OpenFreeEnergy/alchemiscale

View on GitHub

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

Stars: 36
Forks: 11
Open beginner issues: 0
Indexed issues: 72
Avg merge: 8d 11h
Merged PRs (30d): 2

Dominant language: Python
License: No license data
Last GitHub push: Sep 8, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: good first issue

Beginner friendly Everything

Open All

72 open issues indexed

Create `RetainerService` for enforcing data retention policy Open

component-objectstore component-statestore storage

Difficulty 5/5 Over a week Newbie friendliness 42/100

OpenFreeEnergy/alchemiscale#515 · Opened Jul 14, 2026
Handle late `ProtocolDAGResult` uploads from compute services with lost registrations consistently Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

OpenFreeEnergy/alchemiscale#513 · Opened Jul 9, 2026
Hang when running replicates Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

OpenFreeEnergy/alchemiscale#501 · Opened Apr 16, 2026
Add granular `ProtocolDAG` progress reporting by compute services Open

introspection

Difficulty 5/5 Over a week Newbie friendliness 30/100

OpenFreeEnergy/alchemiscale#500 · Opened Apr 15, 2026
Switch `Neo4jStore` to use `AsyncGraphDatabase` Open

component-compute-api component-statestore component-user-api

Difficulty 4/5 3-5 days Newbie friendliness 48/100

OpenFreeEnergy/alchemiscale#492 · Opened Apr 2, 2026
Add `validate` kwarg to `AlchemiscaleClient.create_network`; use process pool if possible Open

component-user-client good first issue

Difficulty 4/5 3-5 days Newbie friendliness 48/100

OpenFreeEnergy/alchemiscale#490 · 4 comments · Opened Mar 17, 2026
Replace `nest_asyncio` if possible in `AlchemiscaleClient` Open

component-user-client good first issue

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#488 · 2 comments · Opened Mar 11, 2026
Update the demo notebook Open

OpenFreeEnergy/alchemiscale#475 · 2 reactions · 2 assignees · Opened Jan 6, 2026
Use `claim_limit` in `ComputeServiceSettings` in `ComputeManager` to determine how many services allowed to be created in call to `create_compute_services` Open

component-compute-manager

Difficulty 3/5 1-2 days Newbie friendliness 48/100

OpenFreeEnergy/alchemiscale#465 · Opened Nov 21, 2025
Make `data` used in `ComputeManager` a dataclass Open

component-compute-manager

Difficulty 3/5 1-2 days Newbie friendliness 48/100

OpenFreeEnergy/alchemiscale#464 · Opened Nov 21, 2025
Find and use alternative to `grolt` for test suite Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#448 · Opened Oct 27, 2025
Add an admin client/API for remote user management Open

OpenFreeEnergy/alchemiscale#447 · 1 assignee · Opened Oct 27, 2025
Add setting to user-facing API to make server read-only Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#446 · Opened Oct 22, 2025
Implement `AsynchronousComputeService` with reactive scheduling Open

OpenFreeEnergy/alchemiscale#432 · 1 assignee · Opened Sep 16, 2025
Add mechanism for introspecting progress of a `ProtocolDAG` as it is running Open

component-compute-api component-compute-client component-compute-service component-statestore introspection

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/alchemiscale#415 · Opened Jun 24, 2025
Add CLI endpoint for replacing identity key Open

bug component-cli component-statestore

Difficulty 3/5 1-2 days Newbie friendliness 42/100

OpenFreeEnergy/alchemiscale#406 · Opened Apr 29, 2025
Weight selection of `AlchemicalNetwork`s for `Task` claiming by `Transformation` count? Open

question

OpenFreeEnergy/alchemiscale#393 · 5 comments · 1 assignee · Opened Apr 1, 2025
Add `AlchemiscaleClient` method for getting percentage of compute consumed currently in given `Scope` relative to all other `Scope`s at same level Open

introspection

Difficulty 5/5 Over a week Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#389 · Opened Mar 18, 2025
Silence pickle warning for ExplicitMoleculeComponent? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#376 · 2 comments · Opened Mar 6, 2025
Add `ProtocolUnit` log preservation to compute services and object store, with reference in state store; expose via `AlchemiscaleClient` Open

component-compute-api component-compute-client component-compute-service component-objectstore component-statestore component-user-api component-user-client introspection

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/alchemiscale#349 · Opened Jan 8, 2025
Change all `AlchemiscaleClient` methods to use `retrieve_*` instead of `get_*` if they return `GufeTokenizable`s Open

component-user-api component-user-client

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#348 · Opened Jan 7, 2025
Expose ability to get stored tracebacks associated with a given `Task` Open

introspection

OpenFreeEnergy/alchemiscale#347 · 1 assignee · Opened Jan 3, 2025
Draft and submit JOSS publication for `alchemiscale` Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

OpenFreeEnergy/alchemiscale#345 · Opened Dec 10, 2024
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 Open

component-compute-api component-compute-client component-compute-service

OpenFreeEnergy/alchemiscale#301 · 1 comment · 1 assignee · Opened Sep 11, 2024
Retain stdout, stderr logs from `ProtocolDAGResult`s; expose access via `AlchemiscaleClient` Open

component-compute-api component-compute-client component-compute-service component-objectstore component-statestore component-user-api component-user-client introspection

