db: drop SA caching_query and FromCache, and thus sql_cache_short beaker cache

It is not a good idea to have dead ORM objects. If we want caching, we should
do it explicit.

It is unknown how much this cache helps, but we can profile and introduce
better caching of simple data where relevant.

scripts: drop isort --wrap-length 160 - it is broken with py3 and not really necessary

Under Python 3, isort 4.3.21 failed with
https://github.com/timothycrosley/isort/issues/741 on
kallithea/controllers/api/api.py :

Traceback (most recent call last):
File "data/env/bin/isort", line 10, in <module>
sys.exit(main())
File ".../env/lib64/python3.7/site-packages/isort/main.py", line 379, in main
for sort_attempt in attempt_iterator:
File ".../env/lib64/python3.7/site-packages/isort/main.py", line 377, in <genexpr>
attempt_iterator = (sort_imports(file_name, **arguments) for file_name in file_names)
File ".../env/lib64/python3.7/site-packages/isort/main.py", line 88, in sort_imports
result = SortImports(file_name, **arguments)
File ".../env/lib64/python3.7/site-packages/isort/isort.py", line 207, in __init__
self._add_formatted_imports()
File ".../env/lib64/python3.7/site-packages/isort/isort.py", line 606, in _add_formatted_imports
self._add_from_imports(from_modules, section, section_output, sort_ignore_case)
File ".../env/lib64/python3.7/site-packages/isort/isort.py", line 526, in _add_from_imports
import_statement = self._multi_line_reformat(import_start, from_import_section, comments)
File ".../env/lib64/python3.7/site-packages/isort/isort.py", line 552, in _multi_line_reformat
dynamic_indent, indent, line_length, comments)
File ".../env/lib64/python3.7/site-packages/isort/isort.py", line 705, in _output_grid
if len(next_statement.split(self.line_separator)[-1]) + 1 > line_length:
TypeError: '>' not supported between instances of 'int' and 'str'

model: name arguments to get_by_group_name

Prepare for refactoring.

flake8: fix some E712 comparison to True should be 'if cond is True:' or 'if cond:'

add_user_to_group is really odd ...

Note that the SqlAlchemy query API cause a lot of this kind of warnings.

codingstyle: trivial whitespace fixes

Reported by flake8.

model: remove BaseModel class

The only remaining purpose of this class was to provide the "sa" field,
allowing a custom SQLAlchemy session to be used for model operations.
However, this never actually worked, nor was it used anywhere.

There's always a global SQLAlchemy session associated with the current
thread; using another session for a single function call does not make
any sense (as sessions cannot be mixed), unless the code works carefully
to ensure the two sessions (and all objects loaded from them) are kept
completely separate. Suffice to say that Kallithea does no such thing,
thus there's no need to pretend to support multiple concurrent sessions.

cleanup: drop superfluous Session.add calls

Session.add should only be called on newly created database objects.

Per the Kallithea contribution guidelines:

When getting an object from the session (via Session().query or
any of the utility functions that look up objects in the database),
it's already part of the session, and should not be added again.

cleanup: do Session.add directly inside _create_default_perms

Let the various _create_default_perms functions add the created object
to the SQLAlchemy database session, instead of having the caller do it.

This is in accordance with the Kallithea contribution guidelines:

When creating an object using a factory function (like create_repo),
the returned object has already (by convention) been added to the
session, and should not be added again.

auth: simplify user group permission checks

In practice, Kallithea has the 'usergroup.admin' permission imply the
'usergroup.write' permission, which again implies 'usergroup.read'.

This codifies this practice by replacing the HasUserGroupPermissionAny
"perm function" with the new HasUserGroupLevel function, reducing the
risk of errors and saving quite a lot of typing.

model: simplify guess_instance invocations

The second argument to the guess_instance classmethod is in practice
fixed for Gist, Permission, RepoGroup, Repository, User, UserGroup;
so might as well move this logic into per-class specializations of
guess_instance.

db: clean up SQLAlchemy session flushes

Many calls to Session().flush() were completely superfluous and have
been removed. (See also the note on "flush" in the contributor docs.)
For the remaining calls, a comment has been added to explain why it's
necessary.

model: move code from __init__.py to base.py

Having too much code, in particular too much imports, inside a package's
__init__.py is a recipe for circular imports, and considered bad practice in
Python [1]

Move out everything from kallithea/model/__init__.py to a new file
kallithea/model/base.py and adapt the existing imports.

[1] http://docs.python-guide.org/en/latest/writing/structure/#packages

cleanup: use obj.foo_id instead of obj.foo.foo_id

Don't use constructs like obj.user.user_id when obj.user_id works
equally well (and potentially saves a database load).

db: PullRequest/Repository/RepoGroup/UserGroup: change 'user' to 'owner'

Rename the 'user' and 'user_id' fields on the four classes to something
more informative. The database column names remain unchanged for now;
a later Alembic script can fix the name of these and other columns to
match their Python name.

This might break rcextensions, though, and external scripts that use
the HTML form interface.

model: refactor and simplify _get_instance

_get_instance is a BaseModel method, but never uses "self". Instead
it takes a class argument, which indicates that it's better suited as
a classmethod on said classes.

Also rename to something more descriptive, remove leading underscore
since it's not a private API, and refactor for readability.

model: drop BaseModel.cls

It no longer serves a purpose.

cleanup: make module self-naming consistent

The self naming is quite pointless ... but at least make it right.

cleanup: check for None object identity in cases where that is what the 'contract' says

Avoid applying bool() on complex objects - it might return something unexpected
such as the key (which might be 0 and thus be false). Checking for None is more
safe and faster.

auth: ignore permissions from in-active user groups (Issue #138)

Tests by Thomas De Schampheleire.

Additionally, rename the unused and seemingly search-replace-massacred
function revokehas_permrevoke_permgrant_perm_perm into revoke_perm.

Second step in two-part process to rename directories.
This is the actual directory rename.