v1.2.2

COBREXA v1.2.2

Diff since v1.2.1

Closed issues:

• Problem converting RECON1 to core/standard model (#563)
• Add name field to StandardModel (#565)
• add CITATION.cff file (#569)

Merged pull requests:

• GRR IDs may contain underscores (#564) (@exaexa)
• Add names field to genes, metabolites and reaction types. (#566) (@stelmo)
• add SBML name accessors, bump SBML compat (#568) (@exaexa)
• add citation information (#570) (@exaexa)
• bump 1.2.2 (#571) (@exaexa)
• develop → master merge for 1.2.2 (#572) (@exaexa)
• docker&singularity autobuild&autopublish (#573) (@exaexa)
• tulip got fixed, we can bump JuMP dep (#576) (@exaexa)
• fix gource link (#577) (@exaexa)
• second and hopefully final develop → master merge for 1.2.2 (#578) (@exaexa)

v1.2.1

COBREXA v1.2.1

Diff since v1.2.0

Closed issues:

• Polishing: add @__FILE__ and other stuff to macro-generated functions (#508)
• WIP: Miscellaneous fixes (#518)
• Are knockouts potentially confusing? (#520)

Merged pull requests:

• CompatHelper: bump compat for "JuMP" to "0.22" (#511) (@github-actions[bot])
• use the keyword arguments in new version of SBML (#544) (@exaexa)
• Revert "Merge pull request #544 from LCSB-BioCore/mk-sbml-091" (#547) (@exaexa)
• Move the changes from #544 to develop (#548) (@exaexa)
• CompatHelper checks the develop branch (#550) (@exaexa)
• Trigger documentation building on master too (#551) (@exaexa)
• explain the multi-gene knockouts better (#553) (@exaexa)
• clean up some leftover unions with Nothing (#555) (@exaexa)
• bemp a small patch release (#556) (@exaexa)
• improve macro-related documentation (#557) (@exaexa)
• Update the dind version in CI (was: fix dind in CI) (#558) (@exaexa)
• Develop → master merge for 1.2.1 (#559) (@exaexa)
• Build docs on PRs to master (to catch doc errors) (#560) (@exaexa)
• COBREXA should be a dep of documentation Project.toml to enforce version checks (#561) (@exaexa)
• postpone JuMP 0.22 compatibility (#562) (@exaexa)

v1.2.0

COBREXA v1.2.0

Diff since v1.1.0

Closed issues:

• Use Dictionary.jl instead of OrderedCollections.jl in StandardModel (#434)
• Add genes and gene reaction rules to CoreModel (#439)
• Fix versioning dropdown in documentation (#498)
• GPU sampler (#524)

Merged pull requests:

• Revert "display banner consistently at each import" (#516) (@exaexa)
• Improve remove_XXX functions (#517) (@stelmo)
• Extend max-min driving force analysis (#519) (@stelmo)
• Gene-reaction rules for CoreModel and CoreModelCoupled #439 (#521) (@htpusa)
• naming & tests for grr vector function (#522) (@exaexa)
• add the (most relevant) old versions of the docs to gh pages (#523) (@exaexa)
• remove some unnecessarily explicit Union types (#525) (@exaexa)
• remove unnecessary documentation deps from the actual package (#526) (@exaexa)
• make sure SBML 0.8.1 doesn't get installed as a dep (#527) (@exaexa)
• fix some wording and make explanation clearer (#529) (@stelmo)
• added change_objective! function and tests (#530) (@stelmo)
• use a precise julia compat entry (#532) (@exaexa)
• upgrade julia from 1.5 to 1.7 (#533) (@laurentheirendt)
• remove duplicate function definitions (#534) (@laurentheirendt)
• clean up the change_objective! overloading, add doc (#535) (@exaexa)
• bump up the "history gif" artifact expiration to 3 months (#536) (@exaexa)
• Regular merge develop→master (#537) (@exaexa)
• Added data source for thermodynamic info in tests (#538) (@stelmo)
• bump version 1.1.1 (#539) (@exaexa)
• fix the versioning for compatibility with General (#540) (@exaexa)
• Merge the fixed develop to master (#541) (@exaexa)

v1.1.0

COBREXA v1.1.0

Diff since v1.0.6

Closed issues:

