
+        self.has_mpi4py = mpi4py_version.split('.',maxsplit=1)[0] in ['2','3','4']
       except ImportError:
         # ignore failing import
         pass
@@ -464,14 +459,16 @@ class lammps(object):
       # need to adjust for type of MPI communicator object
       # allow for int (like MPICH) or void* (like OpenMPI)
       if self.has_mpi_support and self.has_mpi4py:
+        # pylint: disable=C0415
         from mpi4py import MPI
         self.MPI = MPI
 
       if comm is not None:
+        # pylint: disable=I1101
         if not self.has_mpi_support:
-          raise Exception('LAMMPS not compiled with real MPI library')
+          raise RuntimeError('LAMMPS not compiled with real MPI library')
         if not self.has_mpi4py:
-          raise Exception('Python mpi4py version is not 2, 3, or 4')
+          raise RuntimeError('Python mpi4py version is not 2, 3, or 4')
         if self.MPI._sizeof(self.MPI.Comm) == sizeof(c_int):
           MPI_Comm = c_int
         else:
@@ -479,7 +476,7 @@ class lammps(object):
 
         # Detect whether LAMMPS and mpi4py definitely use different MPI libs
         if sizeof(MPI_Comm) != self.lib.lammps_config_has_mpi_support():
-          raise Exception('Inconsistent MPI library in LAMMPS and mpi4py')
+          raise RuntimeError('Inconsistent MPI library in LAMMPS and mpi4py')
 
         narg = 0
         cargs = None
@@ -487,9 +484,9 @@ class lammps(object):
           myargs = ["lammps".encode()]
           narg = len(cmdargs) + 1
           for arg in cmdargs:
-            if type(arg) is str:
+            if isinstance(arg,str):
               myargs.append(arg.encode())
-            elif type(arg) is bytes:
+            elif isinstance(arg,bytes):
               myargs.append(arg)
             else:
               raise TypeError('Unsupported cmdargs type ', type(arg))
@@ -506,15 +503,16 @@ class lammps(object):
 
       else:
         if self.has_mpi4py and self.has_mpi_support:
+          # pylint: disable=I1101
           self.comm = self.MPI.COMM_WORLD
         self.opened = 1
         if cmdargs is not None:
           myargs = ["lammps".encode()]
           narg = len(cmdargs) + 1
           for arg in cmdargs:
-            if type(arg) is str:
+            if isinstance(arg,str):
               myargs.append(arg.encode())
-            elif type(arg) is bytes:
+            elif isinstance(arg,bytes):
               myargs.append(arg)
             else:
               raise TypeError('Unsupported cmdargs type ', type(arg))
@@ -535,7 +533,7 @@ class lammps(object):
 
     # check if library initilialization failed
     if not self.lmp:
-      raise(RuntimeError("Failed to initialize LAMMPS object"))
+      raise RuntimeError("Failed to initialize LAMMPS object")
 
     # optional numpy support (lazy loading)
     self._numpy = None
@@ -545,14 +543,16 @@ class lammps(object):
 
     # check if liblammps version matches the installed python module version
     # but not for in-place usage, i.e. when the version is 0
-    import lammps
-    if lammps.__version__ > 0 and lammps.__version__ != self.lib.lammps_version(self.lmp):
-        raise(AttributeError("LAMMPS Python module installed for LAMMPS version %d, but shared library is version %d" \
-                % (lammps.__version__, self.lib.lammps_version(self.lmp))))
+    # pylint: disable=C0415 disable=C0209
+    import lammps as mylammps
+    if mylammps.__version__ > 0 and mylammps.__version__ != self.lib.lammps_version(self.lmp):
+      raise AttributeError("LAMMPS Python module installed for LAMMPS version %d, but shared library is version %d" \
+                           % (mylammps.__version__, self.lib.lammps_version(self.lmp)))
 
     # add way to insert Python callback for fix external
     self.callback = {}
-    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
+    self.FIX_EXTERNAL_CALLBACK_FUNC = CFUNCTYPE(None, py_object, self.c_bigint, c_int, \
+                                                POINTER(self.c_tagint), POINTER(POINTER(c_double)), POINTER(POINTER(c_double)))
     self.lib.lammps_set_fix_external_callback.argtypes = [c_void_p, c_char_p, self.FIX_EXTERNAL_CALLBACK_FUNC, py_object]
     self.lib.lammps_set_fix_external_callback.restype = None
 
