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Recent Releases of vivarium

vivarium -

- Python
Published by rmudambi 7 months ago

vivarium - v3.4.14

What's Changed

  • Refactor lifecycle system into a package by @rmudambi in https://github.com/ihmeuw/vivarium/pull/638
  • Introduce lifecycle state constants by @rmudambi in https://github.com/ihmeuw/vivarium/pull/639

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.13...v3.4.14

- Python
Published by rmudambi 7 months ago

vivarium - v3.4.13

What's Changed

  • Improve 'simulate profile' by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/637

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.12...v3.4.13

- Python
Published by stevebachmeier 7 months ago

vivarium - v3.4.12

What's Changed

  • Sbachmei/mic 6283/fix stratified observation formatter by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/636

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.11...v3.4.12

- Python
Published by stevebachmeier 8 months ago

vivarium - v3.4.11

What's Changed

  • use numpylt2 dependency by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/635

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.10...v3.4.11

- Python
Published by stevebachmeier 8 months ago

vivarium - v3.4.10

What's Changed

  • Sbachmei/mic 5918/common dependencies by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/633

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.9...v3.4.10

- Python
Published by stevebachmeier 8 months ago

vivarium - v3.4.9

What's Changed

  • fix pandas futurewarnings without pinning pandas by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/634

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.8...v3.4.9

- Python
Published by stevebachmeier 8 months ago

vivarium - v3.4.8

What's Changed

  • Add 'make build-env' by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/632

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.7...v3.4.8

- Python
Published by stevebachmeier 8 months ago

vivarium - v3.4.7

What's Changed

  • Fix dataframegroupby.apply future warnings by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/630

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.6...v3.4.7

- Python
Published by stevebachmeier 9 months ago

vivarium - v3.4.6

What's Changed

  • pin mypy<1.17.0 by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/628
  • Pin vivariumbuildutils by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/627

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.5...v3.4.6

- Python
Published by stevebachmeier 9 months ago

vivarium - v3.4.5

What's Changed

  • typing in population_view.py by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/626

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.4...v3.4.5

- Python
Published by hussain-jafari 10 months ago

vivarium - v3.4.4

What's Changed

  • Albrja/mic-5831/update-package-pins by @albrja in https://github.com/ihmeuw/vivarium/pull/625

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.3...v3.4.4

- Python
Published by albrja 10 months ago

vivarium - v3.4.3

What's Changed

  • Albrja/mic-5621/observer-get-configuration by @albrja in https://github.com/ihmeuw/vivarium/pull/624

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.2...v3.4.3

- Python
Published by albrja 11 months ago

vivarium - v3.4.2

What's Changed

  • Albrja/mic-5653/Fix mypy errors in testing utilities by @albrja in https://github.com/ihmeuw/vivarium/pull/622

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.1...v3.4.2

- Python
Published by albrja 11 months ago

vivarium - v3.4.1

What's Changed

  • typing results/test_context.py by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/621

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.4.0...v3.4.1

- Python
Published by hussain-jafari 11 months ago

vivarium - v3.4.0

What's Changed

  • Albrja/mic-5664/update-rate-to-probability by @albrja in https://github.com/ihmeuw/vivarium/pull/620

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.22...v3.4.0

- Python
Published by albrja 11 months ago

vivarium - v3.3.22

What's Changed

  • Add py.typed marker by @patricktnast in https://github.com/ihmeuw/vivarium/pull/619

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.21...v3.3.22

- Python
Published by patricktnast 11 months ago

vivarium - v3.3.21

What's Changed

  • type hint tests/framework/test_event.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/618

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.20...v3.3.21

- Python
Published by stevebachmeier 11 months ago

vivarium - v3.3.20

What's Changed

  • Fix mypy errors in docs/source/conf and tests/interface/test-utilities by @albrja in https://github.com/ihmeuw/vivarium/pull/617

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.19...v3.3.20

- Python
Published by albrja 11 months ago

vivarium - v3.3.19

What's Changed

  • Albrja/mic-5739/mypy-test-values by @albrja in https://github.com/ihmeuw/vivarium/pull/615
  • type hint tests/framework/test_engine.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/616

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.18...v3.3.19

- Python
Published by stevebachmeier 11 months ago

vivarium - v3.3.18

What's Changed

  • Albrja/mic 5373/all columns required and create column population view by @albrja in https://github.com/ihmeuw/vivarium/pull/610

