cobrexa.jl - v1.5.1

COBREXA v1.5.1

Diff since v1.5.0

Merged pull requests: - make the semantics cut (#776) (@exaexa) - fix sparsevec (#783) (@exaexa)

- Julia
Published by github-actions[bot] almost 3 years ago

cobrexa.jl - v1.5.0

COBREXA v1.5.0

Diff since v1.4.4

Closed issues: - Model type overlay that describes the genetic manipulation (#552) - max_min_driving_force and moment should be a ModelWrapper (#614) - JSON model format incompatible with escher (#758)

Merged pull requests: - pFBA pipe (#747) (@stelmo) - Add test for multiple capacity enzyme bounds (#748) (@stelmo) - Add another convenience constructor for enzyme constrained models (#749) (@stelmo) - Add model annotation details (#750) (@stelmo) - port GRR parsing to 2.0, avoid DNF complexity explosions (#752) (@exaexa) - remove and clean up GeneAssociations alias (#753) (@exaexa) - Remove unnecessary docstrings (#754) (@stelmo) - Fix model accessor bugs (#755) (@stelmo) - Return enzyme concentrations in useful units (#757) (@stelmo) - Make kwargs for convenience enzyme constrained consistent (#759) (@stelmo) - Add plural to changebounds and add changeconstraints (#760) (@stelmo) - Fix and extend reconstruction functions and pipes for objectmodel (#762) (@stelmo) - Result wrapper (#763) (@exaexa) - Fix cFBA implementation (#764) (@stelmo) - Add basic show for ModelWithResult (#766) (@stelmo) - split wrappers off to a separate module (#767) (@exaexa) - unify L2-like QP handling (#769) (@exaexa) - Make kwarg plural (#770) (@stelmo) - Rename GeneAssociation file (#771) (@stelmo) - Extend simplified enzyme model to include multiple capacity constraints (#772) (@stelmo) - implement wrappy pFBA using the normal L2 wrappers (#773) (@exaexa) - Fix EqualGrowthCommunityModel accessors (#774) (@stelmo) - implement expression-limited fluxes (E-Flux like algorihm) (#777) (@exaexa) - fixed merge of #777 (#778) (@exaexa) - Develop → master merge for 1.5.0 (#779) (@exaexa) - fix filename (#781) (@exaexa)

- Julia
Published by github-actions[bot] almost 3 years ago

cobrexa.jl - v1.4.4

COBREXA v1.4.4

Diff since v1.4.3

Closed issues: - Incorrect gene reaction rule parsing (#711)

Merged pull requests: - Turn MMDF analysis into a wrapper (#699) (@stelmo) - Add convenience macro that loads all the functions in modules (#716) (@stelmo) - Implement a variant of Constrained Allocation Flux Balance Analysis (#717) (@stelmo) - Delete reaction overloads (#718) (@stelmo) - Rename GeckoModel to EnzymeConstrainedModel (#719) (@stelmo) - Rename SMomentModel to SimplifiedEnzymeConstrainedModel (#720) (@stelmo) - Rename reactiongeneassociation to reactiongeneassociations (#721) (@stelmo) - Replace uses of :reverse with :backward to be consistent (#722) (@stelmo) - Rename file (#723) (@stelmo) - Add accessors for enzyme associated data (#724) (@stelmo) - Remove crowding (obsolete via SMOMENT) (#725) (@stelmo) - remove obsolete print_banner() from the SIF container (#727) (@exaexa) - LICENSE file type was not markdown (#728) (@exaexa) - CompatHelper: bump compat for SBML to 1, (keep existing compat) (#729) (@github-actions[bot]) - remove a config from local CI (#730) (@exaexa) - add an actual GPA/GRR to DNF parser (#731) (@exaexa) - Fix test bugs in new parser (#732) (@stelmo) - GPA ordering fix (#733) (@exaexa) - fix GRA compat once more (and hopefully the last time) (#734) (@exaexa) - extensible variable semantics (#735) (@exaexa) - Q-opt support (#736) (@exaexa) - version bump for 1.4.4 (#737) (@exaexa) - Develop → master merge for 1.4.4 (#738) (@exaexa) - Add more reconstruction functions to ObjectModel (#739) (@stelmo) - Remove switching argument for reaction constructors (#740) (@stelmo) - Remove double s from enzyme semantics (#741) (@stelmo) - Add some more semantics to EnzymeConstrainedModel (#742) (@stelmo) - Add balance accessor to community model (#743) (@stelmo) - clean up SBML unit-error throwing (#744) (@exaexa) - Homogenize bound kwargs (#746) (@stelmo)