@@ -585,6 +585,7 @@ class lammps(object):
     :rtype: numpy_wrapper
     """
     if not self._numpy:
+      # pylint: disable=C0415
       from .numpy_wrapper import numpy_wrapper
       self._numpy = numpy_wrapper(self)
     return self._numpy
@@ -640,6 +641,7 @@ class lammps(object):
     :rtype: ipython.wrapper
     """
     if not self._ipython:
+      # pylint: disable=C0415
       from .ipython import wrapper
       self._ipython = wrapper(self)
     return self._ipython
@@ -687,8 +689,10 @@ class lammps(object):
     :param error_text:
     :type error_text:  string
     """
-    if error_text: new_error_text = error_text.encode()
-    else: new_error_text = "(unknown error)".encode()
+    if error_text:
+      new_error_text = error_text.encode()
+    else:
+      new_error_text = "(unknown error)".encode()
 
     with ExceptionCheck(self):
       self.lib.lammps_error(self.lmp, error_type, new_error_text)
@@ -735,11 +739,11 @@ class lammps(object):
     """
 
     if self.has_mpi4py and self.has_mpi_support:
+      # pylint: disable=I1101 disable=C0415
       from mpi4py import MPI
       f_comm = self.lib.lammps_get_mpi_comm(self.lmp)
       c_comm = MPI.Comm.f2py(f_comm)
       return c_comm
-    else:
     return None
 
   # -------------------------------------------------------------------------
@@ -767,8 +771,10 @@ class lammps(object):
     :return: expanded string
     :rtype: string
     """
-    if line: newline = line.encode()
-    else: return None
+    if line:
+      newline = line.encode()
+    else:
+      return None
 
     with ExceptionCheck(self):
       strptr = self.lib.lammps_expand(self.lmp, newline)
@@ -797,8 +803,10 @@ class lammps(object):
     :param path: Name of the file/path with LAMMPS commands
     :type path:  string
     """
-    if path: newpath = path.encode()
-    else: return
+    if path:
+      newpath = path.encode()
+    else:
+      return
 
     with ExceptionCheck(self):
       self.lib.lammps_file(self.lmp, newpath)
@@ -814,8 +822,10 @@ class lammps(object):
     :param cmd: a single lammps command
     :type cmd:  string
     """
-    if cmd: newcmd = cmd.encode()
-    else: return
+    if cmd:
+      newcmd = cmd.encode()
+    else:
+      return
 
     with ExceptionCheck(self):
       self.lib.lammps_command(self.lmp, newcmd)
@@ -832,7 +842,7 @@ class lammps(object):
     :param cmdlist: a single lammps command
     :type cmdlist:  list of strings
     """
-    cmds = [x.encode() for x in cmdlist if type(x) is str]
+    cmds = [x.encode() for x in cmdlist if isinstance(x,str)]
     narg = len(cmdlist)
     args = (c_char_p * narg)(*cmds)
     self.lib.lammps_commands_list.argtypes = [c_void_p, c_int, c_char_p * narg]
@@ -852,8 +862,10 @@ class lammps(object):
     :param multicmd: text block of lammps commands
     :type multicmd:  string
     """
-    if type(multicmd) is str: newmulticmd = multicmd.encode()
-    else: newmulticmd = multicmd
+    if isinstance(multicmd,str):
+      newmulticmd = multicmd.encode()
+    else:
+      newmulticmd = multicmd
 
     with ExceptionCheck(self):
       self.lib.lammps_commands_string(self.lmp,c_char_p(newmulticmd))
@@ -942,8 +954,10 @@ class lammps(object):
     :return: value of thermo keyword
     :rtype: double or None
     """
-    if name: newname = name.encode()
-    else: return None
+    if name:
+      newname = name.encode()
+    else:
+      return None
 
     with ExceptionCheck(self):
       return self.lib.lammps_get_thermo(self.lmp, newname)
@@ -972,7 +986,7 @@ class lammps(object):
     :rtype: dict or None
     """
 
-    rv = dict()
+    rv = {}
     mystep = self.last_thermo_step
     if mystep < 0:
       return None
@@ -1020,8 +1034,10 @@ class lammps(object):
     :return: value of the setting
     :rtype: int
     """
-    if name: newname = name.encode()
-    else: return None
+    if name:
+      newname = name.encode()
+    else:
+      return None
     return int(self.lib.lammps_extract_setting(self.lmp, newname))
 
