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fix: duplicates in ExpressionSet - #56

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vmspereira wants to merge 190 commits into

BioSystemsUM:masterfrom

vmspereira:repre2

Commits on Jun 9, 2024
- Merge pull request #2 from vmspereira/vpereira/dev
  vmspereira
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  f7afa08
- [delete] duplicate
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  eb9e757
Commits on Jun 19, 2024
- [UPDATE] Normalize comunity flux option
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Commits on Jun 22, 2024
- version 0.1.35
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- Merge pull request #3 from vmspereira/vpereira/dev
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- Update README
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- Update workflow
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Commits on Jun 24, 2024
- Update notebooks
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  81c5abf
Commits on Jun 28, 2024
- Merge pull request #4 from vmspereira/dev
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- Update notebooks
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- Merge pull request #5 from vmspereira/dev
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Commits on Jun 29, 2024
- Update notebooks
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- Add exchanges analysis for communities
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- Bump to version 0.1.36
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- Merge pull request #6 from vmspereira/dev
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- update docs
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- Merge pull request #7 from vmspereira/dev
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- add readthedocs yaml
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- Merge pull request #8 from vmspereira/dev
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- update docs requirements
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- Merge pull request #9 from vmspereira/dev
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Commits on Dec 14, 2024
- [UPDATE] parsing
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- [UPDATE] copasi function definitions support
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- [ADD] example
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Commits on Dec 15, 2024
- Bump to version 1.0.0
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- update action
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- Merge pull request #10 from vmspereira/dev
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Commits on Jul 30, 2025
- update install and dependencies
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  90a9b91
- update artifacts version
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- update tox & CI
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- Merge pull request #11 from vmspereira/dev/update_install
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- refurbish germ
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- bux fix
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Commits on Nov 24, 2025
- wip
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  b975627
- fix dependencies
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  24a0031
- add PySCIPOpt support
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  9999a7e
- fix unit tests
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- Merge pull request #12 from vmspereira/dev/update_install
  vmspereira
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  b4e6cca
- Merge master into dev/germ: Update dependencies and add PySCIPOpt solver
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  d759979
Commits on Dec 26, 2025
- refactor: clean GERM architecture for cobrapy/reframed integration
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  0039b3e
- Add backwards compatibility for GERM analysis methods
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  5afd093
- clean up
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  0650b1d
- clean up
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  6e7c5d4
- Add convenient factory methods for RegulatoryExtension
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  43aa818
- Change default backend to reframed (more lightweight)
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  85dbfaf
- Fix scientific correctness issues in GERM analysis methods
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- Sprint 1: Code quality quick wins
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- Sprint 2 (partial): API consistency improvements
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- Sprint 4: Tests and migration guide
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  93c71d7
- Add comprehensive improvement summary documentation
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  88fe895
- Fix RFBA test to handle infeasible solutions correctly
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  committed
  649aff2
- clean up
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  committed
  356da0e
- Fix get_reaction AttributeError in GERM analysis methods
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  6952df9
- Fix CPLEX solver to return all variable values
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  872f842
- Fix pFBA to handle dynamic constraints correctly
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- Merge pull request #13 from vmspereira/dev/germ
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- flake8 and black
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  d47d52f
- Merge pull request #14 from vmspereira/linting
  vmspereira
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  d1c7881
- fix(com): correct Big-M constraints in Species Coupling (SC) score
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  77f4b57
- fix(com): deprecate balance_exchange due to mass conservation violation
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  e5c87fc
- fix(com): automatic BigM calculation in SteadyCom based on model bounds
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- docs(com): add comprehensive documentation for critical bug fixes
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  2f3ebe8
- improve(com): add validation, convergence, and consistency improvements
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  68044d2
- refactor(com): performance optimizations and code quality improvements
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  080cff2
- perf(com): optimize community model building for large communities
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- docs(com): organize community documentation in docs/community/
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- linting