• We should eventually use StableRNGs for sampling and all other random number generation. (#84)
• 🚸Explain serialize_model better in docs (#361)
• cannot find kernel - binder (#388)
• add Aqua testing (#389)
• Max-min driving force (#422)
• Add MOMENT algorithm (#446)
• Model modifications for SerializedModel (#456)
• Add screen example to readme (#457)
• The grr parser assigns [[""]] to some reactions when it should be nothing (#463)
• formatting problem in flux_variability_summary (#468)
• Unify the _dict and _vec function variants with some common reusable code (#474)
• Reorganize docs a bit (#479)
• Add FAQ section in docs (#480)
• Check the cause of test failures with OSQP / MOMA (#485)
• unique links to contributing guide (#490)
• link to Edit on Github does not work anymore (#496)
• Rename API reference (#497)
• Rename Detailed tutorial listing (#499)

Merged pull requests:

• Implement max min driving force (#431) (@stelmo)
• Add community functions for StandardModel (#435) (@stelmo)
• Add loopless FBA (#437) (@stelmo)
• Add moment algorithm (#455) (@stelmo)
• fix metabolite vector construction ambiguity (#459) (@exaexa)
• add aqua testing (#460) (@exaexa)
• rewrite julia version in notebooks to one compatible with binder (#461) (@exaexa)
• demonstrate screen() in README (#462) (@exaexa)
• Fix some small docstring issues + small readme changes (#464) (@stelmo)
• Modifications unwrap the serialized model (#465) (@exaexa)
• convert the sampling to stable RNGs (#466) (@exaexa)
• fix docs + naming issue (#467) (@stelmo)
• docfixes (#469) (@exaexa)
• remove binder altogether (#470) (@exaexa)
• explain the use of Serialized models better (#471) (@exaexa)
• moma implementation and tests (#472) (@stelmo)
• try to revive binder (#473) (@exaexa)
• remove some of the repeated code, make MOMA more flexible (#475) (@exaexa)
• silence MOMA tests (#476) (@exaexa)
• run tests&docs on develop, trigger gitlab also on new tags (#477) (@exaexa)
• use the gitlab-documenter integration directly (attempt 1) (#481) (@exaexa)
• reflect the workflow change in contrib guide (#482) (@exaexa)
• temporarily increase tolerance on the MOMA test (needs fixup later) (#484) (@exaexa)
• Polish solution for all QP problems (#486) (@stelmo)
• Reorganize the API docs to nice sections (#487) (@exaexa)
• Try to fix gitlab docbuilding deploy (attempt 2) (#488) (@exaexa)
• fix gitlab docs (attempt 3) (#489) (@exaexa)
• Fix contribution docs (#491) (@exaexa)
• Make the GRR parser a bit more robust (#492) (@exaexa)
• Fix the documentation and some small issues (#493) (@stelmo)
• Polish the notebook/example sections (#494) (@stelmo)
• develop→master (#495) (@exaexa)
• docfixes (#500) (@exaexa)
• reorganize the CI, add a bit of documentation (#501) (@exaexa)
• postpone the external triggers (#502) (@exaexa)
• Mk docfixes 5 (#503) (@exaexa)
• dev→master 20211105 (#504) (@exaexa)
• do not run PR + branch checks together (#505) (@exaexa)
• fix windows compat checks, compat check also BEFORE merging to master (#506) (@exaexa)
• Simplify tests that use OSQP (#507) (@stelmo)
• Develop→master 20211108 (#509) (@exaexa)
• keep Project.toml stuff sorted (#512) (@exaexa)
• [breaking] avoid unnecessary sparsity in lower/upper flux bounds (#513) (@exaexa)
• simplify the _dict and _vec variants of analysis functions (#514) (@exaexa)
• develop→master for 1.1 release (#515) (@exaexa)

v1.0.6

COBREXA v1.0.6

Diff since v1.0.5

Merged pull requests:

