Migrate openforcefield to openff.toolkit

[SimonBoothroyd]

Description

This PR handles the migration over to the new openff-toolkit package name and the namespace migration such that the package will be importable as openff.toolkit rather than openforcefield.

The consensus is that this PR should be merged ready for the first release of this package on C-F, such that the C-F version will only ever contain openff-toolkit >=0.9.0, while the omnia channel will only contain the openforcefield <=0.8.2

Todos

• Tag issue being addressed
• Add tests
• Update docstrings/documentation, if applicable
• Lint codebase
• Update changelog
• Update the openforcefields CI dependencies. This hasn't been changed yet otherwise the CI will fail.

Notes

• This PR updates all links from openforcefield/openforcefield/ to openforcefield/openff-toolkit as the repo will also be renamed as part of the package rename. Until the repo is renamed however the link tests are expected to fail.
• The RTD links will not be updated / changed as there is currently not a clean way to rename a RTD site.
• The swap_existing_ligand_parameters_with_openmmforcefields.ipynb is expected to fail tests as it relies upon the openmmforcefields package which in turn depends upon openforcefield.

Status

• Ready to review
• Ready to merge

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging 1f72fde into a148678 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging 5e0f73b into a148678 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging 81cc2ac into a148678 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[codecov]

Codecov Report

Merging #803 (90fc5a4) into master (68a0881) will decrease coverage by 1.72%.
The diff coverage is 92.59%.

[j-wags]

I spot-checked several changes and didn't find anything objectionable. This looks good to me. Thanks, @SimonBoothroyd! I approve merging this when the process begins.

Is there an overall checklist (when to make specific tags, merge this branch, recommend opening new PRs against a specific branch, make public announcements over various channels, change CI deps in other packages, add deprecation warnings, etc) I can review? Or should we start work on that?

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging ed535e9 into 68a0881 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging 6269894 into 68a0881 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging cc890be into 68a0881 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging 0688faa into 68a0881 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[mattwthompson]

This second sentence could be dropped or changed if it doesn't end up being accurate

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging 5665ae2 into 68a0881 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop

[lgtm-com]

This pull request introduces 1 alert and fixes 4 when merging 90fc5a4 into 68a0881 - view on LGTM.com

new alerts:

• 1 for Module is imported more than once

fixed alerts:

• 2 for Non-callable called
• 1 for Module is imported more than once
• 1 for Non-iterable used in for loop