Running py.test throws a DeprecationWarning w/r/t assertEquals

(gsoc_env) ➜  cohesion git:(master) py.test
============================================= test session starts ==============================================
platform linux -- Python 3.7.4, pytest-5.0.1, py-1.8.0, pluggy-0.12.0
rootdir: /home/jaskaran/packages/cohesion
collected 62 items                                                                                             

tests/test_filesystem.py ...                                                                             [  4%]
tests/test_flake8_extension.py .....                                                                     [ 12%]
tests/test_module.py ................                                                                    [ 38%]
tests/test_parser.py ......................................                                              [100%]

=============================================== warnings summary ===============================================
tests/test_module.py::TestModule::test_module_function_variable
  /home/jaskaran/packages/cohesion/tests/test_module.py:105: DeprecationWarning: Please use assertEqual instead.
    self.assertEquals(result, expected)

-- Docs: https://docs.pytest.org/en/latest/warnings.html
==================================== 62 passed, 1 warnings in 0.12 seconds =====================================

Replacing assertEquals with assertEqual in tests/test_module.py passes tests without the warning above.

For some reason flake8 does not produce any warnings. Even if it should.

Reproduction:

1. create example.py from the readme
2. run flake8 --select=H --cohesion-below=95 example.py

This should raise one error, since the same file produces this output:

» cohesion --below 95 -f example.py
File: example.py
  Class: ExampleClass1 (1:0)
    Function: func1 2/3 66.67%
    Function: func2 1/3 33.33%
    Function: func3 staticmethod
    Total: 33.33%

But, nothing happens. Versions I am using:

{
  "dependencies": [
    {
      "dependency": "setuptools",
      "version": "39.0.1"
    }
  ],
  "platform": {
    "python_implementation": "CPython",
    "python_version": "3.6.5",
    "system": "Darwin"
  },
  "plugins": [
    {
      "is_local": false,
      "plugin": "cohesion",
      "version": "0.9.1"
    },
    {
      "is_local": false,
      "plugin": "mccabe",
      "version": "0.6.1"
    },
    {
      "is_local": false,
      "plugin": "pycodestyle",
      "version": "2.3.1"
    },
    {
      "is_local": false,
      "plugin": "pyflakes",
      "version": "1.6.0"
    }
  ],
  "version": "3.5.0"
}

Hi, thanks for this plugin. I am working on integrating it into our linter: https://github.com/wemake-services/wemake-python-styleguide/issues/134

But, currently there's an issue with configuration.

_______________ FLAKE8-check(ignoring N802 D100 D104 D106 D401) ________________
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py", line 119, in worker
    result = (True, func(*args, **kwds))
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/flake8/checker.py", line 648, in _run_checks
    return checker.run_checks()
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/flake8/checker.py", line 579, in run_checks
    self.run_ast_checks()
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/flake8/checker.py", line 493, in run_ast_checks
    for (line_number, offset, text, check) in runner:
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/cohesion/flake8_extension.py", line 44, in run
    file_module.filter_below(self.cohesion_below)
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/cohesion/module.py", line 79, in filter_below
    self._filter(predicate)
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/cohesion/module.py", line 43, in _filter
    for class_name, class_structure in self.structure.items()
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/cohesion/module.py", line 44, in <dictcomp>
    if predicate(class_name)
  File "/Users/sobolev/Documents/github/wemake-python-styleguide/.venv/lib/python3.6/site-packages/cohesion/module.py", line 77, in predicate
    return operator.le(class_percentage, percentage)
TypeError: '<=' not supported between instances of 'float' and 'str'
"""

The above exception was the direct cause of the following exception:
.venv/lib/python3.6/site-packages/pluggy/hooks.py:258: in __call__
    return self._hookexec(self, self._nonwrappers + self._wrappers, kwargs)
.venv/lib/python3.6/site-packages/pluggy/manager.py:67: in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
.venv/lib/python3.6/site-packages/pluggy/manager.py:61: in <lambda>
    firstresult=hook.spec_opts.get('firstresult'),
.venv/lib/python3.6/site-packages/_pytest/runner.py:111: in pytest_runtest_call
    item.runtest()
.venv/lib/python3.6/site-packages/pytest_flake8.py:117: in runtest
    self.statistics)
.venv/lib/python3.6/site-packages/py/_io/capture.py:150: in call
    res = func(*args, **kwargs)
.venv/lib/python3.6/site-packages/pytest_flake8.py:193: in check_file
    app.run_checks([str(path)])
.venv/lib/python3.6/site-packages/flake8/main/application.py:310: in run_checks
    self.file_checker_manager.run()
.venv/lib/python3.6/site-packages/flake8/checker.py:319: in run
    self.run_parallel()
.venv/lib/python3.6/site-packages/flake8/checker.py:288: in run_parallel
    for ret in pool_map:
/usr/local/Cellar/python/3.6.5/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/pool.py:735: in next
    raise value
E   TypeError: '<=' not supported between instances of 'float' and 'str'

Here's how to reproduce it.

