fix: particle deletion bug

[daniel-ji]

In the current verison of ArtiaX / copick, when a user does the following sequence:

• place particles (any amount)
• delete particle (any amount)
• place particles (more than one)
• delete selected particles (the last selected particle, so one)

The actions work as intended. However, if a user does the following:

• place particles (any amount)
• delete particle (any amount)
• place particles again (one)
• delete selected particles (the last selected particle, so one)

The last delete particle, even though only intended for one particle, deletes all the particles.

This is due to a Numpy broadcasting issue somewhere in the code, which might exist in ChimeraX.

What ends up happening is in (see PR, or src/particle/ParticleList.py):

            position_masks.append(
                np.logical_or(scm.position_mask(), markers.position_mask())
            )

the np.logical_or() evaluates to all true during the bugged action sequence, because scm.position_mask() ends up being all true, Tracing through the inherited classes, we end up with the _position_mask call of the Drawing class in ChimeraX, which seems to possibly be doing some broadcasting errors somewhere in the ChimeraX codebase: https://github.com/RBVI/ChimeraX/blob/56c7172631f802908efe39dda35eb8ec9a6e6baa/src/bundles/graphics/src/drawing.py#L967

    def _position_mask(self, highlighted_only=False):
        dp = self._displayed_positions        # bool array
        if highlighted_only:
            sp = self._highlighted_positions
            if sp is not None:
                import numpy
                dp = sp if dp is None else numpy.logical_and(dp, sp)
        return dp

I can go more down this rabbithole if desired, but the fix I've provided just skips that all entirely and just determines the selected_particles in a more intuitive way.