New msmodelutl by freiburgermsu · Pull Request #18 · cshenry/ModelSEEDpy

Commits on Sep 16, 2021

kinetics and uptake Notebooks
sequoia
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Commits on Sep 17, 2021

FBAHelper unit-test corection

Andrew Freiburger
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Andrew Freiburger
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Merge branch 'main' of https://github.com/freiburgermsu/ModelSEEDpy into main

Andrew Freiburger
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Andrew Freiburger
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FBAHelper unit-test corection

Andrew Freiburger
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Andrew Freiburger
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Commits on Sep 21, 2021

drafting the dFBA package and Notebook example

Andrew Freiburger
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Andrew Freiburger
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Commits on Sep 22, 2021

drafting the dFBA package and Notebook example

Andrew Freiburger
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dFBA package with legacy BaseFBAPkg logic

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final dFBA package logic and Notebook

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Commits on Sep 23, 2021

dFBA unit-test

Andrew Freiburger
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Commits on Apr 27, 2022

resolve merge conflicts

Andrew Freiburger
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Andrew Freiburger
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Commits on May 4, 2022

MSCommunity model+examples, MSmodel pyEDA load, and MScompatibility

Andrew Freiburger
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Commits on May 5, 2022

MScompatibility clarification and polishing

Andrew Freiburger
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Merge branch 'main' into main
freiburgermsu
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MScompatibility finalization and Biohem utils simplification

Andrew Freiburger
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Andrew Freiburger
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Merge branch 'main' of https://github.com/freiburgermsu/ModelSEEDpy into main

Andrew Freiburger
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MScompatibility finalization and Biohem utils simplification

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polishing for PR

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MSCompatibility Notebook

Andrew Freiburger
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MSCompatibility standardize_MSD patch

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quick fix

Andrew Freiburger
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Commits on May 6, 2022

dFBA draft module and preliminary Notebooks and unit-test

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dFBA script and unit-test

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Commits on May 7, 2022

dFBApkg script adjustment, with operational Notebooks

Andrew Freiburger
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dFBA docs and minor edits of dFBAand its Notebooks

Andrew Freiburger
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Commits on May 10, 2022

API docs and ReadTheDocs assemblage

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docs correction

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docs correction

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docs correction

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index copied to the docs root directory

Andrew Freiburger
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update the documentation

Andrew Freiburger
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Update README.rst
freiburgermsu
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Update index.rst
freiburgermsu
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update the docs indices

Andrew Freiburger
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update the docs indices and associated edits to resolve bugs

Andrew Freiburger
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Commits on May 11, 2022

MSCompatibility updates

Andrew Freiburger
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Andrew Freiburger
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Commits on May 13, 2022

MSCompatibility edits

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operational draft of MSCompatibility

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updated draft of MSCompatibility

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Merge branch 'main' into main
freiburgermsu
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Commits on May 14, 2022

refined draft, with extended functionality, of MSCompatibility

Andrew Freiburger
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Andrew Freiburger
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Merge branch 'main' of https://github.com/freiburgermsu/ModelSEEDpy into main

Andrew Freiburger
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export functionality of MSCompatibility and examples files

Andrew Freiburger
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Andrew Freiburger
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Commits on May 15, 2022

network visualization and associated features for MSCommunity +reorganization of the examples folder and files

Andrew Freiburger
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dFBA metabolite variables draft

Andrew Freiburger
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Commits on May 16, 2022

metabolites variables draft dFBA and LPfile

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MSCompatibility fix and updated zip file

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MSCompatibility polishing

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Commits on May 20, 2022

chemostat dFBA

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Commits on May 21, 2022

docs update

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docs update

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docs update

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docs update

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Commits on May 24, 2022

documentation and associated polishing

Andrew Freiburger
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documentation and associated polishing

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Commits on May 25, 2022

fbapkg documentation and associated polishing

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reindexing the docs pages

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polishing the existing docs drafts

Andrew Freiburger
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README updates

Andrew Freiburger
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Update README.rst
freiburgermsu
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Commits on May 27, 2022

core documentation

Andrew Freiburger
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Andrew Freiburger
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Commits on Jun 7, 2022

API doc updates and Julia tests

Andrew Freiburger
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corrected modules and Julia comparison
freiburgermsu
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Commits on Jun 8, 2022

