python: Implement Python high level API in python

[vicentebolea]

Step of #3813

In this PR we move the implementation of File from C++/py11bind to pure Python. In addition to that we also add a High level python API that wraps the python bindings, this high level python API is needed to provide more pythonic supports and to connect the (File)Stream|FileReader with the other ADIOS2 objects (IO, adios, engine...)

• The Python File class has been re-implemented in python in two different classes
  • Stream (for write and read modes)
  • FileReader (for ReadRandomAccess mode)
• More member functions from the ADIOS2 core API has been exposed to the bindings.
• Added several unit tests to test this new API.
• Adds new linters/format (black|pylint|flake8) checks for the format CI build.
• Updaded the readthedocs description for the Python high level API.
• Moved the numpy dependency from the C++ interface to the Python API. This can hinder performance since if the user uses numpy we might incur in an extra memory copy. The reason to remove this was to easy the deployment of this library. @eisenhauer we can rollback this, I wonder what do you think about this.

[vicentebolea]

@dmitry-ganyushin ready for another round of review. I added pylint to the CI and I modify the code so that it satisfies most of the warnings, I disabled a few of them because since we use a C++ generated python module some of the checks do not work properly.

[vicentebolea]

@eisenhauer please review this 👼

[eisenhauer]

@eisenhauer please review this 👼

I only have a little bit of time this morning and there are a lot of changes, so probably won't get through this until the evening, but will do what I can.

[vicentebolea]

@eisenhauer please review this 👼

I only have a little bit of time this morning and there are a lot of changes, so probably won't get through this until the evening, but will do what I can.

Thanks! There has been several reviews from Scott (KW), Berk, and Dmitry, but I have made some changes since they reviewed it.

[eisenhauer]

In py11Engine.cpp, MinBlocksInfo() returns a pointer, and if that pointer is non-null, the caller gains ownership to the created struct, so I think we need a delete of minBlocksInfo at the end of "if (minBlocksInfo)" in Engine::BlocksInfo.

[vicentebolea]

Good catch, find this resolved at the last push

…

On Thu, Dec 28, 2023 at 5:21 PM Greg Eisenhauer ***@***.***> wrote: ***@***.**** requested changes on this pull request. In py11Engine.cpp, MinBlocksInfo() returns a pointer, and if that pointer is non-null, the caller gains ownership to the created struct, so I think we need a delete of nBlocksInfo at the end of "if (mnBlocksInfo)" in Engine::BlocksInfo. — Reply to this email directly, view it on GitHub <#3938 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHFOFWZXDG4XISGXSIQKZDYLXWF3AVCNFSM6AAAAAA7VNKFSGVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTOOJYGQ3TINBWGA> . You are receiving this because you were assigned.Message ID: ***@***.***>

-- [image: logo shows large letter K with the word Kitware below it] <http://www.kitware.com> Vicente Bolea, MSc. *Senior R&D Engineer*

[vicentebolea]

Good catch, find this resolved at the last push
…
On Thu, Dec 28, 2023 at 5:21 PM Greg Eisenhauer @.> wrote: @.* requested changes on this pull request. In py11Engine.cpp, MinBlocksInfo() returns a pointer, and if that pointer is non-null, the caller gains ownership to the created struct, so I think we need a delete of nBlocksInfo at the end of "if (mnBlocksInfo)" in Engine::BlocksInfo. — Reply to this email directly, view it on GitHub <#3938 (review)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAHFOFWZXDG4XISGXSIQKZDYLXWF3AVCNFSM6AAAAAA7VNKFSGVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTOOJYGQ3TINBWGA . You are receiving this because you were assigned.Message ID: @.***>
-- [image: logo shows large letter K with the word Kitware below it] http://www.kitware.com Vicente Bolea, MSc. Senior R&D Engineer

@eisenhauer