Cleanup and releasenotes prep for 0.10.1 (#1112)

* cleanup and releasenotes prep for 0.10.1

* Apply suggestions from code review

Co-authored-by: Matt Thompson <mattwthompson@protonmail.com>

* make CI run without mypy/typing-extensions

* drop deps that are pulling in pydantic --> typing-extensions

* revert changes to pre-release testing

Co-authored-by: Matt Thompson <mattwthompson@protonmail.com>

docs/releasehistory.md

@@ -6,10 +6,18 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 * `minor` increments add features but do not break API compatibility
 * `micro` increments represent bugfix releases or improvements in documentation
 
-## Current development
+## 0.10.1 Minor feature and bugfix release
 
-### New features
+### Behaviors changed and bugfixes
 
+- [PR #1096](https://github.com/openforcefield/openforcefield/pull/1096): Atom names generated by
+  [`Molecule.generate_unique_atom_names`](openff.toolkit.topology.Molecule.generate_unique_atom_names)
+  are now appended with an `"x"`. See the linked issue for more details.
+- [PR #1050](https://github.com/openforcefield/openforcefield/pull/1050): In
+  [`Molecule.generate_conformers`](openff.toolkit.topology.Molecule.generate_conformers), a single
+  toolkit wrapper failing to generate conformers is no longer fatal, but if all wrappers in a registry
+  fail, then a `ValueError` will be raised. This mirrors the behavior of
+  [`Molecule.assign_partial_charges`](openff.toolkit.topology.Molecule.assign_partial_charges).
 - [PR #1050](https://github.com/openforcefield/openforcefield/pull/1050): Conformer generation
   failures in
   [`OpenEyeToolkitWrapper.generate_conformers`](openff.toolkit.utils.toolkits.OpenEyeToolkitWrapper.generate_conformers), and
@@ -20,47 +28,9 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
   [`Molecule.generate_conformers`](openff.toolkit.topology.Molecule.generate_conformers), but only
   when the ``toolkit_registry`` argument is a
   [`ToolkitWrapper`](openff.toolkit.utils.toolkits.ToolkitWrapper), not when it is a
-  [`ToolkitRegistry`](openff.toolkit.utils.toolkits.ToolkitRegistry). See also an entry in the "Behavior changed" section.
-- [PR #1036](https://github.com/openforcefield/openforcefield/pull/1036): SMARTS matching
-  logic for library charges was updated to use only one unique match instead of
-  enumerating all possible matches. This results in faster matching, particularly
-  with larger moldules.
-- [PR #1001](https://github.com/openforcefield/openff-toolkit/pull/1001): Revamped the 
-  [`Molecule.visualize()`](openff.toolkit.topology.Molecule.visualize) method's `rdkit` 
-  backend for more pleasing and idiomatic 2D visualization by default.
-
-
-### Bugfixes
-- [PR #1087](https://github.com/openforcefield/openff-toolkit/pull/1087>): Fixes
-  [Issue #1073](<https://github.com/openforcefield/openff-toolkit/issues/1073>) in which
-  [`Molecule.__repr__`](openff.toolkit.topology.Molecule.__repr__) can fail if the molecule
-  fails by reporting a Hill formula instaed.
-- [PR #1052](https://github.com/openforcefield/openff-toolkit/pull/1052>): Fixes
-  [Issue #986](<https://github.com/openforcefield/openff-toolkit/issues/986>)
-  by raising a subclass of `AttributeError` in
-  `_ParameterAttributeHandler.__getattr__`
-- [PR #1030](https://github.com/openforcefield/openforcefield/pull/1030): Fixes a bug
-  in which capitalization of the `bond_order_model` sometimes matters.
-- [PR #1101](https://github.com/openforcefield/openff-toolkit/pull/1101/files): Fixes a bug
-  in which calling `to_qcschema` on a molecule with no connectivity feeds
-  `QCElemental.Molecule` an empty list for the `connectivity` field; now feeds `None`
-
-### Behavior changed
-
-- [PR #1096](https://github.com/openforcefield/openforcefield/pull/1096): Atom names generated by
-  [`Molecule.generate_unique_atom_names`](openff.toolkit.topology.Molecule.generate_unique_atom_names)
-  are now appended with an `"x"`.
-- [PR #1050](https://github.com/openforcefield/openforcefield/pull/1050): In
