Ecosyste.ms: Issues

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GitHub / segrelab/cometspy issues and pull requests

#54 - merging here all the different docs we had so far

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

#53 - NaN returned in total biomass log due to default biomass parameters

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

#52 - Parsing intermediate files to match final outputs

Issue - State: open - Opened by zoey-rw 7 months ago - 1 comment

#51 - allow objective function to be a sum of multiple reactions

Pull Request - State: closed - Opened by andreastallvik 9 months ago - 1 comment

#50 - 'comets.py' error

Issue - State: open - Opened by 2132030 9 months ago - 20 comments

#49 - error('COMETS_HOME environmental variable is not set')

Issue - State: closed - Opened by 2132030 10 months ago - 1 comment

#48 - Modifying the effect of the death rate

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

#47 - Changing upper bound of objective function to limit growth

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

#46 - UnicodeDecodeError: 'utf-8'

Issue - State: open - Opened by complicatedZ 11 months ago - 4 comments

#45 - Change optimizer from Gurobi to GLPK

Issue - State: closed - Opened by weeklymessage 12 months ago - 9 comments

#44 - Biomass coordinates don't match the flux coordinates

Issue - State: open - Opened by hgscott about 1 year ago - 3 comments

#43 - Print progression messages from COMETS while it is running

Issue - State: open - Opened by hgscott about 1 year ago - 1 comment

#42 - The function or variable 'getSecAbsExcMets' is not recognized

Issue - State: open - Opened by yqq-79 about 1 year ago - 3 comments

#41 - Models input order affect metabolites flux and biomass.

Issue - State: open - Opened by Shlomit840 about 1 year ago - 7 comments

#40 - Add a descriptive landing page to the docs

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

#39 - Add links in the Navigation Pane

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

#38 - Make an installation page

Issue - State: open - Opened by hgscott over 1 year ago

#37 - Make template/set of best practices for writing docstrings

Issue - State: open - Opened by hgscott over 1 year ago

#36 - Write a landing page for the documentation

Issue - State: closed - Opened by hgscott over 1 year ago - 4 comments

#35 - Docs

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

#34 - Change the name of the default branch to main

Issue - State: open - Opened by hgscott over 1 year ago

#33 - `line_terminator` is deprecated

Issue - State: open - Opened by hgscott over 1 year ago - 1 comment

#32 - Add a project description on PyPI

Issue - State: open - Opened by hgscott over 1 year ago
Labels: documentation

#31 - Fix "notable" and set_specific_metabolite bugs

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

#30 - Update documentation

Issue - State: closed - Opened by hgscott over 1 year ago - 10 comments
Labels: documentation

#29 - Automate releases

Issue - State: open - Opened by hgscott over 1 year ago
Labels: enhancement

#28 - Add ignore_index to set_specific_metabolite

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

#27 - Add spaces in warning messages

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

#26 - Pandas errors when checking layout

Issue - State: closed - Opened by hgscott over 1 year ago - 15 comments

#25 - Warning prints “notable” instead of “not able”

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

#24 - Change jamtio.jar to jmatio.jar

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

#23 - Typo in jmatio path

Issue - State: closed - Opened by hgscott over 1 year ago
Labels: bug

#22 - Problem with set_specific_metabolite_at_location.

Issue - State: open - Opened by dukovski almost 2 years ago

#21 - Bump setuptools from 51.0.0 to 65.5.1 in /docs

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

#20 - weird behavior with `static` compounds

Issue - State: open - Opened by hariszaf almost 2 years ago - 3 comments

#19 - Inital pop list

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

#18 - Setting Initial Populations in a Loop

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

#17 - Growth rate after setting media concentration and parame

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

#16 - KeyError: 'COMETS_HOME'

Issue - State: open - Opened by merveyrc over 2 years ago - 12 comments

#15 - the method of cometspy.comets() can not working properly

Issue - State: closed - Opened by wupeng1998 over 2 years ago - 1 comment

#14 - Compatibility issue with different model implementations?

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

#13 - Potential bug in signalling

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

#12 - Using positive lower bound produces unexpected behaviour

Issue - State: closed - Opened by behzadk almost 3 years ago - 19 comments

#10 - error in comets.py: self.total_biomass = self.total_biomass.astype('float')

Issue - State: closed - Opened by beacamara over 3 years ago - 8 comments

#9 - Error when reading a model.cmd

Issue - State: closed - Opened by beacamara over 3 years ago - 4 comments

#8 - Media index bug

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

#6 - signaling bugfixes

Pull Request - State: closed - Opened by jeremymchacon about 4 years ago

#4 - small typo in env variable

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

#3 - fixed path-related bugs when running in Windows

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

#2 - fixed bug where chemostat didnt return layout and parms

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

#1 - added helper utils and fixed bugs

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