Testing for conflicts#84

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cshenry wants to merge 415 commits intoModelSEED:dev_updatefrom

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Commits on Jul 6, 2023

Commits on Jul 8, 2023

Making thresholds on tests more flexible, including supporting media specific multipliers for the threshold
cshenry
committed

Commits on Jul 10, 2023

Commits on Jul 12, 2023

Commits on Jul 17, 2023

Commits on Jul 22, 2023

Improved phenotype functions
cshenry
committed

Commits on Jul 24, 2023

Removing failed ATP gapfillings from gapfilling sensitivity
cshenry
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Adding ATP gapfilled reactions to gapfilling sensitivity
Christopher Henry
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Commits on Jul 25, 2023

Commits on Jul 26, 2023

Commits on Aug 2, 2023

Commits on Aug 3, 2023

Commits on Aug 4, 2023

Commits on Aug 10, 2023

Commits on Aug 17, 2023

Commits on Aug 24, 2023

Adding probabilities for ensemble models
cshenry
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Fixing bug
cshenry
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Fixing bug in report when gapfilling isn't run
cshenry
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Updates to report code
Christopher Henry
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Merge branch 'main' of github.com:cshenry/ModelSEEDpy
Christopher Henry
committed

Commits on Aug 25, 2023

Commits on Aug 26, 2023

Merge pull request #133 from cshenry/main
Fxe
authored

Commits on Aug 28, 2023

Commits on Aug 30, 2023

Commits on Sep 7, 2023

Commits on Sep 9, 2023

Commits on Sep 11, 2023

Fixing report bugs
cshenry
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Commits on Sep 14, 2023

Commits on Sep 15, 2023

Commits on Sep 21, 2023

Adding function template for gapfilling function from PNNL team
cshenry
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Commits on Sep 24, 2023

Commits on Oct 4, 2023

Commits on Oct 5, 2023

Fixing phenotype id code
cshenry
committed

Commits on Oct 6, 2023

Setting debug messages to understanding hanging during sensitivity analysis
cshenry
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Commits on Oct 8, 2023

Fixing problem with solution integration during multigapfill
cshenry
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Commits on Oct 10, 2023

Commits on Oct 11, 2023

Adding function to build modelutl from file
cshenry
committed

Commits on Nov 10, 2023

Commits on Dec 4, 2023

Created Weighting function for gap fill. Example data required for testing.
jjacobson95
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Commits on Dec 7, 2023

Commits on Dec 21, 2023

Commits on Dec 28, 2023

Fixing FBA package and phenotyping
cshenry
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Commits on Jan 4, 2024

Linted
jjacobson95
committed

Commits on Jan 25, 2024

Checking in gapfilling improvements for PNNL use in developing gapfilling method
cshenry
committed

Commits on Feb 6, 2024

Updating code for gapfilling and annotation ontology support
cshenry
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Commits on Feb 9, 2024

rast regex
Fxe
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Commits on Feb 14, 2024

Major updates to weighting / expression data function
jjacobson95
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Commits on Mar 11, 2024

Commits on Mar 17, 2024

Updates to support mscommunity and probabiliy and fixes to ModelSEEDpy
cshenry
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Commits on Mar 19, 2024

Commits on Mar 21, 2024

Commits on Mar 23, 2024

Commits on Mar 25, 2024

Commits on Mar 28, 2024

Finalizing omegga
cshenry
committed

Commits on Mar 30, 2024

Fixing omegga capabilities
cshenry
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Commits on Apr 1, 2024

Working on fbareport for community FBA app and adding debug message when genes are mapped to gapfilled reactions
cshenry
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Commits on Apr 9, 2024

Commits on Apr 28, 2024

Temporarily removing dependency
cshenry
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Commits on May 21, 2024

Fixes to support simulation of uptake and excretion phenotypes
cshenry
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Commits on May 22, 2024

Improving gapfilling and modelutl
cshenry
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Commits on Jun 4, 2024

Adjusting where growth constraint is being removed
cshenry
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Commits on Jun 21, 2024

Commits on Jul 20, 2024

Add pigment and carbohydrate biomass categories
jplfaria
committed

Commits on Jul 22, 2024

Merge remote-tracking branch 'upstream/dev' into dev
jplfaria
committed

Commits on Aug 6, 2024

Checking in various code updates from recent project work.
Christopher Henry
committed

