Fabian Zills

Fix # #### Summary of additions and changes * #### How to test this pull request ``` ```

> We will also need to update the headers of the files, but let's leave that for now. _Originally posted by @SamTov in https://github.com/zincware/MDSuite/issues/589#issuecomment-1429414262_

update ruff excluded

3

After #567 we excluded as many as possible of ruffs errors. We should slowly bring them back. https://github.com/zincware/MDSuite/blob/0b85016999ac93caf52fa10ab7f46df11d7acaa9/pyproject.toml#L13-L20

Fix required packages, clean up dependency management.

requirement resolving could cause issues

1

**Describe the bug** I installed mdsuite via pip on a System with TensorFlow already installed: `ImportError: This version of TensorFlow Probability requires TensorFlow version >= 2.10; Detected an installation of...

Use `conftest.py` to simplify tests

1

See https://docs.pytest.org/en/6.2.x/fixture.html#scope-sharing-fixtures-across-classes-modules-packages-or-session tl;dr Add a file `CI/conftest.py` and put all repeated fixtures there. They will be used automatically and can be removed from the individual tests. https://github.com/zincware/MDSuite/blob/d159167c789a9ced0ab483d03d79c47e10c9435e/CI/integration_tests/calculators/test_green_kubo_distinct_diffusion_coefficients.py#L35-L54

#548 fixed some urgent RTD issue but left open: - [ ] When running `make html` I get the following error (and a lot of warnings about missing docstrings which...

The full code e.g. https://github.com/zincware/MDSuite/blob/55e1ac6ff7c5ac3c08190e8e58c5104b0edd07df/mdsuite/database/scheme.py#L193-L196 is currently not tested in unittests.

rename `box_array` to `cell` or `box`

1

**What feature would you like to see added?** ```py project.experiments.ML_273K.box_array # I think the following attribute names are more convenient than box_array project.experiments.ML_273K.box project.experiments.ML_273K.cell ```