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chore(clang-tidy): Add clang-tidy rules: prefer-member-initializer and optin.performance.Padding (#3716)

* Add clang-tidy prefer-member-initializer

* Fix clang-tdy config

* Fix incorrect change

* Fix sorting of .clang-tidy

clang-tidy automatic changes. NO manual changes.

* override: Fix wrong caching of the overrides

There was a problem when the python type, which was stored in override
cache for C++ functions, was destroyed and  the record wasn't removed from the
override cache. Therefor, dangling pointer was stored there. Then when the
memory was reused and new type was allocated at the given address and the
method with the same name (as previously stored in the cache) was actually
overridden in python, it would wrongly find it in the override cache for C++
functions and therefor override from python wouldn't be called.
The fix is to erase the type from the override cache when the type is destroyed.

* test: Pass by const ref instead of by value (clang-tidy)

* test: Rename classes and move to different files

Rename the classes and files so they're no too generic. Also, better place to
test the stuff is in test_virtual_functions.cpp/.py as we're basically testing
the virtual functions/trampolines.

* Add TODO for erasure code

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Adding google-explicit-constructor to .clang-tidy

* clang-tidy explicit attr.h (all automatic)

* clang-tidy explicit cast.h (all automatic)

* clang-tidy detail/init.h (1 NOLINT)

* clang-tidy detail/type_caster_base.h (2 NOLINT)

* clang-tidy pybind11.h (7 NOLINT)

* clang-tidy detail/common.h (3 NOLINT)

* clang-tidy detail/descr.h (2 NOLINT)

* clang-tidy pytypes.h (23 NOLINT, only 1 explicit)

* clang-tidy eigen.h (7 NOLINT, 0 explicit)

* Adding 2 explicit in functional.h

* Adding 4 explicit in iostream.h

* clang-tidy numpy.h (1 NOLINT, 1 explicit)

* clang-tidy embed.h (0 NOLINT, 1 explicit)

* clang-tidy tests/local_bindings.h (0 NOLINT, 4 explicit)

* clang-tidy tests/pybind11_cross_module_tests.cpp (0 NOLINT, 1 explicit)

* clang-tidy tests/pybind11_tests.h (0 NOLINT, 2 explicit)

* clang-tidy tests/test_buffers.cpp (0 NOLINT, 2 explicit)

* clang-tidy tests/test_builtin_casters.cpp (0 NOLINT, 4 explicit)

* clang-tidy tests/test_class.cpp (0 NOLINT, 6 explicit)

* clang-tidy tests/test_copy_move.cpp (0 NOLINT, 7 explicit)

* clang-tidy tests/test_embed/external_module.cpp (0 NOLINT, 1 explicit)

* clang-tidy tests/test_embed/test_interpreter.cpp (0 NOLINT, 1 explicit)

* clang-tidy tests/object.h (0 NOLINT, 2 explicit)

* clang-tidy batch of fully automatic fixes.

* Workaround for MSVC 19.16.27045.0 C++17 Python 2 C++ syntax error.

* Enable bugprone checks

* Reset delta and massage config

* Start to apply bugprone fixes

* try to fix minor bug

* Fix later

* Fix perfect forwarding bugprone

* Remove nolint

* undo constructor delete

* Fix bugprone-perfect-forwarding again

* Remove TODO

* Add another nolint for bugprone-exception-escape in scoped interpreter

* Fix remaining bugprone errors

* Properly apply bugprone-macro-parantheses

* Redo formatting and remove bugprone nolint

* Add coment and revert more whitespace changes

* Fix typo

* Fix parsing bug

* Add back comma

* Fix clang-tidy issue

* Apply remaining clang-tidy fixes

* Enable clang-tidy else-after-return and redundant void checks

* Fix remaining else-after

* Address reviewer comments

* Fix indentation

* Rerun clang-tidy post merge

* Initial fixes

* Whoops

* Finish clang-tidy manual fixes

* Add two missing fixes

* Revert

* Update clang-tidy

* Try to fix unreachable code error

* Move nolint comment

* Apply missing fix

* Don't override clang-tidy config

* Does this fix clang-tidy?

