Code

Stochastic transitions#474

Code

Draft

RomeshA wants to merge 48 commits intodevelopatomicateam/atomica:developfrom stochastic_transitionsatomicateam/atomica:stochastic_transitionsCopy head branch name to clipboard

+709-165

Commits

Commits on Oct 11, 2021

• Set up stochattic probability-based transitions to allow for measuring probability of e.g. elimination of a disease

  Rowanmh

  committed
  baeafb3

  Copy full SHA for baeafb3

Commits on Oct 12, 2021

• add stochastic_rounding

  Rowanmh

  committed
  4037277

  Copy full SHA for 4037277

Commits on Nov 5, 2021

• Random seed for parset sampling, random.randn -> default_rng sampling

  Rowanmh

  committed
  425223d

  Copy full SHA for 425223d

• default_rng for programs/covouts also

  Rowanmh

  committed
  e3c6285

  Copy full SHA for e3c6285

• Update project.py

  Rowanmh

  committed
  6cbcb6f

  Copy full SHA for 6cbcb6f

• Update project.py

  Rowanmh

  committed
  752154a

  Copy full SHA for 752154a

Commits on Nov 7, 2021

• Pass the same random number generator within a given model run rather than creating local ones

  Rowanmh

  committed
  3965276

  Copy full SHA for 3965276

• Consistent seeding

  Rowanmh

  committed
  ac4e458

  Copy full SHA for ac4e458

• Pass generators within kwargs, and handle that option in parallel_progress

  Rowanmh

  committed
  1e7c94f

  Copy full SHA for 1e7c94f

• Optional acceptance criteria for sampled_sims - to ensure that sampled runs are reasonably matched historically

  Rowanmh

  committed
  930c10e

  Copy full SHA for 930c10e

• Update project.py

  Rowanmh

  committed
  0b4e493

  Copy full SHA for 0b4e493

Commits on Nov 8, 2021

• Acceptance criteria evaluated during runtime or postprocessing as appropriate

  Show description for 0e3bb45
  Rowanmh

  committed
  0e3bb45

  Copy full SHA for 0e3bb45

Commits on Feb 22, 2023

• Merge branch 'develop' into stochastic_transitions

  Rowanmh

  committed
  224c2a6

  Copy full SHA for 224c2a6

Commits on Mar 1, 2023

• Fix ResidualJunctionCompartment not applying stochasticity correctly with a ">" residual link.

  Show description for 211a7fd
  kelvinburke

  committed
  211a7fd

  Copy full SHA for 211a7fd

Commits on Mar 3, 2023

• Whitespace

  Rowanmh

  committed
  98b7274

  Copy full SHA for 98b7274

Commits on May 10, 2023

• Merge pull request #473 from atomicateam/stochastic_transitions_fix

  Show description for b955a10
  Rowanmh

  authored
  b955a10

  Copy full SHA for b955a10

Commits on Jun 18, 2023

• Merge remote-tracking branch 'origin/master' into stochastic_transitions

  RomeshA

  committed
  3188662

  Copy full SHA for 3188662

Commits on Sep 26, 2023

• Merge pull request #486 from atomicateam/develop

  Show description for 33b9da7
  RomeshA

  authored
  33b9da7

  Copy full SHA for 33b9da7

Commits on Oct 20, 2023

• Merge pull request #488 from atomicateam/develop

  Show description for d1839ee
  RomeshA

  authored
  d1839ee

  Copy full SHA for d1839ee

Commits on Nov 1, 2023

• Add rng_sampler=None to Programset.sample()

  kelvinburke

  committed
  a545715

  Copy full SHA for a545715

• Merge branch 'develop' into stochastic_transitions

  Rowanmh

  committed
  61ffc2d

  Copy full SHA for 61ffc2d

Commits on Nov 2, 2023

• Merge branch 'stochastic_transitions' of github.com:atomicateam/atomica into stochastic_transitions