   # -------------------------------------------------------------------------
@@ -1043,8 +1059,10 @@ class lammps(object):
     :return: data type of global property, see :ref:`py_datatype_constants`
     :rtype: int
     """
-    if name: newname = name.encode()
-    else: return None
+    if name:
+      newname = name.encode()
+    else:
+      return None
     return self.lib.lammps_extract_global_datatype(self.lmp, newname)
 
   # -------------------------------------------------------------------------
@@ -1089,8 +1107,10 @@ class lammps(object):
     else:
       veclen = 1
 
-    if name: newname = name.encode()
-    else: return None
+    if name:
+      newname = name.encode()
+    else:
+      return None
 
     if dtype == LAMMPS_INT:
       self.lib.lammps_extract_global.restype = POINTER(c_int32)
@@ -1116,7 +1136,7 @@ class lammps(object):
         for i in range(0,veclen):
           result.append(target_type(ptr[i]))
         return result
-      else: return target_type(ptr[0])
+      return target_type(ptr[0])
     return None
 
   # -------------------------------------------------------------------------
@@ -1145,8 +1165,7 @@ class lammps(object):
 
     if dim < 0:
       return None
-    else:
-      return dim;
+    return dim
 
   # -------------------------------------------------------------------------
   # get access to pair style extractable data
@@ -1178,7 +1197,7 @@ class lammps(object):
     dim = self.extract_pair_dimension(name)
     if dim is None:
       return None
-    elif dim == 0:
+    if dim == 0:
       self.lib.lammps_extract_pair.restype = POINTER(c_double)
     elif dim == 1:
       self.lib.lammps_extract_pair.restype = POINTER(c_double)
@@ -1192,12 +1211,12 @@ class lammps(object):
     if ptr:
       if dim == 0:
         return float(ptr[0])
-      elif dim == 1:
+      if dim == 1:
         result = [0.0]
         for i in range(1,ntypes+1):
           result.append(float(ptr[i]))
         return result
-      elif dim == 2:
+      if dim == 2:
         result = []
         inner = []
         for i in range(0,ntypes+1):
@@ -1209,26 +1228,25 @@ class lammps(object):
             inner.append(float(ptr[i][j]))
           result.append(inner)
         return result
-      else:
       return None
     return None
 
   # -------------------------------------------------------------------------
   # map global atom ID to local atom index
 
-  def map_atom(self, id):
+  def map_atom(self, atomid):
     """Map a global atom ID (aka tag) to the local atom index
 
     This is a wrapper around the :cpp:func:`lammps_map_atom`
     function of the C-library interface.
 
-    :param id: atom ID
-    :type id:  int
+    :param atomid: atom ID
+    :type atomid:  int
     :return: local index
     :rtype: int
     """
 
-    tag = self.c_tagint(id)
+    tag = self.c_tagint(atomid)
     return self.lib.lammps_map_atom(self.lmp, byref(tag))
 
   # -------------------------------------------------------------------------
@@ -1250,8 +1268,10 @@ class lammps(object):
     :return: data type of per-atom property (see :ref:`py_datatype_constants`)
     :rtype: int
     """
-    if name: newname = name.encode()
-    else: return None
+    if name:
+      newname = name.encode()
+    else:
+      return None
     return self.lib.lammps_extract_atom_datatype(self.lmp, newname)
 
   # -------------------------------------------------------------------------
@@ -1278,8 +1298,10 @@ class lammps(object):
     :return: data type of per-atom property (see :ref:`py_datatype_constants`)
     :rtype: int
     """
-    if name: newname = name.encode()
-    else: return None
+    if name:
+      newname = name.encode()
+    else:
+      return None
     return self.lib.lammps_extract_atom_size(self.lmp, newname, dtype)
 
   # -------------------------------------------------------------------------
@@ -1322,8 +1344,10 @@ class lammps(object):
     if dtype == LAMMPS_AUTODETECT:
       dtype = self.extract_atom_datatype(name)
 
-    if name: newname = name.encode()
-    else: return None
+    if name:
+      newname = name.encode()
+    else:
+      return None
 
     if dtype == LAMMPS_INT:
       self.lib.lammps_extract_atom.restype = POINTER(c_int32)
@@ -1340,9 +1364,9 @@ class lammps(object):
     else: return None
 
     ptr = self.lib.lammps_extract_atom(self.lmp, newname)
-    if ptr: return ptr
-    else:   return None
-
+    if ptr:
+      return ptr
+    return None
 