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.17...v3.3.18

- Python
Published by albrja 11 months ago

vivarium - v3.3.17

What's Changed

  • add typevar to nitpick exceptions by @patricktnast in https://github.com/ihmeuw/vivarium/pull/613
  • typing tests/framework/test_lifecycle.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/614

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.16...v3.3.17

- Python
Published by stevebachmeier 12 months ago

vivarium - v3.3.16

What's Changed

  • Typing tests/helpers.py by @patricktnast in https://github.com/ihmeuw/vivarium/pull/612

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.15...v3.3.16

- Python
Published by patricktnast 12 months ago

vivarium - v3.3.15

What's Changed

  • mypy fixes in cli.py and related tests by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/607
  • Albrja/mic-5731/Fix mypy erros in test_configuration.py by @albrja in https://github.com/ihmeuw/vivarium/pull/608
  • Test Disease Model Typing by @patricktnast in https://github.com/ihmeuw/vivarium/pull/609

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.14...v3.3.15

- Python
Published by patricktnast 12 months ago

vivarium - v3.3.14

What's Changed

  • Albrja/mic-5585/load-backup-method by @albrja in https://github.com/ihmeuw/vivarium/pull/604
  • typing result manager test by @patricktnast in https://github.com/ihmeuw/vivarium/pull/606
  • mypy fixes in tests/framework/results/test_interface.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/605

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.13...v3.3.14

- Python
Published by stevebachmeier about 1 year ago

vivarium - v3.3.13

What's Changed

  • mypy fixes for tests/framework/results/test_observer.py by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/601
  • mypy fixes for tests/framework/results/test_stratification.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/602
  • Albjra/mic 5728/mypy test observation by @albrja in https://github.com/ihmeuw/vivarium/pull/603

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.12...v3.3.13

- Python
Published by albrja about 1 year ago

vivarium - v3.3.12

What's Changed

  • mypy fixes for tests/framework/test_plugins.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/600

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.11...v3.3.12

- Python
Published by stevebachmeier about 1 year ago

vivarium - v3.3.11

What's Changed

  • raise error if requested pipeline does not exist in interactive context by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/599

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.10...v3.3.11

- Python
Published by stevebachmeier about 1 year ago

vivarium - v3.3.10

What's Changed

  • Albrja/mic-5737/Fix mypy errors in test time by @albrja in https://github.com/ihmeuw/vivarium/pull/595
  • mypy fixes tests/framework/teststatemachine.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/598

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.9...v3.3.10

- Python
Published by stevebachmeier about 1 year ago

vivarium - v3.3.9

What's Changed

  • Delete .github/workflows/build.yml by @patricktnast in https://github.com/ihmeuw/vivarium/pull/597
  • Typing Test/framework/results/helpers.py by @patricktnast in https://github.com/ihmeuw/vivarium/pull/593
  • Typing testpopulationmanager.py by @patricktnast in https://github.com/ihmeuw/vivarium/pull/596

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.8...v3.3.9

- Python
Published by patricktnast about 1 year ago

vivarium - v3.3.8

What's Changed

  • typing testing/framework/test_utilities.py by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/594

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.7...v3.3.8

- Python
Published by hussain-jafari about 1 year ago

vivarium - v3.3.7

What's Changed

  • fix mypy errors in tests/framework/population/testpopulationview.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/591
  • change Event to a frozen dataclass by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/592

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.6...v3.3.7

- Python
Published by stevebachmeier about 1 year ago

vivarium - v3.3.6

What's Changed

  • tests/framework/randomness/test_stream.py typing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/590

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.5...v3.3.6

- Python
Published by hussain-jafari about 1 year ago

vivarium - v3.3.5

What's Changed

  • Albrja/mic-5722/Fix mypy errors in tests/randomness/test_reproducibility by @albrja in https://github.com/ihmeuw/vivarium/pull/589

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.4...v3.3.5

- Python
Published by albrja about 1 year ago

vivarium - v3.3.4

What's Changed

  • test_lookup.py typing by @patricktnast in https://github.com/ihmeuw/vivarium/pull/588

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.3...v3.3.4

- Python
Published by patricktnast about 1 year ago

vivarium - v3.3.3

What's Changed

  • mypy fixes tests/framework/components/test_manager.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/586

