Ecosyste.ms: Issues

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

GitHub / opencobra/Medusa issues and pull requests

#111 - Bump certifi from 2018.10.15 to 2022.12.7 in /docs

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

#110 - Bump certifi from 2018.10.15 to 2022.12.7

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

#109 - Bump pillow from 9.0.0 to 9.3.0

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

#108 - Bump pillow from 9.0.0 to 9.3.0 in /docs

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

#107 - Bump nbconvert from 5.3.1 to 6.5.1 in /docs

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

#106 - Bump nbconvert from 5.3.1 to 6.5.1

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

#105 - Bump nbconvert from 5.3.1 to 6.3.0 in /docs

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

#104 - Bump nbconvert from 5.3.1 to 6.3.0

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

#103 - Is Medusa obsolete software?

Issue - State: closed - Opened by jeffkimbrel over 2 years ago - 3 comments

#102 - Bump mistune from 0.8.4 to 2.0.3 in /docs

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

#101 - Bump mistune from 0.8.4 to 2.0.3

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

#100 - Bump numpy from 1.15.4 to 1.22.0 in /docs

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

#99 - Bump numpy from 1.15.4 to 1.22.0

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

#98 - Bump notebook from 6.4.1 to 6.4.12 in /docs

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

#97 - Bump notebook from 6.4.1 to 6.4.12

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

#96 - Bump notebook from 6.4.1 to 6.4.10 in /docs

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

#95 - Bump notebook from 6.4.1 to 6.4.10

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

#94 - Bump pillow from 9.0.0 to 9.0.1 in /docs

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

#93 - Bump pillow from 9.0.0 to 9.0.1

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

#92 - Bump ipython from 7.1.1 to 7.16.3 in /docs

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#91 - Bump ipython from 7.1.1 to 7.16.3

Pull Request - State: open - Opened by dependabot[bot] almost 3 years ago
Labels: dependencies

#90 - Bump numpy from 1.15.4 to 1.21.0 in /docs

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

#89 - Bump numpy from 1.15.4 to 1.21.0

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

#88 - Bump pillow from 6.2.0 to 9.0.0 in /docs

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

#87 - Bump pillow from 6.2.0 to 9.0.0

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

#86 - Bump pipenv from 2018.10.13 to 2022.1.8

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

#85 - Bump pipenv from 2018.10.13 to 2022.1.8 in /docs

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

#84 - Bump babel from 2.6.0 to 2.9.1 in /docs

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

#83 - Bump babel from 2.6.0 to 2.9.1

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

#82 - Bump pillow from 6.2.0 to 8.3.2 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 2 comments
Labels: dependencies

#81 - Bump pillow from 6.2.0 to 8.3.2

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

#80 - Bump notebook from 6.1.5 to 6.4.1 in /docs

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

#79 - Bump notebook from 6.1.5 to 6.4.1

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

#78 - Bump jupyterlab from 0.35.4 to 1.2.21 in /docs

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

#77 - Bump jupyterlab from 0.35.4 to 1.2.21

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

#76 - Bump pillow from 6.2.0 to 8.2.0 in /docs

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

#75 - Bump pillow from 6.2.0 to 8.2.0

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

#74 - Bump urllib3 from 1.24.2 to 1.26.5 in /docs

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

#73 - Bump urllib3 from 1.24.2 to 1.26.5

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

#72 - Bump pygments from 2.2.0 to 2.7.4 in /docs

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

#71 - Bump pygments from 2.2.0 to 2.7.4

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

#70 - Bump jinja2 from 2.10 to 2.11.3 in /docs

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

#69 - Bump jinja2 from 2.10 to 2.11.3

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

#68 - Bump pillow from 6.2.0 to 8.1.1 in /docs

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

#67 - Bump pillow from 6.2.0 to 8.1.1

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

#66 - Bump bleach from 3.1.4 to 3.3.0 in /docs

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

#65 - Bump bleach from 3.1.4 to 3.3.0

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

#64 - Bump pillow from 6.2.0 to 7.1.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#63 - Bump pillow from 6.2.0 to 7.1.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#62 - Update expand.py

Pull Request - State: open - Opened by Basie12 almost 4 years ago

#61 - Bump notebook from 5.7.8 to 6.1.5 in /docs

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

#60 - Bump notebook from 5.7.8 to 6.1.5

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

#59 - base_model

Issue - State: open - Opened by Basie12 over 4 years ago - 4 comments

#58 - Bump bleach from 3.0.2 to 3.1.4 in /docs

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

#57 - Bump bleach from 3.0.2 to 3.1.4

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

#56 - Bump bleach from 3.0.2 to 3.1.2 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#55 - Bump bleach from 3.0.2 to 3.1.2

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#54 - Bump bleach from 3.0.2 to 3.1.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#53 - Bump bleach from 3.0.2 to 3.1.1

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#52 - revision and re-running of benchmark docs