• Revert "completely disable JuMP bridge constraints" (#454) (@exaexa)
• bump version to 1.0.6 (#458) (@exaexa)

v1.0.5

COBREXA v1.0.5

Diff since v1.0.4

Merged pull requests:

• more efficient building of sparse stoichiometries (#443) (@exaexa)
• Added repostatus badge (#444) (@stelmo)
• CompatHelper: bump compat for "SBML" to "0.8" (#445) (@github-actions[bot])
• improve parametrization of objective_envelope (#447) (@exaexa)
• slightly improve the objective value handling at FVA (#448) (@exaexa)
• correctly forward the workers parameter (#449) (@exaexa)
• completely disable JuMP bridge constraints (#450) (@exaexa)
• improve the ability of screening functions to use precompiled code (#451) (@exaexa)
• fix the index in remove_metabolites of CoreModel (#452) (@exaexa)
• bump version to 1.0.5 (#453) (@exaexa)

v1.0.4

COBREXA v1.0.4

Diff since v1.0.3

Closed issues:

• establish more elaborate PR and issue templates (#110)
• Make prettyprinting systematic (#154)
• Production envelopes (#267)
• Make model modification functions consistent (#313)
• Tutorials refer to removed functions (#324)
• 🚸Explain FVA better (#345)
• ⚡Conversion to StandardModel is slow, speed it up (#350)
• 🚸make CoreModel add_reactions function more intuitive (#351)
• More running changes (#358)
• 🚸Carefully explain community model construction + pitfalls (#360)
• ✨ Add in place versions of remove_reaction and remove_metabolite + plural variants for CoreModel and StandardModel (#362)
• Change join_with_exchanges to accept a dictionary of external metabolites instead of two vectors (#365)
• Add latex completion hints for non-ascii characters in docs (#382)
• Banner doesn't display (#390)
• Add optimizer modification to make solvers quiet (#391)
• StandardModel does not read in metabolite/reaction/gene names (#392)
• atom_exchange does not weight by flux as stated in the doc string of the function (#393)
• Export function to convert reaction equation into a string (#394)
• Simple export of results in JSON (orig: Should we have a function that exports fluxes in a dict for visualization in Escher?) (#397)
• julia-ize the overloading in change_objective (#405)
• Change set_optmodel_bound! to have kwargs that do not override constraints (#419)
• Implement st-FBA (#423)
• Generalize FBA to include crowding constraints etc. (#436)

Merged pull requests:

• some cosmetic README touches, dev doc links (#384) (@exaexa)
• Fix deployment of container images (#386) (@laurentheirendt)
• Use Makie instead of Plots (#387) (@stelmo)
• improve jsonmodel speed + some extra cleanup (#395) (@exaexa)
• compatibility with SBML 0.6 (#398) (@exaexa)
• unsupport name field in models (#399) (@exaexa)
• slightly more useful issue/PR templates (#400) (@exaexa)
• simplify trigger mechanism (#401) (@laurentheirendt)
• simplify code by removing unnecessary unicode (#402) (@exaexa)
• display banner consistently at each import (#403) (@exaexa)
• Fix error with screen and unregister (#404) (@stelmo)
• implement objective envelopes (aka production envelopes) (#406) (@exaexa)
• document optimize_objective (#409) (@exaexa)
• remove optimize_model (it was not used) (#410) (@exaexa)
• Completely remove all JuMP and COBREXA prefixes where possible (#411) (@exaexa)
• clean up change_objective (#412) (@exaexa)
• Added reaction_equation function and tests (#413) (@stelmo)
• 🪓 some code and streamline utilities for reaction/metabolite balancing (#414) (@stelmo)
• Simple option to silence the JuMP solvers (#415) (@exaexa)
• Update community analysis functions to be more sensible (#416) (@stelmo)
• improve optmodel screening, subsume FVA (#418) (@exaexa)
• Mo tiny fixes (#420) (@stelmo)
• simplify & unsurprise set_optmodel_bound! (#421) (@exaexa)
• Add some more explanations for FVA and add flux_summary usage to notebook (#424) (@stelmo)
• Add in place add_reaction! and add_reactions! (#425) (@stelmo)
• Fix docs (#426) (@stelmo)
• Add back stoichiometry_string (#429) (@stelmo)
• bump SBML compat to 0.7.x (#430) (@exaexa)
• Small fix in docstring + function kwarg (#432) (@stelmo)
• start the grand unification of remove_whatever (#433) (@exaexa)
• Update modifications (#438) (@stelmo)
• MMDF cleanup (#440) (@exaexa)
• add an example for objective_envelope (#441) (@exaexa)
• bump version 1.0.4 (#442) (@exaexa)

