Ecosyste.ms: Issues

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

GitHub / micom-dev/micom issues and pull requests

#190 - Bump actions/setup-python from 5.1.1 to 5.2.0

Pull Request - State: closed - Opened by dependabot[bot] 28 days ago
Labels: dependencies

#188 - Updates to minimal_media and GrowthResults

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

#187 - Hybrid solver broken for numpy 2.0+

Issue - State: closed - Opened by shalabs 2 months ago - 2 comments

#186 - Bump actions/setup-python from 5.1.0 to 5.1.1

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#183 - Bump codecov/codecov-action from 4.4.1 to 4.5.0

Pull Request - State: closed - Opened by dependabot[bot] 3 months ago
Labels: dependencies

#181 - saving intermediate output from "grow"

Issue - State: open - Opened by zoey-rw 4 months ago - 1 comment

#180 - Bump codecov/codecov-action from 4.4.0 to 4.4.1

Pull Request - State: closed - Opened by dependabot[bot] 4 months ago
Labels: dependencies

#179 - Some small fixes

Pull Request - State: closed - Opened by cdiener 5 months ago - 1 comment

#178 - UnboundLocalError when running minimal_media with `summarize=False`

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

#176 - Bump codecov/codecov-action from 4.3.0 to 4.3.1

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago - 1 comment
Labels: dependencies

#174 - Bump peaceiris/actions-gh-pages from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#173 - Bump codecov/codecov-action from 4.2.0 to 4.3.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#172 - Possible Bug in `com.knockout_taxa()`

Issue - State: open - Opened by alejandrocs98 6 months ago - 4 comments

#170 - [feature] Add new interaction analysis API

Pull Request - State: closed - Opened by cdiener 6 months ago - 5 comments

#169 - Bump codecov/codecov-action from 4.1.1 to 4.2.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#168 - Bump actions/setup-python from 5.0.0 to 5.1.0

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#167 - Bump codecov/codecov-action from 4.1.0 to 4.1.1

Pull Request - State: closed - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#166 - Switch the multiprocessing default method to spawn

Issue - State: closed - Opened by cdiener 6 months ago

#165 - "build" step stalling at 99% complete

Issue - State: closed - Opened by zoey-rw 7 months ago - 4 comments

#164 - Analyse sample growth on multiple media (multi threading)

Issue - State: open - Opened by PathogeNish 7 months ago - 3 comments

#163 - Bump codecov/codecov-action from 4.0.2 to 4.1.0

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#162 - Bump codecov/codecov-action from 4.0.1 to 4.0.2

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#161 - Increase the number of threads for grow for a single model

Issue - State: closed - Opened by PathogeNish 8 months ago - 2 comments

#157 - Bump codecov/codecov-action from 3.1.4 to 3.1.5

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#153 - Hotfix to prefix trimming code

Pull Request - State: closed - Opened by cdiener 9 months ago

#152 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#149 - Bump actions/setup-python from 4.7.1 to 5.0.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago
Labels: dependencies

#146 - Make highs work in the CI

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

#145 - allow unifying ranks

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

#144 - Enable the hybrid solver as the new default

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

#143 - Be less strict about medium setting

Pull Request - State: closed - Opened by cdiener 11 months ago - 1 comment
Labels: hacktoberfest-accepted

#142 - Fix the `grow` docstring to mention the correct default strategy.

Pull Request - State: closed - Opened by cdiener 11 months ago - 1 comment
Labels: hacktoberfest-accepted

#139 - Bump actions/setup-python from 4.7.0 to 4.7.1

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: dependencies

#137 - Indicate tested comparison or covariate in test output

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

#136 - Update README.rst

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

#134 - Bump actions/checkout from 3 to 4

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

#131 - Support the `.sbml` extensions for SBML files

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

#127 - Bump actions/setup-python from 4.6.1 to 4.7.0

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

#124 - Bump actions/setup-python from 4.6.0 to 4.6.1

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

#123 - Bump codecov/codecov-action from 3.1.3 to 3.1.4

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

#121 - keyerror: '_gpr' when using 'load_pickle'

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

#118 - Bump codecov/codecov-action from 3.1.2 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#117 - Bump actions/setup-python from 4.5.0 to 4.6.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#116 - Bump codecov/codecov-action from 3.1.1 to 3.1.2

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

#111 - Bump actions/setup-python from 4.4.0 to 4.5.0

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

#109 - Bump actions/setup-python from 4.3.1 to 4.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#108 - Bump actions/setup-python from 4.3.0 to 4.3.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#103 - Bump actions/setup-python from 4.2.0 to 4.3.0

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#102 - Bump codecov/codecov-action from 3.1.0 to 3.1.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#101 - Add a more permissible media completion

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

#95 - Bump actions/setup-python from 4.1.0 to 4.2.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 2 comments
Labels: dependencies