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.2...v3.3.3

- Python
Published by stevebachmeier about 1 year ago

vivarium - v3.3.2

What's Changed

  • test_component.py Typing by @patricktnast in https://github.com/ihmeuw/vivarium/pull/585
  • test_parser typing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/584
  • CHANGELOG test_component hotfix by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/587

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.1...v3.3.2

- Python
Published by hussain-jafari about 1 year ago

vivarium - v3.3.1

What's Changed

  • Albrja/mic-5714/mypy-test-interpolation by @albrja in https://github.com/ihmeuw/vivarium/pull/583

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.3.0...v3.3.1

- Python
Published by albrja about 1 year ago

vivarium - v3.3.0

What's Changed

  • Albrja/mic 5401/lookup dict by @albrja in https://github.com/ihmeuw/vivarium/pull/582

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.20...v3.3.0

- Python
Published by albrja about 1 year ago

vivarium - v3.2.20

What's Changed

  • Albrja/mic-5827/Pin isort by @albrja in https://github.com/ihmeuw/vivarium/pull/581
  • Add python Version json by @patricktnast in https://github.com/ihmeuw/vivarium/pull/579
  • Remove Mocks file by @patricktnast in https://github.com/ihmeuw/vivarium/pull/580

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.19...v3.2.20

- Python
Published by patricktnast about 1 year ago

vivarium - v3.2.19

What's Changed

  • test_hdf typing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/578

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.18...v3.2.19

- Python
Published by hussain-jafari about 1 year ago

vivarium - v3.2.18

What's Changed

  • Albrja/mic-5802/sphinx-config by @albrja in https://github.com/ihmeuw/vivarium/pull/576
  • mypy fixes in artfiact/test_manager.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/577

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.17...v3.2.18

- Python
Published by stevebachmeier about 1 year ago

vivarium - v3.2.17

What's Changed

  • Shared Makefiles by @patricktnast in https://github.com/ihmeuw/vivarium/pull/573
  • Albrja/mic 5720/mypy tests randomness index map by @albrja in https://github.com/ihmeuw/vivarium/pull/574
  • Albrja/mic 5707/mypy test artifact by @albrja in https://github.com/ihmeuw/vivarium/pull/575

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.16...v3.2.17

- Python
Published by albrja about 1 year ago

vivarium - v3.2.16

What's Changed

  • Typing Randomness Manager by @patricktnast in https://github.com/ihmeuw/vivarium/pull/572

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.15...v3.2.16

- Python
Published by patricktnast about 1 year ago

vivarium - v3.2.15

What's Changed

  • Mypy errors test_crn.py by @patricktnast in https://github.com/ihmeuw/vivarium/pull/571

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.14...v3.2.15

- Python
Published by patricktnast about 1 year ago

vivarium - v3.2.14

What's Changed

  • mypy fixes in InteractiveContext by @patricktnast in https://github.com/ihmeuw/vivarium/pull/566
  • mypy fixes in tests/conftest.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/568
  • mypy fixes in tests/randomness/conftest.py by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/569

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.13...v3.2.14

- Python
Published by hussain-jafari about 1 year ago

vivarium - v3.2.13

What's Changed

  • mypy fixes for boids example by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/563

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.12...v3.2.13

- Python
Published by stevebachmeier over 1 year ago

vivarium - v3.2.12

What's Changed

  • Albrja/mic 5649/mypy fraemwork engine by @albrja in https://github.com/ihmeuw/vivarium/pull/562

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.11...v3.2.12

- Python
Published by rmudambi over 1 year ago

vivarium - v3.2.11

What's Changed

  • Try different top-level jenkins agent by @patricktnast in https://github.com/ihmeuw/vivarium/pull/558
  • component parser typing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/561

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.10...v3.2.11

- Python
Published by hussain-jafari over 1 year ago

vivarium - v3.2.10

What's Changed

  • Type-hinting: component manager by @rmudambi in https://github.com/ihmeuw/vivarium/pull/560

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.9...v3.2.10

- Python
Published by rmudambi over 1 year ago

vivarium - v3.2.9

What's Changed

  • lookup int64 processing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/559

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.8...v3.2.9

- Python
Published by hussain-jafari over 1 year ago

vivarium - v3.2.8

What's Changed

  • add test that should be fixed when fixing this bug by @rmudambi in https://github.com/ihmeuw/vivarium/pull/552
  • Albrja/mic 5538/crn additional seed by @albrja in https://github.com/ihmeuw/vivarium/pull/556