v1.0.3

COBREXA v1.0.3

Diff since v1.0.2

Closed issues:

• Overview issue: documentation structure (#137)
• add style guidelines (#163)
• deploy animated history differently (#294)
• 🚸 💄 Informative error message when reaction is not found (#319)
• 🪓 Homogenize set_bound and change_bounds! and make them generic (#329)
• 💄 📝 🚸 Small improvements (#338)
• Make all oneline function definitions const (#356)
• Fix bad references in docs (#370)
• merge or remove docs/src/unmerged.md (#374)
• remove trailing whitespace from everywhere (self-reminder) (#375)
• Bad formatting in some docstrings (#381)

Merged pull requests:

• CompatHelper: bump compat for "SBML" to "0.5" (#339) (@github-actions[bot])
• SBML-0.5.0 compat (#340) (@exaexa)
• better errors for optimizer mods (#341) (@htpusa)
• don't leak the file object when saving JSON (#342) (@exaexa)
• format #341 + add a tiny simplification (#343) (@exaexa)
• fix only compatible SBML versions (#344) (@exaexa)
• Change set_bound to change_bound to fit in with CoreModel functions (#346) (@stelmo)
• documentation fixes and formatting, ... (#347) (@exaexa)
• resolve and build pkgs in docs (#348) (@laurentheirendt)
• Fix small things (#349) (@stelmo)
• Fix dependency in docs environment (#352) (@laurentheirendt)
• fix for double command - pasting error (#353) (@laurentheirendt)
• deploy animated git history differently (#354) (@laurentheirendt)
• use the raw artifact from the last job via URL (#355) (@laurentheirendt)
• add singularity deployment (#357) (@laurentheirendt)
• Added more tests for community model functions (#359) (@stelmo)
• Custom model tutorial+notebook (#366) (@exaexa)
• autoformat code in master (#367) (@exaexa)
• do not deploy notebook build artifacts to docs (#368) (@exaexa)
• change name of secret (#369) (@laurentheirendt)
• make the comment messages useful (#371) (@exaexa)
• do not define function as (non-const) variables (#372) (@exaexa)
• add some common practices and requirements to CONTRIBUTING.md (#373) (@exaexa)
• minimize the change_bound generator macro (#376) (@exaexa)
• code cleanup before release (#377) (@exaexa)
• formatting report fix: break the line after code quote properly (#378) (@exaexa)
• Fix argument error in community model notebook (#379) (@stelmo)
• bump version to 1.0.3 (#380) (@exaexa)
• final doc fixes for 1.0.3 (#383) (@exaexa)

v1.0.2

COBREXA v1.0.2

Diff since v1.0.1

Closed issues:

• speed up testing pipeline (#69)
• Fix samplers and create good tests for them (#82)
• Use normal randoms for generating random directions in samplers (#178)
• Fix rm! to actually keep the model consistent (#197)
• Fix docs of reconstructions/CoreModelCoupled (#255)
• overload Base.copy for all models (so that writing model modifiers is easier) (#256)
• Homogenize add/remove functions and add in place versions (#281)
• solver precompilation in tests blocks unnecessarily (#287)
• Improve coverage of src/base/utils/StandardModel.jl (#288)
• Feature to get atomic counts in reactions (#311)
• generalize get_atom_exchanges (#317)
• 💄 📝 🚸 Usage pointers (#318)
• 💄 🚸 Result summary function (#323)
• 🩹 atom_exchange is not robust to missing formulas (#326)
• 💄 Change order of arguments (#330)

