Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / OpenFreeEnergy/openfe issues and pull requests

#425 - Update links to docs

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#424 - Update equil_rfe_settings.py

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#423 - Fix links in docs

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#422 - Question: OPENFE

Issue - State: closed - Opened by satvikkg over 1 year ago - 1 comment

#420 - Minor docs CSS style improvements

Issue - State: open - Opened by dwhswenson over 1 year ago - 1 comment

#419 - adding style to the docs

Pull Request - State: closed - Opened by RiesBen over 1 year ago - 1 comment

#418 - solvent_padding not showing up in solvent docs

Issue - State: closed - Opened by IAlibay over 1 year ago

#417 - Add comment to docs that first import is slow

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#416 - Fix problem with ligand loading order in test_plan_*_network

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments

#415 - tests qol: add some warnings filters

Issue - State: open - Opened by richardjgowers over 1 year ago - 1 comment

#414 - Regroup CLI Sections

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 2 comments

#412 - Speed up first output from plan-*-network

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#411 - Progress bar for maximal network

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 2 comments

#410 - receptor => complex

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#409 - Rbfe fetch assets

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#408 - change try to be static website

Issue - State: open - Opened by richardjgowers over 1 year ago

#407 - add missing settings docs

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#406 - Forcefield settings now showing up in settings docs

Issue - State: closed - Opened by IAlibay over 1 year ago

#405 - Pull execute dag

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#404 - Add tutorial fetchables

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#403 - Proposal: Reorganize CLI sections

Issue - State: closed - Opened by dwhswenson over 1 year ago

#402 - Remove mapper from plan-*-network command

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#401 - Make docs reasonable to be user facing

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 3 comments

#400 - Pull execute_DAG into `openfe`

Issue - State: closed - Opened by IAlibay over 1 year ago - 1 comment

#399 - Add ligand network output to CLI network planners

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 2 comments

#398 - Silence `openmmtools.multistate` API warnings

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#397 - Fix nesting of shared directory for checkpoint

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments

#396 - Improving our landing page

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 4 comments

#395 - Fix handling of `ThreeParticleAverageSite` virtual sites

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 4 comments

#394 - Copying OpenMM VirtualSite particles from old/new system to hybrid fails

Issue - State: open - Opened by IAlibay over 1 year ago - 2 comments

#393 - Update gather.py - output file refactor

Pull Request - State: closed - Opened by RiesBen over 1 year ago - 1 comment

#392 - Move load_molecules from CLI to core openfe

Pull Request - State: open - Opened by dwhswenson over 1 year ago

#391 - Don't trigger docker build on non-main branch pushes

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 1 comment

#390 - network planners create protocols

Issue - State: closed - Opened by richardjgowers over 1 year ago

#389 - Install docs: Use Mambaforge

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments

#388 - Enable online-analysis by default

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 4 comments

#387 - [RFE protocol] Allow multiple small molecules + allow running with non-OpenFF force fields

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 2 comments

#386 - [ENH] Network from name pairs

Issue - State: closed - Opened by IAlibay over 1 year ago

#385 - autodoc pydantic for openmm_rfe settings

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 4 comments

#384 - CLI: ligand network viewer

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#383 - CLI: mol_dir => molecules

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#382 - CLI: Network Planners: Flatten output directories

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#381 - Update gather.py - protocol failure robustness

Pull Request - State: closed - Opened by RiesBen over 1 year ago - 3 comments

#380 - CLI `fetch` command

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 4 comments

#379 - Make moist tests run on slow only

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 1 comment

#378 - Moist test

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 3 comments

#377 - update offmodels and offtk pins

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 3 comments

#376 - Switching to micromamba for install and add cluster docs

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 10 comments

#375 - Automate Release Version Bumping in Docs

Issue - State: open - Opened by mikemhenry over 1 year ago - 1 comment

#374 - CLI: Remove openfe import required for help

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#373 - `test` CLI command

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments

#372 - [ENH] Have RHTP do the online analysis by default.

