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take Filipe's most recent additions #15

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Commits on Jan 17, 2023

  1. Minor fixes and adding some utility functionality

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    cshenry committed Jan 17, 2023
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  2. Merge commit 'b3d6890dbf5088dbd5c25c455218e9871c9f3c42'

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  3. Merge commit 'eca4cc0d01ed551266214f65f0d095b02fef9b12'

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Commits on Jan 18, 2023

  1. index fix

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    Fxe committed Jan 18, 2023
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Commits on Jan 31, 2023

  1. missing import

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  2. Merge pull request #109 from Fxe/dev 

    minor fixes
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    Fxe committed Jan 31, 2023
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Commits on Feb 1, 2023

  1. fixed builder to detect biomass added compounds

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  2. Merge pull request #110 from Fxe/dev 

    fixed builder to detect biomass added compounds
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Commits on Feb 3, 2023

  1. notebook update

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  2. Merge pull request #111 from Fxe/dev 

    notebook update
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Commits on Feb 9, 2023

  1. Fixes for new biomass code

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  2. Merge commit 'fc5f584bdb5f9ae6c1962de7e3d36c95372d33b4'

    @cshenry
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  3. Formatting with black

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Commits on Feb 14, 2023

  1. biomass fix

    @Fxe
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  2. Merge branch 'ModelSEED:dev' into dev

    @Fxe
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  3. Merge pull request #114 from Fxe/dev 

    biomass update
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  4. bug fix

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  5. Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev

    @Fxe
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  6. Merge branch 'ModelSEED:dev' into dev

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  7. black

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  8. Merge pull request #115 from Fxe/dev 

    biomass bug fix
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  9. Merge pull request #113 from cshenry/main 

    Checking in biomass and gapfilling fixes 2
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Commits on Feb 15, 2023

  1. Updates to fix gapfilling and string concatenation

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  2. Merge pull request #116 from cshenry/main 

    Updates to fix gapfilling and string concatenation
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Commits on Feb 20, 2023

  1. genome feature aliases

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  2. Merge branch 'ModelSEED:dev' into dev

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  3. Merge pull request #117 from Fxe/dev 

    genome feature aliases
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Commits on Feb 21, 2023

  1. template.add_reaction update comcompound references

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  2. Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev

    @Fxe
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  3. Merge pull request #118 from Fxe/dev 

    minor fix
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Commits on Mar 1, 2023

  1. Improving gapfilling and ATP correction

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  2. Merge commit '218f2a119a400c6ccfed29e92125b7c02e3c9659'

    @cshenry
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  3. Merge pull request #119 from cshenry/main 

    Improving Gapfilling and ATP correction
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  4. template species name

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    Fxe committed Mar 1, 2023
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  5. black

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  6. Merge pull request #120 from Fxe/dev 

    template species names
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Commits on Mar 13, 2023

  1. x

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  2. Merge pull request #121 from Fxe/dev 

    building compound in biochme
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Commits on Mar 28, 2023

  1. template format

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  2. Merge branch 'ModelSEED:dev' into dev

    @Fxe
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  3. black

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  4. Merge pull request #123 from Fxe/dev 

    template compound naming
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Commits on Apr 13, 2023

  1. examples

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Commits on Apr 18, 2023

  1. lower/upper case fix

    @Fxe
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  2. Merge branch 'dev' of github.com:ModelSEED/ModelSEEDpy into dev

    @Fxe
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  3. Merge pull request #124 from Fxe/dev 

    Bug Fix
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    Fxe committed Apr 18, 2023
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Commits on May 3, 2023

  1. Implementing multiple gapfill

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Commits on May 16, 2023

  1. Fixing test

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  2. Merge pull request #125 from cshenry/main 

    Implementing multiple gapfill
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Commits on Jun 15, 2023

  1. Renaming ATP

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Commits on Jun 26, 2023

  1. fixes

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  2. black

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  3. Merge pull request #126 from Fxe/dev 

    bug + gz
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Commits on Jul 2, 2023

  1. Changing zero threshold on gapfilling

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Commits on Jul 3, 2023

  1. Adding version printing to ModelSEEDpy so I can be sure what version … 

    …of the code is running
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Commits on Jul 4, 2023

  1. Resetting gapfill threshold for zero

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  2. Restoring small gapfilling threshold

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  3. Fixing gapfilling target issue

    @cshenry
    cshenry committed Jul 4, 2023
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  4. Fixing bug in ATP correction

    @cshenry
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  5. Fixing ATP correction

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  6. Fixing ATP correction media selection

    @cshenry
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  7. Running black

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  8. Merge pull request #127 from cshenry/main 

    Renaming ATP
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  9. minor

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  10. Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev

    @Fxe
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Commits on Jul 6, 2023

  1. added e0 as extracell search for cobrapy

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  2. black

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  3. pre-commit

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    Fxe committed Jul 6, 2023
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  4. Merge pull request #128 from Fxe/dev 

    cobrapy extracell warning
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Commits on Jul 7, 2023

  1. Fixing threshold and adding empty media and fixing thresholds

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  2. Fixing empty media

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  3. Merge branch 'dev' of https://github.com/ModelSEED/ModelSEEDpy

    @cshenry
    cshenry committed Jul 7, 2023
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  4. Fixing git ignore

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Commits on Jul 8, 2023

  1. Making thresholds on tests more flexible, including supporting media … 

    …specific multipliers for the threshold
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Commits on Jul 10, 2023

  1. Improving commenting and improving multi gapfilling

    @cshenry
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  2. Fixing bug in log message

    @cshenry
    cshenry committed Jul 10, 2023
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  3. Update atp_medias.tsv 

    adding methanol and methylamines medias
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  4. Merge pull request #6 from jplfaria/patch-1 

    Update atp_medias.tsv
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  5. Merge branch 'ModelSEED:dev' into dev

    @Fxe
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  6. Merge pull request #129 from Fxe/dev 

    ATP media update
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  7. build biomass index fix

    @Fxe
    Fxe committed Jul 10, 2023
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  8. Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev

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  9. Merge pull request #130 from Fxe/dev 

    biomass index
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Commits on Jul 12, 2023

  1. Fixing various media and element package

    @cshenry
    cshenry committed Jul 12, 2023
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  2. Fixing weird import

    @cshenry
    cshenry committed Jul 12, 2023
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Commits on Jul 13, 2023

  1. Improving phenotype simulations and gapfilling

    @cshenry
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  2. Fixing bug

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  3. Adding MSGrowthPhenotype object

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  4. Adding MSGrowthPhenotype

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  5. Fixing error in simulate arguments

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Commits on Jul 17, 2023

  1. Fixing attributes, improving phenotypes, improving gapfilling

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  2. Fixing attritbute problem and fixing phenotypes

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Commits on Jul 18, 2023

  1. Improving phenotype simulations and enabling use of complete media

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  2. Fixing issue where attributes will be none

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  3. atpcorrection

    @Fxe
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  4. Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev

    @Fxe
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  5. Improving phenotype simulation and making sure parameters are documen… 

    …ted in element uptake
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Commits on Jul 22, 2023

  1. Improved phenotype functions

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Commits on Jul 24, 2023

  1. Removing failed ATP gapfillings from gapfilling sensitivity

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  2. Adding ATP gapfilled reactions to gapfilling sensitivity

    Christopher Henry committed Jul 24, 2023
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Commits on Jul 25, 2023

  1. Fixing bug in gapfill

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  2. Merge branch 'main' of https://github.com/cshenry/ModelSEEDpy

    @cshenry
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Commits on Jul 26, 2023

  1. Fixing bug in ATP media

    @cshenry
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  2. Fixing ATP correction

    Christopher Henry committed Jul 26, 2023
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  3. Merge branch 'main' of github.com:cshenry/ModelSEEDpy

    Christopher Henry committed Jul 26, 2023
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  4. Adding MSModelReport object with Jose's report code

    @cshenry
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  5. Adding filename for report output

    @cshenry
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  6. Fixing report

    @cshenry
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Commits on Aug 2, 2023

  1. Fixing accuracy and output and baseline growth

    @cshenry
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  2. Fixing gapfilling filter saving and complete media

    @cshenry
    cshenry committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. Fixing bug in phenotype accuracy computation

    @cshenry
    cshenry committed Aug 3, 2023
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  2. Fixing gapfilling filter attribute

    @cshenry
    cshenry committed Aug 3, 2023
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  3. Fixing bug in saving of gapfilling filtering

    @cshenry
    cshenry committed Aug 3, 2023
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Commits on Aug 4, 2023

  1. fixing filter saving in attributes

    @cshenry
    cshenry committed Aug 4, 2023
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  2. Removing debugging from filtering code

    @cshenry
    cshenry committed Aug 4, 2023
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Commits on Aug 8, 2023

  1. Adding support for building models from multiple annotations

    @cshenry
    cshenry committed Aug 8, 2023
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  2. Fixing gene hash function

    @cshenry
    cshenry committed Aug 8, 2023
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  3. Fixing add feature function

    @cshenry
    cshenry committed Aug 8, 2023
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  4. Fixing problem with ModelSEEDDatabase reactions

    @cshenry
    cshenry committed Aug 8, 2023
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Commits on Aug 10, 2023

