BUG: restore(clear=False) reflections added to other samples

[prjemian]

In [61]: config.restore(pathlib.Path("fourc-config.json"), clear=True)

In [62]: list_reflections(True)
Sample: main

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   2  0  0      37.000    0.000   90.000   71.500   first        
 1   0  4  0      60.000   30.000   90.000    0.000   second       
============================================================================
Sample: EuAl4

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   0  4  0      60.000   30.000   90.000    0.000   first        
 1   2  0  0      37.000    0.000   90.000   71.500   second       
============================================================================

In [63]: config.restore(pathlib.Path("fourc-config.json"), clear=False)

In [64]: list_reflections(True)
Sample: main

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   2  0  0      37.000    0.000   90.000   71.500   first        
 1   0  4  0      60.000   30.000   90.000    0.000   second       
============================================================================
Sample: EuAl4

 #   H  K  L   Two Theta    Theta      Chi      Phi   orienting   
 0   0  4  0      60.000   30.000   90.000    0.000 
 1   2  0  0      37.000    0.000   90.000   71.500 
 2   2  0  0      37.000    0.000   90.000   71.500 
 3   0  4  0      60.000   30.000   90.000    0.000 
 4   0  4  0      60.000   30.000   90.000    0.000   first        
 5   2  0  0      37.000    0.000   90.000   71.500   second       
============================================================================

It looks like when clear=False, it reads reflections from 'main' also into the following sample.

Originally posted by @strempfer in #279 (comment)

[prjemian]

@strempfer: I have reproduced this situation in test code with the current version and am working on repairs now. In short, the restored samples should each have two reflections in this test. That fails:

        for sample in e4cv.calc._samples.values():
            assert len(sample.reflections) == 2, f"{sample.name=}"
        assert len(e4cv.calc._samples) == 4

        agent = DiffractometerConfiguration(e4cv)
        config = agent.export()

        agent.restore(config, clear=False)
    
        assert len(e4cv.calc._samples) == 4
        for sample in e4cv.calc._samples.values():
>           assert len(sample.reflections) == 2
E           AssertionError: assert 10 == 2

[prjemian]

Those commits should have been on a new branch. Since I've pushed them, will remove the changes with git revert.

[prjemian]

Lots of new errors now in test_configuration.py module.

[prjemian]

All of the form: It is not possible to compute the UB matrix when the given reflections are colinear. When this line is removed, no such error, but reflections are duplicated:

hklpy/hkl/configuration.py

Line 297 in c8163ab

s.remove_reflection(refl)

[prjemian]

... Starving for a sample.update_reflection() method. Alas, v2 item.