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.7...v3.2.8

- Python
Published by albrja over 1 year ago

vivarium - v3.2.7

What's Changed

  • Mypy State Machine by @patricktnast in https://github.com/ihmeuw/vivarium/pull/554

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.6...v3.2.7

- Python
Published by patricktnast over 1 year ago

vivarium - v3.2.6

What's Changed

  • add git branch to conda env name by @patricktnast in https://github.com/ihmeuw/vivarium/pull/555

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.5...v3.2.6

- Python
Published by patricktnast over 1 year ago

vivarium - v3.2.5

What's Changed

  • fix mypy errors: component.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/549
  • Albrja/mic-5603/myppy-results-observer by @albrja in https://github.com/ihmeuw/vivarium/pull/551
  • results/interface.py typing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/550

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.4...v3.2.5

- Python
Published by hussain-jafari over 1 year ago

vivarium - v3.2.4

What's Changed

  • Fix pandas groupby type hints for pandas stubs update by @albrja in https://github.com/ihmeuw/vivarium/pull/548

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.3...v3.2.4

- Python
Published by albrja over 1 year ago

vivarium - v3.2.3

What's Changed

  • mypy fixes in results/manager.py by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/544
  • Lookup Manager Typing by @patricktnast in https://github.com/ihmeuw/vivarium/pull/547
  • allow users to define initialization weights as LookupTableData or an… by @rmudambi in https://github.com/ihmeuw/vivarium/pull/542
  • create DataInput type by @rmudambi in https://github.com/ihmeuw/vivarium/pull/543
  • remove unnecessary layer of indirection by @rmudambi in https://github.com/ihmeuw/vivarium/pull/545
  • add triggered argument to add_transition; return transition by @rmudambi in https://github.com/ihmeuw/vivarium/pull/546

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.2...v3.2.3

- Python
Published by rmudambi over 1 year ago

vivarium - v3.2.2

What's Changed

  • enable adding transition to a state by defining the output state and … by @rmudambi in https://github.com/ihmeuw/vivarium/pull/541

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.1...v3.2.2

- Python
Published by rmudambi over 1 year ago

vivarium - v3.2.1

What's Changed

  • Sbachmei/mic 5549/mypy results context by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/538
  • drop python 3.9 changes by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/540
  • Albrja/mic-5546/mypy framework time by @albrja in https://github.com/ihmeuw/vivarium/pull/539

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.2.0...v3.2.1

- Python
Published by albrja over 1 year ago

vivarium - v3.2.0

What's Changed

  • Release candidate v3.2.0 by @rmudambi in https://github.com/ihmeuw/vivarium/pull/537

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.1.0...v3.2.0

- Python
Published by rmudambi over 1 year ago

vivarium - v3.1.0

What's Changed

  • drop python 3.9 support by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/532

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.18...v3.1.0

- Python
Published by hussain-jafari over 1 year ago

vivarium - v3.0.18

What's Changed

  • Sbachmei/mic 5399/mypy errors logging manager by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/531
  • Albrja/Mic-5462/mypy-results-observation by @albrja in https://github.com/ihmeuw/vivarium/pull/526

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.17...v3.0.18

- Python
Published by albrja over 1 year ago

vivarium - v3.0.17

What's Changed

  • add mypy type checking to configuration.py by @rmudambi in https://github.com/ihmeuw/vivarium/pull/529
  • add mypy type checking to artifact manager by @rmudambi in https://github.com/ihmeuw/vivarium/pull/530

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.16...v3.0.17

- Python
Published by rmudambi over 1 year ago

vivarium - v3.0.16

What's Changed

  • Albrja/mic 5469/add flags to workflow by @albrja in https://github.com/ihmeuw/vivarium/pull/520
  • Remove or replace ignores in plugins by @patricktnast in https://github.com/ihmeuw/vivarium/pull/524
  • table typing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/519
  • Maintain lookup table value column order by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/521
  • fix type handling for clocktime and step_size by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/522
  • typing interface/utilities by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/525
  • Randomness Manager Typing by @patricktnast in https://github.com/ihmeuw/vivarium/pull/523

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.15...v3.0.16

- Python
Published by patricktnast over 1 year ago

vivarium - v3.0.15

What's Changed

  • Sbachmei/mic 5395/mypy event by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/516
  • Albrja/mic 5267/build from vbu by @albrja in https://github.com/ihmeuw/vivarium/pull/517
  • Revert changes to deploy by @albrja in https://github.com/ihmeuw/vivarium/pull/518