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Published by github-actions[bot] about 3 years ago

cobrexa.jl - v1.4.3

COBREXA v1.4.3

Diff since v1.4.2

Merged pull requests: - freeze SBML dictionary ordering (#706) (@exaexa) - bump hotfix release 1.4.3 (#707) (@exaexa) - Develop → master merge for 1.4.3 (#708) (@exaexa)

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Published by github-actions[bot] about 3 years ago

cobrexa.jl - v1.4.2

COBREXA v1.4.2

Diff since v1.4.1

Closed issues: - Consistent argument/kwarg naming (#623) - Add stoichiometry to gene reaction rules (#655) - Organize everything into submodules (#663) - .mat model not loading (#691)

Merged pull requests: - Use smaller organized namespaces. (#674) (@exaexa) - switch tests julia from 1.7 to 1.8 (#680) (@exaexa) - Delete moment algorithm modification (#686) (@stelmo) - Rename MetabolicModel to AbstractMetabolicModel (#687) (@stelmo) - Add ext option (#688) (@josePereiro) - Update gene associations (#689) (@stelmo) - Indent submodule definitions (#690) (@exaexa) - fix loading of matlab version of yeast GEM (#692) (@exaexa) - sync julia version with artenolis (#693) (@exaexa) - Extend community model (#696) (@stelmo) - Remove @add_reactions (#697) (@stelmo) - use a softer failure when unit annotations are missing in SBML (#701) (@exaexa) - use the latest recommended Julia CI on master+develop for generating … (#702) (@exaexa) - Release 1.4.2 (#703) (@exaexa) - Develop → master merge for v1.4.2 (#704) (@exaexa) - upgrade julia version on ci and set mac path (#705) (@laurentheirendt)

- Julia
Published by github-actions[bot] about 3 years ago

cobrexa.jl - v1.4.1

COBREXA v1.4.1

Diff since v1.4.0

Closed issues: - generate FROG reports (models reproducibility) (#609) - pFBA does not fail gracefully (#625) - Gapfilling not giving any solutions (#653) - Drop OSQP and use Clarabel instead for QPs (#666)

Merged pull requests: - remove lots of lb/ub shortcuts from API (#637) (@exaexa) - Remove the banner (#649) (@stelmo) - Add some constructors (#654) (@stelmo) - hotfix: bump CompatHelper version to work with 1.8 (#656) (@exaexa) - Update compathelper CI script (#658) (@exaexa) - Fix pFBA issue with return type nothing (#659) (@stelmo) - Finally add DocStringExtensions 🥳 (#661) (@stelmo) - add an explanation of what happens when you gapfill a feasible model (#662) (@exaexa) - Add SBO terms (#667) (@stelmo) - use Clarabel instd of OSQP (#669) (@exaexa) - CompatHelper: bump compat for SBML to 1, (keep existing compat) (#670) (@github-actions[bot]) - Make the SBML annotations work just like with JSON models (#676) (@exaexa) - docs: reflect the solver change in Project.toml (#677) (@exaexa) - fix docbuild: JuMP MIN_SENSE and MAX_SENSE disappeared (#679) (@exaexa) - remove polish parameter specific to osqp (#681) (@exaexa) - Develop → master merge for v1.4.1 (#682) (@exaexa) - backmerge master changes to develop to resolve merge conflicts (#683) (@exaexa)

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Published by github-actions[bot] over 3 years ago

cobrexa.jl - v1.4.0

COBREXA v1.4.0

Diff since v1.3.1

Closed issues: - Prettyprinting should not hide any information (#77) - change the auto-formatting mechanism (#322) - Switch to ReadableRegex (#601) - Progress meter for long running ops (#626) - fast mmap()able model type (#641)

