Ecosyste.ms: Issues

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

GitHub / biosustain/Maud issues and pull requests

#473 - Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows

Pull Request - State: open - Opened by dependabot[bot] 2 months ago
Labels: dependencies

#472 - Allostery free enzyme ratio bug

Pull Request - State: closed - Opened by teddygroves 3 months ago - 1 comment

#471 - Test case with N_edge > N_enzyme

Issue - State: open - Opened by teddygroves 4 months ago

#470 - Fix indexing on `get_allostery`

Pull Request - State: closed - Opened by carrascomj 4 months ago - 1 comment

#469 - Predict will fail for particular combinations of cmdstan + cmdstanpy

Issue - State: open - Opened by carrascomj 5 months ago - 1 comment

#468 - non-equimolar conserved moieties no implemented

Issue - State: open - Opened by NicholasCowie 5 months ago

#467 - Safety error in tox for jinja

Issue - State: open - Opened by NicholasCowie 5 months ago
Labels: bug

#466 - Separate docs and development dependencies

Issue - State: closed - Opened by carrascomj 5 months ago - 1 comment

#465 - Fix wrong kcat indexing

Pull Request - State: closed - Opened by carrascomj 5 months ago - 2 comments

#464 - Build wheels for apple silicon

Issue - State: open - Opened by teddygroves 8 months ago

#463 - Fixed dgf bug

Pull Request - State: closed - Opened by teddygroves 8 months ago - 1 comment

#462 - Init free dGfs properly

Issue - State: closed - Opened by carrascomj 8 months ago
Labels: bug

#461 - Update cmdstanpy

Pull Request - State: open - Opened by NicholasCowie 9 months ago

#460 - Model without unbalanced metabolites

Issue - State: open - Opened by carrascomj 10 months ago

#459 - Conserved moieties

Pull Request - State: closed - Opened by NicholasCowie 11 months ago - 1 comment

#458 - Bump version

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#457 - Fix Predict

Pull Request - State: closed - Opened by NicholasCowie about 1 year ago

#456 - Move back to JSON

Issue - State: open - Opened by NicholasCowie about 1 year ago

#455 - bump version

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#454 - bug: json rearranges indexes

Pull Request - State: closed - Opened by NicholasCowie about 1 year ago

#453 - bump version

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#452 - Laplace and pathfinder commands

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#451 - Don't use priors for fixed dgfs

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#450 - fix: remove reject_non_steady flag

Pull Request - State: closed - Opened by carrascomj about 1 year ago - 1 comment

#449 - Fix dgfs

Pull Request - State: closed - Opened by teddygroves about 1 year ago - 1 comment

#448 - refactor: unify some train/test code

Pull Request - State: closed - Opened by carrascomj about 1 year ago - 3 comments

#447 - Pydantic v2

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#446 - Hybrid algebra/ode solver

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#445 - Methionine fix

Pull Request - State: closed - Opened by NicholasCowie about 1 year ago

#444 - Update Stan models for latest cmdstan

Pull Request - State: closed - Opened by teddygroves about 1 year ago

#443 - Expand troubleshooting documentation

Issue - State: open - Opened by teddygroves about 1 year ago

#442 - Fix any parameter

Issue - State: open - Opened by teddygroves about 1 year ago

#441 - E. coli glycolysis example input

Issue - State: open - Opened by teddygroves about 1 year ago

#440 - Add case study to documentation

Issue - State: open - Opened by teddygroves about 1 year ago

#439 - Update methionine input

Issue - State: open - Opened by teddygroves about 1 year ago

#438 - MCA

Issue - State: open - Opened by teddygroves about 1 year ago

#437 - Copy error on fresh install

Issue - State: open - Opened by teddygroves about 1 year ago
Labels: bug

#436 - MCA implementation

Pull Request - State: closed - Opened by NicholasCowie about 1 year ago

#435 - Merge non_steady config

Issue - State: open - Opened by carrascomj about 1 year ago

#434 - Include the deviation from the steady state in the likelihood

Pull Request - State: closed - Opened by carrascomj over 1 year ago - 5 comments

#433 - Steady state deviation in the likelihood

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

#432 - [WIP] Fix methionine

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

#431 - adjoint and algebra solver

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

#430 - Fix missing methionine input

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

#428 - Update docs

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

#427 - point build-wheels workflow at real PyPI

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

#426 - Bundle stan models

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

#425 - Update tooling

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

#424 - Simulate no concs bug

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

#423 - feat: optimize model

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

#422 - Feat: specify initial concentrations individually for the ODE state vector

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

#421 - Generated idata fails to be deserialized

Issue - State: closed - Opened by carrascomj over 1 year ago - 2 comments

#420 - Units

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

#419 - Feat: print more debug info on steady state failure

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

#418 - Default factories

Pull Request - State: closed - Opened by teddygroves almost 2 years ago

#417 - Bug: fix a few small errors in example inputs

Pull Request - State: closed - Opened by teddygroves almost 2 years ago - 1 comment