Merged pull requests:

• add singularity container (#263) (@laurentheirendt)
• ✨ Basic community model construction functions (#270) (@stelmo)
• Clean up test data handling (#289) (@exaexa)
• Deleted unnecessary dependency (#291) (@stelmo)
• Small fixes (#292) (@exaexa)
• re-add missing directories in ignore (#293) (@laurentheirendt)
• change singularity base img (#295) (@laurentheirendt)
• add tulip to singularity container (#296) (@laurentheirendt)
• ✨ Add looks_like_xxx functions to make finding specific reaction/metabolite types easy (#297) (@stelmo)
• 🚚 Rename add! and rm! functions for StandardModel (#298) (@stelmo)
• 🪓 Remove exchange_reactions (#299) (@stelmo)
• 🩹 fix docs (#301) (@stelmo)
• 💄 Update pretty printing of models (#302) (@stelmo)
• warmup jump+tulip code to save much time later in testing (#303) (@exaexa)
• 📝 Add emoji references (#304) (@stelmo)
• add shallow copying of StandardModel stuff, useful for writing custom… (#306) (@exaexa)
• Missing functions for CoreModelCoupled (#307) (@laurentheirendt)
• 💄 ⚠️ OSQP (#308) (@stelmo)
• 🩹 ✨ Atoms in reactions and overall flux (#312) (@stelmo)
• backwards compatibility with find_exchange_reactions and pals (#314) (@exaexa)
• clean up exchanges a bit (#316) (@exaexa)
• just reformat everything (#320) (@exaexa)
• Screening cleanup + tutorial (#321) (@exaexa)
• 📝 🚧 Community model construction (#325) (@stelmo)
• 🩹 Make atom_exchage robust to metabolites missing formulas (#327) (@stelmo)
• 🚸💄 Added summarize function (#328) (@stelmo)
• make atom_exchange and metabolite_fluxes a bit more generic (#331) (@exaexa)
• fix screening doc build (#332) (@exaexa)
• reformat the community model tutorial (#333) (@exaexa)
• clean up analysis documentation and examples (#334) (@exaexa)
• 💄 Another example (#335) (@stelmo)
• bump version (#336) (@exaexa)

v1.0.1

COBREXA v1.0.1

Diff since v1.0.0

Closed issues:

• fluxVariabilityAnalysis doesn't check termination status (#5)
• add travis and github actions (#70)
• FVA does not include optimization problem modifications (#219)
• change suggested solved in README from GLPK to Tulip (#232)
• fix Edit on Github button on index.md (#245)
• Register COBREXA.jl (#249)
• add backlink from docs (#250)
• unify contributing.md and howToContribute sections (#253)
• remove Random dependency? (#280)

Merged pull requests:

• Fix hit and run sampler (#251) (@stelmo)
• add the abstract screening helper + on-disk externalized models (#254) (@exaexa)
• Revert "change installation to git (temporarily)" (#257) (@laurentheirendt)
• clean up docs badges and acks (#264) (@exaexa)
• switch README to Tulip (#265) (@exaexa)
• add support for travis CI (#268) (@laurentheirendt)
• increase coverage of serialization + fixes (#271) (@exaexa)
• fix banner on 80col terminal (#272) (@exaexa)
• fix a problem in screening (#273) (@exaexa)
• unify contribution guides (#274) (@exaexa)
• Clean up FVA (#275) (@exaexa)
• disable the edit link in docs (#276) (@exaexa)
• Clean up tests (#277) (@exaexa)
• replace index.md link (#278) (@laurentheirendt)
• fix directory in doc deployment (#282) (@laurentheirendt)
• Clean up hit-and-run sampling (#284) (@exaexa)
• docs: improve the contribution edit link (#285) (@exaexa)
• bump to 1.0.1 (#286) (@exaexa)