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.14...v3.0.15

- Python
Published by albrja over 1 year ago

vivarium - v3.0.14

What's Changed

  • Randomness Stream typing by @patricktnast in https://github.com/ihmeuw/vivarium/pull/509
  • Albrja/mic 5397/mypy artifact by @albrja in https://github.com/ihmeuw/vivarium/pull/508

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.13...v3.0.14

- Python
Published by albrja over 1 year ago

vivarium - v3.0.13

What's Changed

  • Albrja/Mic-5240/Slack developer on build failure by @albrja in https://github.com/ihmeuw/vivarium/pull/502
  • interpolation typing by @hussain-jafari in https://github.com/ihmeuw/vivarium/pull/495

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.12...v3.0.13

- Python
Published by hussain-jafari over 1 year ago

vivarium - v3.0.12

What's Changed

  • Bugfix for values typing by @patricktnast in https://github.com/ihmeuw/vivarium/pull/500

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.11...v3.0.12

- Python
Published by patricktnast over 1 year ago

vivarium - v3.0.11

What's Changed

  • fix mypy typing Values by @patricktnast in https://github.com/ihmeuw/vivarium/pull/494

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.10...v3.0.11

- Python
Published by patricktnast over 1 year ago

vivarium - v3.0.10

What's Changed

  • Albrja/mic 5383/add-number-steps-method by @albrja in https://github.com/ihmeuw/vivarium/pull/493

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.9...v3.0.10

- Python
Published by albrja over 1 year ago

vivarium - v3.0.9

What's Changed

  • fix mypy typing: logging utilities by @rmudambi in https://github.com/ihmeuw/vivarium/pull/492

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.8...v3.0.9

- Python
Published by rmudambi over 1 year ago

vivarium - v3.0.8

What's Changed

  • Albrja/Mic-5340/mypy-artifact-hdf by @albrja in https://github.com/ihmeuw/vivarium/pull/491
  • Sbachmei/mic 5347/mypy resources by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/490

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.7...v3.0.8

- Python
Published by stevebachmeier over 1 year ago

vivarium - v3.0.7

What's Changed

  • Enable population manager and population view methods to accept strings by @rmudambi in #485
  • Fix mypy errors: vivarium/framework/lifecycle.py by @hussain-jafari in #486
  • Fix mypy errors: vivarium/framework/population/manager.py by @rmudambi in #483
  • Fix mypy errors: vivarium/framework/population/population_view.py by @rmudambi in #483
  • Fix mypy errors: vivarium/framework/plugins.py by @albrja in #484
  • Fix mypy errors: vivarium/framework/results/stratification.py by @patricktnast in #487

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.6...v3.0.7

- Python
Published by patricktnast over 1 year ago

vivarium - v3.0.6

What's Changed

  • mypy fix index_map.py by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/482

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.5...v3.0.6

- Python
Published by stevebachmeier over 1 year ago

vivarium - v3.0.5

What's Changed

  • pin sphinx <8 by @patricktnast in https://github.com/ihmeuw/vivarium/pull/481

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.4...v3.0.5

- Python
Published by patricktnast over 1 year ago

vivarium - v3.0.4

What's Changed

  • introduce static type checking with mypy by @rmudambi in https://github.com/ihmeuw/vivarium/pull/479
  • improve time types; fix mypy errors in utilities by @rmudambi in https://github.com/ihmeuw/vivarium/pull/480

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.3...v3.0.4

- Python
Published by rmudambi over 1 year ago

vivarium - v3.0.3

What's Changed

  • raise an error if a component attempts to access a non-existent population_view by @rmudambi in https://github.com/ihmeuw/vivarium/pull/478

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.2...v3.0.3

- Python
Published by rmudambi over 1 year ago

vivarium - v3.0.2

What's Changed

  • Mic 5211/cron job by @albrja in https://github.com/ihmeuw/vivarium/pull/466
  • Epic/results documentation by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/477

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.1...v3.0.2

- Python
Published by stevebachmeier over 1 year ago

vivarium - v3.0.1

What's Changed

  • create a script to find matching dependency branches by @rmudambi in https://github.com/ihmeuw/vivarium/pull/470
  • Add category exclusions test by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/468