* Make all clang-tidy errors visible

* Add comments about NOLINTs and remove a few

* Fix typo

* WIP: module -> module_ without typedef

* refactor: allow py::module to work again

* fix: use OVERRIDE instead of OVERLOAD

* docs: more accurate statement

Resolve empty statement warning when using PYBIND11_OVERLOAD_PURE_NAME and PYBIND11_OVERLOAD_PURE (#2325)

* Wrap PYBIND11_OVERLOAD_NAME and PYBIND11_OVERLOAD_PURE_NAME in do { ... } while (false), and resolve trailing semicolon

* Deprecate PYBIND11_OVERLOAD_* and get_overload in favor of PYBIND11_OVERRIDE_* and get_override

* Correct erroneous usage of 'overload' instead of 'override' in the implementation and internals

* Fix tests to use non-deprecated PYBIND11_OVERRIDE_* macros

* Update docs to use override instead of overload where appropriate, and add warning about deprecated aliases

* Add semicolons to deprecated PYBIND11_OVERLOAD macros to match original behavior

* Remove deprecation of PYBIND11_OVERLOAD_* macros and get_overload

* Add note to changelog and upgrade guide

* Added guards to the includes

Added new CI config

Added new trigger

Changed CI workflow name

Debug CI

Debug CI

Debug CI

Debug CI

Added flags fro PGI

Disable Eigen

Removed tests that fail

Uncomment lines

* fix: missing include

fix: minor style cleanup

tests: support skipping

ci: remove and tighten a bit

fix: try msvc workaround for pgic

* tests: split up prealoc tests

* fix: PGI compiler fix

* fix: PGI void_t only

* fix: try to appease nvcc

* ci: better ordering for slow tests

* ci: minor improvements to testing

* ci: Add NumPy to testing

* ci: Eigen generates CUDA warnings / PGI errors

* Added CentOS7 back for a moment

* Fix YAML

* ci: runs-on missing

* centos7 is missing pytest

* ci: use C++11 on CentOS 7

* ci: test something else

* Try just adding flags on CentOS 7

* fix: CentOS 7

* refactor: move include to shared location

* Added verbose flag

* Try to use system cmake3 on CI

* Try to use system cmake3 on CI, attempt2

* Try to use system cmake3 on CI, attempt3

* tests: not finding pytest should be a warning, not a fatal error

* tests: cleanup

* Weird issue?

* fix: final polish
Co-authored-by: Andrii Verbytskyi <andrii.verbytskyi@mpp.mpg.de>
Co-authored-by: Henry Schreiner <henryschreineriii@gmail.com>
Co-authored-by: Andrii Verbytskyi <averbyts@cern.ch>

* fix: support nvcc and test

* fixup! fix: support nvcc and test

* docs: mention what compilers fail

* fix: much simpler logic

* refactor: slightly faster / clearer

* Fix warning that not including a cmake source or build dir will be a fatal error (it is now on newest CMakes)
    * Fixes appveyor
* Travis uses CMake 3.9 for more than a year now
* Travis dropped sudo: false in December
* Dropping Sphinx 2
- clang7: Suppress self-assign warnings; fix missing virtual dtors
- pypy:
  - Keep old version (newer stuff breaks)
  - Pin packages to extra index for speed
- travis:
  - Make docker explicit; remove docker if not needed
  - Make commands more verbose (for debugging / repro)
  - Make Ubuntu dist explicit per job
- Fix Windows
- Add names to travis

Fixes #1401

- PYBIND11_MAKE_OPAQUE now takes ... rather than a single argument and
  expands it with __VA_ARGS__; this lets templated, comma-containing
  types get through correctly.
- Adds a new macro PYBIND11_TYPE() that lets you pass the type into a
  macro as a single argument, such as:

      PYBIND11_OVERLOAD(PYBIND11_TYPE(R<1,2>), PYBIND11_TYPE(C<3,4>), func)

  Unfortunately this only works for one macro call: to forward the
  argument on to the next macro call (without the processor breaking it
  up again) requires also adding the PYBIND11_TYPE(...) to type macro
  arguments in the PYBIND11_OVERLOAD_... macro chain.
- updated the documentation with these two changes, and use them at a couple
  places in the test suite to test that they work.

