pyproject.toml

# Python code analysis settings

# For Python version 3.10

# Contents:
# black (details: https://black.readthedocs.io/en/stable/usage_and_configuration/the_basics.html)
# mypy (details: https://mypy.readthedocs.io/en/stable/config_file.html)
# poetry (details: https://python-poetry.org/docs/managing-dependencies/)
# pytest (details: pytest -h)
# pylint (details: https://pylint.pycqa.org/en/latest/user_guide/configuration/all-options.html#ignore)

# -----BLACK--------------------------------------------------------------------
[tool.black]
line-length = 100 # Number of characters in a line, the same as in Pacer
target-version = ["py311"] # Adjusted to Python 3.11
include = '''
 cardiac_mesh_construction.*py$|
 '''
# ------------------------------------------------------------------------------

# -----MYPY---------------------------------------------------------------------
# global options
[tool.mypy]
python_version = "3.11"
platform = "linux"

ignore_missing_imports = true
ignore_errors = true
namespace_packages = true
disallow_any_explicit = true
disallow_untyped_calls = false
strict_equality = true

warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true
warn_unreachable = true

show_error_context = true
show_column_numbers = true
show_error_codes = true
exclude = ['build']

# mypy per-mopdule options
[[tool.mypy.overrides]]
module = [
    "cardiac_mesh_construction.*",
]
ignore_errors = false
disallow_untyped_defs = true

# ------------------------------------------------------------------------------

# -----POETRY-------------------------------------------------------------------
[tool.poetry]
name = "CardiacMeshConstruction"
version = "0.1.0"
description = "The package to generate artificial cardiac meshes."
authors = [
    "Maciej Marciniak <maciej.mar92@gmail.com>",
]
license = "MIT"
readme = "README.md"
packages = [{ include = "cardiac_mesh_construction" }]

[tool.poetry.dependencies]
python = "^3.11, <3.12"
numpy = "^1.26.0"
plotly = "^5.10.0"
lxml = "^4.9.3"
scikit-learn = "^1.3.1"
pandas = "^2.1.1"
matplotlib = "^3.8.0"
Pillow = "^10.0.1"
regex = "^2023.8.8"
scipy = "^1.11.3"
vtk = "^9.2.6"
matplotlib-stubs = "^0.2.0"


[tool.poetry.group.dev.dependencies]
black = { extras = ["d"], version = "^23.9.1" }
pandas-stubs = "^1.5.0.221012"
pre-commit = "^3.4.0"
pytest = "^7.1.2"
pylint = "^2.17.7"
loguru = "^0.6.0"
tqdm = "^4.64.1"

[build-system]
build-backend = "poetry.core.masonry.api"
# ------------------------------------------------------------------------------

# -----PYTEST-------------------------------------------------------------------
[tool.pytest.ini_options]
addopts = "-x --color=yes --code-highlight=no "
testpaths = ["tests"]
# ------------------------------------------------------------------------------

# -----PYLINT-------------------------------------------------------------------
# This setup contains a best-effort configuration to uphold the
# best-practices and style described in the Google Python style guide:
#   https://google.github.io/styleguide/pyguide.html
#
# Its canonical open-source location is:
#   https://google.github.io/styleguide/pylintrc
# List of checkers:
# MAIN
# MESSAGES CONTROL
# REPORTS
# BASIC
# TYPECHECK
# MISCELLANEOUS
# STRING
# VARIABLES
# LOGGING
# SIMILARITIES
# SPELLING
# IMPORTS
# CLASSES
# EXCEPTIONS

[tool.pylint.MAIN]

# Files or directories to be skipped. They should be base names, not paths.
ignore = []

# Files or directories matching the regex patterns are skipped. The regex
# matches against base names, not paths.
ignore-patterns = ['test_(.)*\.py']

# Pickle collected data for later comparisons.
persistent = 'no'

# List of plugins (as comma separated values of python modules names) to load,
# usually to register additional checkers.
load-plugins = []

# Use multiple processes to speed up Pylint.
jobs = 8

# Allow loading of arbitrary C extensions. Extensions are imported into the
# active Python interpreter and may run arbitrary code.
unsafe-load-any-extension = 'no'


[tool.pylint.'MESSAGES CONTROL']

# Only show warnings with the listed confidence levels. Leave empty to show
# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED
confidence = []

