update pyproject.toml

[ErikSieburgh]

Update the pyproject.toml such that new users can easily create an venv with the dependencies. I left the gpu dependencies out of the toml, since this is specified in the README.
After starting the venv, I can run most of the test. The test_probes.py seems problematic. It takes a very long time and writes coordinates to a csv in working directory.

(pysemtools-env) eriksieburgh@n171-p50 pySEMTools % mpirun -n 1 pytest -v tests/ --ignore=tests/test_probes.py -x

========================================= test session starts ==========================================
platform darwin -- Python 3.12.8, pytest-8.4.2, pluggy-1.6.0 -- /Volumes/sourcecode/Python/kth/pySEMTools/pysemtools-env/bin/python3.12
cachedir: .pytest_cache
rootdir: /Volumes/sourcecode/Python/kth/pySEMTools
configfile: pyproject.toml
collected 32 items

tests/test_autograd.py::test_autograd PASSED [ 3%]
tests/test_coef.py::test_coef_2d PASSED [ 6%]
tests/test_coef.py::test_coef_3d PASSED [ 9%]
tests/test_dssum.py::test_dssum PASSED [ 12%]
tests/test_interpolator.py::test_single_point_interpolator PASSED [ 15%]
tests/test_interpolator.py::test_multiple_point_interpolator_numpy PASSED [ 18%]
tests/test_interpolator.py::test_multiple_point_interpolator_torch PASSED [ 21%]
tests/test_interpolator.py::test_multiple_point_interpolator_torch_autograd SKIPPED (Interpo...) [ 25%]
tests/test_io_data_types.py::test_read_data_single PASSED [ 28%]
tests/test_io_data_types.py::test_wrapper PASSED [ 31%]
tests/test_io_data_types.py::test_read_data_double PASSED [ 34%]
tests/test_io_data_types.py::test_write_data_single PASSED [ 37%]
tests/test_io_data_types.py::test_write_data_double PASSED [ 40%]
tests/test_io_data_types.py::test_write_data_single_no_mesh PASSED [ 43%]
tests/test_io_data_types.py::test_write_data_double_no_mesh PASSED [ 46%]
tests/test_io_data_types_2D.py::test_read_data_single PASSED [ 50%]
tests/test_io_data_types_2D.py::test_read_data_double PASSED [ 53%]
tests/test_io_data_types_2D.py::test_write_data_single PASSED [ 56%]
tests/test_io_data_types_2D.py::test_write_data_double PASSED [ 59%]
tests/test_io_data_types_2D.py::test_write_data_single_no_mesh PASSED [ 62%]
tests/test_io_data_types_2D.py::test_write_data_double_no_mesh PASSED [ 65%]
tests/test_io_hdf5.py::test_io_hdf5 PASSED [ 68%]
tests/test_ppymech.py::test_read_double PASSED [ 71%]
tests/test_ppymech.py::test_read_single PASSED [ 75%]
tests/test_ppymech.py::test_write_double PASSED [ 78%]
tests/test_ppymech.py::test_write_single PASSED [ 81%]
tests/test_rom.py::test_POD PASSED [ 84%]
tests/test_rotations.py::test_cartesian_to_cylindrical PASSED [ 87%]
tests/test_statistics.py::test_time_averaging_1_batches PASSED [ 90%]
tests/test_statistics.py::test_time_averaging_2_batches PASSED [ 93%]
tests/test_statistics.py::test_space_averaging PASSED [ 96%]
tests/test_uq.py::test_NOBM PASSED [100%]

============================== 31 passed, 1 skipped in 213.00s (0:03:32) ===============================
(pysemtools-env) eriksieburgh@n171-p50 pySEMTools %