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  7c4d264
- style(tests): apply flake8 and black formatting to test files
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- style(com): apply black formatting to community module source files
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  47337c3
- Merge pull request #15 from vmspereira/communities
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Commits on Dec 27, 2025
- security(kinetic): fix critical code injection vulnerabilities
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  fd674f0
- fix(kinetic): fix high priority code quality issues
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  99c46de
- perf(kinetic): fix medium priority code quality and performance issues
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  c5be96b
- docs(kinetic): fix low priority documentation and style issues
  vmspereira
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  3c2aac4
- Fix critical mathematical bugs in kinetic deriv() path
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  58ef155
- build: add numexpr dependency for kinetic security fixes
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  ca10fb4
- Merge pull request #16 from vmspereira/kinetic
  vmspereira
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  fa9b1dd
- fix(omics): fix high priority issues in omics module
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  bd71594
- perf(omics): fix medium priority code quality issues
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  dd6759b
- docs(omics): fix low priority documentation and style issues
  vmspereira
  committed
  86802dc
- fix(omics): fix high priority issues in integration methods
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  850e653
- docs(omics): add comprehensive analysis of integration methods
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  803f0b5
- docs(omics): improve GIMME documentation and code clarity
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  28253a4
- feat(omics): add build_model parameter to E-Flux and iMAT for API consistency
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  1ff94ed
- fix(omics): correct iMAT MILP constraint formulation with proper big-M method
  vmspereira
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  060cacf
- Merge pull request #17 from vmspereira/omics
  vmspereira
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  98d22c6
- fix(cobra): fix critical bugs in convert_gpr_to_dnf and minimal_medium
  vmspereira
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  73482dc
- fix(cobra): fix all code quality issues in cobra module
  vmspereira
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  52d295d
- style: fix import sorting issues with isort
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  8e5bfc5
- Merge pull request #18 from vmspereira/cobra
  vmspereira
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  ef5a090
- fix(simulation): fix critical bugs in simulation module
  vmspereira
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  4346fc5
- fix(simulation): fix high priority issues in simulation module
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  a4b0354
- fix(simulation): fix medium priority issues in simulation module
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  committed
  0749851
- fix(simulation): fix low priority issues in simulation module
  vmspereira
  committed
  10adb6a
- style(simulation): fix flake8 and black formatting issues
  vmspereira
  committed
  298fcd9
- Merge pull request #19 from vmspereira/simulation
  vmspereira
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  825c505
- fix(optimization): fix critical bugs in optimization module
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  committed
  1d9c98b
- docs(optimization): add comprehensive code quality analysis report
  vmspereira
  committed
  58aba49
- Fix high priority issues in optimization module
  vmspereira
  committed
  545ac73
- Fix medium priority issues in optimization module
  vmspereira
  committed
  4408fc5
- Fix low priority issues in optimization module
  vmspereira
  committed
  829932a
- Apply black formatting to optimization module
  vmspereira
  committed
  b0e8ae1
- Merge pull request #20 from vmspereira/optimisation
  vmspereira
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  551ddab
- Fix critical issues in problems module
  vmspereira
  committed
  76fc81b
- Fix high priority issues in problems module
  vmspereira
  committed
  2773870
- Fix medium priority issues in problems module
  vmspereira
  committed
  fd218eb
- Fix low priority issues in problems module
  vmspereira
  committed
  821c7ba
- Merge pull request #21 from vmspereira/problem
  vmspereira
  authored
  7155a09
- Fix critical issues in util module
  vmspereira
  committed
  bded85f
- Fix high priority issues in util module
  vmspereira
  committed
  1318890
- Fix medium priority issues in util module
  vmspereira
  committed
  397d9b6
- Fix low priority issues in util module
  vmspereira
  committed
  6dbf7d4
- Fix import ordering in parsing.py
  vmspereira
  committed
  96d418f
- Merge pull request #22 from vmspereira/utils
  vmspereira
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  bff0ef6
- Fix security vulnerabilities by removing unsafe eval() usage
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  committed
  381ed33
- Fix jmetalpy 1.7.0 compatibility: correct BinaryTournamentSelection import
  vmspereira
  committed
  b1a98e5
- Fix pandas 3.0 compatibility in cobra.py
  vmspereira
  committed
  f3b0015
- Add SCIP solver support to simulation framework
  vmspereira
  committed
  1ea86de
- Fix Python 3.11 compatibility: explicitly clear __abstractmethods__ in jmetal Solution classes
  vmspereira
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  face4b1
- Improve Python 3.11 compatibility: use decorator to clear __abstractmethods__
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  20fa4f8
- Fix Python 3.11 and jmetalpy 1.9+ compatibility: implement abstract variables property
  vmspereira
  committed
  cc6454e
- Merge pull request #23 from vmspereira/eval
  vmspereira
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  5dd40b8
- Fix EA engines compatibility and multiprocessing issues
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  committed
  c09c1db
- Fix multiprocessing by setting start method to 'fork'
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  committed
  d9cb741
- Merge pull request #24 from vmspereira/dev-validate
  vmspereira
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  099520a
- Make Ray mandatory dependency and fix multiprocessing start method ordering
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  committed
  4fb00db
- Add community models multiprocessing verification
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  af8a232
- Fix EA crash on infeasible solutions