# 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=

# 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 reenable 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 = [
    # Default keywords
    'apply-builtin',
    'bad-option-value',
    'basestring-builtin',
    'buffer-builtin',
    'cmp-builtin',
    'cmp-method',
    'coerce-builtin',
    'coerce-method',
    'delslice-method',
    'div-method',
    'eq-without-hash',
    'execfile-builtin',
    'file-builtin',
    'filter-builtin-not-iterating',
    'fixme',
    'getslice-method',
    'hex-method',
    'idiv-method',
    'input-builtin',
    'intern-builtin',
    'invalid-str-codec',
    'locally-disabled',
    'long-builtin',
    'long-suffix',
    'map-builtin-not-iterating',
    'metaclass-assignment',
    'next-method-called',
    'next-method-defined',
    'no-absolute-import',
    'no-member',
    'no-name-in-module',
    'no-self-use',
    'nonzero-method',
    'oct-method',
    'old-division',
    'old-ne-operator',
    'old-octal-literal',
    'old-raise-syntax',
    'parameter-unpacking',
    'print-statement',
    'raising-string',
    'raw_input-builtin',
    'rdiv-method',
    'reduce-builtin',
    'relative-import',
    'reload-builtin',
    'round-builtin',
    'setslice-method',
    'signature-differs',
    'standarderror-builtin',
    'sys-max-int',
    'too-few-public-methods',
    'too-many-ancestors',
    'too-many-arguments',
    'too-many-boolean-expressions',
    'too-many-branches',
    'too-many-instance-attributes',
    'too-many-locals',
    'too-many-nested-blocks',
    'too-many-public-methods',
    'too-many-return-statements',
    'too-many-statements',
    'trailing-newlines',
    'unichr-builtin',
    'unicode-builtin',
    'unpacking-in-except',
    'using-cmp-argument',
    'xrange-builtin',
    'zip-builtin-not-iterating',

    # Project keywords
    'missing-module-docstring',
    'unspecified-encoding',
]


[tool.pylint.REPORTS]

# Set the output format. Available formats are text, parseable, colorized, msvs
# (visual studio) and html. You can also give a reporter class, eg
# mypackage.mymodule.MyReporterClass.
output-format = 'colorized'

# Tells whether to display a full report or only the messages
reports = 'no'

# Python expression which should return a note less than 10 (10 is the highest
# note). You have access to the variables errors warning, statement which
# respectively contain the number of errors / warnings messages and the total
# number of statements analyzed. This is used by the global evaluation report
# (RP0004).
evaluation = '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=


[tool.pylint.BASIC]

# Good variable names which should always be accepted, separated by a comma
good-names = ['main', '_']

# Bad variable names which should always be refused, separated by a comma
bad-names = ['test', 'param', 'arg']

# Colon-delimited sets of names that determine each other's naming style when
# the name regexes allow several styles.
name-group = []

# Include a hint for the correct naming format with invalid-name
include-naming-hint = 'yes'

# List of decorators that produce properties, such as abc.abstractproperty. Add
# to this list to register other decorators that produce valid properties.
property-classes = [
    'abc.abstractproperty',
    'cached_property.cached_property',
    'cached_property.threaded_cached_property',
    'cached_property.cached_property_with_ttl',
    'cached_property.threaded_cached_property_with_ttl',
]

# Regular expression matching correct function names
function-rgx = '^(?:(?P<exempt>setUp|tearDown|setUpModule|tearDownModule)|(?P<camel_case>_?[A-Z][a-zA-Z0-9]*)|(?P<snake_case>_?[a-z][a-z0-9_]*))$'

# Regular expression matching correct variable names
variable-rgx = '^[a-z][a-z0-9_]*$'

# Regular expression matching correct constant names
const-rgx = '^(_?[A-Z][A-Z0-9_]*|__[a-z0-9_]+__|_?[a-z][a-z0-9_]*)$'

# Regular expression matching correct attribute names
attr-rgx = '^_{0,2}[a-z][a-z0-9_]*$'

# Regular expression matching correct argument names
argument-rgx = '^[a-z][a-z0-9_]*$'

# Regular expression matching correct class attribute names
class-attribute-rgx = '^(_?[A-Z][A-Z0-9_]*|__[a-z0-9_]+__|_?[a-z][a-z0-9_]*)$'

# Regular expression matching correct inline iteration names
inlinevar-rgx = '^[a-z][a-z0-9_]*$'

# Regular expression matching correct class names
class-rgx = '^_?[A-Z][a-zA-Z0-9]*$'

# Regular expression matching correct module names
module-rgx = '^(_?[a-z][a-z0-9_]*|__init__)$'

# Regular expression matching correct method names
method-rgx = '(?x)^(?:(?P<exempt>_[a-z0-9_]+__|runTest|setUp|tearDown|setUpTestCase|tearDownTestCase|setupSelf|tearDownClass|setUpClass|(test|assert)_*[A-Z0-9][a-zA-Z0-9_]*|next)|(?P<camel_case>_{0,2}[A-Z][a-zA-Z0-9_]*)|(?P<snake_case>_{0,2}[a-z][a-z0-9_]*))$'

# Regular expression which should only match function or class names that do
# not require a docstring.
no-docstring-rgx = '(__.*__|main|test.*|.*test|.*Test)$'

# Minimum line length for functions/classes that require docstrings, shorter
# ones are exempt.
docstring-min-length = 10


[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',
    'contextlib2.contextmanager',
]

# Tells whether missing members accessed in mixin class should be ignored. A
# mixin class is detected if its name ends with "mixin" (case insensitive).
ignore-mixin-members = 'yes'

# List of module names for which member attributes should not be checked
# (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 = []

# 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']

# 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 = []


[tool.pylint.FORMAT]

# TODO(https://github.com/PyCQA/pylint/issues/3352): Direct pylint to exempt
# lines made too long by directives to pytype.