Commits on Jun 10, 2022

docs, package edits, and organization

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minor edits for TRAVIS

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passing unit tests

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Commits on Jun 11, 2022

docs updates before upstream fetch

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merged with Chris' MSCommunity in the core directory

Andrew Freiburger
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Commits on Jun 13, 2022

docs and removed self-referential import in requirements

Andrew Freiburger
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Update requirements.txt
freiburgermsu
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remove versions from requirement.txt, ReadTheDocs
freiburgermsu
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RSTedits for improves ReadTheDocs

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Merge branch 'main' of https://github.com/freiburgermsu/ModelSEEDpy into main

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docs indices were updated

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final core docs drafts

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operational code logic

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republicized function names, main setup path, and relocated requiremenets.txt file

Andrew Freiburger
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Commits on Jun 15, 2022

reverted revisions

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improved revisions

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improved revisions

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Commits on Jun 20, 2022

community and FBAHelper additions

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dfbapkg minor edit

Andrew Freiburger
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Andrew Freiburger
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Commits on Jun 22, 2022

exceptions file and dfba edits

Andrew Freiburger
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Merge branch 'main' into MSmain
freiburgermsu
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Merge pull request #2 from freiburgermsu/MSmain
freiburgermsu
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concessions for modelseed PR

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edits for modelseed PR

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mild edits for main PR

Andrew Freiburger
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Merge pull request #3 from freiburgermsu/MSmain
freiburgermsu
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Merge branch 'main' of https://github.com/freiburgermsu/ModelSEEDpy into main

Andrew Freiburger
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Andrew Freiburger
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Commits on Jun 25, 2022

exceptions and gapfill concession

Andrew Freiburger
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Commits on Jun 26, 2022

Commits on Jun 28, 2022

parse_df update to proper np.arrays

Andrew Freiburger
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Commits on Jun 29, 2022

fbahelper polishing

Andrew Freiburger
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fbahelper polishing

Andrew Freiburger
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Commits on Jun 30, 2022

fbahelper polishing

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Commits on Jul 1, 2022

exceptions expansion

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Commits on Jul 2, 2022

msmodelutl edits

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inital commit

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msmodelutls polishing

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msmodelutls polishing

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exceptions.py expansion

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rearrange the fullthermo functions

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Commits on Jul 3, 2022

initial commit

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polishing edits

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polishing edits

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polishing edits

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polishing edits

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polishing edits

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initial ocmmit

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initial ocmmit

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initial ocmmit

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initial ocmmit

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polishing edits

Andrew Freiburger
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initial commit

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polishing edits

Andrew Freiburger
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polishing edits

Andrew Freiburger
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Commits on Jul 4, 2022

docs and example integration

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restoration of the source docs directory

Andrew Freiburger
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update the requirements TXTfor ReadTheDaocs

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adjust the autoAPI import for ReadTheDaocs

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comment-out logic for autogeneration of documentation

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move index to the main docs page

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ReadTheDocs YAML addition

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slimmed requirements and deleted redundant index file

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removed readthedocs.yaml file

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restored readthedocs.yaml file and blank line in toctree

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adjust docs index and add Notebook extensions to stimulate.rst

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docs dorrections

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relocate simulate_nb and justified case-sensitive directory references

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docs updates and polishing

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polishing Notebooks

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polishing Notebooks

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polishing Notebooks

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API includehidden tag

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updated docs and associated examples for the docs

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webinar links

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Merge branch 'main' into docs_examples
freiburgermsu
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Merge pull request #5 from freiburgermsu/docs_examples
freiburgermsu
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update docs and examples

Andrew Freiburger
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update docs and examples

Andrew Freiburger
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Commits on Jul 6, 2022

Update index.ipynb
freiburgermsu
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Commits on Jul 9, 2022

API landing page update

Andrew Freiburger
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Andrew Freiburger
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Merge branch 'main' of https://github.com/freiburgermsu/ModelSEEDpy into main

Andrew Freiburger
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Commits on Jul 10, 2022

API landing update and lowercase API titles

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update toctree spacing in API landing

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final API landing update

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final API landing update

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headers for API landing

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Commits on Jul 12, 2022

Merge pull request #75 from ModelSEED/dev
Fxe
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Commits on Jul 16, 2022

MSCommFitting API docs and community docs polishing

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MSCommFitting API docs and community docs polishing

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MSCommFitting added to the community index

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removed individual directory indices

