From 04f069bb0458aaee95f99e2629c09047a96ba087 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Fri, 10 Nov 2023 10:04:27 +0000 Subject: [PATCH 1/4] Adds pre-commit configuration (& markdownlint-cli2) Closes #5 --- .markdownlint-cli2.yaml | 17 +++++++++++ .pre-commit-config.yaml | 66 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 .markdownlint-cli2.yaml create mode 100644 .pre-commit-config.yaml diff --git a/.markdownlint-cli2.yaml b/.markdownlint-cli2.yaml new file mode 100644 index 0000000..a245804 --- /dev/null +++ b/.markdownlint-cli2.yaml @@ -0,0 +1,17 @@ +# Configuration +config: + # MD013 - line-length + line_length: + line_length: 120 + code_blocks: false + tables: false + html: + allowed_elements: + - div + +# Globs +globs: + - "**/*.md" + +# Fix any fixable errors +fix: true diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..05de10c --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,66 @@ +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.5.0 # Use the ref you want to point at + hooks: + - id: check-case-conflict + - id: check-docstring-first + - id: check-merge-conflict + - id: check-toml + - id: check-yaml + - id: end-of-file-fixer + types: [python] + - id: fix-byte-order-marker + - id: name-tests-test + args: ["--pytest-test-first"] + - id: requirements-txt-fixer + - id: trailing-whitespace + types: [python, yaml, markdown] + + - repo: https://github.com/DavidAnson/markdownlint-cli2 + rev: v0.10.0 + hooks: + - id: markdownlint-cli2 + args: [] + + - repo: https://github.com/asottile/pyupgrade + rev: v3.15.0 + hooks: + - id: pyupgrade + args: [--py38-plus] + + - repo: https://github.com/astral-sh/ruff-pre-commit + # Ruff version. + rev: v0.1.4 + hooks: + - id: ruff + args: [ --fix, --exit-non-zero-on-fix ] + + - repo: https://github.com/psf/black + rev: 23.10.1 + hooks: + - id: black + types: [python] + additional_dependencies: ['click==8.0.4'] + args: ["--extend-exclude", "topostats/plotting.py"] + - id: black-jupyter + + - repo: https://github.com/kynan/nbstripout + rev: 0.6.1 + hooks: + - id: nbstripout + + - repo: local + hooks: + - id: pylint + args: ["--rcfile=.pylintrc"] + name: Pylint + entry: python -m pylint + language: system + files: \.py$ + +ci: + autofix_prs: true + autofix_commit_msg: '[pre-commit.ci] Fixing issues with pre-commit' + autoupdate_schedule: weekly + autoupdate_commit_msg: '[pre-commit.ci] pre-commit-autoupdate' + skip: [pylint] # Optionally list ids of hooks to skip on CI From 24d3fce700e6feb7d028f98bc120a8c00adf2a29 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Fri, 10 Nov 2023 10:07:36 +0000 Subject: [PATCH 2/4] Adding .pylintrc Forgot to copy over `.pylintrc`. --- .pylintrc | 583 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 583 insertions(+) create mode 100644 .pylintrc diff --git a/.pylintrc b/.pylintrc new file mode 100644 index 0000000..269b895 --- /dev/null +++ b/.pylintrc @@ -0,0 +1,583 @@ +[MASTER] + +# 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 to be exceeded before program exits with error. +fail-under=10.0 + +# Files or directories to be skipped. They should be base names, not paths. +ignore=CVS, + _version.py, + dnatracing.py, + dnacurvature.py, + conf.py, + test_dnacurvature.py, + __main__.py + +# Add files or directories matching the regex patterns to the ignore-list. The +# regex matches against paths and can be in Posix or Windows format. +ignore-paths= + +# Files or directories matching the regex patterns are skipped. The regex +# matches against base names, not paths. +ignore-patterns=tracingfuncs.py + +# 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. +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=yes + +# Minimum Python version to use for version dependent checks. Will default to +# the version used to run pylint. +py-version=3.9 + +# When enabled, pylint would attempt to guess common misconfiguration and emit +# user-friendly hints instead of false-positive error messages. +suggestion-mode=yes + +# Allow loading of arbitrary C extensions. Extensions are imported into the +# active Python interpreter and may run arbitrary code. +unsafe-load-any-extension=no + + +[MESSAGES CONTROL] + +# Only show warnings with the listed confidence levels. Leave empty to show +# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED. +confidence= + +# 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=C0103, + E1131, + R0801, + raw-checker-failed, + bad-inline-option, + locally-disabled, + logging-fstring-interpolation, + file-ignored, + suppressed-message, + useless-suppression, + deprecated-pragma, + 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=c-extension-no-member + + +[REPORTS] + +# Python expression which should return a score less than or equal to 10. You +# have access to the variables 'error', 'warning', 