Merged pull requests: - Fix small error with gapfill modifications (#622) (@stelmo) - fix example formatting in addmomentconstraints (#624) (@exaexa) - sampling improvements (#627) (@exaexa) - docs reorganization (#628) (@exaexa) - Add examples (#631) (@stelmo) - allow hyphens in gene names in GRRs (#634) (@exaexa) - Merge autoformatter improvements from SBML.jl (#635) (@exaexa) - make reactionatombalance have generic MetabolicModel as type (#636) (@HettieC) - support SBML writing (#639) (@exaexa) - HDF5 model storage and fast memory mapping support (#642) (@exaexa) - Adds more details to mmdf and gecko (#643) (@stelmo) - extend the autoformatting priveleges a bit (#644) (@exaexa) - unify the reference section with the rest of the docs (#645) (@exaexa) - Small docs fixes (#646) (@stelmo) - Add better links (#647) (@stelmo) - version bump for 1.4 (#650) (@exaexa) - Develop → master merge for 1.4 (#651) (@exaexa)

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Published by github-actions[bot] over 3 years ago

cobrexa.jl - v1.3.1

COBREXA v1.3.1

Diff since v1.3.0

Closed issues: - generate and deploy docker & singularity containers (#68) - Implement GECKO (#574) - Implement sMOMENT (#575) - fix import of yeast GEM models (#600) - use asyncmap instead of map to collect information from workers (#603)

Merged pull requests: - switch to asyncmap for fetching results from multiple workers (#610) (@exaexa) - load more metadata from models (#611) (@exaexa) - Update mods to handle gecko model (#612) (@stelmo) - Check format using github actions, implement the /format command (#615) (@exaexa) - Explain reactions better (#616) (@exaexa) - Add a gap filling algorithm (#617) (@stelmo) - clean up the gapfilling code (#618) (@exaexa) - bemp version 1.3.1 (#619) (@exaexa) - Develop→master for 1.3.1 (#620) (@exaexa) - fix documentation issues and warnings (#621) (@exaexa)

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Published by github-actions[bot] almost 4 years ago

cobrexa.jl - v1.3.0

COBREXA v1.3.0

Diff since v1.2.3

Closed issues: - Moment modification deletes ATPM bounds (#542)

Merged pull requests: - banner again! (#585) (@exaexa) - Implement GECKO and SMOMENT (#586) (@stelmo) - CompatHelper: bump compat for "JuMP" to "0.23" (#587) (@github-actions[bot]) - prepare a macro for inheriting the accessors for model data (#588) (@exaexa) - Fixing typos (#589) (@htpusa) - Fix argument forwarding in find_biomass_reaction_ids (#590) (@exaexa) - CompatHelper: bump compat for "DistributedData" to "0.2" (#593) (@github-actions[bot]) - CompatHelper: bump compat for "JuMP" to "1" (#594) (@github-actions[bot]) - Add deprecation warning (#595) (@stelmo) - Systematic model wrappers (#597) (@exaexa) - make stoichiometries easily extensible to encompass more complicated analyses (#598) (@exaexa) - Add some accessors for MATModel (#602) (@stelmo) - "minor" fixes for enzyme-constrained models (#604) (@exaexa) - Small fixes to enzyme PR (#605) (@stelmo) - Small fixes (#606) (@stelmo) - Bump version 1.3.0 (#607) (@stelmo) - develop -> master for v1.3.0 (#608) (@stelmo)

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Published by github-actions[bot] almost 4 years ago

cobrexa.jl - v1.2.3

COBREXA v1.2.3

Diff since v1.2.2

Merged pull requests: - Fix small error (#579) (@stelmo) - prevent more directional typos (#580) (@exaexa) - fix pretty reaction builders (#581) (@exaexa) - docker build from gitlab (#582) (@exaexa) - bump version 1.2.3 (#583) (@exaexa) - Develop → master merge for 1.2.3 (#584) (@exaexa)

- Julia
Published by github-actions[bot] about 4 years ago

cobrexa.jl - 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)

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Published by github-actions[bot] about 4 years ago

cobrexa.jl - 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)

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Published by github-actions[bot] about 4 years ago

cobrexa.jl - 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)

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Published by github-actions[bot] about 4 years ago

cobrexa.jl - 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)

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Published by github-actions[bot] over 4 years ago

cobrexa.jl - 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)

- Julia
Published by github-actions[bot] over 4 years ago

cobrexa.jl - 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 objectiveenvelope (#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 removemetabolites of CoreModel (#452) (@exaexa) - bump version to 1.0.5 (#453) (@exaexa)

