fix: NumPy slice error

[eagmon]

This PR fixes a long-standing NumPy error in which a slice object can no longer be used as an index. Instead, I am pulling the ranges out of the slice object and using them directly.

I also fixed some listing errors and matplotlib deprecation errors, but left 4 tests still failing, down from 13 failing before this PR:

1. FAILED tests/model_lang/bngl/test_bngl_utils.py::BgnlUtilsTestCase::test_get_parameters_variables_for_simulation_with_empty_sample_times - AssertionError: “failed to parse action” does not match “Model file /home/runner/work/Biosimulators_utils/Biosimulators_utils/tests/model_lang/bngl/../../fixtures/bngl/empty-sample-times.bngl is not a valid BNGL or BNGL XML file.
2. FAILED tests/sedml/test_sedml_validation.py::ValidationTestCase::test_validate_calculation - AssertionError: ‘The syntax’ not found in ‘- The mathematical expression a * is invalid.\n - unexpected EOF while parsing (, line 1)’
3. FAILED tests/combine/test_combine_exec.py::ExecCombineTestCase::test_1 - AssertionError: None != {‘sim.sedml’: {‘report1’: ‘ABC’, ‘report2’: ‘DEF’}}
4. FAILED tests/combine/test_combine_exec.py::ExecCombineTestCase::test_2 - AssertionError: Lists differ: [‘log.yml’] != [‘dir1’, ‘log.yml’, ‘plots.zip’, ‘reports.zip’]

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