   # -------------------------------------------------------------------------
 
@@ -1367,8 +1391,10 @@ class lammps(object):
     :return: requested data as scalar, pointer to 1d or 2d double array, or None
     :rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType
     """
-    if cid: newcid = cid.encode()
-    else: return None
+    if cid:
+      newcid = cid.encode()
+    else:
+      return None
 
     if ctype == LMP_TYPE_SCALAR:
       if cstyle == LMP_STYLE_GLOBAL:
@@ -1376,9 +1402,9 @@ class lammps(object):
         with ExceptionCheck(self):
           ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype)
         return ptr[0]
-      elif cstyle == LMP_STYLE_ATOM:
+      if cstyle == LMP_STYLE_ATOM:
         return None
-      elif cstyle == LMP_STYLE_LOCAL:
+      if cstyle == LMP_STYLE_LOCAL:
         self.lib.lammps_extract_compute.restype = POINTER(c_int)
         with ExceptionCheck(self):
           ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype)
@@ -1397,14 +1423,14 @@ class lammps(object):
       return ptr
 
     elif ctype == LMP_SIZE_COLS:
-      if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_ATOM or cstyle == LMP_STYLE_LOCAL:
+      if cstyle in (LMP_STYLE_GLOBAL,LMP_STYLE_ATOM,LMP_STYLE_LOCAL):
         self.lib.lammps_extract_compute.restype = POINTER(c_int)
         with ExceptionCheck(self):
           ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype)
         return ptr[0]
 
-    elif ctype == LMP_SIZE_VECTOR or ctype == LMP_SIZE_ROWS:
-      if cstyle == LMP_STYLE_GLOBAL or cstyle == LMP_STYLE_LOCAL:
+    elif ctype in (LMP_SIZE_VECTOR,LMP_SIZE_ROWS):
+      if cstyle in (LMP_STYLE_GLOBAL,LMP_STYLE_LOCAL):
         self.lib.lammps_extract_compute.restype = POINTER(c_int)
         with ExceptionCheck(self):
           ptr = self.lib.lammps_extract_compute(self.lmp,newcid,cstyle,ctype)
@@ -1452,8 +1478,10 @@ class lammps(object):
     :rtype: c_double, ctypes.POINTER(c_double), ctypes.POINTER(ctypes.POINTER(c_double)), or NoneType
 
     """
-    if fid: newfid = fid.encode()
-    else: return None
+    if fid:
+      newfid = fid.encode()
+    else:
+      return None
 
     if fstyle == LMP_STYLE_GLOBAL:
       if ftype in (LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
@@ -1463,15 +1491,14 @@ class lammps(object):
         result = ptr[0]
         self.lib.lammps_free(ptr)
         return result
-      elif ftype in (LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
+      if ftype in (LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS):
         self.lib.lammps_extract_fix.restype = POINTER(c_int)
         with ExceptionCheck(self):
           ptr = self.lib.lammps_extract_fix(self.lmp,newfid,fstyle,ftype,nrow,ncol)
         return ptr[0]
-      else:
       return None
 
-    elif fstyle == LMP_STYLE_ATOM:
+    if fstyle == LMP_STYLE_ATOM:
       if ftype == LMP_TYPE_VECTOR:
         self.lib.lammps_extract_fix.restype = POINTER(c_double)
       elif ftype == LMP_TYPE_ARRAY:
@@ -1484,10 +1511,9 @@ class lammps(object):
         ptr = self.lib.lammps_extract_fix(self.lmp,newfid,fstyle,ftype,nrow,ncol)
       if ftype == LMP_SIZE_COLS:
         return ptr[0]
-      else:
       return ptr
 
-    elif fstyle == LMP_STYLE_LOCAL:
+    if fstyle == LMP_STYLE_LOCAL:
       if ftype == LMP_TYPE_VECTOR:
         self.lib.lammps_extract_fix.restype = POINTER(c_double)
       elif ftype == LMP_TYPE_ARRAY:
@@ -1500,9 +1526,7 @@ class lammps(object):
         ptr = self.lib.lammps_extract_fix(self.lmp,newfid,fstyle,ftype,nrow,ncol)
       if ftype in (LMP_TYPE_VECTOR, LMP_TYPE_ARRAY):
         return ptr
-      else:
       return ptr[0]
-    else:
     return None
 