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Published by github-actions[bot] over 4 years ago

cobrexa.jl - 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 optimizemodel (it was not used) (#410) (@exaexa) - Completely remove all JuMP and COBREXA prefixes where possible (#411) (@exaexa) - clean up `changeobjective(#412) (@exaexa) - Addedreactionequationfunction 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 & unsurprisesetoptmodelbound!(#421) (@exaexa) - Add some more explanations for FVA and addfluxsummaryusage to notebook (#424) (@stelmo) - Add in placeaddreaction!andaddreactions!(#425) (@stelmo) - Fix docs (#426) (@stelmo) - Addback stoichiometrystring` (#429) (@stelmo) - bump SBML compat to 0.7.x (#430) (@exaexa) - Small fix in docstring + function kwarg (#432) (@stelmo) - start the grand unification of removewhatever (#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)

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Published by github-actions[bot] over 4 years ago

cobrexa.jl - 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)

- Julia
Published by github-actions[bot] over 4 years ago

cobrexa.jl - 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 findexchangereactions 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 atomexchange and metabolitefluxes 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)

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Published by github-actions[bot] over 4 years ago

cobrexa.jl - 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)

- Julia
Published by github-actions[bot] over 4 years ago

cobrexa.jl - v1.0.0

COBREXA v1.0.0

Closed issues: - storage of large model (#2) - i/o of SBML files (#3) - Expand IO (MAT) (#4) - Migration to github.com (#6) - loadModel is broken (#12) - Some SBML formats (level 3?) are not read correctly (#18) - Wildcard documentation building (#26) - Name functions consistently with JuMP style? (#32) - SBMLModel should just be CobraModel (#36) - Implement function callbacks to make function modifications uniform and streamlined (#37) - Automatic file loading (#38) - fluxBalanceAnalysisVec seems to be missing (#39) - Clean-up downloading of test models (#40) - change badge links to cobrexa (#41) - reorganize file contents (#42) - remove PyCall Dependency (#45) - clean up error handling and warnings (#47) - Change CobraModel to FullModel (#54) - Implement macros for all functions (where appropriate) (#61) - Regroup tests to files that match src/ (#65) - add CodeCov (#67) - trigger test pipelines in external repos (#71) - Implement knockouts in an efficient way (#72) - add doc test to pipeline (#74) - fix badges of CI in readme (#75) - Add references to methods where possible (#76) - Explain the need of modifying the sampling defaults in docs (#80) - replace format check with bot action to fix automagically (#86) - Ongoing design considerations (#92) - Homogenize tests (#96) - Make sure the accessors for MetabolicModel kinda feature-complete (#100) - Community model + tutorial (#103) - Bounds should not be sparse vectors, maybe a new data type... (#112) - Fix the code examples after StandardModel has changed (#117) - improve readme for beginners (#123) - generate html files from tutorials automatically (#145) - Consistent model variable naming (#152) - File cleanup + housekeeping (#155) - Making error messages more informative (#160) - integrate tutorial testing in ci pipeline (#165) - document internal functions, at least with comments (#179) - Change add_reactions! to accept string ids as inputs (#193)