Non-user facing. 
Found using `codespell -q 3`

This reimplements the py::init<...> implementations using the various
functions added to support `py::init(...)`, and moves the implementing
structs into `detail/init.h` from `pybind11.h`.  It doesn't simply use a
factory directly, as this is a very common case and implementation
without an extra lambda call is a small but useful optimization.

This, combined with the previous lazy initialization, also avoids
needing placement new for `py::init<...>()` construction: such
construction now occurs via an ordinary `new Type(...)`.

A consequence of this is that it also fixes a potential bug when using
multiple inheritance from Python: it was very easy to write classes
that double-initialize an existing instance which had the potential to
leak for non-pod classes.  With the new implementation, an attempt to
call `__init__` on an already-initialized object is now ignored.  (This
was already done in the previous commit for factory constructors).

This change exposed a few warnings (fixed here) from deleting a pointer
to a base class with virtual functions but without a virtual destructor.
These look like legitimate warnings that we shouldn't suppress; this
adds virtual destructors to the appropriate classes.

This allows you to use:

    cls.def(py::init(&factory_function));

where `factory_function` returns a pointer, holder, or value of the
class type (or a derived type).  Various compile-time checks
(static_asserts) are performed to ensure the function is valid, and
various run-time type checks where necessary.

Some other details of this feature:
- The `py::init` name doesn't conflict with the templated no-argument
  `py::init<...>()`, but keeps the naming consistent: the existing
  templated, no-argument one wraps constructors, the no-template,
  function-argument one wraps factory functions.
- If returning a CppClass (whether by value or pointer) when an CppAlias
  is required (i.e. python-side inheritance and a declared alias), a
  dynamic_cast to the alias is attempted (for the pointer version); if
  it fails, or if returned by value, an Alias(Class &&) constructor
  is invoked.  If this constructor doesn't exist, a runtime error occurs.
- for holder returns when an alias is required, we try a dynamic_cast of
  the wrapped pointer to the alias to see if it is already an alias
  instance; if it isn't, we raise an error.
- `py::init(class_factory, alias_factory)` is also available that takes
  two factories: the first is called when an alias is not needed, the
  second when it is.
- Reimplement factory instance clearing.  The previous implementation
  failed under python-side multiple inheritance: *each* inherited
  type's factory init would clear the instance instead of only setting
  its own type value.  The new implementation here clears just the
  relevant value pointer.
- dealloc is updated to explicitly set the leftover value pointer to
  nullptr and the `holder_constructed` flag to false so that it can be
  used to clear preallocated value without needing to rebuild the
  instance internals data.
- Added various tests to test out new allocation/deallocation code.
- With preallocation now done lazily, init factory holders can
  completely avoid the extra overhead of needing an extra
  allocation/deallocation.
- Updated documentation to make factory constructors the default
  advanced constructor style.
- If an `__init__` is called a second time, we have two choices: we can
  throw away the first instance, replacing it with the second; or we can
  ignore the second call.  The latter is slightly easier, so do that.

This udpates all the remaining tests to the new test suite code and
comment styles started in #898.  For the most part, the test coverage
here is unchanged, with a few minor exceptions as noted below.

- test_constants_and_functions: this adds more overload tests with
  overloads with different number of arguments for more comprehensive
  overload_cast testing.  The test style conversion broke the overload
  tests under MSVC 2015, prompting the additional tests while looking
  for a workaround.