1. install flake8 and cohesion
2. create setup.cfg with the following contents:

[flake8]
cohesion-below = 100.0

3. Run flake8 on any file with a class inside, for example the one from the readme.

Here's related flake8 information:

{
  "dependencies": [
    {
      "dependency": "setuptools",
      "version": "39.0.1"
    }
  ],
  "platform": {
    "python_implementation": "CPython",
    "python_version": "3.6.5",
    "system": "Darwin"
  },
  "plugins": [
    {
      "is_local": false,
      "plugin": "cohesion",
      "version": "0.8.0"
    },
    {
      "is_local": false,
      "plugin": "pycodestyle",
      "version": "2.3.1"
    },
    {
      "is_local": false,
      "plugin": "pyflakes",
      "version": "1.6.0"
    }
  ],
  "version": "3.5.0"
}

After updating to 0.9.1 I have faced a new issue:

1. create an example.py file from the readme
2. run cohesion -f example.py, output will be:

File: example.py
  Class: ExampleClass1 (1:0)
    Function: func1 2/3 66.67%
    Function: func2 1/3 33.33%
    Function: func3 staticmethod
    Total: 33.33%
  Class: ExampleClass2 (22:0)
    Function: func1 1/1 100.00%
    Total: 100.00%

3. then run cohesion --below 100 -f example.py, output will not change

File: example.py
  Class: ExampleClass1 (1:0)
    Function: func1 2/3 66.67%
    Function: func2 1/3 33.33%
    Function: func3 staticmethod
    Total: 33.33%
  Class: ExampleClass2 (22:0)
    Function: func1 1/1 100.00%
    Total: 100.00%

However, 100 is not below 100. It is equal.

Just for the reference, running cohesion --below 99 -f example.py:

File: example.py
  Class: ExampleClass1 (1:0)
    Function: func1 2/3 66.67%
    Function: func2 1/3 33.33%
    Function: func3 staticmethod
    Total: 33.33%

It works well.

http://flake8.pycqa.org/en/2.5.5/extensions.html

This will also provide some added community visibility to this project. We'll probably need some kind of filter capability in order to perform linting. I.e. we'll want to only show classes whose cohesion is less than 50%, etc.

I ran the lib cohesion over my code and return me the result.. what the lib analyze ?

 Function: __eq__ 1/3 33.33%
    Function: __init__ 1/3 33.33%
    Function: __repr__ 2/3 66.67%
    Function: change_bit 2/3 66.67%
    Function: is_valid 1/3 33.33%
    Total: 46.67%
  Class: Hamming
    Function: __init__ 1/13 7.69%
    Function: __repr__ 2/13 15.38%
    Function: bits_verified_by 3/13 23.08%
    Function: calculate_parity 2/13 15.38%
    Function: check 4/13 30.77%
    Function: divisors 1/13 7.69%
    Function: encode 8/13 61.54%
    Function: fix 3/13 23.08%
    Function: is_power 2/13 15.38%
    Function: wrong_position 4/13 30.77%
    Total: 23.08%

I ran the command:

pip install cohesion

and show me result :

Downloading/unpacking cohesion
  Could not find any downloads that satisfy the requirement cohesion
No distributions at all found for cohesion
Storing complete log in /home/cliente/.pip/pip.log

Seeing the pip.log file:

Downloading/unpacking cohesion

  Getting page http://pypi.python.org/simple/cohesion
  URLs to search for versions for cohesion:
  * http://pypi.python.org/simple/cohesion/
  Getting page http://pypi.python.org/simple/cohesion/
  Analyzing links from page https://pypi.python.org/simple/cohesion/
    Skipping link https://pypi.python.org/packages/9d/56/536846a677d672f6176eccbc66d4da05101960ef755e865d36df3a3fbc25/cohesion-0.5.0-py2.py3-none-any.whl#md5=f735e4fa689b77313edb46c6434e7df5 (from https://pypi.python.org/simple/cohesion/); unknown archive format: .whl
    Skipping link https://pypi.python.org/packages/e1/db/2b29b55958681a994a52a06767465426cf1952ea9218a73f9c00926694c3/cohesion-0.5.1-py2.py3-none-any.whl#md5=0b5fc31e76753afb20c7e320318295a5 (from https://pypi.python.org/simple/cohesion/); unknown archive format: .whl
  Could not find any downloads that satisfy the requirement cohesion