   # -------------------------------------------------------------------------
@@ -1538,32 +1562,40 @@ class lammps(object):
     :return: the requested data
     :rtype: c_double, (c_double), or NoneType
     """
-    if name: newname = name.encode()
-    else: return None
-    if group: newgroup = group.encode()
-    else: newgroup = None
+    if name:
+      newname = name.encode()
+    else:
+      return None
+    if group:
+      newgroup = group.encode()
+    else:
+      newgroup = None
     if vartype is None :
       vartype = self.lib.lammps_extract_variable_datatype(self.lmp, newname)
     if vartype == LMP_VAR_EQUAL:
       self.lib.lammps_extract_variable.restype = POINTER(c_double)
       with ExceptionCheck(self):
         ptr = self.lib.lammps_extract_variable(self.lmp, newname, newgroup)
-      if ptr: result = ptr[0]
-      else: return None
+      if ptr:
+        result = ptr[0]
+      else:
+        return None
       self.lib.lammps_free(ptr)
       return result
-    elif vartype == LMP_VAR_ATOM:
+    if vartype == LMP_VAR_ATOM:
       nlocal = self.extract_global("nlocal")
       result = (c_double*nlocal)()
       self.lib.lammps_extract_variable.restype = POINTER(c_double)
       with ExceptionCheck(self):
         ptr = self.lib.lammps_extract_variable(self.lmp, newname, newgroup)
       if ptr:
-        for i in range(nlocal): result[i] = ptr[i]
+        for i in range(nlocal):
+          result[i] = ptr[i]
         self.lib.lammps_free(ptr)
-      else: return None
+      else:
+        return None
       return result
-    elif vartype == LMP_VAR_VECTOR :
+    if vartype == LMP_VAR_VECTOR :
       nvector = 0
       self.lib.lammps_extract_variable.restype = POINTER(c_int)
       ptr = self.lib.lammps_extract_variable(self.lmp, newname,
@@ -1581,9 +1613,8 @@ class lammps(object):
           result[i] = values[i]
         # do NOT free the values pointer (points to internal vector data)
         return result
-      else:
       return None
-    elif vartype == LMP_VAR_STRING :
+    if vartype == LMP_VAR_STRING :
       self.lib.lammps_extract_variable.restype = c_char_p
       with ExceptionCheck(self) :
         ptr = self.lib.lammps_extract_variable(self.lmp, newname, newgroup)
@@ -1592,7 +1623,7 @@ class lammps(object):
 
   # -------------------------------------------------------------------------
 
-  def clearstep_compute(self, nextstep):
+  def clearstep_compute(self):
     with ExceptionCheck(self):
       return self.lib.lammps_clearstep_compute(self.lmp)
 
@@ -1637,10 +1668,14 @@ class lammps(object):
     :return: either 0 on success or -1 on failure
     :rtype: int
     """
-    if name: newname = name.encode()
-    else: return -1
-    if value: newvalue = str(value).encode()
-    else: return -1
+    if name:
+      newname = name.encode()
+    else:
+      return -1
+    if value:
+      newvalue = str(value).encode()
+    else:
+      return -1
     with ExceptionCheck(self):
       return self.lib.lammps_set_variable(self.lmp, newname, newvalue)
 
@@ -1661,10 +1696,14 @@ class lammps(object):
     :return: either 0 on success or -1 on failure
     :rtype: int
     """
-    if name: newname = name.encode()
-    else: return -1
-    if value: newvalue = str(value).encode()
-    else: return -1
+    if name:
+      newname = name.encode()
+    else:
+      return -1
+    if value:
+      newvalue = str(value).encode()
+    else:
+      return -1
     with ExceptionCheck(self):
       return self.lib.lammps_set_string_variable(self.lmp,newname,newvalue)
 
@@ -1685,8 +1724,10 @@ class lammps(object):
     :return: either 0 on success or -1 on failure
     :rtype: int
     """
-    if name: newname = name.encode()
-    else: return -1
+    if name:
+      newname = name.encode()
+    else:
+      return -1
     with ExceptionCheck(self):
       return self.lib.lammps_set_internal_variable(self.lmp,newname,value)
 
@@ -1707,8 +1748,10 @@ class lammps(object):
     :rtype: c_double
     """
 
