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Linting - #55

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vmspereira wants to merge 57 commits into

BioSystemsUM:masterfrom

vmspereira:linting

Commits on Jun 9, 2024
- Merge pull request #2 from vmspereira/vpereira/dev
  vmspereira
  authored
  f7afa08
- [delete] duplicate
  vmspereira
  committed
  eb9e757
Commits on Jun 19, 2024
- [UPDATE] Normalize comunity flux option
  vmspereira
  committed
  aedf204
Commits on Jun 22, 2024
- version 0.1.35
  vmspereira
  committed
  4234559
- Merge pull request #3 from vmspereira/vpereira/dev
  vmspereira
  authored
  65aebb4
- Update README
  vmspereira
  committed
  550b66b
- Update workflow
  vmspereira
  committed
  0296164
Commits on Jun 24, 2024
- Update notebooks
  vmspereira
  committed
  81c5abf
Commits on Jun 28, 2024
- Merge pull request #4 from vmspereira/dev
  vmspereira
  authored
  02b5b00
- Update notebooks
  vmspereira
  committed
  f8e2dd9
- Merge pull request #5 from vmspereira/dev
  vmspereira
  authored
  d20a7ef
Commits on Jun 29, 2024
- Update notebooks
  vmspereira
  committed
  c4f94f1
- Add exchanges analysis for communities
  vmspereira
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  07b14e4
- Bump to version 0.1.36
  vmspereira
  committed
  49b6be4
- Merge pull request #6 from vmspereira/dev
  vmspereira
  authored
  987c45c
- update docs
  vmspereira
  committed
  3388664
- Merge pull request #7 from vmspereira/dev
  vmspereira
  authored
  b2b286c
- add readthedocs yaml
  vmspereira
  committed
  96c6583
- Merge pull request #8 from vmspereira/dev
  vmspereira
  authored
  b8d0ed1
- update docs requirements
  vmspereira
  committed
  cfb45a0
- Merge pull request #9 from vmspereira/dev
  vmspereira
  authored
  fa50d7e
Commits on Dec 14, 2024
- [UPDATE] parsing
  vmspereira
  committed
  f708998
- [UPDATE] copasi function definitions support
  vmspereira
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  a31b911
- [ADD] example
  vmspereira
  committed
  d197ecb
Commits on Dec 15, 2024
- Bump to version 1.0.0
  vmspereira
  committed
  d0b0fe8
- update action
  vmspereira
  committed
  3bf69b0
- Merge pull request #10 from vmspereira/dev
  vmspereira
  authored
  dc21b32
Commits on Jul 30, 2025
- update install and dependencies
  vpereira01
  committed
  90a9b91
- update artifacts version
  vpereira01
  committed
  3213fa6
- update tox & CI
  vpereira01
  committed
  3b9243e
- Merge pull request #11 from vmspereira/dev/update_install
  vmspereira
  authored
  519fd04
- refurbish germ
  vpereira01
  committed
  0ebfab6
- bux fix
  vpereira01
  committed
  f7e2582
Commits on Nov 24, 2025
- wip
  vpereira01
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  b975627
- fix dependencies
  vpereira01
  committed
  24a0031
- add PySCIPOpt support
  vpereira01
  committed
  9999a7e
- fix unit tests
  vpereira01
  committed
  221ccfe
- Merge pull request #12 from vmspereira/dev/update_install
  vmspereira
  authored
  b4e6cca
- Merge master into dev/germ: Update dependencies and add PySCIPOpt solver
  vpereira01
  committed
  d759979
Commits on Dec 26, 2025
- refactor: clean GERM architecture for cobrapy/reframed integration
  vpereira01
  committed
  0039b3e
- Add backwards compatibility for GERM analysis methods
  vpereira01
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  5afd093
- clean up
  vpereira01
  committed
  0650b1d
- clean up
  vpereira01
  committed
  6e7c5d4
- Add convenient factory methods for RegulatoryExtension
  vmspereira
  committed
  43aa818
- Change default backend to reframed (more lightweight)
  vmspereira
  committed
  85dbfaf
- Fix scientific correctness issues in GERM analysis methods
  vmspereira
  committed
  c8814a2
- Sprint 1: Code quality quick wins
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  681f33f
- Sprint 2 (partial): API consistency improvements
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  committed
  f262bac
- Sprint 4: Tests and migration guide
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  committed
  93c71d7
- Add comprehensive improvement summary documentation
  vmspereira
  committed
  88fe895
- Fix RFBA test to handle infeasible solutions correctly
  vmspereira
  committed
  649aff2
- clean up
  vmspereira
  committed
  356da0e
- Fix get_reaction AttributeError in GERM analysis methods
  vmspereira
  committed
  6952df9
- Fix CPLEX solver to return all variable values
  vmspereira
  committed
  872f842
- Fix pFBA to handle dynamic constraints correctly
  vmspereira
  committed
  8fffa5c
- Merge pull request #13 from vmspereira/dev/germ
  vmspereira
  authored
  3ff01e1
- flake8 and black
  vmspereira
  committed
  d47d52f

Commits

Commits on Jun 9, 2024

Commits on Jun 19, 2024

Commits on Jun 22, 2024

Commits on Jun 24, 2024

Commits on Jun 28, 2024

Commits on Jun 29, 2024

Commits on Dec 14, 2024

Commits on Dec 15, 2024

Commits on Jul 30, 2025

Commits on Nov 24, 2025

Commits on Dec 26, 2025