Fast-fix-palooza

[j-wags]

• Fix Update docs to clearly indicate shape any type of inputs for Quantities #421 - Indicate shape/type of Molecule.conformers and Molecule.partial_charges in all docstrings
• Fix Remove unused files #424 - Delete gbsaforces.py and test_smirnoff.py since they're not used at all and have confused a bunch of people by having spurious code.
• Fix Can't pickle ValidatedList #411 - @trevorgokey's easy patch to enable pickling of FF's, associated tests
• Fix Make OpenEye loading failure explicitly say "Warning" #410 - Make all toolkit warnings begin with Warning: to reduce user confusion
• Fix Produce a more informative error when someone asks RDKit to load mol2 #407 - Add extra text explaining why we don't let RDKit load mol2
• Remove ForceField._parameters, since that has probably been a mistake all along
• Update docstrings/documentation, if applicable
• Update changelog

Status

• Ready for review
• Ready for merge

[lgtm-com]

This pull request fixes 1 alert when merging 35e50b0 into bc89224 - view on LGTM.com

fixed alerts:

• 1 for 'import *' may pollute namespace

[lgtm-com]

This pull request introduces 1 alert and fixes 1 when merging 058b5d5 into bc89224 - view on LGTM.com

new alerts:

• 1 for Unused import

fixed alerts:

• 1 for 'import *' may pollute namespace

[codecov-io]

Codecov Report

Merging #425 into master will increase coverage by 1.53%.
The diff coverage is 53.06%.

@@            Coverage Diff             @@
##           master     #425      +/-   ##
==========================================
+ Coverage   49.35%   50.89%   +1.53%     
==========================================
  Files          35       33       -2     
  Lines        9583     9292     -291     
==========================================
- Hits         4730     4729       -1     
+ Misses       4853     4563     -290

Impacted Files	Coverage Δ
openforcefield/typing/engines/smirnoff/__init__.py	100% <ø> (ø)	⬆️
openforcefield/tests/test_forcefield.py	0% <0%> (ø)	⬆️
openforcefield/topology/molecule.py	86.22% <100%> (+0.04%)	⬆️
...enforcefield/typing/engines/smirnoff/forcefield.py	80.52% <100%> (-0.06%)	⬇️
openforcefield/utils/collections.py	96% <100%> (+0.16%)	⬆️
openforcefield/utils/toolkits.py	88.07% <100%> (+0.02%)	⬆️
...enforcefield/typing/engines/smirnoff/parameters.py	85.59% <100%> (+0.02%)	⬆️
openforcefield/utils/structure.py	51.14% <50%> (-0.09%)	⬇️

---

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[lgtm-com]

This pull request introduces 1 alert and fixes 1 when merging 7834f92 into bc89224 - view on LGTM.com

new alerts:

• 1 for Unused import

fixed alerts:

• 1 for 'import *' may pollute namespace

[lgtm-com]

This pull request introduces 1 alert and fixes 1 when merging 4eff2d2 into bc89224 - view on LGTM.com

new alerts:

• 1 for Unused import

fixed alerts:

• 1 for 'import *' may pollute namespace

[lgtm-com]

This pull request introduces 1 alert and fixes 1 when merging e094e40 into bc89224 - view on LGTM.com

new alerts:

• 1 for Unused import

fixed alerts:

• 1 for 'import *' may pollute namespace

[lgtm-com]

This pull request fixes 1 alert when merging 5551d05 into bc89224 - view on LGTM.com

fixed alerts:

• 1 for 'import *' may pollute namespace

[jchodera]

Looks good!

I am uncertain about using __reduce__ as an alternative to overriding __setstate__/__getstate__ and what that might mean for forward-compatibility of serialized versions.

If we're not 100% sure of our approach, perhaps we want to note that pickle/serialization support is still experimental and we cannot guarantee future versions of the toolkit will be able to read pickled/serialized objects from this version of the toolkit?

[j-wags]

If we're not 100% sure of our approach, perhaps we want to note that pickle/serialization support is still experimental and we cannot guarantee future versions of the toolkit will be able to read pickled/serialized objects from this version of the toolkit?

Agreed -- added

  Note that, while XML representations of ``ForceField``s are stable and conform to the SMIRNOFF
  specification, the pickled ``ForceField``s that this functionality enables are not guaranteed
  to be compatible with future toolkit versions.

to release notes

[lgtm-com]

This pull request fixes 1 alert when merging 7f4844d into bc89224 - view on LGTM.com

fixed alerts:

• 1 for 'import *' may pollute namespace