Merged pull requests: - formatting of license (#1) (@laurentheirendt) - Community docs (#7) (@laurentheirendt) - add parallel FVA (#8) (@htpusa) - Make the banner fit to 80column terminal. (#9) (@exaexa) - SBML loading (#10) (@exaexa) - various minor fixes (#11) (@exaexa) - simplify reader (#13) (@htpusa) - [WIP] distributed FVA (#15) (@exaexa) - Writer (#16) (@htpusa) - clean-up before API changes (#17) (@exaexa) - remove dup entries in toml (#20) (@laurentheirendt) - add workflow to contributing guide (#22) (@laurentheirendt) - Make analysis functions generic and easily extensible (#23) (@exaexa) - fix docs (#24) (@stelmo) - simplify the use of devel command for contribution guide (#25) (@exaexa) - parametrize FVA (#27) (@htpusa) - Add a test for γ-parametrized FVA (#28) (@exaexa) - Support wildcards in documentation building (#29) (@exaexa) - WIP: integrate generic interface & cobratools (#30) (@stelmo) - Docs standardization (#31) (@exaexa) - add additional FBA output formats (#33) (@exaexa) - Properly support multiple model types and conversions (#34) (@exaexa) - fix new-master and cobratools remaining integration issues (#35) (@stelmo) - reduce size of favicon (#43) (@laurentheirendt) - fixes for links (#44) (@laurentheirendt) - fix the nice FBA variants (again) (#46) (@exaexa) - clean-up downloading of files for testing (#48) (@exaexa) - Minor package changes (#50) (@laurentheirendt) - Cherries from PR49 (#51) (@laurentheirendt) - pause CI gh action (#52) (@laurentheirendt) - implement callbacks to make problem modification pretty (#53) (@stelmo) - Move JuliaFormatter to Gitlab CI (#55) (@laurentheirendt) - add master runs to test and format (#56) (@laurentheirendt) - add native linux, mac, and windows nodes (#57) (@laurentheirendt) - Simplifications (#58) (@exaexa) - Add reaction macro (#59) (@marvinvanaalst) - Added loopless fba (#60) (@marvinvanaalst) - remove Conda dep (#62) (@laurentheirendt) - Add default_constants tuple to reduce number of hard coded constants (#63) (@stelmo) - Generic io interface (#64) (@stelmo) - Deleted geometric fba (#66) (@stelmo) - cleaning & recontenting the file structure (#78) (@exaexa) - Reduce the number of constants (#79) (@exaexa) - add logos for README (#81) (@exaexa) - format check returns the failure properly (#83) (@exaexa) - add codecov and bot for formatting (#85) (@laurentheirendt) - add automated documentation tests (#87) (@laurentheirendt) - Small fixes (#88) (@stelmo) - add docker img for deploy doc stage (#89) (@laurentheirendt) - The Big Rename of LinearModel to CoreModel (#91) (@exaexa) - make the abstract interface easily implementable (#95) (@exaexa) - Prepare accessors for genetic and chemical information (#97) (@exaexa) - Conversion + genetics and chemical interface for SBML (#99) (@exaexa) - support ngenes accessor (#101) (@exaexa) - add annotations (#102) (@exaexa) - Separated-out JSONModel commits (from elmo) (#104) (@exaexa) - remove some unneeded dependencies (#107) (@exaexa) - Implement pretty printing (#108) (@stelmo) - Add generic interface for StandardModels (#111) (@stelmo) - Implement conditional logging switches (#114) (@exaexa) - MATModel: generic interface + conversions + test (#115) (@exaexa) - add the forgotten MATModel conversion tests (#118) (@exaexa) - IO code cleanup (#119) (@exaexa) - fixed small issues (#120) (@stelmo) - MetabolicModel→StandardModel conversion (#121) (@stelmo) - prettyprinting hints & minor fixes (#122) (@exaexa) - slightly new structure (#124) (@laurentheirendt) - Add remaining accessors function to MetabolicModel (#125) (@stelmo) - Add accessors to StandardModel, add tests and doctests (#126) (@stelmo) - Change defaults of fields in Reaction, Gene and Metabolite to nothing (#127) (@stelmo) - Add github action with custom docker img (#128) (@laurentheirendt) - add generic prettyprinting (fixes ppr(nothing) bug) (#129) (@exaexa) - test the prettyprinting correctly (allow some formatting freedom) (#130) (@exaexa) - Fix JSON code to work with new accessors (#131) (@exaexa) - add flags to gh action (#132) (@laurentheirendt) - use precompiled docker img (#133) (@laurentheirendt) - finalized SBML accessors (#134) (@exaexa) - avoid uncertainty creep (#135) (@exaexa) - Steamlined Gene tests (#136) (@stelmo) - updated readme (#138) (@laurentheirendt) - Mo tutorial 1 (merge into #139!!) (#140) (@stelmo) - Added quick start (#141) (@stelmo) - make MATModel work with the abstract interface (#142) (@exaexa) - add stage to generate gource history automatically (#143) (@laurentheirendt) - Simplified example in quick start (#144) (@stelmo) - add gitattributes file (#146) (@laurentheirendt) - added tutorial 2 - (merge into #140!!) (#148) (@stelmo) - fix welcome contributions button (#150) (@laurentheirendt) - Mva knockout 2 (#151) (@marvinvanaalst) - Automatic conversion of Jupyter notebooks (#153) (@laurentheirendt) - Analysis problem modifications: make generic (#156) (@stelmo) - Instructions for adding solver (#157) (@laurentheirendt) - support some additional possibilities of MAT file content (#158) (@exaexa) - Added fba tutorial (merge into #148) (#159) (@stelmo) - Fix small things in `checkduplicate_annotations(#161) (@stelmo) - Fix docs and some functions that useStandardModel` (#162) (@stelmo) - Code docstrings and structure finalization (#164) (@exaexa) - Removal of stuff that won't go to 1.0 + some cleaning (#167) (@exaexa) - simplify&fix namespace resolution in parallel FVA (#169) (@exaexa) - Fix small things in stmodel specific functions (#172) (@stelmo) - add docker container generation (#174) (@laurentheirendt) - fixed fva tests (checked externally) (#175) (@stelmo) - Fixed small pfba error (#176) (@stelmo) - Implement analysis functions for CoreModelCoupled (#177) (@stelmo) - Export MAX/MIN, squash optimality check, relocate modifications (#180) (@stelmo) - Fix knockouts (#181) (@stelmo) - Add Literate.jl (#182) (@laurentheirendt) - Convert loading notebook to literate file (#183) (@stelmo) - fix the polymorphism of knockout mod (#184) (@exaexa) - Literally the basic usage tutorial (#185) (@stelmo) - literate structure-up (#186) (@exaexa) - Basic usage of standardmodel (#187) (@stelmo) - Normalize variable naming in models (#188) (@exaexa) - Basic usage of core and coupled models (#189) (@stelmo) - Document small accessor functions (#190) (@exaexa) - fix notebooks after master collision (#192) (@exaexa) - remove notebook converter (#194) (@laurentheirendt) - Model construction, modification and joining (#195) (@stelmo) - trigger external repo (#196) (@laurentheirendt) - skip ci for automatic formatting changes (#198) (@laurentheirendt) - Housekeeping 🪓 🧟 (#199) (@stelmo) - Improve how to contribute docs (#200) (@stelmo) - clean up tutorial 1 (#203) (@exaexa) - Small cosmetic fixes (#204) (@stelmo) - debug external trigger (#205) (@laurentheirendt) - [skip ci] trigger pipeline via API (#206) (@laurentheirendt) - revert the skip ci for the formatting bot (#207) (@laurentheirendt) - tutorial2 + notebook2 (#209) (@exaexa) - Cut example from readme (#210) (@stelmo) - [skip ci] simplify generating of the doc index (#211) (@exaexa) - [skip ci] tutorial 3 (#212) (@exaexa) - Add error message (#213) (@stelmo) - Improve standardmodel modifications (#214) (@stelmo) - Add references to analysis functions (#215) (@stelmo) - change curl command to docker (#218) (@laurentheirendt) - [skip ci] remove curl output (#220) (@laurentheirendt) - Add history image to main page of doc (#221) (@laurentheirendt) - tutorial 4 (#222) (@exaexa) - move gource asset (#223) (@laurentheirendt) - fix location (#224) (@laurentheirendt) - [skip ci] fix assets (#225) (@laurentheirendt) - new logos (#226) (@laurentheirendt) - release doc (#227) (@laurentheirendt) - new banner (#229) (@stelmo) - Slight improvement to banner (#230) (@stelmo) - format banner (#231) (@laurentheirendt) - fix doc deployment (#233) (@laurentheirendt) - set env for PR/MR (#234) (@laurentheirendt) - fix syntax for doc deployment (#235) (@laurentheirendt) - change installation to git (temporarily) (#236) (@exaexa) - fix issue with travis branch (#237) (@laurentheirendt) - add tag bot and compathelper (#238) (@laurentheirendt) - technical changes for doc deployment (#239) (@laurentheirendt) - bump version for release (#240) (@laurentheirendt) - Small fixes to the docs (#241) (@stelmo) - cleanup of dependencies (#242) (@exaexa) - use a gray filter for all console text (#243) (@exaexa) - remove devurl (#244) (@laurentheirendt) - fix nb viewer link (#246) (@laurentheirendt) - fix nb viewer - second round (#247) (@laurentheirendt) - fix nb viewer (#248) (@laurentheirendt)

- Julia
Published by github-actions[bot] almost 5 years ago