Bump development tools: mypy, codespell, isort, ...

Move all tools configuration in pyproject.toml.

Remove no longer needed mypy overrides.

Related to swh/meta#5075.

Prevent timestamps in node properties from being shifted according to the timezone WriteNodeProperties is being run in.

Due to our ORC exports using the `timestamp` instead of the `timestamp with timezone`, reader and writer need to agree out of bound on the timezone used in files they exchange.

However, we don't do this:

* `swh-dataset` uses pyorc, which uses the C++ ORC library, which assumes users (us) always write in GMT
* `swh-graph` uses the Java ORC library, which assumes the system timezone (or `$TZ` if set)

So when reading with a non-UTC timezone, the Java ORC library interprets timestamps in the dataset as being in the local timezone, and converts them to UNIX timestamps (number of seconds since epoch); then we use these converted timestamps and write them to `.property.author_timestamp.bin` and `.property.committer_timestamp.bin`.

This commit regenerates the example graph to have the correct timestamps. It also applies the 39ed0d17 change that removes useless padding at the end of all property files.

Resolves #4788

Related to swh/meta#4960

Jérémy Bobbio (Lunar) authored 2 years ago and Jérémy Bobbio (Lunar) committed 2 years ago

Related to swh/meta#4959

They tend to be forgotten; this will make sure that running 'tox' will
run Java tests as well as Python tests.

It will also make it easier to run Java tests on the CI

whitelist_externals is deprecated since v3.18, and removed since v4.0

- pre-commit from 4.1.0 to 4.3.0,
- codespell from 2.2.1 to 2.2.2,
- black from 22.3.0 to 22.10.0 and
- flake8 from 4.0.1 to 5.0.4. Also freeze flake8 dependencies.

Also change flake8's repo config to github (the gitlab mirror
being outdated).

black is considered stable since release 22.1.0 and the version
we are currently using is quite outdated and not compatible with
click 8.1.0, so it is time to bump it to its latest stable release.

Please note that E501 pycodestyle warning related to line length
is replaced by B950 one from flake8-bugbear as recommended by black.
https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html#line-length

Related to T3922

This also drops spurious copyright headers to those files if present.

Related to T3812

Enable to check package documentation can be built without producing
sphinx warnings.

The sphinx environment is designed to be used in continuous integration
in order to prevent breaking documentation build when committing changes.

The sphinx-dev environment is designed to be used inside a full swh
development environment.

Related to T3258

- blackify all the python files,
- enable black in pre-commit,
- add a black tox environment.

no longer needed extra indirection

thanks to @olasd for the tip

Closes T2054

it is possible we want to actually define it, as it is in swh-py-template,
but there is a more general issue of how to keep that tox.ini in sync with
all other repos --- which is postponed for now

- Move 'api/client' to the root
- Move 'api/server' into 'java/server'