Merge pull request #2 from fkie-cad/removing_deprecated_function

Removing deprecated function

.isort.cfg

+[settings]
+line_length=120
+default_section = THIRDPARTY
+multi_line_output=6

.pre-commit-config.yaml

+default_stages: [commit, push]
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.2.3
+    hooks:
+    -   id: check-added-large-files
+        args: [--maxkb=10000]
+
+    -   id: check-json
+
+    -   id: check-merge-conflict
+
+    -   id: check-yaml
+
+    -   id: end-of-file-fixer
+        types: [python]
+
+    -   id: fix-encoding-pragma
+        args: [--remove]
+
+    -   id: flake8
+        args: [--ignore="E501,W503", --select=W504]
+
+    -   id: forbid-new-submodules
+
+    -   id: no-commit-to-branch
+
+    -   id: pretty-format-json
+        args: [--autofix]
+
+    -   id: trailing-whitespace
+        types: [python]
+
+
+-   repo: https://github.com/pre-commit/mirrors-pylint
+    rev: v2.3.1
+    hooks:
+    -   id: pylint
+        language: system
+        args: [--rcfile=.pylintrc]
+
+-   repo: https://github.com/jumanjihouse/pre-commit-hooks
+    rev: 1.11.0
+    hooks:
+    -   id: shellcheck
+
+-   repo: https://github.com/pryorda/dockerfilelint-precommit-hooks
+    rev: v0.1.0
+    hooks:
+    -   id: dockerfilelint
+
+-   repo: https://github.com/pre-commit/mirrors-jshint
+    rev: v2.10.2
+    hooks:
+    -   id: jshint
+
+-   repo: https://github.com/pre-commit/mirrors-isort
+    rev: v4.3.20
+    hooks:
+    -   id: isort

