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Develop → master merge for v1.4.1 #682

Merged
merged 79 commits into from
Oct 14, 2022
Merged

Develop → master merge for v1.4.1 #682

merged 79 commits into from
Oct 14, 2022

Commits on Aug 5, 2022

  1. remove banner

    @stelmo
    stelmo committed Aug 5, 2022
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Commits on Aug 30, 2022

  1. bump CompatHelper version to work with 1.8

    @exaexa
    exaexa committed Aug 30, 2022
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  2. update to latest compathelper script version

    @exaexa
    exaexa committed Aug 30, 2022
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  3. Merge pull request #658 from LCSB-BioCore/mk-fix-ch-dev 

    Update compathelper CI script
    @laurentheirendt
    laurentheirendt committed Aug 30, 2022
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  4. fix return bug

    @stelmo
    stelmo committed Aug 30, 2022
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  5. add DSE and update analysis

    @stelmo
    stelmo committed Aug 30, 2022
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  6. done log and macros (left some)

    @stelmo
    stelmo committed Aug 30, 2022
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  7. log

    @stelmo
    stelmo committed Aug 30, 2022
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  8. done types functions

    @stelmo
    stelmo committed Aug 30, 2022
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  9. done with functions

    @stelmo
    stelmo committed Aug 30, 2022
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  10. done with fields and types

    @stelmo
    stelmo committed Aug 30, 2022
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  11. fix fields

    @stelmo
    stelmo committed Aug 30, 2022
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Commits on Aug 31, 2022

  1. add DSE compat entry (silence Aqua)

    @exaexa
    exaexa committed Aug 31, 2022
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  2. fix review

    @stelmo
    stelmo committed Aug 31, 2022
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  3. add DSE for reaction math

    @stelmo
    stelmo committed Aug 31, 2022
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  4. add DSe for model wrappers

    @stelmo
    stelmo committed Aug 31, 2022
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  5. Merge branch 'mo-dse' of https://github.com/LCSB-BioCore/COBREXA.jl i… 

    …nto mo-dse
    @stelmo
    stelmo committed Aug 31, 2022
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  6. automatic formatting 

    triggered by @stelmo on PR #661
    @stelmo
    stelmo committed Aug 31, 2022
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  7. Merge pull request #661 from LCSB-BioCore/mo-dse 

    Finally add DocStringExtensions 🥳
    @stelmo
    stelmo committed Aug 31, 2022
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  8. add metabolite constructor

    @stelmo
    stelmo committed Aug 31, 2022
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  9. add gene constructor and format

    @stelmo
    stelmo committed Aug 31, 2022
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  10. remove hidden constructor

    @stelmo
    stelmo committed Aug 31, 2022
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  11. add default arg

    @stelmo
    stelmo committed Aug 31, 2022
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  12. add DSEs

    @stelmo
    stelmo committed Aug 31, 2022
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  13. automatic formatting 

    triggered by @stelmo on PR #654
    @stelmo
    stelmo committed Aug 31, 2022
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  14. Merge pull request #659 from LCSB-BioCore/mo-pfba-fix 

    Fix pFBA issue with return type nothing
    @exaexa
    exaexa committed Aug 31, 2022
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  15. Merge pull request #654 from LCSB-BioCore/mo-constructors 

    Add some constructors
    @stelmo
    stelmo committed Aug 31, 2022
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Commits on Sep 2, 2022

  1. add an explanation of what happens when you gapfill a feasible model 

    Closes #653
    @exaexa
    exaexa committed Sep 2, 2022
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  2. Merge pull request #662 from LCSB-BioCore/mk-gapfill-doc 

    add an explanation of what happens when you gapfill a feasible model
    @exaexa
    exaexa committed Sep 2, 2022
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  3. add banner to module docstring

    @stelmo
    stelmo committed Sep 2, 2022
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  4. fix alignment

    @stelmo
    stelmo committed Sep 2, 2022
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  5. add back some consts and make docstring nicer

    @stelmo
    stelmo committed Sep 2, 2022
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  6. tune up the ?COBREXA docstring

    @exaexa
    exaexa committed Sep 2, 2022
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  7. Merge pull request #649 from LCSB-BioCore/mo-remove-banner 

    Remove the banner
    @stelmo
    stelmo committed Sep 2, 2022
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Commits on Sep 3, 2022

  1. add sbo constants

    @stelmo
    stelmo committed Sep 3, 2022
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  2. add exchange reaction

    @stelmo
    stelmo committed Sep 3, 2022
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  3. Update src/base/sbo.jl 

    Co-authored-by: Mirek Kratochvil <exa.exa@gmail.com>
    @stelmo @exaexa
    stelmo and exaexa committed Sep 3, 2022
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  4. fix module

    @stelmo
    stelmo committed Sep 3, 2022
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  5. make future proof

    @stelmo
    stelmo committed Sep 3, 2022
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  6. format and change names

    @stelmo
    stelmo committed Sep 3, 2022
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  7. update modules

    @stelmo
    stelmo committed Sep 3, 2022
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  8. use all the macros!

