matthiaskoenig/fbc_curation issues and pull requests

#99 - Compat with frog spec 0.1.3

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

#98 - `runfrog` does not work via github actions or local installation

Issue - State: open - Opened by famosab almost 2 years ago - 1 comment
Labels: bug

#97 - Allow comparison to be used from command line

Pull Request - State: open - Opened by fbergmann about 2 years ago

#96 - Incorrect flux written in FVA for objective

Issue - State: closed - Opened by matthiaskoenig about 2 years ago
Labels: bug

#95 - Update from develop

Pull Request - State: closed - Opened by github-actions[bot] about 2 years ago - 1 comment

#94 - Fix naming issues (harmonization)

Issue - State: closed - Opened by matthiaskoenig about 2 years ago - 1 comment

#93 - Websocket communication between frontend and backend

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: website

#92 - Split execution of tasks in multiple subtasks & feedback

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: feature, website

#91 - Render results in tables/metadata

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: website

#90 - Fix NaN serialization issue

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: website

#89 - Fix and update docker containers/dependencies

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: website

#88 - Add tests for celery worker

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: website

#87 - Update website dependencies

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: website

#86 - Update readthedocs

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: website

#85 - Add documentation to webpage

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: documentation, website

#84 - changes for version 0.2.0

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

#83 - New website release

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: website

#82 - Update documentation with latest commands and outputs

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: documentation

#81 - Support comparison with other reference files

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: feature

#80 - Fix mypy issues

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: testing

#79 - Fix flake8 issues

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

#78 - Fix failing tests

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

#77 - Rename master to main branch

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

#76 - Add icon and description to release notes

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

#75 - Updates towards v0.2.0

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

#74 - Better filename for OMEX archive

Issue - State: closed - Opened by matthiaskoenig over 2 years ago - 3 comments
Labels: documentation, website

#73 - Better documentation of FROG report

Issue - State: closed - Opened by matthiaskoenig over 2 years ago
Labels: documentation, website

#72 - Update documentation of comparison with reference files

Issue - State: closed - Opened by matthiaskoenig over 2 years ago - 1 comment
Labels: documentation

#71 - Fix 500 issue and crashes with Pedro model

Issue - State: closed - Opened by matthiaskoenig over 2 years ago - 1 comment
Labels: bug, website

#70 - Add JSON output for tool

Issue - State: open - Opened by matthiaskoenig over 2 years ago
Labels: feature

#69 - Bug when running FROG: cannot import name 'soft_unicode' from 'markupsafe'

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

#68 - Link fbc_curation and other tools on runfrog.de

Issue - State: open - Opened by matthiaskoenig almost 3 years ago
Labels: documentation, website

#67 - Update SSL certificates

Issue - State: closed - Opened by matthiaskoenig almost 3 years ago

#66 - Upgrade to cameo 0.13.6

Issue - State: closed - Opened by matthiaskoenig almost 3 years ago

#65 - Upgrade to cobra 0.24.0

Issue - State: closed - Opened by matthiaskoenig almost 3 years ago

#64 - Support python 3.10

Issue - State: closed - Opened by matthiaskoenig almost 3 years ago

#63 - fbc_curation does not set the solver and metadata can be misleading

Issue - State: open - Opened by glucksfall almost 3 years ago
Labels: bug

#62 - valid SBML-file throws non-valid SBML error

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

#61 - Update to cameo==0.13.6

Issue - State: closed - Opened by matthiaskoenig about 3 years ago - 1 comment

#60 - Improve API error handling

Issue - State: open - Opened by matthiaskoenig about 3 years ago
Labels: bug, website

#59 - Handle paths with special characters

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: bug

#58 - Run benchmark evaluation

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

#57 - New package release

Issue - State: closed - Opened by matthiaskoenig over 3 years ago

#56 - Issue with COVID model

Issue - State: closed - Opened by matthiaskoenig over 3 years ago - 1 comment
Labels: bug

#55 - Improve FROG webservice/site

Issue - State: closed - Opened by matthiaskoenig over 3 years ago - 1 comment
Labels: website

#54 - Error when uploading a model or creating a report via the web interface of runfrog.de

Issue - State: closed - Opened by draeger over 3 years ago - 1 comment
Labels: bug

#53 - Forward www.runfrog.de

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

#52 - Implement rounding for reproducible results

Issue - State: closed - Opened by matthiaskoenig over 3 years ago - 1 comment
Labels: bug

#51 - Bug reading serialized JSON due to infeasible values

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

#50 - Document metadata

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: documentation

#49 - Document NaN representation of missing values

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: documentation

#48 - Document identifiers.org URLS

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: documentation

#47 - Document and provide JSON schema in documentation

Issue - State: open - Opened by matthiaskoenig over 3 years ago
Labels: documentation

#46 - Run tasks in task queue

Issue - State: closed - Opened by matthiaskoenig over 3 years ago - 1 comment
Labels: website

