MIRA v0.9.0

What's Changed

• Update URLs for DKG service by @bgyori in #386
• Add model parameters to safe parse of distribution parameters by @djinnome in #390
• Propagate concept descriptions by @nanglo123 in #392
• Process distributions from SBML models by @bgyori in #393
• Handle null input or outputs when ingesting petrinet amr transitions by @nanglo123 in #397
• Extend SBML distribution processing by @bgyori in #395
• Processing ODE equations into a template model by @bgyori in #398
• Improve sympy extraction and ODE simulation by @bgyori in #401
• Update Docker build, pin pyobo by @kkaris in #400
• Enhanced model comparison by @bgyori in #403
• Hackathon 2024.12 initial materials by @bgyori in #404
• Precompile patterns and use cache when parsing by @bgyori in #405
• Various improvements by @bgyori in #406

Full Changelog: 0.8.0...0.9.0

MIRA v0.8.0

What's Changed

• Add resources to DKG by @nanglo123 in #344
• Implement new templates to model metabolism by @bgyori in #347
• Change new transition naming upon stratification by @bgyori in #349
• Add updated notebooks and exports for 2024.08 scenarios by @bgyori in #350
• Support expressions in parameters of distributions by @bgyori in #358
• Addition of ontology terms and subtree terms by @nanglo123 in #363
• Update dkg links in notebooks by @nanglo123 in #365
• Implement adding observables by pattern by @bgyori in #364
• Add obo pickled graphs to docker build by @nanglo123 in #367
• Fix sbml amr export by @nanglo123 in #368
• Only filter cities by minimum population by @nanglo123 in #373
• Update code to be compatible with Pydantic2 by @nanglo123 in #360
• Add all geonames admin2 regions by @nanglo123 in #375
• Propogate param_renaming_uses_strata_names argument from stratify endpoint to stratify method by @nanglo123 in #377
• Fix the epidemology DKG construction pipeline and docker container startup by @nanglo123 in #376
• Add "rdfs:subclassof" as a refinement relation by @nanglo123 in #380
• Fix unit processing for model ingestion by @nanglo123 in #381
• Update util.py by @djinnome in #379
• Speed up model composition by referring a singleton refinement closure by @nanglo123 in #383
• Generalize SBML initial condition extraction by @bgyori in #382
• Explicitly filter excluded controllers when considering cartesian product by @bgyori in #385

New Contributors

• @djinnome made their first contribution in #379

Full Changelog: 0.7.0...0.8.0

MIRA v0.7.0

What's Changed

• New features in rate law settings and ODE simulation + photosynthesis model by @bgyori in #316
• Handle superscripts in expressions by @bgyori in #317
• Recursively reason over flow control relationships by @cthoyt in #302
• Evaluation epi scenario 1 example model by @kkaris in #315
• Move evaluation notebooks into dedicated folders by @bgyori in #318
• Update evaluation 2024.03 epi scenario 4 notebook by @nanglo123 in #319
• Update way in which we identify controllers for rate laws when importing from Vensim by @nanglo123 in #320
• Evaluation scenario 2 by @bgyori in #323
• Eval sc1 initials by @kkaris in #324
• Add evaluation scenario 3 notebook and model by @bgyori in #326
• Create Notebook for evaluation2024.03 epi_scenario_1 model b by @nanglo123 in #321
• Add control variables to the mapping of parameters for a MIRA template model ingested from a Vensim model by @nanglo123 in #327
• Fix multiple stratification of templates with excluded concepts by @bgyori in #330
• Add support for sbml qual models by @nanglo123 in #328
• Reimplement stratification logic for parameter consistency by @bgyori in #332
• Add visualization for DKG relations by @nanglo123 in #333
• Fix dkg viz edge naming by @nanglo123 in #334
• Change link for budyko-sellers decapode example by @nanglo123 in #337
• Rename templates during stratification by @bgyori in #338
• Implement model composition by @nanglo123 in #335
• Fix serialization for datetime by @nanglo123 in #340
• Extend DKG Instance by @nanglo123 in #342
• Adjust test that are affected by the sympy 1.13 update by @nanglo123 in #343