'refactor', and 'convention' +# 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=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, json +# and msvs (visual studio). You can also give a reporter class, e.g. +# mypackage.mymodule.MyReporterClass. +output-format=text + +# Tells whether to display a full report or only the messages. +reports=no + +# Activate the evaluation score. +score=yes + + +[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 + + +[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 + + +[SPELLING] + +# Limits count of emitted suggestions for spelling mistakes. +max-spelling-suggestions=4 + +# Spelling dictionary name. Available dictionaries: none. To make it work, +# install the 'python-enchant' package. +spelling-dict= + +# List of comma separated words that should be considered directives if they +# appear and 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=no + + +[MISCELLANEOUS] + +# List of note tags to take in consideration, separated by a comma. +notes=XXX, + TODO + +# Regular expression of note tags to take in consideration. +#notes-rgx= + + +[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=torch.* + +# 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. +ignore-mixin-members=yes + +# Tells whether to warn about missing members when the owner of the attribute +# is inferred to be None. +ignore-none=yes + + +# 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=yes + +# 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 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= + +# 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=yes + +# The minimum 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 ignore-mixin- +# members is set to 'yes' +mixin-class-rgx=.*[Mm]ixin + +# List of decorators that change the signature of a decorated function. +signature-mutators= + + +[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=yes + +# 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. Default to name +# with leading underscore. +ignored-argument-names=_.*|^ignored_|^unused_ + +# Tells whether we should check for unused import in __init__ files. +init-import=no + +# List of qualified module names which can have objects that can redefine +# builtins. +redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io + + +[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*(# )??$ + +# Number of spaces of indent required inside a hanging or continued line. +indent-after-paren=4 + +# 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=120 + +# Maximum number of lines in a module. +max-module-lines=1000 + +# Allow the body of a class to be on the same line as the declaration if body +# contains single statement. +single-line-class-stmt=no + +# Allow the body of an if to be on the same line as the test if there is no +# else. +single-line-if-stmt=no + + +[SIMILARITIES] + +# Comments are removed from the similarity computation +ignore-comments=yes + +# Docstrings are removed from the similarity computation +ignore-docstrings=yes + +# Imports are removed from the similarity computation +ignore-imports=no + +# Signatures are removed from the similarity computation +ignore-signatures=no + +# Minimum lines number of a similarity. +min-similarity-lines=4 + + +[BASIC] + +# Naming style matching correct argument names. +argument-naming-style=snake_case + +# Regular expression matching correct argument names. Overrides argument- +# 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. +#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. +#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. +#class-const-rgx= + +# Naming style matching correct class names. +class-naming-style=PascalCase + +# Regular expression matching correct class names. Overrides class-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. +#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. +#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=no + +# Naming style matching correct inline iteration names. +inlinevar-naming-style=any + +# Regular expression matching correct inline iteration names. Overrides +# inlinevar-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. +#method-rgx= + +# Naming style matching correct module names. +module-naming-style=snake_case + +# Regular expression matching correct module names. Overrides module-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 + +# Naming style matching correct variable names. +variable-naming-style=snake_case + +# Regular expression matching correct variable names. Overrides variable- +# naming-style. +#variable-rgx= + + +[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=no + +# This flag controls whether the implicit-str-concat should generate a warning +# on implicit string concatenation in sequences defined over several