-    if expr: newexpr = expr.encode()
-    else: return None
+    if expr:
+      newexpr = expr.encode()
+    else:
+      return None
 
     with ExceptionCheck(self):
       return self.lib.lammps_eval(self.lmp, newexpr)
@@ -1725,8 +1768,10 @@ class lammps(object):
   #   e.g. for Python list or NumPy or ctypes
 
   def gather_atoms(self,name,dtype,count):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     natoms = self.get_natoms()
     with ExceptionCheck(self):
       if dtype == 0:
@@ -1742,8 +1787,10 @@ class lammps(object):
   # -------------------------------------------------------------------------
 
   def gather_atoms_concat(self,name,dtype,count):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     natoms = self.get_natoms()
     with ExceptionCheck(self):
       if dtype == 0:
@@ -1757,8 +1804,10 @@ class lammps(object):
     return data
 
   def gather_atoms_subset(self,name,dtype,count,ndata,ids):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     with ExceptionCheck(self):
       if dtype == 0:
         data = ((count*ndata)*c_int)()
@@ -1782,16 +1831,20 @@ class lammps(object):
   #   e.g. for Python list or NumPy or ctypes
 
   def scatter_atoms(self,name,dtype,count,data):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     with ExceptionCheck(self):
       self.lib.lammps_scatter_atoms(self.lmp,newname,dtype,count,data)
 
   # -------------------------------------------------------------------------
 
   def scatter_atoms_subset(self,name,dtype,count,ndata,ids,data):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     with ExceptionCheck(self):
       self.lib.lammps_scatter_atoms_subset(self.lmp,newname,dtype,count,ndata,ids,data)
 
@@ -1899,8 +1952,10 @@ class lammps(object):
   # NOTE: need to ensure are converting to/from correct Python type
   #   e.g. for Python list or NumPy or ctypes
   def gather(self,name,dtype,count):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     natoms = self.get_natoms()
     with ExceptionCheck(self):
       if dtype == 0:
@@ -1914,8 +1969,10 @@ class lammps(object):
     return data
 
   def gather_concat(self,name,dtype,count):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     natoms = self.get_natoms()
     with ExceptionCheck(self):
       if dtype == 0:
@@ -1929,8 +1986,10 @@ class lammps(object):
     return data
 
   def gather_subset(self,name,dtype,count,ndata,ids):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     with ExceptionCheck(self):
       if dtype == 0:
         data = ((count*ndata)*c_int)()
@@ -1952,14 +2011,18 @@ class lammps(object):
   #   e.g. for Python list or NumPy or ctypes
 
   def scatter(self,name,dtype,count,data):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     with ExceptionCheck(self):
       self.lib.lammps_scatter(self.lmp,newname,dtype,count,data)
 
   def scatter_subset(self,name,dtype,count,ndata,ids,data):
-    if name: newname = name.encode()
-    else: newname = None
+    if name:
+      newname = name.encode()
+    else:
+      newname = None
     with ExceptionCheck(self):
       self.lib.lammps_scatter_subset(self.lmp,newname,dtype,count,ndata,ids,data)
 
@@ -2006,15 +2069,15 @@ class lammps(object):
 
   # create N atoms on all procs
   # N = global number of atoms
-  # id = ID of each atom (optional, can be None)
-  # type = type of each atom (1 to Ntypes) (required)
+  # atomid = ID of each atom (optional, can be None)
+  # atype = type of each atom (1 to Ntypes) (required)
   # x = coords of each atom as (N,3) array (required)
   # v = velocity of each atom as (N,3) array (optional, can be None)
   # NOTE: how could we ensure are passing correct type to LAMMPS
   #   e.g. for Python list or NumPy, etc
   #   ditto for gather_atoms() above
 
-  def create_atoms(self,n,id,type,x,v=None,image=None,shrinkexceed=False):
+  def create_atoms(self,n,atomid,atype,x,v=None,image=None,shrinkexceed=False):
     """
     Create N atoms from list of coordinates and properties
 
@@ -2034,10 +2097,10 @@ class lammps(object):
 