.pylintrc

+[MASTER]
+
+# Add files or directories to the blacklist. They should be base names, not
+# paths.
+ignore=CVS
+
+# Add files or directories matching the regex patterns to the blacklist. The
+# regex matches against base names, not paths.
+
+# Pickle collected data for later comparisons.
+persistent=yes
+
+# List of plugins (as comma separated values of python modules names) to load,
+# usually to register additional checkers.
+load-plugins=pylint.extensions.bad_builtin,pylint.extensions.mccabe
+
+# Use multiple processes to speed up Pylint.
+jobs=2
+
+# Allow loading of arbitrary C extensions. Extensions are imported into the
+# active Python interpreter and may run arbitrary code.
+unsafe-load-any-extension=no
+
+# 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-whitelist=
+
+# Allow optimization of some AST trees. This will activate a peephole AST
+# optimizer, which will apply various small optimizations. For instance, it can
+# be used to obtain the result of joining multiple strings with the addition
+# operator. Joining a lot of strings can lead to a maximum recursion error in
+# Pylint and this flag can prevent that. It has one side effect, the resulting
+# AST will be different than the one from reality. This option is deprecated
+# and it will be removed in Pylint 2.0.
+optimize-ast=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)
+disable=missing-docstring,locally-disabled,logging-format-interpolation
+
+
+[REPORTS]
+
+# Set the output format. Available formats are text, parseable, colorized, html
+output-format=colorized
+
+# Put messages in a separate file for each module / package specified on the
+# command line instead of printing them on stdout. Reports (if any) will be
+# written in a file name "pylint_global.[txt|html]". This option is deprecated
+# and it will be removed in Pylint 2.0.
+files-output=no
+
+# 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="{path}:{line}: [{symbol}:{obj}] {msg}"
+
+
+[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=_$|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.moves,future.builtins
+
+
+[TYPECHECK]
+
+# 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 classes names for which member attributes should not be checked
+# (useful for classes with attributes dynamically set). This supports can work
+# with qualified names.
+ignored-classes=
+
+# 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=
+
+# 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
+
+
+[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
+
+
+[SIMILARITIES]
+
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+
+# Ignore comments when computing similarities.
+ignore-comments=yes
+
+# Ignore docstrings when computing similarities.
+ignore-docstrings=yes
+
+# Ignore imports when computing similarities.
+ignore-imports=no
+
+
+[MISCELLANEOUS]
+
+# List of note tags to take in consideration, separated by a comma.
+notes=FIXME,XXX
+
+
+[LOGGING]
+
+# Logging modules to check that the string format arguments are in logging
+# function parameter format
+logging-modules=logging
+
+
+[FORMAT]
+
+# Maximum number of characters on a single line.
+max-line-length=200
+
+# Regexp for a line that is allowed to be longer than the limit.
+ignore-long-lines=^\s*(# )?<?https?://\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=no
+
+# List of optional constructs for which whitespace checking is disabled. `dict-
+# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
+# `trailing-comma` allows a space between comma and closing bracket: (a, ).
+# `empty-line` allows space-only lines.
+no-space-check=trailing-comma,dict-separator
+
+# Maximum number of lines in a module
+max-module-lines=1000
+
+# String used as indentation unit. This is usually "    " (4 spaces) or "\t" (1
+# tab).
+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=
+
+
+[BASIC]
+
+# List of builtins function names that should not be used, separated by a comma
+bad-functions=map,filter
+
+# Good variable names which should always be accepted, separated by a comma
+good-names=i,j,k,ex,Run,_
+
+# Bad variable names which should always be refused, separated by a comma
+bad-names=foo,bar,baz,toto,tutu,tata
+
+# 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=no
+
+# 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
+
+# Regular expression matching correct method names
+method-rgx=[a-z_][a-z0-9_]{2,50}$
+
+# Naming hint for method names
+method-name-hint=[a-z_][a-z0-9_]{2,50}$
+
+# Regular expression matching correct attribute names
+attr-rgx=[a-z_][a-z0-9_]{1,30}$
+
+# Naming hint for attribute names
+attr-name-hint=[a-z_][a-z0-9_]{1,30}$
+
+# Regular expression matching correct class names
+class-rgx=[A-Z_][a-zA-Z0-9]+$
+
+# Naming hint for class names
+class-name-hint=[A-Z_][a-zA-Z0-9]+$
+
+# Regular expression matching correct module names
+module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Naming hint for module names
+module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
+
+# Regular expression matching correct function names
+function-rgx=[a-z_][a-z0-9_]{2,33}$
+
+# Naming hint for function names
+function-name-hint=[a-z_][a-z0-9_]{2,33}$
+
+# Regular expression matching correct inline iteration names
+inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
+
+# Naming hint for inline iteration names
+inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
+
+# Regular expression matching correct argument names
+argument-rgx=[a-z_][a-z0-9_]{1,30}$
+
+# Naming hint for argument names
+argument-name-hint=[a-z_][a-z0-9_]{1,30}$
+
+# Regular expression matching correct variable names
+variable-rgx=[a-z_][a-z0-9_]{1,30}$
+
+# Naming hint for variable names
+variable-name-hint=[a-z_][a-z0-9_]{1,30}$
+
+# Regular expression matching correct class attribute names
+class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
+
+# Naming hint for class attribute names
+class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
+
+# Regular expression matching correct constant names
+const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+
+# Naming hint for constant names
+const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
+
+# Regular expression which should only match function or class names that do
+# not require a docstring.
+no-docstring-rgx=^_
+
+# Minimum line length for functions/classes that require docstrings, shorter
+# ones are exempt.
+docstring-min-length=-1
+
+
+[ELIF]
+
+# Maximum number of nested blocks for function / method body
+max-nested-blocks=5
+
+
+[IMPORTS]
+
+# Deprecated modules which should not be used, separated by a comma
+deprecated-modules=optparse
+
+# 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
+
+# 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
+
+
+[DESIGN]
+
+# McCabe complexity cyclomatic threshold
+max-complexity=7
+
+# Maximum number of arguments for function / method
+max-args=7
+
+# Argument names that match this expression will be ignored. Default to name
+# with leading underscore
+ignored-argument-names=_.*
+
+# Maximum number of locals for function / method body
+max-locals=15
+
+# Maximum number of return / yield for function / method body
+max-returns=6
+
+# Maximum number of branch for function / method body
+max-branches=12
+
+# Maximum number of statements in function / method body
+max-statements=50
+
+# Maximum number of parents for a class (see R0901).
+max-parents=7
+
+# Maximum number of attributes for a class (see R0902).
+max-attributes=7
+
+# Minimum number of public methods for a class (see R0903).
+min-public-methods=0
+
+# Maximum number of public methods for a class (see R0904).
+max-public-methods=40
+
+# Maximum number of boolean expressions in a if statement
+max-bool-expr=5
+
+
+[CLASSES]
+
+# List of method names used to declare (i.e. assign) instance attributes.
+defining-attr-methods=__init__,__new__,setUp
+
+# 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
+
+# List of member names, which should be excluded from the protected access
+# warning.
+exclude-protected=_asdict,_fields,_replace,_source,_make
+
+
+[EXCEPTIONS]
+
+# Exceptions that will emit a warning when being caught. Defaults to
+# "Exception"
+overgeneral-exceptions=Exception

