GeomScale/dingo issues and pull requests

#99 - fix typo in slow_fba, and a bug in fast_fba

Pull Request - State: closed - Opened by KeShih about 2 months ago - 1 comment

#98 - new interface for samples and fba, fva solutions and workaround for #96

Pull Request - State: open - Opened by hariszaf 2 months ago

#97 - rename biomass_function to objective_function, fixes issue #82

Pull Request - State: closed - Opened by hritikb 2 months ago

#96 - Error using fva after sampling

Issue - State: open - Opened by vfisikop 3 months ago - 6 comments

#95 - Redundant methods in MetabolicNetwork

Issue - State: open - Opened by vfisikop 3 months ago - 3 comments

#93 - Refactor mmcs algorithm

Issue - State: open - Opened by vfisikop 3 months ago

#92 - Fix rounding test

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

#91 - Update README installation instructions to be more user friendly #89

Pull Request - State: closed - Opened by rkstu 4 months ago

#90 - solve issue #83: generate_steady_states fails when you edit a model's optimal percentage twice #83

Pull Request - State: closed - Opened by rkstu 4 months ago - 3 comments

#89 - Update README installation instructions to be more user friendly

Issue - State: closed - Opened by rkstu 4 months ago - 5 comments
Labels: documentation

#88 - Build volestipy with lpsolve

Pull Request - State: closed - Opened by vfisikop 5 months ago

#87 - Update dingo to use volesti develop instead of volesti4dingo branch

Pull Request - State: closed - Opened by vfisikop 5 months ago

#86 - loopless sampling

Issue - State: open - Opened by hariszaf 5 months ago - 1 comment
Labels: enhancement

#85 - solve issue #83: generate_steady_states fails when you edit a model's optimal percentage twice #83

Pull Request - State: closed - Opened by rkstu 5 months ago - 4 comments

#84 - Modernize LP solver interface

Issue - State: open - Opened by vissarion 6 months ago - 1 comment
Labels: enhancement

#83 - `generate_steady_states` fails when you edit a model's optimal percentage twice

Issue - State: open - Opened by hariszaf 7 months ago

#82 - Consider renaming `biomass_function` routine

Issue - State: closed - Opened by hariszaf 7 months ago - 3 comments
Labels: code style

#81 - Create redundant_facet_removal_backup.py

Pull Request - State: closed - Opened by nitishmalang 9 months ago - 2 comments

#80 - Create imp-16.py

Pull Request - State: closed - Opened by nitishmalang 10 months ago

#79 - Dockerfile is added to the codebase

Pull Request - State: open - Opened by ai-naymul 10 months ago - 8 comments

#78 - Consider a docker image

Issue - State: open - Opened by hariszaf 10 months ago
Labels: enhancement

#77 - Error in installation (incompatible versions of Python and numpy)

Issue - State: closed - Opened by savvas-paragkamian 10 months ago - 17 comments

#76 - support of medium modification and cobra model loading

Pull Request - State: closed - Opened by hariszaf 10 months ago - 2 comments

#75 - alternative suffix for sbml models

Issue - State: closed - Opened by hariszaf 10 months ago

#74 - Modify model's medium

Issue - State: closed - Opened by TolisChal 10 months ago - 1 comment

#73 - Expose HMC walks with Gaussian and exponential distributions

Pull Request - State: closed - Opened by stormaths 11 months ago

#72 - rounding.py is excluded from github actions

Issue - State: open - Opened by TolisChal 11 months ago - 5 comments
Labels: tests

#71 - Update README.md

Pull Request - State: closed - Opened by nitishmalang 12 months ago - 2 comments

#70 - Fix bug in retrieving samples

Pull Request - State: closed - Opened by TolisChal 12 months ago

#69 - Update README.md

Pull Request - State: closed - Opened by nitishmalang 12 months ago

#68 - Exposed two HMC walks with exponential and Gaussian sampling from Volesti

Pull Request - State: closed - Opened by stormaths 12 months ago - 2 comments

#67 - Sampling on the flux space of multiple metabolic networks

Issue - State: open - Opened by vissarion about 1 year ago - 2 comments
Labels: enhancement

#66 - non-uniqueness issue in dynamic FBA

Issue - State: open - Opened by hariszaf about 1 year ago - 1 comment
Labels: enhancement

#65 - sample asking for a min/max value of the objective function

Issue - State: closed - Opened by hariszaf about 1 year ago - 3 comments
Labels: enhancement

#64 - Add volume computation support and motivation

Issue - State: open - Opened by vissarion about 1 year ago
Labels: enhancement

#63 - fix magic command denoter; issue #60

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

#62 - Fix poetry version 1.3.2 in actions.