     :param n: number of atoms for which data is provided
     :type n: int
-    :param id: list of atom IDs with at least n elements or None
-    :type id: list of lammps.tagint
-    :param type: list of atom types
-    :type type: list of int
+    :param atomid: list of atom IDs with at least n elements or None
+    :type atomid: list of lammps.tagint
+    :param atype: list of atom types
+    :type atype: list of int
     :param x: list of coordinates for x-, y-, and z (flat list of 3n entries)
     :type x: list of float
     :param v: list of velocities for x-, y-, and z (flat list of 3n entries) or None (optional)
@@ -2049,10 +2112,10 @@ class lammps(object):
     :return: number of atoms created. 0 if insufficient or invalid data
     :rtype: int
     """
-    if id is not None:
+    if atomid is not None:
       id_lmp = (self.c_tagint*n)()
       try:
-        id_lmp[:] = id[0:n]
+        id_lmp[:] = atomid[0:n]
       except ValueError:
         return 0
     else:
@@ -2060,7 +2123,7 @@ class lammps(object):
 
     type_lmp = (c_int*n)()
     try:
-      type_lmp[:] = type[0:n]
+      type_lmp[:] = atype[0:n]
     except ValueError:
       return 0
 
@@ -2103,7 +2166,7 @@ class lammps(object):
 
   # -------------------------------------------------------------------------
 
-  def create_molecule(self, id, jsonstr):
+  def create_molecule(self, molid, jsonstr):
     """ Create new molecule template from string with JSON data
 
     .. versionadded:: TBD
@@ -2111,15 +2174,19 @@ class lammps(object):
     This is a wrapper around the :cpp:func:`lammps_create_molecule` function
     of the library interface.
 
-    :param id: molecule-id of the new molecule template
+    :param molid: molecule-id of the new molecule template
     :type name: string
     :param jsonstr: JSON data defining a new molecule template
     :type jsonstr: string
     """
-    if id: newid = id.encode()
-    else: newid = None
-    if id: newjsonstr = jsonstr.encode()
-    else: newjsonstr = None
+    if molid:
+      newid = molid.encode()
+    else:
+      newid = None
+    if jsonstr:
+      newjsonstr = jsonstr.encode()
+    else:
+      newjsonstr = None
     with ExceptionCheck(self):
       self.lib.lammps_create_molecule(self.lmp, newid, newjsonstr)
 
@@ -2476,7 +2543,7 @@ class lammps(object):
 
   # -------------------------------------------------------------------------
 
-  def available_plugins(self, category):
+  def available_plugins(self, category=None):
     """Returns a list of plugins available for a given category
 
     .. versionadded:: 10Mar2021
@@ -2494,6 +2561,7 @@ class lammps(object):
     nam = create_string_buffer(LMP_BUFSIZE)
     for idx in range(num):
       self.lib.lammps_plugin_name(idx, sty, nam, LMP_BUFSIZE)
+      if not category or (category == sty.value):
         available_plugins.append([sty.value.decode(), nam.value.decode()])
     return available_plugins
 
@@ -2618,7 +2686,7 @@ class lammps(object):
 
     nlocal = self.extract_setting('nlocal')
     if len(eatom) < nlocal:
-      raise Exception('per-atom energy list length must be at least nlocal')
+      raise ValueError('per-atom energy list length must be at least nlocal')
     ceatom = (nlocal*c_double)(*eatom)
     with ExceptionCheck(self):
       return self.lib.lammps_fix_external_set_energy_peratom(self.lmp, fix_id.encode(), ceatom)
@@ -2642,10 +2710,10 @@ class lammps(object):
     # copy virial data to C compatible buffer
     nlocal = self.extract_setting('nlocal')
     if len(vatom) < nlocal:
-      raise Exception('per-atom virial first dimension must be at least nlocal')
+      raise ValueError('per-atom virial first dimension must be at least nlocal')
     if len(vatom[0]) != 6:
-      raise Exception('per-atom virial second dimension must be 6')
-    vbuf = (c_double * 6)
+      raise ValueError('per-atom virial second dimension must be 6')
+    vbuf = c_double * 6
     vptr = POINTER(c_double)
     c_virial = (vptr * nlocal)()
     for i in range(nlocal):

python/lammps/pylammps.py

@@ -16,10 +16,6 @@
 # Written by Richard Berger <richard.berger@outlook.com>
 ################################################################################
 
-# for python2/3 compatibility
-
-from __future__ import print_function
-
 import io
 import os
 import re
@@ -762,7 +758,7 @@ class PyLammps(object):
     if self.comm_me > 0:
       raise Exception("PyLammps.eval() may only be used on MPI rank 0")
 
-    value = self.lmp_print('"$(%s)"' % expr).strip()
+    value = print('"$(%s)"' % expr).strip()
     try:
       return float(value)
     except ValueError:
@@ -847,10 +843,6 @@ class PyLammps(object):
       elements.append(element)
     return elements
 