    @stelmo
    stelmo committed Sep 3, 2022
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  9. automatic formatting 

    triggered by @stelmo on PR #667
    @stelmo
    stelmo committed Sep 3, 2022
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  10. add tests

    @stelmo
    stelmo committed Sep 3, 2022
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  11. Merge branch 'mo-sbo' of https://github.com/LCSB-BioCore/COBREXA.jl i… 

    …nto mo-sbo
    @stelmo
    stelmo committed Sep 3, 2022
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  12. automatic formatting 

    triggered by @stelmo on PR #667
    @stelmo
    stelmo committed Sep 3, 2022
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  13. less strings

    @stelmo
    stelmo committed Sep 3, 2022
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  14. fix docstring

    @stelmo
    stelmo committed Sep 3, 2022
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  15. automatic formatting 

    triggered by @stelmo on PR #667
    @stelmo
    stelmo committed Sep 3, 2022
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  16. add notes to docstrings

    @stelmo
    stelmo committed Sep 3, 2022
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  17. Merge branch 'mo-sbo' of https://github.com/LCSB-BioCore/COBREXA.jl i… 

    …nto mo-sbo
    @stelmo
    stelmo committed Sep 3, 2022
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  18. automatic formatting 

    triggered by @stelmo on PR #667
    @stelmo
    stelmo committed Sep 3, 2022
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  19. fix docstring

    @stelmo
    stelmo committed Sep 3, 2022
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  20. Merge branch 'mo-sbo' of https://github.com/LCSB-BioCore/COBREXA.jl i… 

    …nto mo-sbo
    @stelmo
    stelmo committed Sep 3, 2022
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  21. automatic formatting 

    triggered by @stelmo on PR #667
    @stelmo
    stelmo committed Sep 3, 2022
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  22. Merge pull request #667 from LCSB-BioCore/mo-sbo 

    Add SBO terms
    @stelmo
    stelmo committed Sep 3, 2022
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Commits on Sep 5, 2022

  1. change OSQP to Clarabel in tests 

    Currently this requires a #dev version of Clarabel
    @exaexa
    exaexa committed Sep 5, 2022
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  2. fmt

    @exaexa
    exaexa committed Sep 5, 2022
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Commits on Sep 10, 2022

  1. CompatHelper: bump compat for SBML to 1, (keep existing compat)

    CompatHelper Julia committed Sep 10, 2022
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Commits on Sep 11, 2022

  1. be a bit more careful with SBML version bounds

    @exaexa
    exaexa committed Sep 11, 2022
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  2. Merge pull request #670 from LCSB-BioCore/compathelper/new_version/20… 

    …22-09-10-02-40-32-218-02454686738

CompatHelper: bump compat for SBML to 1, (keep existing compat)
    @exaexa
    exaexa committed Sep 11, 2022
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Commits on Sep 14, 2022

  1. bump Clarabel compat

    @exaexa
    exaexa committed Sep 14, 2022
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  2. limit jump versions to prevent MAX_SENSE breakage

    @exaexa
    exaexa committed Sep 14, 2022
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  3. limit more

    @exaexa
    exaexa committed Sep 14, 2022
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  4. ok JuMP we'll use your senses

    @exaexa
    exaexa committed Sep 14, 2022
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Commits on Sep 22, 2022

  1. Merge pull request #669 from LCSB-BioCore/mk-clarabel 

    use Clarabel instd of OSQP
    @stelmo
    stelmo committed Sep 22, 2022
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Commits on Sep 27, 2022

  1. improve SBML import and export 

    - support CVTerms-based annotations in the usual way
  (thanks COBRApy for inspiration!)
- fix minor issues with notes and formula export
- prevent problems when exporting (some) non-SBMLizable metabolite names
    @exaexa
    exaexa committed Sep 27, 2022
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  2. bump minor version 

    (I need to depend on the fixes here)
    @exaexa
    exaexa committed Sep 27, 2022
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  3. fix missing formulas

    @exaexa
    exaexa committed Sep 27, 2022
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  4. Merge pull request #676 from LCSB-BioCore/mk-sbml-annot 

    Make the SBML annotations work just like with JSON models
    @exaexa
    exaexa committed Sep 27, 2022
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  5. docs: reflect the solver change in Project.toml

    @exaexa
    exaexa committed Sep 27, 2022
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  6. Merge pull request #677 from LCSB-BioCore/mk-clean-osqp 

    docs: reflect the solver change in Project.toml
    @exaexa
    exaexa committed Sep 27, 2022
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Commits on Oct 13, 2022

  1. import JuMP to allow touching MAX/MIN_SENSE

    @exaexa
    exaexa committed Oct 13, 2022
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  2. Merge pull request #679 from LCSB-BioCore/mk-fix-doc-build-jump-sense 

    fix docbuild: JuMP `MIN_SENSE` and `MAX_SENSE` disappeared
    @exaexa
    exaexa committed Oct 13, 2022
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Commits on Oct 14, 2022

  1. remove polish parameter specific to osqp

    @exaexa
    exaexa committed Oct 14, 2022
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  2. automatic formatting 

    triggered by @exaexa on PR #681
    @exaexa
    exaexa committed Oct 14, 2022
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  3. Merge pull request #681 from LCSB-BioCore/mk-remove-osqp-remains 

    remove `polish` parameter specific to osqp
    @exaexa
    exaexa committed Oct 14, 2022
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  4. Merge branch 'master' into mk-fix-mergeability

    @exaexa
    exaexa committed Oct 14, 2022
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  5. Merge pull request #683 from LCSB-BioCore/mk-fix-mergeability 

    backmerge `master` changes to `develop` to resolve merge conflicts
    @exaexa
    exaexa committed Oct 14, 2022
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