-  [`Molecule.generate_conformers`](openff.toolkit.topology.Molecule.generate_conformers), a single
-  toolkit wrapper failing to generate conformers is no longer fatal, but if all wrappers in a registry
-  fail, then a `ValueError` will be raised. This mirrors the behavior of
-  [`Molecule.assign_partial_charges`](openff.toolkit.topology.Molecule.assign_partial_charges).
+  [`ToolkitRegistry`](openff.toolkit.utils.toolkits.ToolkitRegistry). 
 - [PR #1046](https://github.com/openforcefield/openforcefield/pull/1046): Changes OFFXML output to
   replace tabs with 4 spaces to standardize representation in different text viewers. 
-- [PR #1036](https://github.com/openforcefield/openforcefield/pull/1036): SMARTS matching
-  logic for library charges was updated to use only one unique match. No adverse side effects
-  were found in testing, but could bad behavior may possibly exist in some unknown caes.
-  Note that the default behavior for other parameter handlers was not updated.
 - [PR #1001](https://github.com/openforcefield/openff-toolkit/pull/1001): RDKit `Mol` objects 
   created through the [`Molecule.to_rdkit()`](openff.toolkit.topology.Molecule.to_rdkit)
   method have the `NoImplicit` property set to `True` on all atoms. This prevents RDKit from
@@ -71,6 +41,29 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
   [`Topology.from_parmed`](openff.toolkit.topology.Topology.from_parmed).
 - [PR #1065](https://github.com/openforcefield/openforcefield/pull/1065): The example `conformer_energies.py` script
   now uses the Sage 2.0.0 force field.
+- [PR #1036](https://github.com/openforcefield/openforcefield/pull/1036): SMARTS matching
+  logic for library charges was updated to use only one unique match instead of
+  enumerating all possible matches. This results in faster matching, particularly
+  with larger molecules. No adverse side effects
+  were found in testing, but bad behavior may possibly exist in some unknown cases.
+  Note that the default behavior for other parameter handlers was not updated.
+- [PR #1001](https://github.com/openforcefield/openff-toolkit/pull/1001): Revamped the 
+  [`Molecule.visualize()`](openff.toolkit.topology.Molecule.visualize) method's `rdkit` 
+  backend for more pleasing and idiomatic 2D visualization by default.
+- [PR #1087](https://github.com/openforcefield/openff-toolkit/pull/1087): Fixes
+  [Issue #1073](https://github.com/openforcefield/openff-toolkit/issues/1073) in which
+  [`Molecule.__repr__`](openff.toolkit.topology.Molecule.__repr__) fails if the molecule can not be represented as 
+  a SMILES pattern. Now, if SMILES generation fails, the molecule will be described by its Hill formula.
+- [PR #1052](https://github.com/openforcefield/openff-toolkit/pull/1052): Fixes
+  [Issue #986](https://github.com/openforcefield/openff-toolkit/issues/986)
+  by raising a subclass of `AttributeError` in
+  `_ParameterAttributeHandler.__getattr__`
+- [PR #1030](https://github.com/openforcefield/openforcefield/pull/1030): Fixes a bug
+  in which the expectations for capitalization for values of `bond_order_model` attributes and 
+  keywords are inconsistent.
+- [PR #1101](https://github.com/openforcefield/openff-toolkit/pull/1101): Fixes a bug
+  in which calling `to_qcschema` on a molecule with no connectivity feeds
+  `QCElemental.Molecule` an empty list for the `connectivity` field; now feeds `None`.
 
 ### Tests updated
 

openff/toolkit/topology/molecule.py

@@ -2362,7 +2362,10 @@ def has_unique_atom_names(self):
     def generate_unique_atom_names(self):
         """
         Generate unique atom names using element name and number of times that element has occurred
-        e.g. 'C1', 'H1', 'O1', 'C2', ...
+        e.g. 'C1x', 'H1x', 'O1x', 'C2x', ...
+
+        The character 'x' is appended to these generated names to reduce the odds that they clash with an atom name or
+        type imported from another source.
 
         """
         from collections import defaultdict