#91 - Adding coupling constraint to a coupling model

Issue - State: closed - Opened by Ilhem36 about 2 years ago

#89 - Bump actions/setup-python from 4.0.0 to 4.1.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#85 - Bump actions/setup-python from 3.1.2 to 4.0.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#84 - Bump codecov/codecov-action from 3.0.0 to 3.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#82 - Bump actions/setup-python from 3.1.1 to 3.1.2

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#81 - Improve the Gurobi support in MICOM

Pull Request - State: closed - Opened by cdiener over 2 years ago - 2 comments
Labels: numeric

#79 - Bump actions/upload-artifact from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#78 - Bump codecov/codecov-action from 2.1.0 to 3.0.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#77 - Bump actions/setup-python from 3.1.0 to 3.1.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#76 - Bump actions/setup-python from 2 to 3.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#72 - Error while copying model using model.copy()

Issue - State: open - Opened by cdiener over 2 years ago - 2 comments

#67 - Bump actions/checkout from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#66 - Bump actions/setup-python from 2 to 3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#64 - Improve the warning for media metabolites with a missing transport reaction

Issue - State: closed - Opened by cdiener almost 3 years ago - 1 comment

#59 - Bump codecov/codecov-action from 2.0.3 to 2.1.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#56 - Adjust active demands when loading models

Issue - State: closed - Opened by cdiener about 3 years ago - 3 comments

#54 - Bump codecov/codecov-action from 2.0.2 to 2.0.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#51 - Bump codecov/codecov-action from 1 to 2.0.2

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#43 - Update and fix the docs

Issue - State: open - Opened by cdiener over 3 years ago

#39 - Fix #37 by allowing the user to define the compression...

Pull Request - State: closed - Opened by nigiord over 3 years ago - 5 comments

#38 - interpretation of plot_exchanges_per_sample default behavior

Issue - State: closed - Opened by mmp3 over 3 years ago - 6 comments

#37 - Give the option to increase the compresslvl of model databases

Issue - State: closed - Opened by nigiord over 3 years ago - 1 comment

#36 - Support for GTDB taxonomy?

Issue - State: open - Opened by nick-youngblut over 3 years ago - 8 comments

#35 - Enable OSQP support

Pull Request - State: closed - Opened by cdiener over 3 years ago - 1 comment

#34 - [MICOM 1.0 API] Proposed new format for fluxes

Issue - State: open - Opened by cdiener over 3 years ago - 2 comments
Labels: feature

#31 - "Metrics are only available for models build using a model database" when using custom SBML files

Issue - State: closed - Opened by mmp3 over 3 years ago - 3 comments
Labels: bug

#30 - Different cooperative tradeoff solutions between first and second run

Issue - State: closed - Opened by gzampieri over 3 years ago - 1 comment

#29 - Fraction variation influences "status"

Issue - State: closed - Opened by arianccbasile over 3 years ago - 5 comments

#26 - Implement more checks and help for model tables

Issue - State: open - Opened by cdiener over 3 years ago

#24 - Workflows are broken with Gurobi

Issue - State: closed - Opened by cdiener over 3 years ago - 1 comment

#15 - minimal_medium() returns more reactions than initially present

Issue - State: closed - Opened by nigiord about 4 years ago - 2 comments
Labels: question, numeric

#14 - Mention and link where to ask questions

Issue - State: closed - Opened by cdiener about 4 years ago - 1 comment
Labels: feature

#13 - Add basic installation instructions for QP solvers to the docs

Issue - State: closed - Opened by jfoldi81 about 4 years ago - 4 comments

#12 - Error occurs when joining two models after changing their metabolite IDs

Issue - State: closed - Opened by wintermute221 about 4 years ago - 4 comments

#11 - Why is cooperative_tradeoff with "fluxes=True" not feasible sometimes?

Issue - State: closed - Opened by cymee95 about 4 years ago - 3 comments
Labels: numeric, done

#10 - Export optcom results

Issue - State: closed - Opened by arianccbasile over 4 years ago - 2 comments

#9 - exchanges not identified correctly in CarveME models

Issue - State: closed - Opened by arianccbasile about 5 years ago - 14 comments

#8 - ValueError is raised with custom reaction identifiers

Issue - State: closed - Opened by mostueve about 5 years ago - 2 comments

#7 - Should warn about mismatched IDs

Issue - State: open - Opened by cdiener about 5 years ago

#6 - Question on setting import flux upper bounds

Issue - State: closed - Opened by krcurtis about 5 years ago - 1 comment
Labels: question

#5 - Question on units for media fluxes

Issue - State: closed - Opened by krcurtis over 5 years ago - 1 comment

#4 - Issue importing

Issue - State: closed - Opened by arianccbasile over 5 years ago - 3 comments

#3 - Optimize community growth to match known relative abundance

Issue - State: closed - Opened by krcurtis over 5 years ago - 5 comments

#2 - Verbose messages from gurobi when loading community model

Issue - State: closed - Opened by mmundy42 almost 7 years ago - 3 comments