Fix mass and charge in GSD writer; Add angles and dihedrals to GSD writer

[chrisjonesBSU]

This helps address #678 where the gsd writer was trying to perform math operations with NoneType objects.

Still need to add a unit test

Edit: Some other errors popped up, and I ended up totally revamping the gsd writer. It is writing out angles and dihedrals now.

Edit: I edited the title again to better reflect the changes by the PR. After talking with Cal in #678 there aren't any changes to default mass and charge values.

[chrisjonesBSU]

This also contains another fix where the gsd writer was trying to call on t.atom_type and t.name when t1 and t2 were already the types or names.

[lgtm-com]

This pull request introduces 1 alert when merging a537c3e into 2970412 - view on LGTM.com

new alerts:

• 1 for Unused import

[chrisjonesBSU]

So, it looks like f-string formatting doesn't work when using it with warnings.warn?

[daico007]

hmm, that should not be the case, I used f-string with warnings.warn in multiple occasions before. What's the error message are you getting?

[lgtm-com]

This pull request introduces 3 alerts when merging 918425b into c336588 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[chrisjonesBSU]

I'm not getting an error, but when running in a notebook, the variable name with brackets is in the warning statement rather than it actually performing the string formatting and printing the variable's value.

I think I am missing a couple f".." in the warning statements..oops

[codecov]

Codecov Report

Merging #680 (847e4b0) into develop (0a11627) will increase coverage by 0.24%.
The diff coverage is 98.66%.

@@             Coverage Diff             @@
##           develop     #680      +/-   ##
===========================================
+ Coverage    91.22%   91.47%   +0.24%     
===========================================
  Files           63       63              
  Lines         5172     5217      +45     
===========================================
+ Hits          4718     4772      +54     
+ Misses         454      445       -9     

Impacted Files	Coverage Δ
gmso/formats/gsd.py	98.62% <98.66%> (+3.62%)	⬆️
gmso/utils/geometry.py	88.88% <0.00%> (+11.11%)	⬆️
gmso/utils/sorting.py	100.00% <0.00%> (+100.00%)	⬆️

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

[lgtm-com]

This pull request introduces 3 alerts when merging 0d3f4f1 into c336588 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[lgtm-com]

This pull request introduces 3 alerts when merging 9d1d195 into c336588 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[chrisjonesBSU]

Before we merge this, let me test it out with some more compounds from mBuild and make sure the information the gsd file is correct and makes sense.

[lgtm-com]

This pull request introduces 3 alerts when merging 4d0d34a into c336588 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[lgtm-com]

This pull request introduces 3 alerts when merging 2fbc265 into c336588 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[lgtm-com]

This pull request introduces 3 alerts when merging 36f30a4 into c336588 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[chrisjonesBSU]

The workflow in the latest unit test I added also solves mosdef-hub/mbuild#1025

[lgtm-com]

This pull request introduces 3 alerts when merging 3ac2565 into cc23eb8 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[lgtm-com]

This pull request introduces 3 alerts when merging 2ec890a into 0a11627 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import

[daico007]

Slight update to docstring, the rest LGTM!

[CalCraven]

LGTM! Would like some testing for more ways to write out GSD files and testing them, but until we have a more extensive set of things we want to be sure to support, I think we're good.

[lgtm-com]

This pull request introduces 3 alerts when merging 847e4b0 into 0a11627 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 1 for Unused import