.travis.yml

@@ -13,7 +13,7 @@ install:
   - "sudo apt-get install -y mongodb-org" 
   - "sudo service mongod start"
   - "python setup.py -q install"
-  - "pip install --upgrade pytest pytest-pep8 pytest-cov codecov"
+  - "pip install --upgrade pytest pytest-flake8 pytest-cov codecov"
 # command to run tests
 script: "pytest --cov-config .coveragerc --cov=./"
 after_success:

common_helper_mongo/__init__.py

+from .aggregate import (
+    get_field_average, get_field_execute_operation, get_field_sum, get_list_of_all_values,
+    get_objects_and_count_of_occurrence
+)
 from .gridfs import overwrite_file
-from .aggregate import get_objects_and_count_of_occurrence, get_field_average, get_field_sum, get_field_execute_operation, get_list_of_all_values, get_list_of_all_values_and_collect_information_of_additional_field
 
 __all__ = [
     'overwrite_file',
@@ -8,5 +11,4 @@ __all__ = [
     'get_field_sum',
     'get_field_execute_operation',
     'get_list_of_all_values',
-    'get_list_of_all_values_and_collect_information_of_additional_field'
 ]

common_helper_mongo/aggregate.py

@@ -2,7 +2,6 @@ import logging
 from typing import List, Optional
 
 from bson.son import SON
-from pymongo.command_cursor import CommandCursor
 
 
 def get_list_of_all_values(collection, object_path, unwind=False, match=None):
@@ -27,28 +26,6 @@ def get_list_of_all_values(collection, object_path, unwind=False, match=None):
     return result
 
 
-def get_list_of_all_values_and_collect_information_of_additional_field(
-        collection, object_path, additional_information_object_path, unwind=False, match=None):
-    '''
-    Get a list of unique values and a collection of additional information on a specific object path in a collection.
-    An Optional search string (match) can be added.
-
-    :param collection: mongo collection to look at
-    :type collection: pymongo.collection.Collection
-    :param object_path: mongo object path
-    :type object_path: str
-    :param additional_information_object_path: field of the additional information
-    :type additional_information_object_path: str
-    :param unwind: if true: handle list entries as single values
-    :type unwind: bool
-    :param match: mongo search string
-    :type match: dict, optional
-    :return: {<VALUE>:[<ADDITIONAL_INFORMATION_1>, ...], ...}
-    '''
-    logging.warning('deprecation warning: this method will be removed in a future release')
-    return get_all_value_combinations_of_fields(collection, object_path, additional_information_object_path, unwind, match)
-
-
 def get_all_value_combinations_of_fields(collection, primary_field, secondary_field, unwind=False, match=None):
     '''
     Get a dictionary with all unique values of a field as keys and a list of all unique values that a second field takes

pytest.ini

 [pytest]
-addopts = --pep8 -v
-pep8ignore = 
-    *.py E501
+addopts = --flake8 -v
+flake8-ignore =
+    *.py E501 W503
+flake8-select =
+    *.py W504

tests/test_aggregate.py

 from common_helper_mongo.aggregate import (
     get_all_value_combinations_of_fields, get_field_average, get_field_sum, get_list_of_all_values,
-    get_list_of_all_values_and_collect_information_of_additional_field, get_objects_and_count_of_occurrence,
+    get_objects_and_count_of_occurrence
 )
 from tests.base_class_database_test import MongoDbTest
 
@@ -81,9 +81,3 @@ class TestAggregate(MongoDbTest):
     def test_get_field_execute_operation_empty(self):
         result = get_field_sum(self.test_collection, "$test_int")
         self.assertEqual(result, 0)
-
-    def test_get_list_of_all_values_and_collect_information_of_additional_field(self):
-        self.add_list_test_data()
-        with self.assertLogs() as logger:
-            get_list_of_all_values_and_collect_information_of_additional_field(self.test_collection, "$test_list", "$_id", unwind=True)
-            assert 'deprecation warning' in logger.output.pop()