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test enhancement and code clean up. (#1424)

- Make faster test
   On my mac:
```bash
pytest -vs tests/ -vs --duration 10 -n 4

========================================================= slowest 10 test durations =========================================================
8.17s call     tests/test_analysis/test_volmap.py::TestVolmap::test_volmap
6.68s call     tests/test_analysis/test_closest.py::TestClosest::test_closest
4.53s call     tests/test_analysis/test_pca.py::TestPCA::test_pca_with_ref_with_different_mask_from_matrix
3.10s call     tests/test_analysis/test_vector_analysis.py::TestVectorAnalysisModule::test_ired_vector
2.41s call     tests/test_analysis/test_watershell.py::TestWatershell::test_watershell
2.39s call     tests/test_io/test_io.py::test_iterload_comprehensive
2.36s call     tests/test_analysis/test_ired.py::test_ired_simple_for_coverage
2.17s call     tests/test_analysis/test_density.py::TestDensity::test_density
2.12s call     tests/test_iterator/test_iter_not_same_frame.py::Test::test_0
2.10s call     tests/test_io/test_io.py::test_load_comprehensive

418 passed, 52 skipped in 39.37 seconds
```
- `pytest -vs tests` work now 
- yapf 0.18.0

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