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

#61 - update colab; fix #60

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

#60 - Error importing MetabolicNetwork class from dingo package in Google Colab (GSoC 2023)

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

#59 - Adding CodeCov

Pull Request - State: closed - Opened by bsarthak16 over 1 year ago

#58 - Edits on copula illustration and export

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

#57 - Improve copula illustration and export

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

#56 - Bump future from 0.18.2 to 0.18.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#54 - Move the documentation to readme

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

#53 - Expose rounding methods

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

#52 - implement copula illustration in dingo pipeline

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

#51 - Add cobra package as a dependence.

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

#50 - Load models

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

#49 - reorder sections and minor edits

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

#48 - Update poetry installation CI command

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

#47 - segmentation fault when ESS low

Issue - State: open - Opened by hariszaf almost 2 years ago
Labels: bug

#45 - Experiments

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

#44 - include volume approximation

Issue - State: open - Opened by Patrickens almost 2 years ago - 1 comment
Labels: enhancement

#40 - Expose uniform random walks

Pull Request - State: closed - Opened by Kostas-Pallikaris almost 2 years ago - 1 comment
Labels: enhancement

#39 - Update mention of unit tests in main README

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

#38 - Move updated tutorial to tutorials folder and copyedit

Pull Request - State: closed - Opened by dymil almost 2 years ago - 3 comments

#37 - Make changes to code style

Pull Request - State: closed - Opened by dymil about 2 years ago - 3 comments
Labels: code style

#36 - Copyedit main README + comments in volestipy.pyx

Pull Request - State: closed - Opened by dymil about 2 years ago - 1 comment

#35 - Fix typo in tutorial README

Pull Request - State: closed - Opened by dymil about 2 years ago - 1 comment

#34 - sampling using the maximum entropy probability distribution

Issue - State: open - Opened by hariszaf over 2 years ago - 2 comments
Labels: enhancement

#33 - Support ellipsoid sampling methods

Issue - State: closed - Opened by vissarion over 2 years ago - 2 comments
Labels: enhancement

#32 - code coverage for dingo

Issue - State: open - Opened by vissarion over 2 years ago
Labels: tests, Hacktoberfest

#31 - Add a boolean to control the preprocessing method

Pull Request - State: closed - Opened by TolisChal over 2 years ago
Labels: enhancement

#30 - For Begginer

Issue - State: closed - Opened by nikdantani over 2 years ago - 2 comments

#29 - Fix the bug in sample_from_polytope function

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

#28 - Fix compile errors

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

#27 - Improve preprocessing

Pull Request - State: closed - Opened by TolisChal over 2 years ago
Labels: enhancement

#26 - Read `.xml` models

Issue - State: closed - Opened by hariszaf almost 3 years ago - 4 comments
Labels: enhancement, good first issue, Hacktoberfest

#25 - Read `.mat` models

Issue - State: closed - Opened by hariszaf almost 3 years ago
Labels: enhancement, good first issue, Hacktoberfest

#24 - `NameError` when using the `sample_from_polytope` function

Issue - State: closed - Opened by hariszaf almost 3 years ago
Labels: bug

#23 - Compartments

Issue - State: closed - Opened by hariszaf almost 3 years ago - 2 comments
Labels: question

#22 - Fix/json biomass index value

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

#21 - sampler does not converge with iLJ478 model

Issue - State: closed - Opened by vissarion almost 3 years ago - 2 comments
Labels: bug

#20 - fast_inner_ball computes negative radius

Issue - State: closed - Opened by vissarion almost 3 years ago
Labels: bug

#19 - Error with biomass index handling after parsing json files

Issue - State: closed - Opened by vissarion almost 3 years ago
Labels: bug

#18 - Sampling on the flux space of multiple metabolic networks

Pull Request - State: closed - Opened by hariszaf almost 3 years ago - 3 comments
Labels: enhancement

#17 - dingo tutorial notebook

Pull Request - State: closed - Opened by hariszaf almost 3 years ago - 9 comments
Labels: tutorial

#16 - dingo crashes with various metabolic models

Issue - State: closed - Opened by vissarion about 3 years ago - 4 comments
Labels: bug

#15 - Add examples and use-cases

Issue - State: closed - Opened by vissarion about 3 years ago - 3 comments
Labels: good first issue, help wanted, Hacktoberfest

#14 - Add Contribution guidelines

Issue - State: closed - Opened by vissarion about 3 years ago - 1 comment
Labels: good first issue

#13 - Knock out a reaction flux

Pull Request - State: closed - Opened by TolisChal about 3 years ago
Labels: enhancement

#12 - Set Black code style

Pull Request - State: closed - Opened by TolisChal about 3 years ago
Labels: code style

#11 - Fix tests

Pull Request - State: closed - Opened by TolisChal about 3 years ago
Labels: tests

#10 - Add github actions

Pull Request - State: closed - Opened by vissarion about 3 years ago
Labels: tests

#9 - Improve Python code

Pull Request - State: closed - Opened by TolisChal about 3 years ago

#8 - Update boost download link

Pull Request - State: closed - Opened by vissarion about 3 years ago

#7 - Restructure of Python code

Pull Request - State: closed - Opened by TolisChal about 3 years ago