- test_eigen: this dropped the unused functions `get_cm_corners` and
  `get_cm_corners_const`--these same tests were duplicates of the same
  things provided (and used) via ReturnTester methods.

- test_opaque_types: this test had a hidden dependence on ExampleMandA
  which is now fixed by using the global UserType which suffices for the
  relevant test.

- test_methods_and_attributes: this required some additions to UserType
  to make it usable as a replacement for the test's previous SimpleType:
  UserType gained a value mutator, and the `value` property is not
  mutable (it was previously readonly).  Some overload tests were also
  added to better test overload_cast (as described above).

- test_numpy_array: removed the untemplated mutate_data/mutate_data_t:
  the templated versions with an empty parameter pack expand to the same
  thing.

- test_stl: this was already mostly in the new style; this just tweaks
  things a bit, localizing a class, and adding some missing
  `// test_whatever` comments.

- test_virtual_functions: like `test_stl`, this was mostly in the new
  test style already, but needed some `// test_whatever` comments.
  This commit also moves the inherited virtual example code to the end
  of the file, after the main set of tests (since it is less important
  than the other tests, and rather length); it also got renamed to
  `test_inherited_virtuals` (from `test_inheriting_repeat`) because it
  tests both inherited virtual approaches, not just the repeat approach.

This adds a static local variable (in dead code unless actually needed)
in the overload code that is used for storage if the overload is for
some convert-by-value type (such as numeric values or std::string).

This has limitations (as written up in the advanced doc), but is better
than simply not being able to overload reference or pointer methods.

Minor change that makes this example more compliant with the C++ Core
Guidelines.

This allows a slightly cleaner base type specification of:

    py::class_<Type, Base>("Type")

as an alternative to

    py::class_<Type>("Type", py::base<Base>())

As with the other template parameters, the order relative to the holder
or trampoline types doesn't matter.

This also includes a compile-time assertion failure if attempting to
specify more than one base class (but is easily extendible to support
multiple inheritance, someday, by updating the class_selector::set_bases
function to set multiple bases).

With this change both C++ and Python write to sys.stdout which resolves
the capture issues noted in #351. Therefore, the related workarounds are
removed.

The current pybind11::class_<Type, Holder, Trampoline> fixed template
ordering results in a requirement to repeat the Holder with its default
value (std::unique_ptr<Type>) argument, which is a little bit annoying:
it needs to be specified not because we want to override the default,
but rather because we need to specify the third argument.

This commit removes this limitation by making the class_ template take
the type name plus a parameter pack of options.  It then extracts the
first valid holder type and the first subclass type for holder_type and
trampoline type_alias, respectively.  (If unfound, both fall back to
their current defaults, `std::unique_ptr<type>` and `type`,
respectively).  If any unmatched template arguments are provided, a
static assertion fails.

What this means is that you can specify or omit the arguments in any
order:

    py::class_<A, PyA> c1(m, "A");
    py::class_<B, PyB, std::shared_ptr<B>> c2(m, "B");
    py::class_<C, std::shared_ptr<C>, PyB> c3(m, "C");

It also allows future class attributes (such as base types in the next
commit) to be passed as class template types rather than needing to use
a py::base<> wrapper.

Adding or removing tests is a little bit cumbersome currently: the test
needs to be added to CMakeLists.txt, the init function needs to be
predeclared in pybind11_tests.cpp, then called in the plugin
initialization.  While this isn't a big deal for tests that are being
committed, it's more of a hassle when working on some new feature or
test code for which I temporarily only care about building and linking
the test being worked on rather than the entire test suite.

This commit changes tests to self-register their initialization by
having each test initialize a local object (which stores the
initialization function in a static variable).  This makes changing the
set of tests being build easy: one only needs to add or comment out
test names in tests/CMakeLists.txt.

