Commits · master · LCSB-BioCore / COBREXA.jl

This project is mirrored from https://github.com/LCSB-BioCore/COBREXA.jl.git. Pull mirroring updated Jul 29, 2021.

28 Jul, 2021 5 commits
- Merge pull request #401 from LCSB-BioCore/simplify-mechanism · 3a65889b
  Miroslav Kratochvil authored Jul 28, 2021
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simplify trigger mechanism
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  3a65889b
- simplify trigger mechanism · a467ea98
  Laurent Heirendt authored Jul 28, 2021
  
  a467ea98
- Merge pull request #400 from LCSB-BioCore/mk-issue-templates · 51f6f8f3
  Miroslav Kratochvil authored Jul 28, 2021
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slightly more useful issue/PR templates
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  51f6f8f3
- a new PR template · 20bd283e
  Miroslav Kratochvil authored Jul 28, 2021
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closes #110
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  20bd283e
- slightly more useful issue templates · 543971c2
  Miroslav Kratochvil authored Jul 28, 2021
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refs #110
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  543971c2
27 Jul, 2021 6 commits
- Merge pull request #399 from LCSB-BioCore/mk-clean-name · 9a2b22ee
  Miroslav Kratochvil authored Jul 27, 2021
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unsupport `name` field in models
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  9a2b22ee
- unsupport `name` field in models · ec9b7e1b
  Miroslav Kratochvil authored Jul 27, 2021
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It looks great but we aren't going to support it in core MetabolicModel
interface. Moreover, it's only a prettification, which the users may manage
externally.

Closes #392 (name support will be implemented elsewhere)
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  ec9b7e1b
- Merge pull request #398 from LCSB-BioCore/mk-sbml06-compat · 37d30cb8
  Miroslav Kratochvil authored Jul 27, 2021
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compatibility with SBML 0.6
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  37d30cb8
- compatibility with SBML 0.6 · bacd6f6d
  Miroslav Kratochvil authored Jul 27, 2021
  
  bacd6f6d
- Merge pull request #395 from LCSB-BioCore/mk-model-cleanup · 1b2fa49e
  Laurent Heirendt authored Jul 27, 2021
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improve jsonmodel speed + some extra cleanup
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  1b2fa49e
- explain new JSONModel structure · b513e824
  Miroslav Kratochvil authored Jul 27, 2021
  
  b513e824
26 Jul, 2021 4 commits
- finish the cleanup, fix bug, format · 7c96bbd9
  Miroslav Kratochvil authored Jul 26, 2021
  
  7c96bbd9
- clean up reaction_stoichiometry comments · b46d0045
  Miroslav Kratochvil authored Jul 26, 2021
  
  b46d0045
- style and clean up some code, esp. unify reaction_stoichiometry · 25577855
  Miroslav Kratochvil authored Jul 26, 2021
  
  25577855
- clean up in JSONModel, use indexes to avoid linear array search · fbf9afdd
  Miroslav Kratochvil authored Jul 26, 2021
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Closes #350
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  fbf9afdd
21 Jul, 2021 1 commit
- Merge pull request #387 from LCSB-BioCore/mo-makie · ad76b3e2
  Laurent Heirendt authored Jul 21, 2021
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Use Makie instead of Plots
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  ad76b3e2
20 Jul, 2021 6 commits
- increase number of displayed reactions · 70edc80f
  St. Elmo authored Jul 20, 2021
  
  70edc80f
- format · da87177b
  St. Elmo authored Jul 20, 2021
  
  da87177b
- added Makie · 9ec83298
  St. Elmo authored Jul 20, 2021
  
  9ec83298
- Merge pull request #386 from LCSB-BioCore/lh-fix-cd-containers · 6ea062d4
  Laurent Heirendt authored Jul 20, 2021
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Fix deployment of container images
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  6ea062d4
- add specific rule for singularity deployment · a9145852
  Laurent Heirendt authored Jul 20, 2021
  
  a9145852
- add specific rule for docker deployment · a8a2026c
  Laurent Heirendt authored Jul 20, 2021
  
  a8a2026c
15 Jul, 2021 1 commit
- Merge pull request #384 from LCSB-BioCore/mk-dev-docs-link · fed7cfe1
  Laurent Heirendt authored Jul 15, 2021
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some cosmetic README touches, dev doc links
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  fed7cfe1
10 Jul, 2021 15 commits
- some cosmetic README touches, dev doc links · e12e1712
  Miroslav Kratochvil authored Jul 10, 2021
  
  e12e1712
- Merge pull request #383 from LCSB-BioCore/mk-final-doc-fixes · f5c7abc7
  Miroslav Kratochvil authored Jul 10, 2021
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final doc fixes for 1.0.3
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  f5c7abc7
- fix Reaction docs · da3def7b
  Miroslav Kratochvil authored Jul 10, 2021
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closes #381
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  da3def7b
- finalize docs for 1.0.3 · f14566e6
  Miroslav Kratochvil authored Jul 10, 2021
  
  f14566e6
- eradicate with_set_bound · 266edf66
  Miroslav Kratochvil authored Jul 10, 2021
  
  266edf66
- Merge pull request #380 from LCSB-BioCore/mk-bump-103 · fa0f82f2
  Miroslav Kratochvil authored Jul 10, 2021
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bump version to 1.0.3
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  fa0f82f2
- bump version · d485aed5
  Miroslav Kratochvil authored Jul 10, 2021
  
  d485aed5
- Merge pull request #379 from LCSB-BioCore/mo-doc-fix-change-bounds · 1c17b4fe
  Miroslav Kratochvil authored Jul 10, 2021
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Fix argument error in community model notebook
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  1c17b4fe
- Merge pull request #378 from LCSB-BioCore/mk-format-fix · 97be9bbb
  Miroslav Kratochvil authored Jul 10, 2021
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formatting report fix: break the line after code quote properly
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  97be9bbb
- Merge pull request #377 from LCSB-BioCore/mk-rm-trailing-ws · cec68ffa
  Miroslav Kratochvil authored Jul 10, 2021
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code cleanup before release
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  cec68ffa
- fix doc error · ea1a1c14
  St. Elmo authored Jul 10, 2021
  
  ea1a1c14
- Merge pull request #372 from LCSB-BioCore/mk-const-functions · 17a761ce
  Miroslav Kratochvil authored Jul 10, 2021
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do not define function as (non-const) variables
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  17a761ce
- remove leftover documentation · 552f105d
  Miroslav Kratochvil authored Jul 10, 2021
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Fixes #374
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  552f105d
- fix all whitespace errors and trails · c70eb6ef
  Miroslav Kratochvil authored Jul 10, 2021
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Closes #375
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  c70eb6ef
- Merge pull request #346 from LCSB-BioCore/mo-homo-set-change-bound · fcaedc5b
  Miroslav Kratochvil authored Jul 10, 2021
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Change `set_bound` to `change_bound` to fit in with `CoreModel` functions
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  fcaedc5b
09 Jul, 2021 2 commits
- Merge pull request #376 from LCSB-BioCore/mk-homo-set-minimize · a67eaec3
  St. Elmo authored Jul 09, 2021
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minimize the change_bound generator macro
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  a67eaec3
- minimize the change_bound generator macro · 412a0061
  Miroslav Kratochvil authored Jul 09, 2021
  
  412a0061