OpenFreeEnergy/alchemiscale#295 · 1 comment · 1 assignee · Opened Aug 27, 2024
Add `AlchemiscaleClient` methods `set_tasks` and `set_transformations_tasks` Open

component-statestore component-user-api component-user-client

OpenFreeEnergy/alchemiscale#293 · 1 comment · 1 assignee · Opened Aug 23, 2024
Add `metadata` kwarg to `AlchemiscaleClient.create_network` Open

component-objectstore component-statestore component-user-api component-user-client

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/alchemiscale#290 · Opened Aug 16, 2024
Make `TaskHub`s only eligible for `Task` claims from compute services if they are associated with an `'active'` `AlchemicalNetwork` Open

component-compute-api component-compute-client component-statestore

Difficulty 3/5 1-2 days Newbie friendliness 45/100

OpenFreeEnergy/alchemiscale#261 · Opened Mar 27, 2024
Add configurable list of `Scope`s and permissions server-side for unauthenticated users Open

component-user-api component-user-client enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

OpenFreeEnergy/alchemiscale#247 · Opened Feb 23, 2024
Scope weighting for compute service Open

OpenFreeEnergy/alchemiscale#241 · 1 reaction · 1 assignee · Opened Feb 14, 2024
Add `AlchemiscaleClient.copy_network`, `.merge_networks`, and `.merge_scopes` methods Open

component-statestore component-user-api component-user-client

OpenFreeEnergy/alchemiscale#221 · 1 reaction · 1 assignee · Opened Jan 9, 2024
Add `Task` indicators, methods for getting these in `AlchemiscaleClient`, for introspection of `Task` history and running state Open

component-statestore component-user-api component-user-client enhancement introspection

Difficulty 5/5 Over a week Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#211 · Opened Dec 5, 2023
Expand testing section in developer docs Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

OpenFreeEnergy/alchemiscale#205 · Opened Dec 1, 2023
Set `Task` to `error` upon failure to `create` a `ProtocolDAG` from a `Transformation`; add `reason` field and populate it Open

component-compute-api component-compute-client component-compute-service component-statestore component-user-api component-user-client introspection

OpenFreeEnergy/alchemiscale#195 · 1 assignee · Opened Oct 25, 2023
`py2neo` `Transaction.merge` doesn't allow for multiple relationships of the same type between the same two nodes, even with differing attributes Open

bug component-statestore user-story

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/alchemiscale#187 · 2 comments · Opened Oct 6, 2023
Add note about AWS logging in deployment doc Open

documentation

OpenFreeEnergy/alchemiscale#184 · 1 reaction · 1 assignee · Opened Sep 27, 2023
Refactor `Task` system to retain `ProtocolDAG`, upload `ProtocolUnitResult`s and `ResultFile`s as they complete Open

component-compute-api component-compute-client component-compute-service component-objectstore component-statestore

OpenFreeEnergy/alchemiscale#180 · 2 comments · 1 assignee · Opened Sep 19, 2023
Add instructions for adding users, authorized scopes for a Kubernetes deployment in operations docs Open

documentation

OpenFreeEnergy/alchemiscale#179 · 1 assignee · Opened Sep 8, 2023
Server throws 500 error instead of 403 when credentials are invalid Open

component-compute-api component-user-api

Difficulty 3/5 1-2 days Newbie friendliness 42/100

OpenFreeEnergy/alchemiscale#171 · 1 comment · Opened Aug 24, 2023
Build initial migration machinery for `alchemiscale`; must capture data model changes in `gufe`, `openfe`, `perses` Open

OpenFreeEnergy/alchemiscale#168 · 1 assignee · Opened Aug 22, 2023
Add client-server version comparison check for major libraries Open

component-user-api component-user-client good first issue

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#159 · 1 comment · Opened Aug 3, 2023
Add enforced `max_batch_size` configurable for API services Open

component-user-api

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#151 · Opened Jun 27, 2023
Add `limit` and `skip` to all `AlchemiscaleClient.query_*` methods Open

component-statestore component-user-api component-user-client good first issue

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#149 · Opened Jun 20, 2023
Enforce `ScopedKey`s of specific types in `Neo4jStore`, API endpoints as appropriate Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

OpenFreeEnergy/alchemiscale#145 · Opened Jun 15, 2023
py2neo now EOL Open

OpenFreeEnergy/alchemiscale#144 · 2 comments · 1 assignee · Opened Jun 13, 2023
[ENH] Seeing the total available resources being consumed by alchemiscale Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/alchemiscale#137 · Opened May 1, 2023
Create API-enforced, configurable upper bounds on number of 'waiting' `Task`s on a `Transformation`, number of `Task`s ACTIONed on a `TaskHub` Open

good first issue

OpenFreeEnergy/alchemiscale#134 · 1 assignee · Opened Apr 27, 2023
Make `max_time` in `SynchronousComputeService.start` check occur in separate thread Open

component-compute-service

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#124 · 1 comment · Opened Apr 17, 2023
`SynchronousComputeService` dies if `transformation.create` throws exception Open

component-compute-service

Difficulty 5/5 Over a week Newbie friendliness 25/100

OpenFreeEnergy/alchemiscale#122 · Opened Apr 16, 2023
Add `PeriodicsService` for performing periodic database operations, such as expiring stale `ComputeServiceRegistration`s Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

OpenFreeEnergy/alchemiscale#109 · Opened Mar 31, 2023

OpenFreeEnergy/alchemiscale

Get new issues in your inbox