lines. +check-str-concat-over-line-jumps=no + + +[IMPORTS] + +# List of modules that can be imported at any level, not just the top level +# one. +allow-any-import-level= + + +# Allow wildcard imports from modules that define __all__. +allow-wildcard-with-all=no + +# 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 + +# 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= + + +[CLASSES] + +# Warn about protected attribute access inside special methods +check-protected-access-in-special-methods=no + +# List of method names used to declare (i.e. assign) instance attributes. +defining-attr-methods=__init__, + __new__, + setUp, + __post_init__ + + +# 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 + +# List of valid names for the first argument in a metaclass class method. +valid-metaclass-classmethod-first-arg=cls + + +[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=7 # Raised this from 5 + +# Maximum number of attributes for a class (see R0902). +max-attributes=7 + +# 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=12 + +# Maximum number of locals for function / method body. +max-locals=15 + + +# Maximum number of parents for a class (see R0901). +max-parents=7 + +# Maximum number of public methods for a class (see R0904). +max-public-methods=20 + +# Maximum number of return / yield for function / method body. +max-returns=6 + +# Maximum number of statements in function / method body. +max-statements=50 + +# Minimum number of public methods for a class (see R0903). +min-public-methods=2 + + + +[EXCEPTIONS] + +# Exceptions that will emit a warning when being caught. Defaults to +# "BaseException, Exception". +overgeneral-exceptions=builtins.BaseException, + builtins.Exception From 336cd81a7622532e5a0033ee0fc304212db22c55 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Fri, 10 Nov 2023 10:13:47 +0000 Subject: [PATCH 3/4] Adds configuration of black and ruff to pyproject.toml In my haste I forgot to actually add the configuration. Also... * Include `pytest-cov` * Order `dev` option-dependencies alphabetically. * Add keywords to package metadata. --- pyproject.toml | 99 +++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 97 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e7872ea..b5ad02f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,11 +18,106 @@ classifiers = [ "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", ] +keywrods = [ + "afm", + "image processing" +] dependencies = ["numpy"] [project.optional-dependencies] -dev = ["pytest", "black", "pylint"] +dev = [ + "black", + "pytest", + "pytest-cov", + "pylint", + "ruff" +] [project.urls] "Homepage" = "https://github.com/AFM-SPM/topofileformats" -"Bug Tracker" = "https://github.com/AFM-SPM/topofileformats/issues" \ No newline at end of file +"Bug Tracker" = "https://github.com/AFM-SPM/topofileformats/issues" + +[tool.pytest.ini_options] +minversion = "7.0" +addopts = "--cov --mpl" +testpaths = [ + "tests", +] +filterwarnings = [ + "ignore::DeprecationWarning", + "ignore::PendingDeprecationWarning", + "ignore::UserWarning" +] + +[tool.black] +line-length = 120 +target-version = ['py38'] +exclude = ''' + +( + /( + \.eggs # exclude a few common directories in the + | \.git # root of the project + | \.venv + )/ +) +''' + +[tool.ruff] +exclude = [ + "*.ipynb", + ".bzr", + ".direnv", + ".eggs", + ".git", + ".hg", + ".mypy_cache", + ".nox", + ".pants.d", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + "__pycache__", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "docs/conf.py", + "node_modules", + "pygwytracing.py", + "tests/tracing/test_dnacurvature.py", + "tests/tracing/test_dnatracing.py", + "tests/tracing/test_tracing_dna.py", + "topostats/plotting.py", + "topostats/tracing/dnatracing.py", + "topostats/tracing/tracing_dna.py", + "topostats/tracing/tracingfuncs.py", + "venv", +] +# per-file-ignores = [] +line-length = 120 +target-version = "py310" +select = ["A", "B", "C", "D", "E", "F", "PT", "PTH", "R", "S", "W", "U"] +ignore = [ + "B905", + "E501", + "S101", + "T201"] +# Allow autofix for all enabled rules (when `--fix`) is provided. +fixable = ["A", "B", "C", "D", "E", "F", "PT", "PTH", "R", "S", "W", "U"] +unfixable = [] + +[tool.ruff.flake8-quotes] +docstring-quotes = "double" + +[tool.ruff.isort] +case-sensitive = true + +[tool.ruff.pydocstyle] +convention = "numpy" + +[tool.ruff.flake8-pytest-style] +fixture-parentheses = true From 7e62c3ad9a7161be56297026a545793dce8dfb37 Mon Sep 17 00:00:00 2001 From: Neil Shephard Date: Fri, 10 Nov 2023 13:44:32 +0000 Subject: [PATCH 4/4] Correcting tpyo --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index b5ad02f..62f6d8c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ classifiers = [ "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", ] -keywrods = [ +keywords = [ "afm", "image processing" ]