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v3.0.0...v3.0.1

- Python
Published by stevebachmeier over 1 year ago

vivarium - v3.0.0

What's Changed

Breaking changes: - Remove the unnecessary metrics pipeline - Refactor lookup table creation and allow configuration of lookup columns - Refactor results manager to process results directly

Major changes: - Move results controller and interface from managers to default plugins - Add a getconfiguration method and configuration attribute to Component - Enable buildlookup_table to accept a list as input data - Implement an Observation dataclass - Remove --location/-l option from simulate run command - Change the metrics/ folder to results/; refer to "results" instead of "metrics" throughout - Implement multiple new interface functions for registering stratifications and observations - Implement multiple new Observer types - Implement simulation backups - Implement excluding results categories via the configuration

Other changes: - Use layered-config-tree package instead of local ConfigTree class - Add a report emitter to the SimulationContext - Check for and log unused stratifications and raise for missing required stratifications - Move all steps of running a simulation into a run_simulation instance method - Add simulate run e2e test - Stop writing seed and draw columns to the results - Install matching upstream branches in github builds - Automatically run Jenkins builds on push or pull request - Add type hints throughout results modules - Various other minor updates

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.8...v3.0.0

- Python
Published by stevebachmeier over 1 year ago

vivarium - v2.3.8

What's Changed

  • Mic-5121/Hotfix/pin numpy below 2.0 by @albrja in https://github.com/ihmeuw/vivarium/pull/434

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.7...v2.3.8

- Python
Published by albrja almost 2 years ago

vivarium - v2.3.7

What's Changed

  • Feature/sbachmei/mic 4944 config tree deprecation warning by @stevebachmeier in https://github.com/ihmeuw/vivarium/pull/391

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.6...v2.3.7

- Python
Published by stevebachmeier about 2 years ago

vivarium - v2.3.6

What's Changed

  • Update population keys by @albrja in https://github.com/ihmeuw/vivarium/pull/390

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.5...v2.3.6

- Python
Published by albrja about 2 years ago

vivarium - v2.3.5

What's Changed

  • Continue boids tutorial by @zmbc in https://github.com/ihmeuw/vivarium/pull/383

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.4...v2.3.5

- Python
Published by rmudambi about 2 years ago

vivarium - v2.3.4

What's Changed

  • Update CODEOWNERS by @patricktnast in https://github.com/ihmeuw/vivarium/pull/387
  • Parse metrics without stratification by @albrja in https://github.com/ihmeuw/vivarium/pull/388

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.3...v2.3.4

- Python
Published by albrja about 2 years ago

vivarium - v2.3.3

What's Changed

  • Improve readability of api reference docs by @rmudambi in https://github.com/ihmeuw/vivarium/pull/386

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.2...v2.3.3

- Python
Published by rmudambi about 2 years ago

vivarium - v2.3.2

What's Changed

  • Docs bug fixes by @rmudambi in https://github.com/ihmeuw/vivarium/pull/385

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.1...v2.3.2

- Python
Published by rmudambi about 2 years ago

vivarium - v2.3.1

What's Changed

  • Update pypi publish with 2FA by @patricktnast in https://github.com/ihmeuw/vivarium/pull/384

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.3.0...v2.3.1

- Python
Published by patricktnast about 2 years ago

vivarium - v2.3.0

What's Changed

  • Mic-4666/Fix schedule tests by @albrja in https://github.com/ihmeuw/vivarium/pull/369
  • Individual Clocks v1 by @patricktnast in https://github.com/ihmeuw/vivarium/pull/382
  • Document how to remove components from an interactive simulation by @zmbc in https://github.com/ihmeuw/vivarium/pull/379
  • Update code in docs to match current implementation by @aflaxman in https://github.com/ihmeuw/vivarium/pull/375

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.2.1...v2.3.0

- Python
Published by patricktnast over 2 years ago

vivarium - v2.2.1

What's Changed

  • Mic-4384/Notify when cron or deploy builds fail by @albrja in https://github.com/ihmeuw/vivarium/pull/365
  • fix ScalarValue import by @rmudambi in https://github.com/ihmeuw/vivarium/pull/368