Commits on Sep 4, 2024

genome
Fxe
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Commits on Sep 26, 2024

Commits on Oct 8, 2024

Fixes for expression fba and ATP
Christopher Henry
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Commits on Nov 5, 2024

Fixing error with bio reaction, fixing check for compounds in template, setting failure testing to false, and fixing report
Christopher Henry
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Commits on Nov 7, 2024

Merge pull request #148 from jplfaria/dev
Fxe
authored

Commits on Nov 9, 2024

genome
Fxe
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b
Fxe
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Commits on Nov 20, 2024

Fixing media forcing; fixing ensemble modeling; fixing aliases in genomes; fixing msexpression
Christopher Henry
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Commits on Nov 21, 2024

Removing pyeda dependency
Christopher Henry
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Removing solution printing that was used for debugging
Christopher Henry
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Setting config for KBase deploy
Christopher Henry
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Commits on Nov 29, 2024

Commits on Dec 28, 2024

Fixing global gapfilling
Christopher Henry
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Commits on Jan 20, 2025

Commits on Feb 13, 2025

Improvements to support building models from other annotations
Christopher Henry
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Adding support for pigment and carbohydrate
Christopher Henry
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Adding defaults for new fields pigment and carbohydrate
Christopher Henry
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Fixing ModelSEEDDatabase calls in utils
Christopher Henry
committed
Fixing reaction scoring
Christopher Henry
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Fixing reaction scoring
Christopher Henry
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Fixing reaction scoring
Christopher Henry
committed

Commits on Feb 14, 2025

Attempting to fix variable mismatch
Christopher Henry
committed

Commits on Feb 15, 2025

Trying to fix bug with problem replication with gurobi
Christopher Henry
committed

Commits on Feb 22, 2025

Fixing bugs in gapfilling
Christopher Henry
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Commits on Feb 23, 2025

Debugging global gapfill solution saving
Christopher Henry
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Debugging gene finder for gapfilled reactions
Christopher Henry
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Adding time import
Christopher Henry
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Fixing gapfilling
Christopher Henry
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Removing debugging print
Christopher Henry
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Commits on Feb 24, 2025

Debugging issue with reaction bounds on gapfilled reactions
Christopher Henry
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Fixing bug in debuging prints
Christopher Henry
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Fixing phenotype simulation and gapfilling debugging
Christopher Henry
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Commits on Feb 25, 2025

Fixing ensemble and gapfilling
Christopher Henry
committed
Fixing bug
Christopher Henry
committed
Fixing bug causing gapfilled reactions to be KO during testing
Christopher Henry
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Fixing ensemble and removing prints
Christopher Henry
committed

Commits on Feb 26, 2025

Fixing ensemble code and annotation ontology
Christopher Henry
committed

Commits on Mar 3, 2025

genome loader
Fxe
committed

Commits on Mar 6, 2025

Commits on Apr 4, 2025

Fixing path to ModelSEEDDatanase in config file for KBase app
Christopher Henry
committed
mstemplate biomass
Fxe
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Merge pull request #154 from Fxe/dev
Fxe
authored

Commits on Apr 5, 2025

Adding objective package
Christopher Henry
committed
Merge commit 'cc095d6d49959f1d9018ec71e6f31ee3eb8a2d25'
Christopher Henry
committed

Commits on Oct 11, 2025

Checking in latest code with new fba packages and fixes to phenotype simulation, biochemistry, and gapfilling
Christopher Henry
committed

Commits on Oct 16, 2025

feat: add fit_model_flux_to_data function to MSExpression class
Christopher Henry
committed

Commits on Oct 17, 2025

Adding new reference flux and fold change analysis scripts
Christopher Henry
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Removing start imports which cause immediate breaks in environments that lack all dependencies
Christopher Henry
committed
Removing MSCommunity temporarily
Christopher Henry
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Debugging large coefficients
Christopher Henry
committed
Debugging
Christopher Henry
committed
Fixing bug
Christopher Henry
committed

Commits on Oct 18, 2025

Fix build_reaction_expression to support direct gene ID matching

Christopher Henry
and
claude
committed

Commits on Nov 4, 2025

Commits on Nov 10, 2025

Adding claude commands and system prompt to hopefully improve performance of claude web
Christopher Henry
committed