@LecrisUT thanks very much for pushing forward with this!

Unfortunately it doesn't seem to fix our specific case:

(This is using the example data in the doped GitHub, with the spglib version from #457)
The full error output is:

spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 0 tolerance = 1.000000e-02 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 1 tolerance = 9.500000e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 0 tolerance = 1.000000e-02 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 1 tolerance = 9.500000e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: ssm_get_exact_positions failed (attempt=0). (line 115, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/site_symmetry.c).
spglib: ssm_get_exact_positions failed (attempt=1). (line 115, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/site_symmetry.c).
spglib: ssm_get_exact_positions failed (attempt=2). (line 115, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/site_symmetry.c).
spglib: ssm_get_exact_positions failed (attempt=3). (line 115, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/site_symmetry.c).
spglib: ssm_get_exact_positions failed (attempt=4). (line 115, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/site_symmetry.c).
spglib: ssm_get_exact_positions failed. (line 479, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/refinement.c).
spglib: get_bravais_exact_positions_and_lattice failed. (line 336, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/refinement.c).
spglib: ref_get_exact_structure_and_symmetry failed. (line 82, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/determination.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 0 tolerance = 9.000000e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 1 tolerance = 8.550000e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 2 tolerance = 8.122500e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 3 tolerance = 7.716375e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 4 tolerance = 7.330556e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 5 tolerance = 6.964028e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).

If I rerun this cell, the output gets shortened to:

spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 0 tolerance = 1.000000e-02 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).
spglib: No point group was found (line 405, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/pointgroup.c).
spglib: Attempt 1 tolerance = 9.500000e-03 failed(line 800, /Users/runner/miniforge3/conda-bld/spglib_1707625470649/work/src/spacegroup.c).

I played around with trying to capture these warnings with warnings, StringIO() (for stdout/stderr), but none of these work either

Most of warning_print should should not be displayed. #338

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