Alchemiscale

New Contributors
* mattwthompson made their first contribution in https://github.com/openforcefield/alchemiscale/pull/253

**Full Changelog**: https://github.com/openforcefield/alchemiscale/compare/v0.3.0...v0.4.0

This release focused on improving users' ability to influence compute effort allocation on their `Task`s, as well as enabling support for large `AlchemicalNetwork`s. This includes:
- the ability to set and get `Task` `priority`, set and get `AlchemicalNetwork` `weight` relative to others, and set and get actioned `Task` `weight`s. These give users several levers of control for getting results of greater interest more quickly. Big thanks to ianmkenney for working on these pieces in detail.
- vast improvement to `AlchemicalNetwork` submission and `AlchemicalNetwork`, `Transformation`, and `ChemicalSystem` retrieval through smarter serialization via use of keyed `dict`s, thanks to work by ianmkenney and dotsdl to solve alchemiscale216:
- users should see very fast submission times compared to previously, even on relatively slow internet connections
- "large" networks (>1000 chemical systems) should be ingestible without issue

What's Changed
* Set minimum for openmmforcefields version in conda envs to 0.12.0 by dotsdl in https://github.com/openforcefield/alchemiscale/pull/193
* Fixing broken CI due to lomap import failures by dotsdl in https://github.com/openforcefield/alchemiscale/pull/196
* Update prod envs to use gufe 0.9.5, openfe 0.14.0 by dotsdl in https://github.com/openforcefield/alchemiscale/pull/197
* Make test env use latest release of openfe and gufe instead of `main` by dotsdl in https://github.com/openforcefield/alchemiscale/pull/203
* Add the `visualize` kwarg to the `create_network` method by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/207
* Add ability to sort `ScopedKey`s by dotsdl in https://github.com/openforcefield/alchemiscale/pull/199
* Remove `return_gufe` kwarg from `AlchemiscaleClient.query_networks` by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/206
* Add client/API getter and setter methods for network weights by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/212
* Add `weight` kwarg to `AlchemiscaleClient.action_tasks` method by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/209
* Add getters and setters for Task priority in AlchemiscaleClient by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/213
* Add `get_network_actioned_tasks` and `get_task_actioned_networks` to `AlchemicaleClient` by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/214
* Network representation optimizations for JSON encoding by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/217
* Optimization to `gufe_to_digraph` to avoid repeated traversals, calls to `GufeTokenizable.to_shallow_dict` by dotsdl in https://github.com/openforcefield/alchemiscale/pull/219
* Added docs on getting and setting AlchemicalNetwork weights, Task actioned weights, and Task priorities by dotsdl in https://github.com/openforcefield/alchemiscale/pull/223
* Attempting to fix seemingly random failures on CI by dotsdl in https://github.com/openforcefield/alchemiscale/pull/224
* Adding KeyedChain class by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/227
* QA tests for impending 0.3.0 release by dotsdl in https://github.com/openforcefield/alchemiscale/pull/226


**Full Changelog**: https://github.com/openforcefield/alchemiscale/compare/v0.2.1...v0.3.0

This is a bugfix release for the v0.2.x release series.

What's Changed
* Added `n_retries` usage for `SynchronousComputeService` by dotsdl in https://github.com/openforcefield/alchemiscale/pull/186
* Added validation guardrail for AlchemicalNetworks with self-Transformations by dotsdl in https://github.com/openforcefield/alchemiscale/pull/189
* Updates for release 0.2.1 by dotsdl in https://github.com/openforcefield/alchemiscale/pull/190


**Full Changelog**: https://github.com/openforcefield/alchemiscale/compare/v0.2.0...v0.2.1

This release focused on adding documentation for `alchemiscale`, including a [user guide](https://docs.alchemiscale.org/en/latest/user_guide.html), a [first tutorial](https://docs.alchemiscale.org/en/latest/tutorials/demo/Alchemiscale%20Demo.html), [deployment](https://docs.alchemiscale.org/en/latest/deployment.html), [compute](https://docs.alchemiscale.org/en/latest/compute.html), and [operations](https://docs.alchemiscale.org/en/latest/operations.html) guides, a [developer guide](https://docs.alchemiscale.org/en/latest/development.html), and an [API reference](https://docs.alchemiscale.org/en/latest/api.html). It also added efficient methods for getting network-wide results to the `AlchemiscaleClient` in #178, and some smaller fixes to the `alchemiscale` CLI.