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  committed
  11aa8ab
Commits on Dec 28, 2025
- Add documentation for infeasibility handling in EA
  vmspereira
  committed
  643800c
- Fix black formatting in process.py
  vmspereira
  committed
  75147d0
- Merge pull request #25 from vmspereira/dev-validate
  vmspereira
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  8cd80c7
- Fix matplotlib 3.4+ compatibility: handle set_window_title deprecation
  vmspereira
  committed
  d886c3d
- Merge pull request #26 from vmspereira/canvas
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  73a07c0
- Fix matplotlib 3.4+ compatibility: handle set_window_title deprecation
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  committed
  16f8b1c
- print observers
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  committed
  50e747c
- Add logging configuration to MEWpy
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  committed
  963989a
- logger observer
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  committed
  02f4910
- Fix import ordering with isort
  vmspereira
  committed
  cdc15c1
- Merge pull request #27 from vmspereira/observers
  vmspereira
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  39f6a05
- Fix StreamingPlot axis creation for 2D and 3D plots
  vmspereira
  committed
  1a38c4e
- Improve kinetic model LaTeX rendering for Jupyter notebooks
  vmspereira
  committed
  838eee8
- Merge pull request #28 from vmspereira/observers
  vmspereira
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  96fe24b
- Improve kinetic model LaTeX rendering for Jupyter notebooks
  vmspereira
  committed
  4a3e3e0
- Merge branch 'master' into observers
  vmspereira
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  eca2fae
- Merge pull request #29 from vmspereira/observers
  vmspereira
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  84eb64f
- clean up
  vmspereira
  committed
  91f0aea
- Merge pull request #30 from vmspereira/clean-up
  vmspereira
  authored
  3f34137
- Optimize SCIP solver performance and fix GERM notebook compatibility
  vmspereira
  committed
  67b2cd2
- Fix LaTeX rendering errors for values with underscores in notebooks
  vmspereira
  committed
  f9d9017
- Fix black formatting in solution.py
  vmspereira
  committed
  6fec983
- Merge pull request #31 from vmspereira/reg
  vmspereira
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  45833a9
- Implement rich table representation for analysis instances
  vmspereira
  committed
  6061ec1
- Add rich representations for Solution, Summary, and multi-solution classes
  vmspereira
  committed
  de41988
- Implement Phase 1 rich representations for core user-facing classes
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  committed
  cf325a5
- Implement Phase 2 rich representations for optimization and regulatory classes
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  committed
  0d88689
- Implement Phase 3 rich representations for advanced features
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  committed
  29bbfb9
- Merge pull request #32 from vmspereira/germ_notebook
  vmspereira
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  9e0bb1a
- Implement rich representation for SimulationResult
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  committed
  b55c853
- Implement rich representations for ODEModel and CommunityModel
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  7e19430
Commits on Dec 29, 2025
- Add pandas-like HTML representations for Jupyter notebooks
  vmspereira
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  ece4868
- Add pandas-like HTML representations to all core classes
  vmspereira
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  2f635b6
Commits on Jan 2, 2026
- Remove unused lp module
  vmspereira
  committed
  4ca3ea1
- Simplify GERM analysis API by making FBA/pFBA private
  vmspereira
  committed
  58307ad
- Remove redundant slim_fba and slim_pfba functions
  vmspereira
  committed
  c29281b
- Fix SRFBA boolean variable creation for RegulatoryExtension models
  vmspereira
  committed
  efdaf39
- Fix RFBA gene ID mismatch and dynamic mode issues
  vmspereira
  committed
  4bd58fd
- Fix CoRegFlux implementation and document PROM issues
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  committed
  f522945
- Fix PROM implementation - all API compatibility issues resolved
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  committed
  f3221e2
- Update PROM and CoRegFlux documentation and examples
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  committed
  2af2500
- Fix dynamic simulation iteration in CoRegFlux example
  vmspereira
  committed
  a363259
- Add error handling for infeasible solutions in regulatory extension example
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  committed
  d4431bc
- Fix import and path issues in regulatory extension example
  vmspereira
  committed
  fe15155
- Fix flake8 line length violations in PROM and CoRegFlux
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  committed
  18b3696
- Fix flake8 F541 errors in example files
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  committed
  29bdbf4
- Apply black formatting and deprecate legacy model tests
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  5e6f019
- Apply black and isort formatting to test files
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  committed
  d85d430
- Fix RFBA/SRFBA test failures
  vmspereira
  committed
  8e83d4f
- Fix duplicate 'constraints' keyword argument in RFBA
  vmspereira
  committed
  a783eb6
- Fix undefined fba and pfba variables in test_d_models.py
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  committed
  54058f3
- Add graceful skip for missing scipy/sklearn dependencies
  vmspereira
  committed
  4602ffd
- Add scikit-learn and scipy to optional dependencies
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  committed
  22c5992
- Make __repr__ return clean format for dict keys
  vmspereira
  committed
  10ba51b
- Add HTML representation to Solution class
  vmspereira
  committed
  e6bc699
- Enhance Solution.to_dataframe() to include shadow prices and reduced costs
  vmspereira
  committed
  eab6c06
- Fix SRFBA GPR linearization to handle both Symbolic and Expression types
  vmspereira
  committed
  3d47b83
- Enhance Regulator HTML representation with additional fields
  vmspereira
  committed
  55a61c3
- Enhance Gene HTML representation with additional fields
  vmspereira
  committed
  c5c1bd7
- Enhance HTML representations for Target, Reaction, Metabolite, and Interaction
  vmspereira
  committed
  b3614ed
- Fix Solution.to_summary() to populate inputs and outputs DataFrames
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  committed
  0311d9d
Commits on Jan 3, 2026
- Add duplicate handling to ExpressionSet with 'suffix' as default
  vmspereira
  committed
  846e81a

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