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Commits on Jul 23, 2022

exceptions update and setup correction to permit downloads

Andrew Freiburger
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msmodelutl polishing

Andrew Freiburger
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revert multi-statement line and logger location
freiburgermsu
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Commits on Jul 27, 2022

MSCommunity and edits associated with SMETANA

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merge conflicts

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MSCommunity debugging

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MSCommunity debugging and FBAHelper expansion

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Commits on Jul 28, 2022

MSCommunity debugging

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Commits on Aug 3, 2022

MSCommunity debugging and Utility function additions

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Commits on Aug 4, 2022

MSCommunity and FBAHelper edits

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Commits on Aug 5, 2022

MSCommunity, MSCompatability, and associated edits

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Commits on Aug 6, 2022

community edits

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Commits on Aug 17, 2022

MSCompibility edits

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MSCompibility edits

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MSCompibility edits

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Commits on Aug 18, 2022

MSCompibility and MSCommunity edits

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Commits on Aug 19, 2022

MSCompibility staticmethod completion and the associated updates to the documentation

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Commits on Aug 23, 2022

Commits on Aug 24, 2022

MSCompatibility edits
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Commits on Aug 25, 2022

MSCompatilibity and MSCommunity edits

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MSCompatilibity merge correction

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Commits on Aug 26, 2022

MSCompatilibity updates towards debugging the jenga method

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Commits on Aug 27, 2022

OptlangHelper expansion with a recursive expression definition

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Commits on Aug 28, 2022

OptlangHelper expansion with dot products

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Commits on Aug 29, 2022

OptlangHelper finalization and mscompatibility updates

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Commits on Aug 30, 2022

MSCompatibility and minimal_media updates

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Compatibility edits
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Commits on Aug 31, 2022

MSSCommFitting dictionary composition

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remove print debugger from OptlganHelper

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finalized MSCompatibility package and Notebook

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Commits on Sep 2, 2022

minor MSCompatibility edits ; setup dependencies

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Commits on Sep 3, 2022

minor Jenga edits in MSCommunity

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Commits on Sep 6, 2022

Cleaning directories and Jenga method edits

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Commits on Sep 8, 2022

MILP ReactionUsePkg Minimal Media progress

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Commits on Sep 10, 2022

MinimalMediaPkg development and JENGA method relocation

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Commits on Sep 13, 2022

Commits on Sep 14, 2022

Commits on Sep 15, 2022

reorganization; build_from_species and mscompatibility edits; and __init__ corrections

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final polish

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Commits on Sep 16, 2022

build_from_species and minimal media operations

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Commits on Sep 18, 2022

basefba merge conflict resolution

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bilevel merge conflict resolution

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flexiblebiomass merge conflict resolution

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fluxfittingpkg and reactionusepkg merge conflict resolutions

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Merge branch 'ModelSEED:main' into main
freiburgermsu
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MSCompatibility and MinimalMediaPkg edits

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Commits on Sep 19, 2022

MSCompatibility and build_from_species edits

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Commits on Sep 21, 2022

MSSmetana addition and reorganized community sub-library

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Commits on Sep 23, 2022

MSSmetana & MinimalMediaPkg editsin complete draft

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Commits on Sep 30, 2022

examine community pairs in SMETNAA

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10-member pairs

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Commits on Oct 2, 2022

MSSmetana assessment with 10-member comm pairs

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rename to MSMinimalMedia

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correct rename in MSMinimalMedia

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statistical assessment of the pairs via SMETANA

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Commits on Oct 6, 2022

merge conflict resolution with Chris' fork
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Commits on Oct 11, 2022

SMETANA code revision and Notebook expansion for PMI presentation

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Commits on Oct 18, 2022

CommKinetics and MSCommunity edits

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Commits on Oct 20, 2022

parsed SteadyCom and CommHelper from MSCommunity ; simulations for All-Hands presentation

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Commits on Oct 21, 2022

rename steadycom

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pair Notebook revision for Alexis

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New msmodelutl#18freiburgermsu wants to merge 231 commits intocshenry:devcshenry/ModelSEEDpy:devfrom freiburgermsu:new_msmodelutlfreiburgermsu/ModelSEEDpy:new_msmodelutlCopy head branch name to clipboard

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New msmodelutl#18
freiburgermsu wants to merge 231 commits intocshenry:devfrom
freiburgermsu:new_msmodelutl