Pull Request - State: closed - Opened by gregmedlock almost 5 years ago

#51 - benchmarking notebook pull request

Pull Request - State: closed - Opened by Tjmoutinho almost 5 years ago

#50 - clarify batch_load_from_files docstrings, variable names, and SBML/json checking

Issue - State: open - Opened by gregmedlock almost 5 years ago
Labels: development

#49 - Benchmarking: ensemble memory

Issue - State: closed - Opened by gregmedlock almost 5 years ago - 1 comment
Labels: Documentation

#48 - Benchmarking: FBA

Issue - State: closed - Opened by gregmedlock almost 5 years ago - 1 comment
Labels: Documentation

#47 - Update for compatibility with newer cobrapy versions

Issue - State: open - Opened by gregmedlock almost 5 years ago
Labels: development

#46 - Package-wide linting

Issue - State: open - Opened by gregmedlock almost 5 years ago
Labels: cleaning

#45 - Parametrize tests

Issue - State: open - Opened by gregmedlock almost 5 years ago
Labels: testing

#44 - Bump notebook from 5.7.2 to 5.7.8

Pull Request - State: closed - Opened by dependabot[bot] almost 5 years ago
Labels: dependencies

#43 - Bump urllib3 from 1.24.1 to 1.24.2

Pull Request - State: closed - Opened by dependabot[bot] almost 5 years ago
Labels: dependencies

#42 - Bump notebook from 5.7.2 to 5.7.8 in /docs

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

#41 - Bump typed-ast from 1.3.0 to 1.3.2 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 5 years ago
Labels: dependencies

#40 - Bump pillow from 5.3.0 to 6.2.0 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago
Labels: dependencies

#39 - Bump pillow from 5.3.0 to 6.2.0

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago
Labels: dependencies

#38 - Bump urllib3 from 1.24.1 to 1.24.2 in /docs

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

#36 - Reassignment of member ids does not reindex

Issue - State: closed - Opened by gregmedlock about 5 years ago - 1 comment

#35 - Order of min/max columns in cobrapy has changed

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

#34 - Load from file function

Pull Request - State: closed - Opened by Tjmoutinho over 5 years ago - 1 comment

#33 - Add utility functions for extracting useful information about an ensemble

Issue - State: open - Opened by gregmedlock over 5 years ago - 1 comment
Labels: enhancement

#32 - Implement multiprocessing for iterative gapfilling

Issue - State: open - Opened by gregmedlock almost 6 years ago
Labels: enhancement

#31 - Enable AutoAPI creation from docstrings

Issue - State: closed - Opened by gregmedlock almost 6 years ago
Labels: Documentation

#30 - Include simpler analyses in examples within documentation

Issue - State: open - Opened by gregmedlock almost 6 years ago
Labels: Documentation

#29 - Expand on analogies between Medusa containers/objects and cobrapy objects

Issue - State: closed - Opened by gregmedlock almost 6 years ago
Labels: Documentation

#28 - Merging again for 0.2 release.

Pull Request - State: closed - Opened by gregmedlock almost 6 years ago

#27 - Remove transporter search from gapfilling example

Issue - State: closed - Opened by gregmedlock almost 6 years ago
Labels: Documentation

#25 - Implement randomization strategies for iterative gapfilling

Issue - State: open - Opened by gregmedlock almost 6 years ago

#24 - implement multiprocessing for ensembleFBA

Issue - State: closed - Opened by gregmedlock almost 6 years ago - 1 comment
Labels: enhancement

#23 - PR for release 0.2

Pull Request - State: closed - Opened by gregmedlock almost 6 years ago

#22 - Add dataframe state output function

Issue - State: open - Opened by gregmedlock almost 6 years ago
Labels: enhancement

#21 - Sort requirements into requirements, develop, and doc

Issue - State: open - Opened by gregmedlock almost 6 years ago

#20 - Profile runtime of continuous gapfilling

Issue - State: open - Opened by gregmedlock almost 6 years ago
Labels: enhancement

#19 - Create "Gallery" section of examples of ensemble analyses

Issue - State: open - Opened by gregmedlock almost 6 years ago
Labels: Documentation

#18 - fix local sphinx vs. readthedocs rendering differences

Issue - State: closed - Opened by gregmedlock almost 6 years ago - 1 comment

#17 - Add documentation for updating documentation deployment in Sphinx/Readthedocs

Issue - State: open - Opened by gregmedlock about 6 years ago
Labels: Documentation

#16 - Add documentation for updating deployed release to contribution guide

Issue - State: open - Opened by gregmedlock about 6 years ago
Labels: Documentation

#15 - enable pip installation of development branch

Issue - State: open - Opened by Tjmoutinho about 6 years ago - 1 comment

#14 - Add json IO for ensembles

Issue - State: open - Opened by gregmedlock about 6 years ago
Labels: enhancement

#12 - Setup Sphinx documentation

Issue - State: closed - Opened by gregmedlock over 6 years ago
Labels: Documentation

#11 - Add wrapper for add_models to create ensemble from collection of files

Issue - State: closed - Opened by gregmedlock over 6 years ago - 4 comments
Labels: enhancement