A couple other minor changes that go along with this:

- test_eigen.cpp is now included in the test list, then removed if eigen
  isn't available.  This lets you disable the eigen tests by commenting
  it out, just like all the other tests, but keeps the build working
  without eigen eigen isn't available.  (Also, if it's commented out, we
  don't even bother looking for and reporting the building with/without
  eigen status message).

- pytest is now invoked with all the built test names (with .cpp changed
  to .py) so that it doesn't try to run tests that weren't built.

Problem
=======

The template trampoline pattern documented in PR #322 has a problem with
virtual method overloads in intermediate classes in the inheritance
chain between the trampoline class and the base class.

For example, consider the following inheritance structure, where `B` is
the actual class, `PyB<B>` is the trampoline class, and `PyA<B>` is an
intermediate class adding A's methods into the trampoline:

    PyB<B> -> PyA<B> -> B -> A

Suppose PyA<B> has a method `some_method()` with a PYBIND11_OVERLOAD in
it to overload the virtual `A::some_method()`.  If a Python class `C` is
defined that inherits from the pybind11-registered `B` and tries to
provide an overriding `some_method()`, the PYBIND11_OVERLOADs declared
in PyA<B> fails to find this overloaded method, and thus never invoke it
(or, if pure virtual and not overridden in PyB<B>, raises an exception).

This happens because the base (internal) `PYBIND11_OVERLOAD_INT` macro
simply calls `get_overload(this, name)`; `get_overload()` then uses the
inferred type of `this` to do a type lookup in `registered_types_cpp`.
This is where it fails: `this` will be a `PyA<B> *`, but `PyA<B>` is
neither the base type (`B`) nor the trampoline type (`PyB<B>`).  As a
result, the overload fails and we get a failed overload lookup.

The fix
=======

The fix is relatively simple: we can cast `this` passed to
`get_overload()` to a `const B *`, which lets get_overload look up the
correct class.  Since trampoline classes should be derived from `B`
classes anyway, this cast should be perfectly safe.

This does require adding the class name as an argument to the
PYBIND11_OVERLOAD_INT macro, but leaves the public macro signatures
unchanged.

- ICPC can't handle the NCVirt trampoline which returns a non-copyable
  type, which is likely due to a constexpr/SFINAE issue. This disables
  the test on that compiler so that at least the rest can be tested.

Use simple asserts and pytest's powerful introspection to make testing
simpler. This merges the old .py/.ref file pairs into simple .py files
where the expected values are right next to the code being tested.

This commit does not touch the C++ part of the code and replicates the
Python tests exactly like the old .ref-file-based approach.

This commit rewrites the examples that look for constructor/destructor
calls to do so via static variable tracking rather than output parsing.

The added ConstructorStats class provides methods to keep track of
constructors and destructors, number of default/copy/move constructors,
and number of copy/move assignments.  It also provides a mechanism for
storing values (e.g. for value construction), and then allows all of
this to be checked at the end of a test by getting the statistics for a
C++ (or python mapping) class.

By not relying on the precise pattern of constructions/destructions,
but rather simply ensuring that every construction is matched with a
destruction on the same object, we ensure that everything that gets
created also gets destroyed as expected.

This replaces all of the various "std::cout << whatever" code in
constructors/destructors with
`print_created(this)`/`print_destroyed(this)`/etc. functions which
provide similar output, but now has a unified format across the
different examples, including a new ### prefix that makes mixed example
output and lifecycle events easier to distinguish.

With this change, relaxed mode is no longer needed, which enables
testing for proper destruction under MSVC, and under any other compiler
that generates code calling extra constructors, or optimizes away any
constructors.  GCC/clang are used as the baseline for move
constructors; the tests are adapted to allow more move constructors to
be evoked (but other types are constructors much have matching counts).

This commit also disables output buffering of tests, as the buffering
sometimes results in C++ output ending up in the middle of python
output (or vice versa), depending on the OS/python version.