  1. Fixing annotation ontology and build from annotation ontology

    @cshenry
    cshenry committed Aug 10, 2023
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  2. Correcting message output in ontology builder

    @cshenry
    cshenry committed Aug 10, 2023
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Commits on Aug 17, 2023

  1. Checking in first draft of tempalte

    @cshenry
    cshenry committed Aug 17, 2023
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  2. Fixing template

    @cshenry
    cshenry committed Aug 17, 2023
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  3. Updating template

    @cshenry
    cshenry committed Aug 17, 2023
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Commits on Aug 24, 2023

  1. Adding probabilities for ensemble models

    @cshenry
    cshenry committed Aug 24, 2023
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  2. Fixing bug

    @cshenry
    cshenry committed Aug 24, 2023
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  3. Fixing bug in report when gapfilling isn't run

    @cshenry
    cshenry committed Aug 24, 2023
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  4. Updates to report code

    Christopher Henry committed Aug 24, 2023
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  5. Merge branch 'main' of github.com:cshenry/ModelSEEDpy

    Christopher Henry committed Aug 24, 2023
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Commits on Aug 25, 2023

  1. Merge branch 'main' of https://github.com/cshenry/ModelSEEDpy into dev

    @jplfaria
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  2. adding multi tab model report

    @jplfaria
    jplfaria committed Aug 25, 2023
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Commits on Aug 26, 2023

  1. Merge pull request #133 from cshenry/main 

    Checking in annotation ontology model building, biochemistry fixes, growth phenotype analysis, improvements to ATP and gapfilling, and report improvements
    @Fxe
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Commits on Aug 28, 2023

  1. changes to multitab report and redoing gapfilling and atp analysis re… 

    …port
    @jplfaria
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  2. Merge pull request #134 from jplfaria/dev 

    Improvements to Model Report
    @Fxe
    Fxe committed Aug 28, 2023
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Commits on Aug 30, 2023

  1. Fixing bug in report

    @cshenry
    cshenry committed Aug 30, 2023
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  2. Fixing report bug

    @cshenry
    cshenry committed Aug 30, 2023
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Commits on Sep 7, 2023

  1. Debugging media

    @cshenry
    cshenry committed Sep 7, 2023
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  2. Removing debugging

    @cshenry
    cshenry committed Sep 7, 2023
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Commits on Sep 9, 2023

  1. Fixing report

    @cshenry
    cshenry committed Sep 9, 2023
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  2. Fixing report

    @cshenry
    cshenry committed Sep 9, 2023
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  3. Fixing report

    @cshenry
    cshenry committed Sep 9, 2023
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  4. Fixing report

    @cshenry
    cshenry committed Sep 9, 2023
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  5. Slight report correction

    @cshenry
    cshenry committed Sep 9, 2023
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Commits on Sep 11, 2023

  1. Fixing report bugs

    @cshenry
    cshenry committed Sep 11, 2023
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Commits on Sep 13, 2023

  1. Fixing model report encoding

    @cshenry
    cshenry committed Sep 13, 2023
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  2. Fixing report for empty gapfillling data

    @cshenry
    cshenry committed Sep 13, 2023
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  3. Adding annotationontology class to module

    @cshenry
    cshenry committed Sep 13, 2023
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  4. Fixing report for models where gapfilling has an empty solution

    @cshenry
    cshenry committed Sep 13, 2023
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Commits on Sep 14, 2023

  1. utl

    @Fxe
    Fxe committed Sep 14, 2023
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  2. Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev

    @Fxe
    Fxe committed Sep 14, 2023
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  3. balck

    @Fxe
    Fxe committed Sep 14, 2023
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  4. precommit

    @Fxe
    Fxe committed Sep 14, 2023
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  5. ignore examples

    @Fxe
    Fxe committed Sep 14, 2023
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  6. no examples

    @Fxe
    Fxe committed Sep 14, 2023
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Commits on Sep 15, 2023

  1. version bump and atpcorrection media id check

    @Fxe
    Fxe committed Sep 15, 2023
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  2. black

    @Fxe
    Fxe committed Sep 15, 2023
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  3. Merge pull request #136 from Fxe/dev 

    fixing pre commit
    @Fxe
    Fxe committed Sep 15, 2023
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Commits on Sep 21, 2023

  1. Adding function template for gapfilling function from PNNL team

    @cshenry
    cshenry committed Sep 21, 2023
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Commits on Sep 23, 2023

  1. Fixing bug in model reconstruction

    @cshenry
    cshenry committed Sep 23, 2023
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  2. Running black

    @cshenry
    cshenry committed Sep 23, 2023
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  3. Beginning implementation of global gapfill method

    @cshenry
    cshenry committed Sep 23, 2023
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  4. Merge commit '59f7c857b38f55de4ca86b5fc97f07b1e98d8553' 

