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fix: fix .show() crash when restraints weren't added add_soft_bounds() - #227
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@sbillinge ready for review, The description is very claude-y 😂 but i felt it did a good job describing the changes |
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #227 +/- ##
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+ Coverage 71.63% 84.70% +13.07%
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Files 25 43 +18
Lines 3437 4805 +1368
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+ Hits 2462 4070 +1608
+ Misses 975 735 -240
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I think codecov isnt happy because |
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yes, claudy but easy to follow. It will be work to test those string methods and if we change them the test will break for no particularly good reason, so I think this is ok as it is. |
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What problem does this PR address?
Closes #24
show()crashed with anAttributeErrorwhenever a recipe held a restraint that wasn't made byadd_soft_bounds. That includes:restrainBVS()Restraintadded directly withregister_soft_bounds()Why:
show()printed every restraint aseqstr: lower_bound = ..., upper_bound = ..., sig = ..., scaled = .... Only restraints made byadd_soft_boundshave those attributes. The others store different information. For example, an ObjCryst restraint only wraps a pyobjcryst object, soshow()failed when it tried to read them.Fix: Each restraint class now describes itself through
__str__, andshow()prints what each restraint returns:show()add_soft_bounds("p", 0, 2)(unchanged)p: lower_bound = 0.000000, upper_bound = 2.000000, sig = 1.000000, scaled = FalseRestraintviaregister_soft_boundseq_p: lower_bound = 0.000000, upper_bound = 2.000000, sig = 1.000000, scaled = FalseBVS of nacl: sig = 0.500000, scaled = TrueC0-C5: length = 3.300000, sigma = 0.100000, delta = 0.200000, scaled = FalseC0-C5-C7: angle = 1.000000, sigma = 0.100000, delta = 0.200000, scaled = FalseBefore:
After: the Restraints section lists
BVS of nacl: sig = 1.000000, scaled = False.Changes:
Restraintsetseqstrto the equation's name by default, so a restraint built by hand has something to show.add_soft_boundsstill overrides it as before.Restraint,BVSRestraintandObjCrystMoleculeRestrainteach get a__str__. The ObjCryst one also covers restraints wrapped from an existing molecule withwrapRestraints().Tests: I added
show()tests for each kind of restraint intest_recipeorganizer.py,test_diffpyparset.pyandtest_objcrystparset.py.What should the reviewer(s) do?
Please review and merge. One point you may want to check:
ObjCrystMoleculeRestraint.__str__decides between a bond length and an angle by checkinghasattr(res, "GetLength0"). It has to work this way because restraints wrapped from an existing molecule (wrapRestraints()) are plainObjCrystMoleculeRestraintobjects, not the bond-length or angle subclasses.