Issue - State: closed - Opened by IAlibay over 1 year ago - 1 comment

#371 - update package versions

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 4 comments

#370 - Clean up install docs

Issue - State: closed - Opened by dwhswenson over 1 year ago - 1 comment

#369 - Issue 368 init docs

Pull Request - State: closed - Opened by richardjgowers over 1 year ago

#368 - Some API docs missing init sections

Issue - State: closed - Opened by richardjgowers over 1 year ago
Labels: documentation

#367 - Update hash for hmass change upstream

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 1 comment

#366 - Add timemachine mapper

Issue - State: open - Opened by IAlibay over 1 year ago

#365 - [WIP] Fix docker build issues

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 3 comments

#364 - lomap mapper updates for 2.3.0

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#362 - image building is failing

Issue - State: closed - Opened by IAlibay over 1 year ago - 4 comments

#361 - Fix analyzer cleaning up scope issues

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 1 comment

#359 - Remove test skipping

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 6 comments

#358 - Fix test incompatibility

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 2 comments

#357 - Warning error during equilibration!!

Issue - State: closed - Opened by mayank-kohli over 1 year ago - 12 comments

#356 - openmm_rfe: make repeat_ids non 0 assuming

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 2 comments

#355 - Fixes ProtocolResult aggregation for get_estimate, get_uncertainty

Pull Request - State: closed - Opened by dotsdl over 1 year ago - 2 comments

#354 - Cleanup contexts upon calculation completion, failure

Pull Request - State: closed - Opened by dotsdl over 1 year ago - 32 comments

#353 - Push Apptainer Image to GHCR + Build Installer & Docker Image using Conda-Forge Package

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 2 comments

#352 - only build installer on demand

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#351 - Use pip instead of conda for sphinx-toolbox

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 2 comments

#350 - Capitalize all instances of `protocol`?

Issue - State: open - Opened by IAlibay over 1 year ago - 2 comments

#349 - Settle down on recommendation for repeats

Issue - State: open - Opened by IAlibay over 1 year ago - 1 comment

#348 - mapping option in Lomap

Issue - State: open - Opened by xy127 over 1 year ago - 3 comments

#347 - Add Docs for Containers and Single File Installer

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 2 comments

#346 - [OpenMM RFE] clarify `scratch_basepath`

Issue - State: open - Opened by IAlibay over 1 year ago

#345 - Issue 292 rfe context usage

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 2 comments

#343 - Add debug logging conf file

Issue - State: open - Opened by dwhswenson over 1 year ago

#342 - Weird failures when running tests in docker image

Issue - State: closed - Opened by mikemhenry over 1 year ago - 6 comments

#341 - DOCS: Cleanup guide intro

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 4 comments

#340 - DOCS: Core models and CLI usage

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 6 comments

#339 - fix issue where we would get a key error if `OFE_SLOW_TESTS` was unset

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 2 comments

#338 - py3dmol optional import not quite working

Issue - State: open - Opened by richardjgowers over 1 year ago

#335 - use FloatQuantity from openff models

Issue - State: open - Opened by richardjgowers over 1 year ago - 2 comments
Labels: openmm_rbfe

#332 - Swap LangevinSplittingDynamicMove to LangevinDynamicsMove

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 2 comments

#325 - Start adding API docs

Pull Request - State: closed - Opened by dwhswenson over 1 year ago - 2 comments

#321 - Add image building

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 7 comments
Labels: enhancement, priority:high, deployment

#320 - [WIP] conda release cron job

Pull Request - State: open - Opened by IAlibay over 1 year ago - 2 comments

#319 - Don't exclude py3.10 macos runners

Pull Request - State: closed - Opened by IAlibay over 1 year ago - 3 comments

#318 - cookbook docs

Pull Request - State: closed - Opened by richardjgowers over 1 year ago - 1 comment

#315 - inconsistent on 3D vs 3d

Issue - State: open - Opened by richardjgowers over 1 year ago

#312 - [docs] add docs badge

Issue - State: open - Opened by IAlibay over 1 year ago - 2 comments

#308 - Fix single file installer

Pull Request - State: closed - Opened by mikemhenry over 1 year ago - 1 comment

#305 - [release] Do an RC release of 0.7

Issue - State: closed - Opened by IAlibay over 1 year ago

#302 - [docs] Dealing with Protocols docs

Issue - State: open - Opened by IAlibay over 1 year ago - 3 comments
Labels: documentation, userguide