# Regexp for a line that is allowed to be longer than the limit.
ignore-long-lines = '(?x)(^\s*(\#\ )?<?https?://\S+>?$|^\s*(from\s+\S+\s+)?import\s+.+$)'

# Allow the body of an if to be on the same line as the test if there is no
# else.
single-line-if-stmt = 'yes'

# Maximum number of lines in a module
max-module-lines = 99999

# String used as indentation unit.  The internal Google style guide mandates 2
# spaces.  Google's externaly-published style guide says 4, consistent with
# PEP 8.  Here, we use 2 spaces, for conformity with many open-sourced Google
# projects (like TensorFlow).
indent-string = '    '

# Number of spaces of indent required inside a hanging  or continued line.
indent-after-paren = 4

# Expected format of line ending, e.g. empty (any line ending), LF or CRLF.
expected-line-ending-format = ''


[tool.pylint.MISCELLANEOUS]

# List of note tags to take in consideration, separated by a comma.
notes = ['TODO']


[tool.pylint.STRING]

# This flag controls whether inconsistent-quotes generates a warning when the
# character used as a quote delimiter is used inconsistently within a module.
check-quote-consistency = 'yes'


[tool.pylint.VARIABLES]

# Tells whether we should check for unused import in __init__ files.
init-import = 'no'

# A regular expression matching the name of dummy variables (i.e. expectedly
# not used).
dummy-variables-rgx = '^\*{0,2}(_$|unused_|dummy_)'

# List of additional names supposed to be defined in builtins. Remember that
# you should avoid to define new builtins when possible.
additional-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']

# List of qualified module names which can have objects that can redefine
# builtins.
redefining-builtins-modules = [
    'six',
    'six.moves',
    'past.builtins',
    'future.builtins',
    'functools',
]


[tool.pylint.LOGGING]

# Logging modules to check that the string format arguments are in logging
# function parameter format
logging-modules = ['logging', 'absl.logging', 'tensorflow.io.logging']


[tool.pylint.SIMILARITIES]

# Minimum lines number of a similarity.
min-similarity-lines = 5

# Ignore comments when computing similarities.
ignore-comments = 'yes'

# Ignore docstrings when computing similarities.
ignore-docstrings = 'yes'

# Ignore imports when computing similarities.
ignore-imports = 'no'


[tool.pylint.SPELLING]

# Spelling dictionary name. Available dictionaries: none. To make it working
# install python-enchant package.
spelling-dict = ''

# List of comma separated words that should not be checked.
spelling-ignore-words = []

# A path to a file that contains private dictionary; one word per line.
spelling-private-dict-file = ''

# Tells whether to store unknown words to indicated private dictionary in
# --spelling-private-dict-file option instead of raising a message.
spelling-store-unknown-words = 'no'


[tool.pylint.IMPORTS]

# Deprecated modules which should not be used, separated by a comma
deprecated-modules = ['regsub', 'TERMIOS', 'Bastion', 'rexec', 'sets']

# Create a graph of every (i.e. internal and external) dependencies in the
# given file (report RP0402 must not be disabled)
import-graph = ''

# Create a graph of external dependencies in the given file (report RP0402 must
# not be disabled)
ext-import-graph = ''

# Create a graph of internal dependencies in 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', 'absl']

# 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 = 'no'


[tool.pylint.CLASSES]

# List of method names used to declare (i.e. assign) instance attributes.
defining-attr-methods = ['__init__', '__new__', 'setUp']

# List of member names, which should be excluded from the protected access
# warning.
exclude-protected = ['_asdict', '_fields', '_replace', '_source', '_make']

# List of valid names for the first argument in a class method.
valid-classmethod-first-arg = ['cls', 'class_']

# List of valid names for the first argument in a metaclass class method.
valid-metaclass-classmethod-first-arg = ['mcs']


[tool.pylint.EXCEPTIONS]

# Exceptions that will emit a warning when being caught. Defaults to
# "Exception"
overgeneral-exceptions = [
    'builtins.StandardError',
    'builtins.Exception',
    'builtins.BaseException',
]