OpenFreeEnergy / alchemiscale

a high-throughput alchemical free energy execution system for use with HPC, cloud, bare metal, and Folding@Home

http://alchemiscale.org

OpenFreeEnergy/alchemiscale Issues

Update deployment docs to point to new Docker image registry location
Updated a month ago
Replace "passlib" with direct calls to bcrypt
Updated a month ago1
Create `alchemiscale.org` Hugo site as project hub
Closed a month ago1
Add user-settable server-side `Task` restart policy, per-`AlchemicalNetwork`
Updated a month ago4
Add use of zstd compression on compute services for pushing to API service, storing at-rest, and fast decompression on retreival via clients
Updated a month ago2
Query 'active' networks without having to check every network in org
Closed a month ago6
Update `alchemiscale` tutorial for `openfe` and `gufe` 1.0 use, current `cinnabar`
Updated a month ago1
Add periodic checks by compute services that their claimed `Task`s are actioned by at least one active `AlchemicalNetwork`; halt execution and drop claim for those `Task`s that are not
Updated a month ago1
Passing in malformed inputs as "ScopedKeys" gives raw 500 error
Updated a month ago
Improve performance of `Neo4jStore.cancel_tasks` by using UNWIND
Closed a month ago
Update `alchemiscale` test suite to use `neo4j` 5.23
Updated a month ago
Deprecation warnings from `neo4j`: "The query used a deprecated function: `id`"
Updated a month ago
Retain stdout, stderr logs from `ProtocolDAGResult`s; expose access via `AlchemiscaleClient`
Updated 2 months ago1
Make `AlchemiscaleClient.get_transformation_chemicalsystems` return a `tuple`, ordered by `(<state>)`
Updated 2 months ago
Add `AlchemiscaleClient` methods `set_tasks` and `set_transformations_tasks`
Updated 2 months ago1
Add `metadata` kwarg to `AlchemiscaleClient.create_network`
Updated 2 months ago
Drop `perses` from all deployment environments; switch to `feflow`
Closed 2 months ago1
`alchemiscale-client` conda package for v0.4.0 reports `0.0.0` in `alchemiscale.__version__`
Updated 3 months ago2
Initial design proposal for `Strategy`s
Updated 3 months ago
Remove `scopes` validation from `alchemiscale compute synchronous` CLI endpoint; enforce as validator in `ComputeServiceSettings`
Updated 3 months ago
`Neo4jStore.query_networks` doesn't yield `AlchemicalNetwork`s with `name = None`
Closed 4 months ago
Add `AlchemiscaleClient` method for producing archival-quality extracts of `AlchemicalNetwork`s and their existing results
Updated 5 months ago1
Add server-side memory of `ComputeServiceRegistrations` that consistently fail jobs?
Updated 6 months ago
`AlchemicalNetwork` retrieval is slow for large networks
Updated 6 months ago
Cinnabar analysis is outdated in the tutorial demo
Updated 6 months ago1
Add `AlchemiscaleClient.copy_network`, `.merge_networks`, and `.merge_scopes` methods
Updated 6 months ago
Decrease Docker image size
Updated 6 months ago
Add concept of user-settable network `state`
Closed 6 months ago1
Add `get_networks_weight` and `set_networks_weight` methods as bulk methods to `AlchemiscaleClient`
Closed 7 months ago
Add `get_networks_status` and `get_networks_actioned_tasks` as bulk methods to `AlchemiscaleClient`
Closed 7 months ago
Make `TaskHub`s only eligible for `Task` claims from compute services if they are associated with an `'active'` `AlchemicalNetwork`
Updated 7 months ago
Use query parameters wherever possible in `Neo4jStore` instead of f-string substitutions
Updated 7 months ago
Deprecate `AlchemiscaleClient.get_scoped_key`
Closed 7 months ago
Expand testing section in developer docs
Updated 8 months ago
allow setting of `task_status` to "error"
Closed 8 months ago6
Add configurable list of `Scope`s and permissions server-side for unauthenticated users
Updated 8 months ago
Need to enforce ligand names, or auto-assign
Closed 8 months ago4
Scope weighting for compute service
Updated 8 months ago
Add discussion of task actioning weight to user guide
Closed 8 months ago1
Strategy: task prioritization of 'core' of network
Updated 8 months ago1
Add section to user guide on how to mark tasks as `invalid`, `deleted`
Closed 9 months ago1
Not possible to select different docs version from bottom left flyout menu on ReadTheDocs
Updated 9 months ago1
Add `scopes-exclude` config option for compute services
Updated 9 months ago
Add `weight` argument to `AlchemiscaleClient.action_tasks`
Closed 10 months ago
Implement methods to get and set `Task` priorities to `AlchemiscaleClient`
Closed 10 months ago
Expose setting `TaskHub` weight to `AlchemiscaleClient`
Closed 10 months ago
`AlchemiscaleClient.create_network` scales poorly with increasing `AlchemicalNetwork` size
Closed 9 months ago
Default ACTION weight difference between user interface and statestore levels
Closed 10 months ago1
Add `Task` indicators, methods for getting these in `AlchemiscaleClient`, for introspection of `Task` history and running state
Updated 10 months ago
Make `ScopedKey`s sortable
Closed 10 months ago1