  RomeshA

  committed
  da06bbb

  Copy full SHA for da06bbb

• Keep "Output" column in worksheet and don't group by output, just print the whole dataframe as it is

  kelvinburke

  committed
  72f231d

  Copy full SHA for 72f231d

• Also make sure the required_width of a column fits the column name

  kelvinburke

  committed
  76a1dba

  Copy full SHA for 76a1dba

Commits on Nov 6, 2023

• Add "constant" to reserved_keywords

  Rowanmh

  committed
  1ee101c

  Copy full SHA for 1ee101c

Commits on Nov 10, 2023

• Merge remote-tracking branch 'origin/databook_fixes' into stochastic_transitions

  Rowanmh

  committed
  efcf4c2

  Copy full SHA for efcf4c2

• Merge remote-tracking branch 'origin/dont-group-results-excel' into stochastic_transitions

  Rowanmh

  committed
  eb464d0

  Copy full SHA for eb464d0

Commits on Nov 24, 2023

• Use ax = fig.gca() instead of ax = plt.gca() so that you can have multiple figures plotting in parallel

  kelvinburke

  committed
  70f34cd

  Copy full SHA for 70f34cd

• Improve error message when different y-labels

  kelvinburke

  committed
  02c4cb9

  Copy full SHA for 02c4cb9

Commits on Feb 5, 2024

• Merge pull request #495 from atomicateam/develop

  Show description for 17efbee
  RomeshA

  authored
  17efbee

  Copy full SHA for 17efbee

Commits on Apr 11, 2024

• Add test_tox_markovchain.py

  kelvinburke

  committed
  269f712

  Copy full SHA for 269f712

Commits on Jun 5, 2024

• Merge remote-tracking branch 'origin/stochastic_transitions' into stochastic_transitions

  RomeshA

  committed
  c9dfa22

  Copy full SHA for c9dfa22

• Merge remote-tracking branch 'origin/develop' into stochastic_transitions

  RomeshA

  committed
  c6d990c

  Copy full SHA for c6d990c

Commits on Jun 7, 2024

• Fix tests

  RomeshA

  committed
  9dcb653

  Copy full SHA for 9dcb653

• Fix seed selection

  RomeshA

  committed
  e39b780

  Copy full SHA for e39b780

• Implement very simple example of test reordering for further use later

  RomeshA

  committed
  8abb36a

  Copy full SHA for 8abb36a

• Formatting pass

  RomeshA

  committed
  2a8bc1e

  Copy full SHA for 2a8bc1e

Commits on Jun 26, 2024

• Update to Python 3.12

  RomeshA

  committed
  3e76bf7

  Copy full SHA for 3e76bf7

Commits on Jun 27, 2024

• Enable auto calibration of transfers

  RomeshA

  committed
  a8ef28d

  Copy full SHA for a8ef28d

• Update test pipeline

  RomeshA

  committed
  c6dbf4b

  Copy full SHA for c6dbf4b

• Update documentation

  RomeshA

  committed
  5af7e4b

  Copy full SHA for 5af7e4b

• Update setup.py

  RomeshA

  committed
  9a353e1

  Copy full SHA for 9a353e1

• Merge remote-tracking branch 'origin/develop' into enable-transfer-calibration

  RomeshA

  committed
  8a1b0c1

  Copy full SHA for 8a1b0c1

Commits on Jun 28, 2024

• Update deprecated scipy function

  RomeshA

  committed
  6a49703

  Copy full SHA for 6a49703

• Merge branch 'enable-transfer-calibration' into stochastic_transitions

  RomeshA

  committed
  222ad88

  Copy full SHA for 222ad88

Commits on Aug 19, 2024

• Rename stochastic to multinomial

  RomeshA

  committed
  c2fe4ae

  Copy full SHA for c2fe4ae

Commits on Sep 2, 2024

• Prefill interaction tables with Y/N more logically

  Show description for d1c2223
  Rowanmh

  committed
  d1c2223

  Copy full SHA for d1c2223

• More informative sc.prepr output (useful when debugging)

  Rowanmh

  committed
  c752086

  Copy full SHA for c752086