-  def lmp_print(self, s):
-    """ needed for Python2 compatibility, since print is a reserved keyword """
-    return self.__getattr__("print")(s)
-
   def __dir__(self):
     return sorted(set(['angle_coeff', 'angle_style', 'atom_modify', 'atom_style', 'atom_style',
     'bond_coeff', 'bond_style', 'boundary', 'change_box', 'communicate', 'compute',

unittest/python/python-commands.py

@@ -122,7 +122,7 @@ create_atoms 1 single &
         x = [ 1.0, 1.0, 1.0,  1.0, 1.0, 1.5 ]
         types = [1, 1]
 
-        self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2)
+        self.assertEqual(self.lmp.create_atoms(2, atomid=None, atype=types, x=x), 2)
         nlocal = self.lmp.extract_global("nlocal")
         self.assertEqual(nlocal, 2)
 
@@ -167,7 +167,7 @@ create_atoms 1 single &
         tags = [1, 2, 3, 4, 5, 6, 7]
         types = [1, 1, 1, 1, 1, 1, 1]
 
-        self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
+        self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7)
         nlocal = self.lmp.extract_global("nlocal")
         self.assertEqual(nlocal, 7)
 
@@ -207,7 +207,7 @@ create_atoms 1 single &
         tags = [1, 2, 3, 4, 5, 6, 7]
         types = [1, 1, 1, 1, 1, 1, 1]
 
-        self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
+        self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7)
         nlocal = self.lmp.extract_global("nlocal")
         self.assertEqual(nlocal, 7)
 
@@ -237,7 +237,7 @@ create_atoms 1 single &
         tags = [1, 2, 3, 4, 5, 6, 7]
         types = [1, 1, 1, 1, 1, 1, 1]
 
-        self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
+        self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7)
         nlocal = self.lmp.extract_global("nlocal")
         self.assertEqual(nlocal, 7)
 
@@ -276,7 +276,7 @@ create_atoms 1 single &
         tags = [1, 2, 3, 4, 5, 6, 7]
         types = [1, 1, 1, 1, 1, 1, 1]
 
-        self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
+        self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7)
         nlocal = self.lmp.extract_global("nlocal")
         self.assertEqual(nlocal, 7)
 
@@ -310,7 +310,7 @@ create_atoms 1 single &
         tags = [1, 2, 3, 4, 5, 6, 7]
         types = [1, 1, 1, 1, 2, 2, 2]
 
-        self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
+        self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7)
         nlocal = self.lmp.extract_global("nlocal")
         self.assertEqual(nlocal, 7)
 
@@ -378,7 +378,7 @@ create_atoms 1 single &
         tags = [1, 2, 3, 4, 5, 6, 7]
         types = [1, 1, 1, 1, 1, 1, 1]
 
-        self.assertEqual(self.lmp.create_atoms(7, id=tags, type=types, x=x), 7)
+        self.assertEqual(self.lmp.create_atoms(7, atomid=tags, atype=types, x=x), 7)
         nlocal = self.lmp.extract_global("nlocal")
         self.assertEqual(nlocal, 7)
 
@@ -522,7 +522,7 @@ create_atoms 1 single &
 
         types = [1, 1]
 
-        self.assertEqual(self.lmp.create_atoms(2, id=None, type=types, x=x), 2)
+        self.assertEqual(self.lmp.create_atoms(2, atomid=None, atype=types, x=x), 2)
         self.lmp.command("variable a atom x*x+y*y+z*z")
         a = self.lmp.extract_variable("a", "all", LMP_VAR_ATOM)
         self.assertEqual(a[0], x[0]*x[0]+x[1]*x[1]+x[2]*x[2])
@@ -573,7 +573,7 @@ create_atoms 1 single &
         ]
 
         types = [1, 1]
-        self.lmp.create_atoms(2, id=None, type=types, x=x)
+        self.lmp.create_atoms(2, atomid=None, atype=types, x=x)
 
         state = {
             "step": 0,
@@ -611,7 +611,7 @@ create_atoms 1 single &
           1.5, 1.5, 1.5
         ]
         types = [1, 1]
-        self.lmp.create_atoms(2, id=None, type=types, x=x)
+        self.lmp.create_atoms(2, atomid=None, atype=types, x=x)
 
         self.assertEqual(self.lmp.last_thermo(), None)
         self.lmp.command("run 2 post no")