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.2.0...v2.2.1

- Python
Published by rmudambi over 2 years ago

vivarium - v2.2.0

What's Changed

  • Release/v2.2.0 by @rmudambi in https://github.com/ihmeuw/vivarium/pull/367

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.1.1...v2.2.0

- Python
Published by rmudambi over 2 years ago

vivarium - v2.1.1

What's Changed

  • Refactor ComponentConfigurationParser creating Components as they are parsed by @rmudambi in https://github.com/ihmeuw/vivarium/pull/356
  • enable RandomnessStream to sample from distributions by @rmudambi in https://github.com/ihmeuw/vivarium/pull/357

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.1.0...v2.1.1

- Python
Published by rmudambi over 2 years ago

vivarium - v2.1.0

What's Changed

  • Release v2.1.0 by @rmudambi in https://github.com/ihmeuw/vivarium/pull/354

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.0.1...v2.1.0

- Python
Published by rmudambi over 2 years ago

vivarium - v2.0.1

What's Changed

  • Set pipeline's returned Series' name to the pipeline's name by @rmudambi in https://github.com/ihmeuw/vivarium/pull/353

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v2.0.0...v2.0.1

- Python
Published by rmudambi over 2 years ago

vivarium - v2.0.0

What's Changed

  • Mic 3237/readme update by @albrja in https://github.com/ihmeuw/vivarium/pull/342
  • Mic-4057/Update ci button by @albrja in https://github.com/ihmeuw/vivarium/pull/345
  • datetime and Timestamp are incompatible in run_until by @patricktnast in https://github.com/ihmeuw/vivarium/pull/343
  • Mic-4379/schedule-builds by @albrja in https://github.com/ihmeuw/vivarium/pull/346
  • Add default to Register Observation pop filter by @patricktnast in https://github.com/ihmeuw/vivarium/pull/344
  • Mic-4379/change cron time by @albrja in https://github.com/ihmeuw/vivarium/pull/348
  • Mic 4380/full test suites schedule by @albrja in https://github.com/ihmeuw/vivarium/pull/349
  • Mic-4381/Run all tests on deploy by @albrja in https://github.com/ihmeuw/vivarium/pull/351
  • Component Standardization by @rmudambi in https://github.com/ihmeuw/vivarium/pull/350
  • Mic-4381/Add runslow to conftest so deploy will work by @albrja in https://github.com/ihmeuw/vivarium/pull/352

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v1.2.8...v2.0.0

- Python
Published by rmudambi over 2 years ago

vivarium - Patch Release v1.2.8

What's Changed

  • Unpin Pandas by @patricktnast in https://github.com/ihmeuw/vivarium/pull/340

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v1.2.7...v1.2.8

- Python
Published by patricktnast over 2 years ago

vivarium - Patch Release v1.2.7

What's Changed

  • Upgrade Pandas to 2.0 by @patricktnast in https://github.com/ihmeuw/vivarium/pull/339

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v1.2.6...v1.2.7

- Python
Published by patricktnast over 2 years ago

vivarium - Patch Release v1.2.6

What's Changed

  • Mic-4382/lint-before-tests by @albrja in https://github.com/ihmeuw/vivarium/pull/336
  • Address Pandas >2.0.0 FutureWarnings by @patricktnast in https://github.com/ihmeuw/vivarium/pull/338

New Contributors

  • @albrja made their first contribution in https://github.com/ihmeuw/vivarium/pull/336
  • @patricktnast made their first contribution in https://github.com/ihmeuw/vivarium/pull/338

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v1.2.5...v1.2.6

What's Changed

  • Mic-4382/lint-before-tests by @albrja in https://github.com/ihmeuw/vivarium/pull/336
  • Address Pandas >2.0.0 FutureWarnings by @patricktnast in https://github.com/ihmeuw/vivarium/pull/338

New Contributors

  • @albrja made their first contribution in https://github.com/ihmeuw/vivarium/pull/336

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v1.2.5...v1.2.6

- Python
Published by patricktnast over 2 years ago

vivarium - Patch release v1.2.5

What's Changed

  • Make ConfigTree objects pickleable by @rmudambi in https://github.com/ihmeuw/vivarium/pull/335

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v1.2.4...v1.2.5

- Python
Published by rmudambi over 2 years ago

vivarium - Patch release v1.2.4

What's Changed

  • create type alias for LookupTable source data by @rmudambi in https://github.com/ihmeuw/vivarium/pull/333

Full Changelog: https://github.com/ihmeuw/vivarium/compare/v1.2.3...v1.2.4

- Python
Published by rmudambi over 2 years ago