#416 - Feat: example output

Pull Request - State: closed - Opened by teddygroves almost 2 years ago - 1 comment

#415 - Move example inputs into package

Pull Request - State: closed - Opened by teddygroves almost 2 years ago - 1 comment

#414 - Chore: remove unused dependencies and fix tox isort warning

Pull Request - State: closed - Opened by teddygroves almost 2 years ago

#413 - Simulate fails when there are no concentration measurements

Issue - State: closed - Opened by teddygroves almost 2 years ago
Labels: bug

#412 - Fully toml user input

Pull Request - State: closed - Opened by teddygroves almost 2 years ago

#411 - Updating Version

Pull Request - State: closed - Opened by NicholasCowie about 2 years ago

#410 - Bug: add contributing page to documentation index

Pull Request - State: closed - Opened by teddygroves about 2 years ago

#409 - chore: change split ids in conc_unbalanced

Pull Request - State: closed - Opened by NicholasCowie about 2 years ago

#408 - including split ids

Pull Request - State: closed - Opened by NicholasCowie about 2 years ago

#407 - Bug: fix #397

Pull Request - State: closed - Opened by teddygroves about 2 years ago

#406 - Fix a couple of bugs

Pull Request - State: closed - Opened by teddygroves about 2 years ago
Labels: bug

#405 - Opposite Km parameters of irreversible reactions are included

Issue - State: closed - Opened by ShannaraTP about 2 years ago - 1 comment
Labels: bug

#404 - Chore: Bump version

Pull Request - State: closed - Opened by teddygroves about 2 years ago

#403 - Update setup.cfg

Pull Request - State: closed - Opened by teddygroves about 2 years ago

#402 - Update setup.cfg

Pull Request - State: closed - Opened by teddygroves about 2 years ago

#401 - Simulate input bug

Pull Request - State: closed - Opened by teddygroves about 2 years ago

#400 - chore: pin arviz and pydantic deps

Pull Request - State: closed - Opened by carrascomj about 2 years ago

#399 - Customise starting ode state vector

Pull Request - State: closed - Opened by teddygroves about 2 years ago - 2 comments

#398 - Bug: Fix unbalanced mic concentration stan variable and validate

Pull Request - State: closed - Opened by teddygroves over 2 years ago
Labels: bug

#397 - Bug: can't differentiate between allosteric activators or inhibitors via allostery ID

Issue - State: closed - Opened by NicholasCowie over 2 years ago - 4 comments
Labels: bug

#396 - Move data files inside package

Pull Request - State: closed - Opened by teddygroves over 2 years ago - 2 comments
Labels: bug

#395 - Example model is not included when pip install maud-metabolic-models

Issue - State: closed - Opened by viktorht over 2 years ago - 1 comment
Labels: internal

#394 - Feat: Workflow for releasing new versions of maud and setup.cfg fix

Pull Request - State: closed - Opened by teddygroves over 2 years ago - 1 comment

#393 - Implement promiscuous enzymes [WIP]

Pull Request - State: closed - Opened by teddygroves over 2 years ago - 1 comment

#392 - Better errors for generated inits

Issue - State: open - Opened by carrascomj over 2 years ago - 1 comment

#391 - Multi-compartment membrane potential

Issue - State: open - Opened by carrascomj over 2 years ago

#390 - Feat: add version to metadata in setup.cfg, delete versioneer

Pull Request - State: closed - Opened by teddygroves over 2 years ago

#389 - Test case for irreversible mechanism

Issue - State: closed - Opened by teddygroves over 2 years ago - 1 comment

#388 - Refactor to accommodate promiscuous enzymes

Pull Request - State: closed - Opened by teddygroves over 2 years ago

#387 - Feat transported charge

Pull Request - State: closed - Opened by carrascomj over 2 years ago - 3 comments

#386 - MCA design docs

Pull Request - State: closed - Opened by NicholasCowie over 2 years ago

#384 - Doc: adr document for moving non-core functionality to a new repo

Pull Request - State: closed - Opened by teddygroves over 2 years ago - 1 comment

#383 - Make some hard coded numbers configurable

Issue - State: closed - Opened by teddygroves over 2 years ago

#382 - Add windows installation and testing to github actions

Issue - State: closed - Opened by teddygroves over 2 years ago

#381 - Water and small fix

Pull Request - State: closed - Opened by NicholasCowie over 2 years ago

#380 - Bug: fix wrong metabolite order in equilibrator script

Pull Request - State: closed - Opened by teddygroves over 2 years ago
Labels: bug

#379 - Feat: transform dgf prior means

Pull Request - State: closed - Opened by teddygroves over 2 years ago

#378 - Variational inference and setting stanc and c++ options

Pull Request - State: closed - Opened by teddygroves over 2 years ago

#377 - Feat: let user configure steady state check thresholds

Pull Request - State: closed - Opened by teddygroves almost 3 years ago

#376 - Improved steady state checking

Pull Request - State: closed - Opened by teddygroves almost 3 years ago

#375 - 2021 01 24 tidyup

Pull Request - State: closed - Opened by teddygroves almost 3 years ago