#45 - Register `runfrog` command

Issue - State: closed - Opened by matthiaskoenig over 3 years ago

#44 - Rename package and rebrand

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

#43 - Add frog icon

Issue - State: closed - Opened by matthiaskoenig over 3 years ago

#42 - Support python 3.9

Issue - State: closed - Opened by matthiaskoenig over 3 years ago

#41 - Update dependencies

Issue - State: closed - Opened by matthiaskoenig over 3 years ago

#40 - Zenodo metadata

Issue - State: closed - Opened by matthiaskoenig over 3 years ago

#39 - Rich logging

Issue - State: closed - Opened by matthiaskoenig over 3 years ago
Labels: feature

#38 - Add exact solver solution with cobrapy `glpk_exact`

Issue - State: open - Opened by matthiaskoenig almost 4 years ago
Labels: feature

#37 - Add fraction_optimum column to FVA report

Issue - State: closed - Opened by matthiaskoenig about 4 years ago
Labels: bug

#36 - Add percentage change for gene and reaction deletion

Issue - State: closed - Opened by matthiaskoenig about 4 years ago - 1 comment
Labels: bug

#35 - Update from develop

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago

#34 - Error while running `fbc_curation_examples`

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

#33 - additional curation metadata

Issue - State: closed - Opened by bgoli over 4 years ago - 1 comment
Labels: feature, metadata

#32 - metadata extended and less required attributes

Issue - State: closed - Opened by bgoli over 4 years ago - 3 comments
Labels: metadata

#31 - metadata fields

Issue - State: closed - Opened by bgoli over 4 years ago - 2 comments
Labels: metadata

#30 - Update from develop

Pull Request - State: closed - Opened by github-actions[bot] over 4 years ago

#29 - Fix negative values in FVA results

Issue - State: closed - Opened by matthiaskoenig over 4 years ago

#28 - Reaction identifiers do not match SBML identifiers in FVA

Issue - State: closed - Opened by matthiaskoenig over 4 years ago

#27 - Store infeasible values as NA instead of empty

Issue - State: closed - Opened by matthiaskoenig over 4 years ago - 1 comment
Labels: bug

#26 - Fix failing CI test

Issue - State: closed - Opened by matthiaskoenig over 4 years ago

#25 - Clearly state the percent of optimum in FVA (100%) in documentation

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: documentation

#24 - FVA should include the reference flux value

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: bug

#23 - Use SBML filename in output report

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: bug

#22 - Create tool metadata

Issue - State: closed - Opened by matthiaskoenig over 4 years ago

#21 - Fix issues with cobrapy 0.19.0

Issue - State: closed - Opened by matthiaskoenig over 4 years ago

#20 - FVA result output

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

#19 - Move to github actions

Issue - State: closed - Opened by matthiaskoenig over 4 years ago

#18 - Provide files as JSON (with json schema)

Issue - State: closed - Opened by matthiaskoenig over 4 years ago - 1 comment
Labels: feature

#17 - Examples are not distributed with pip package

Issue - State: closed - Opened by matthiaskoenig over 4 years ago - 1 comment

#16 - Changes for release fbc_curation-v0.1.0

Pull Request - State: closed - Opened by matthiaskoenig over 4 years ago

#15 - Support python 3.8

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: wontfix

#14 - Add webservice for simple creation of the files

Issue - State: closed - Opened by matthiaskoenig over 4 years ago
Labels: feature, website

#13 - Add memote report for simple evaluation of results

Issue - State: closed - Opened by matthiaskoenig over 4 years ago - 1 comment

#12 - Changes for v0.0.6

Pull Request - State: closed - Opened by matthiaskoenig almost 5 years ago - 1 comment

#11 - fbc_curation_example bug

Issue - State: closed - Opened by matthiaskoenig almost 5 years ago - 1 comment

#10 - Changes for v0.0.5 release

Pull Request - State: closed - Opened by matthiaskoenig almost 5 years ago - 1 comment

#9 - Run example on HepatoNet1 & additional examples

Issue - State: closed - Opened by matthiaskoenig almost 5 years ago

#8 - Unbound errors in biomodels in FVA

Issue - State: closed - Opened by matthiaskoenig almost 5 years ago - 2 comments
Labels: bug

#7 - Add support for omex files as input and output

Issue - State: closed - Opened by matthiaskoenig almost 5 years ago - 1 comment
Labels: feature

#6 - Support multiple objectives

Issue - State: open - Opened by matthiaskoenig almost 5 years ago
Labels: feature

#5 - Changes for v0.0.4

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

#4 - Changes for v0.0.3

Pull Request - State: closed - Opened by matthiaskoenig almost 5 years ago - 1 comment

#3 - Example files are not packaged

Issue - State: closed - Opened by matthiaskoenig almost 5 years ago

#2 - Changes for v0.0.2

Pull Request - State: closed - Opened by matthiaskoenig almost 5 years ago - 1 comment

#1 - Changes for v0.0.1 release

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

GitHub / matthiaskoenig/fbc_curation issues and pull requests