What's Changed
* Fixed version mismatch of alchemiscale in conda environments by ianmkenney in https://github.com/openforcefield/alchemiscale/pull/165
* Add user guide to docs, restructure some other documentation pages by dotsdl in https://github.com/openforcefield/alchemiscale/pull/166
* Added compute doc, adding other operations docs (e.g. backups) by dotsdl in https://github.com/openforcefield/alchemiscale/pull/167
* Support adding and removing multiple scopes from identity with single CLI call by dotsdl in https://github.com/openforcefield/alchemiscale/pull/172
* Add developer-facing docs by dotsdl in https://github.com/openforcefield/alchemiscale/pull/175
* Review and refinement of API docs by dotsdl in https://github.com/openforcefield/alchemiscale/pull/177
* Added `get_network_results` method to `AlchemiscaleClient` by dotsdl in https://github.com/openforcefield/alchemiscale/pull/178
* Add Alchemiscale Demo as first tutorial by dotsdl in https://github.com/openforcefield/alchemiscale/pull/174
* Updated prod-oriented conda envs to use latest openfe, gufe, and python 3.11 by dotsdl in https://github.com/openforcefield/alchemiscale/pull/181

New Contributors
* ianmkenney made their first contribution in https://github.com/openforcefield/alchemiscale/pull/165

**Full Changelog**: https://github.com/openforcefield/alchemiscale/compare/v0.1.4...v0.2.0

This release focused on bugfixes for user-facing issues, in particular opportunities for mismatches between `Transformation` and `ProtocolDAGResult` `gufe` keys in the objectstore and statestore (161). It also added initial documentation structure (157), and guardrails on the allowed `Task` statuses for actioning (162).

What's Changed
* Update prod envs to use openfe 0.11.0 by dotsdl in https://github.com/openforcefield/alchemiscale/pull/158
* Add deplyoment docs v2 by mikemhenry in https://github.com/openforcefield/alchemiscale/pull/157
* Make `ProtocolDAGResult` push and pull keys self-consistent by dotsdl in https://github.com/openforcefield/alchemiscale/pull/161
* Set pydantic version less than 2.0 for all conda envs by dotsdl in https://github.com/openforcefield/alchemiscale/pull/160
* Only action `Task`s that are `status` 'waiting', 'error', or 'running' by dotsdl in https://github.com/openforcefield/alchemiscale/pull/162


**Full Changelog**: https://github.com/openforcefield/alchemiscale/compare/v0.1.3...v0.1.4

This release focused on bugfixes and user-facing features and performance improvements in the `AlchemiscaleClient`. In particular, it added:
- visual feedback for method calls that push or retrieve large data structures
- `asyncio`-based result retrieval
- LRU caching where appropriate to methods that retrieve large data structures, allowing for fast repeated calls for the same objects
- bulk API points for methods that get or set properties of many individual objects, allowing efficient batching and fast execution
- `Task` status methods at the `scope` and `network` levels
- fast accessor methods for related components, such as `get_transformation_tasks`, `get_chemicalsystem_networks`, `get_network_transformations`, etc.

Mismatches in the `gufe` key of an object between the client and the server should also no longer lock users out of their data, using the accessor methods mentioned above.

What's Changed
* Update deployment envs with openfe=0.7.4, gufe=0.7.3 by dotsdl in https://github.com/openforcefield/alchemiscale/pull/135
* Use pyproject.toml by mikemhenry in https://github.com/openforcefield/alchemiscale/pull/141
* Add AlchemiscaleClient API points for simpler status, result retrieval by dotsdl in https://github.com/openforcefield/alchemiscale/pull/143
* AlchemiscalClient async+bulk for results, other methods; add request, response compression for large objects by dotsdl in https://github.com/openforcefield/alchemiscale/pull/150
* `AlchemiscaleClient` LRU caching by dotsdl in https://github.com/openforcefield/alchemiscale/pull/155
* Updated dependencies in conda envs, both testing and deployment by dotsdl in https://github.com/openforcefield/alchemiscale/pull/152


**Full Changelog**: https://github.com/openforcefield/alchemiscale/compare/v0.1.2...v0.1.3