Full Changelog: 0.6.0...0.7.0

MIRA v0.6.0

What's Changed

• Process ODE semantics from regnet AMR by @bgyori in #305
• Improve assembly and recognition of replications by @bgyori in #306
• Fix sign on intrinsic decay for regnet AMR by @bgyori in #308
• Handle float and int in expression constructor by @bgyori in #309
• Update code in notebooks for LLM ingestion by @nanglo123 in #310
• Comparison colors by @kkaris in #311
• Fix observable handling in stock and flow by @bgyori in #313
• Scenario5 by @bgyori in #314

Full Changelog: 0.5.0...0.6.0

MIRA v0.5.0

What's Changed

• Fix expression creation for Stella by @nanglo123 in #277
• Consolidate November 2023 Hackathon Notebook by @nanglo123 in #278
• Add regnet demo notebook by @bgyori in #279
• Preprocess stella expressions for PySD parsing and add error handling for currently unparseable expressions by @nanglo123 in #280
• Handle non-standard unicode characters in models by @bgyori in #282
• Process SIF models and export to regnets by @bgyori in #283
• Add Regnet AMR export of COVID-19 Disease Map by @bgyori in #284
• Implement replication templates by @bgyori in #285
• Improve Vensim Processing for Hackathon Vensim File by @nanglo123 in #286
• Add notebook for scenario 5 of 02/2024 hackathon by @nanglo123 in #288
• Improve scenario 5 import by @cthoyt in #289
• Implement safe parsing of curly braces by @bgyori in #290
• Fix bug in regnet initial export by @bgyori in #293
• Improve Vensim parser for scenario 5 by @cthoyt in #294
• Allow floats in regnet initials by @bgyori in #295
• Handle non-Lotka-Volterra kinetics for regnet models by @bgyori in #296
• Support missing input/output and missing rate law by @bgyori in #298
• Improve vensim import by @cthoyt in #300
• Fix TemplateModel json I/O by @kkaris in #301
• Add epi scenario1 notebook and artifacts by @kkaris in #299
• Add Hunt model for Scenario 6 by @bgyori in #303

Full Changelog: 0.4.0...0.5.0

MIRA v0.4.0

What's Changed

• Improve handling of stock and flow ACSets by @nanglo123 in #273
• Add total node count to DKG homepage by @cthoyt in #274
• Improve entity similarity endpoint by @cthoyt in #271
• Parse Vensim/Stella models into MIRA template models by @nanglo123 in #272
• Improvements to regnet export by @bgyori in #276

Full Changelog: 0.3.0...0.4.0

MIRA v0.3.0

What's Changed

• Add provenance and parents to climate ontology by @cthoyt in #255
• Use grounded names when renaming in stratification by @kkaris in #252
• Get physical constants from Wikidata by @cthoyt in #256
• Notebook benchmarking model comparison with/without grounding by @bgyori in #258
• Ingest a Decapode Compute Graph JSON Object and a Decaexpr Computation Tree JSON Object and Parse their content by @nanglo123 in #260
• Add entity similarity endpoint by @cthoyt in #261
• Fix awkward wording and typo in cells summarizing results of comparing all covid model comparisons for benchmarking dkg by @nanglo123 in #259
• Extract Climate Information from the EIFFEL Ontology to be added to the DKG by @nanglo123 in #262
• Improve DKG assembly of physical constants by @cthoyt in #263
• Major documentation update by @kkaris in #265
• Create TA1 Extraction Evaluation.ipynb by @cthoyt in #253
• Fix bug where we set initials dict to return of initials.update rather than just calling initials.update by @nanglo123 in #268
• Update required packages and README by @nanglo123 in #269
• Handle digesting budyko-sellers decapode. by @nanglo123 in #266

Full Changelog: 0.2.1...0.3.0