No distributions at all found for cohesion

Exception information:
Traceback (most recent call last):
  File "/home/cliente/Dev/Apps/redes/tests/local/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/basecommand.py", line 104, in main
    status = self.run(options, args)
  File "/home/cliente/Dev/Apps/redes/tests/local/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/commands/install.py", line 245, in run
    requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
  File "/home/cliente/Dev/Apps/redes/tests/local/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/req.py", line 978, in prepare_files
    url = finder.find_requirement(req_to_install, upgrade=self.upgrade)
  File "/home/cliente/Dev/Apps/redes/tests/local/lib/python2.7/site-packages/pip-1.1-py2.7.egg/pip/index.py", line 157, in find_requirement
    raise DistributionNotFound('No distributions at all found for %s' % req)
DistributionNotFound: No distributions at all found for cohesion

For example:

$ cat example.py 
class ExampleClass1(object):
    class_variable1 = 5
    class_variable2 = 6

    def func1(self):
        self.instance_variable = 6

        def inner_func(b):
            return b + 5

        local_variable = self.class_variable1

        return local_variable

    def func2(self):
        print(self.class_variable2)

    @staticmethod
    def func3(variable):
        return variable + 7

class ExampleClass2(object):
    def func1(self):
        self.instance_variable1 = 7

Without the --debug flag:

$ PYTHONPATH=lib/ python -m cohesion -f example.py 
File: example.py
  Class: ExampleClass2 (22:0)
    Function: func1 1/1 100.00%
    Total: 100.00%
  Class: ExampleClass1 (1:0)
    Function: func3 staticmethod
    Function: func2 1/3 33.33%
    Function: func1 2/3 66.67%
    Total: 33.33%

With the --debug flag:

$ PYTHONPATH=lib/ python -m cohesion --debug -f example.py 
{
    "ExampleClass2": {
        "cohesion": null,
        "variables": [
            "instance_variable1"
        ],
        "lineno": 22,
        "col_offset": 0,
        "functions": {
            "func1": {
                "classmethod": false,
                "variables": [
                    "instance_variable1"
                ],
                "bounded": true,
                "staticmethod": false
            }
        }
    },
    "ExampleClass1": {
        "cohesion": null,
        "variables": [
            "class_variable2",
            "class_variable1",
            "instance_variable"
        ],
        "lineno": 1,
        "col_offset": 0,
        "functions": {
            "func3": {
                "classmethod": false,
                "variables": [],
                "bounded": false,
                "staticmethod": true
            },
            "func2": {
                "classmethod": false,
                "variables": [
                    "class_variable2"
                ],
                "bounded": true,
                "staticmethod": false
            },
            "func1": {
                "classmethod": false,
                "variables": [
                    "class_variable1",
                    "instance_variable"
                ],
                "bounded": true,
                "staticmethod": false
            }
        }
    }
}

Notice the cohesion value is null with debugging turned on. It looks like this value is calculated differently depending on if debugging is turned on. We should remedy this.

E.g. if we only want to see classes or modules that meet some criteria, like high cohesion percentage than X%.

We'll probably want a way to perform this via library calls and a way to specify it from the command line.

$ cat example.py 
class ExampleClass1(object):
    def func1(self):
        print("HAI")

    def func4(self):
        self.func1()

$ cohesion -f example.py -x
{
    "ExampleClass1": {
        "variables": [
            "func1"
        ],
        "functions": {
            "func1": {
                "classmethod": false,
                "variables": [],
                "bounded": true,
                "staticmethod": false
            },
            "func4": {
                "classmethod": false,
                "variables": [
                    "func1"
                ],
                "bounded": true,
                "staticmethod": false
            }
        }
    }
}

The cohesion calculation should also be for classes that contain either no methods or only static, class or abstract methods, because the cohesion will be 0 %. This is annoying when dealing with abstract classes that will implement methods on subclasses.

Suppose you have this module:

class Data(object):
    def __init__(self, data):
        if not isinstance(data, list):
            raise ValueError('Data: Input arg must be list')
        self.data = data

    def get_value_at_start(self):
        return self.get_value_at_index(0)

    def get_value_at_index(self, index):
        return self.data[index]

data = Data([1, 3, 5, 7])
print 'Data 0: {}'.format(data.get_value_at_start())
print 'Data 2: {}'.format(data.get_value_at_index(2))

cohesion gives 0.00% for Function: get_value_at_start. IMO this is incorrect. By the definition you have in your documentation (extracted from wikipedia): "[...] cohesion refers to the degree to which the elements of a module belong together". Getting a cohesion of 0% would mean that the method does not belong to the class. However, it does; it's only that we're avoiding code repetition. If the function did 'return self.data[0]' we'd get cohesion score=100%, but this would go against good practices, because if later we change something in how we access data points, we need to change it in two places. What do you think?