    # Conflicts:
#	modelseedpy/__init__.py
#	modelseedpy/core/msmodelreport.py
    @cshenry
    cshenry committed Sep 23, 2023
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Commits on Sep 24, 2023

  1. Merge pull request #137 from cshenry/main 

    Fixes related to deploy of MS2 app
    @Fxe
    Fxe committed Sep 24, 2023
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Commits on Oct 10, 2023

  1. update rast call

    @Fxe
    Fxe committed Oct 10, 2023
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  2. Merge branch 'ModelSEED:dev' into dev

    @Fxe
    Fxe committed Oct 10, 2023
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  3. Merge pull request #138 from Fxe/dev 

    remove annotate_proteins_kmer_v1
    @Fxe
    Fxe committed Oct 10, 2023
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Commits on Dec 4, 2023

  1. Created Weighting function for gap fill. Example data required for te… 

    …sting.
    @jjacobson95
    jjacobson95 committed Dec 4, 2023
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Commits on Dec 7, 2023

  1. updated cobra version and template reaction type fix

    @Fxe
    Fxe committed Dec 7, 2023
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  2. format

    @Fxe
    Fxe committed Dec 7, 2023
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  3. Merge pull request #141 from Fxe/dev 

    minor fix
    @Fxe
    Fxe committed Dec 7, 2023
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Commits on Jan 4, 2024

  1. Linted

    @jjacobson95
    jjacobson95 committed Jan 4, 2024
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Commits on Feb 9, 2024

  1. rast regex

    @Fxe
    Fxe committed Feb 9, 2024
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Commits on Feb 14, 2024

  1. Major updates to weighting / expression data function

    @jjacobson95
    jjacobson95 committed Feb 14, 2024
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Commits on Mar 21, 2024

  1. Merge pull request #140 from jjacobson95/dev 

    Created Weighting function for gap fill. Example data needed for testing function.
    @cshenry
    cshenry committed Mar 21, 2024
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Commits on Mar 22, 2024

  1. Update msgapfill.py

    @jjacobson95
    jjacobson95 committed Mar 22, 2024
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  2. linted

    @jjacobson95
    jjacobson95 committed Mar 22, 2024
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  3. re-linted msgapfill.py

    @jjacobson95
    jjacobson95 committed Mar 22, 2024
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Commits on Mar 25, 2024

  1. Merge pull request #142 from jjacobson95/dev 

    Major speed increase for the omics weighting function and edge case bug fix.
    @cshenry
    cshenry committed Mar 25, 2024
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Commits on Apr 9, 2024

  1. Merge branch 'ModelSEED:dev' into dev

    @Fxe
    Fxe committed Apr 9, 2024
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  2. fixes

    @Fxe
    Fxe committed Apr 9, 2024
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  3. black

    @Fxe
    Fxe committed Apr 9, 2024
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  4. added py311

    @Fxe
    Fxe committed Apr 9, 2024
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  5. Merge pull request #144 from Fxe/dev 

    Fix RAST parsing
    @Fxe
    Fxe committed Apr 9, 2024
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Commits on Jun 21, 2024

  1. biochem

    @Fxe
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  2. Merge branch 'ModelSEED:dev' into dev

    @Fxe
    Fxe committed Jun 21, 2024
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Commits on Jul 9, 2024

  1. bump 4.0 swapped pyeda for sympy

    @Fxe
    Fxe committed Jul 9, 2024
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  2. Merge branch 'dev' of github.com:Fxe/ModelSEEDpy into dev

    @Fxe
    Fxe committed Jul 9, 2024
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  3. mixed line endings

    @Fxe
    Fxe committed Jul 9, 2024
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  4. pragmas

    @Fxe
    Fxe committed Jul 9, 2024
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  5. Merge pull request #145 from Fxe/dev 

    bumped to version 0.4.0
    @Fxe
    Fxe committed Jul 9, 2024
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  6. readne

    @Fxe
    Fxe committed Jul 9, 2024
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  7. Merge branch 'ModelSEED:dev' into dev

    @Fxe
    Fxe committed Jul 9, 2024
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  8. Merge pull request #146 from Fxe/dev 

    readme
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    Fxe committed Jul 9, 2024
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Commits on Sep 4, 2024

  1. genome

    @Fxe
    Fxe committed Sep 4, 2024
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Commits on Sep 26, 2024

  1. reaction pathways

    @Fxe
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  2. black

    @Fxe
    Fxe committed Sep 26, 2024
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  3. Merge pull request #149 from Fxe/dev 

    msatpcorrection.py default path + reactions pathways
    @Fxe
    Fxe committed Sep 26, 2024
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