Code

Release cycle, December 2024#375

Code

Merged

TimothyWillard merged 174 commits intomainHopkinsIDD/flepiMoP:mainfrom devHopkinsIDD/flepiMoP:devCopy head branch name to clipboardDec 11, 2024

+5,811-19,809

Commits

Commits on Sep 16, 2024

• fixes the argument call to the plot of emcee chains

  jcblemai

  committed
  8974cc4

• finish the plot

  jcblemai

  committed
  1453303

• fix emcee rmse error spotted by Tim in #300

  jcblemai

  committed
  e4bbd8c

Commits on Sep 17, 2024

• Save seir, spar and snpi on save, + made more granullar to access a funciton that just run a simulation

  jcblemai

  committed
  311a20b

• fix

  jcblemai

  committed
  80e63b8

• change the order so it fails fast if something already exist

  jcblemai

  committed
  bf7c37a

Commits on Sep 18, 2024

• a very hacky and stupid batch hack to fight memory creep...

  jcblemai

  committed
  6725bf6

Commits on Sep 19, 2024

• trying to trigger a llik reevaluation

  jcblemai

  committed
  70bbee8

• solve #316: likelihood are discarded during resume

  jcblemai

  committed
  465d0bb

Commits on Sep 20, 2024

• upgrade plot to show the transformed data

  jcblemai

  committed
  2c54cfd

Commits on Sep 25, 2024

• plotting proections

  jcblemai

  committed
  f1ecbe6

• file structure

  jcblemai

  committed
  b5409a7

• add poisson likelihood

  twallema

  committed
  ebbf2c2

• add new distributions - retain old distributions

  twallema

  committed
  589af08

• miscopied the poisson from pySODM

  twallema

  committed
  b797cf7

• match data format gempyor --> not summed over dates --> happens after

  twallema

  committed
  3ca0c7a

Commits on Sep 26, 2024

• fix plot-fit for one outcome

  twallema

  committed
  88686cd

• tentative: propose cocktail of emcee "moves"

  twallema

  committed
  1b1ddb2

Commits on Sep 27, 2024

• compatibility with python on longleaf. To remove ?

  jcblemai

  committed
  7e2a061

• Merge branch 'emcee_batch' of https://github.com/HopkinsIDD/flepiMoP into emcee_batch

  jcblemai

  committed
  8849b24

Commits on Sep 28, 2024

• plot fix

  jcblemai

  committed
  6caa83f

• Merge branch 'emcee_batch' of https://github.com/HopkinsIDD/flepiMoP into emcee_batch

  jcblemai

  committed
  a843710

• nicer grid

  jcblemai

  committed
  ae86e52

Commits on Sep 30, 2024

• simplify my life

  jcblemai

  committed
  965ef19

Commits on Oct 3, 2024

• reload groundtruth to help with usage

  jcblemai

  committed
  33bd35c

• default to making config plots

  jcblemai

  committed
  b590d92

• new config

  jcblemai

  committed
  5ee0f2b

• cocktail change

  jcblemai

  committed
  ce59add

• energy savings :D

  jcblemai

  committed
  fabc759

Commits on Oct 4, 2024

• add a precheck for config sensitivity after what happen on Flu R1 2024

  jcblemai

  committed
  d80f213

• error

  jcblemai

  committed
  fb5618f

Commits on Oct 15, 2024

• this check is vad...

  jcblemai

  committed
  823d81f

• postprocessing script

  jcblemai

  committed
  88e305b

• gen markdown

  jcblemai

  committed
  ec12e4b

Commits on Oct 30, 2024

• draft of modifiers support of out of reach subpops, still unsafe

  jcblemai

  committed
  37f7901

Commits on Oct 31, 2024

• remove print

  jcblemai

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  f186244

• temp

  jcblemai

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  a18d170

• merge

  jcblemai

  committed
  b99afec

Commits on Nov 7, 2024

• very iugly code for cli that plot modifiers activation and time series

  jcblemai

  committed
  3ddc975

• add outcoems parameters

  jcblemai

  committed
  5ea3d41

• tried the outcoems NPI plot

  jcblemai

  committed
  a3541d5

• tried the outcoems NPI plot

  jcblemai

  committed
  6da7439

• fix one subpop

  jcblemai

  committed
  29de35e

Commits on Nov 8, 2024

• Modify GitHub actions to work on dev branch

  Show description for d827993
  TimothyWillard

  committed
  d827993

• initial demo for patching configs capability

  

  pearsonca

  authored and

  TimothyWillard

  committed
  8cf5cf0

• add config patching

  

  pearsonca

  authored and

  TimothyWillard

  committed
  83584d5

• address cleanup comments

  

  pearsonca

  authored and

  TimothyWillard

  committed
  0f314fd

• Update flepimop/gempyor_pkg/src/gempyor/cli.py

  

  pearsonca

  authored and

  TimothyWillard

  committed
  9c32070

• further pare down tutorial configs

  

  pearsonca

  authored and

  TimothyWillard

  committed
  ea7d701

• expand cli coverage

  

  pearsonca

  authored and

  TimothyWillard

  committed
  6c18229

• remove non-used click imports

  

  pearsonca

  authored and

  TimothyWillard

  committed
  a19fda1

• update tutorial testing

  

  pearsonca

  authored and

  TimothyWillard

  committed
  148eabf

• adding internal comments to cli.py

  

  pearsonca

  authored and

  TimothyWillard

  committed
  29edd64

• non-working WIP; issue with (non)scenario parsing

  

  pearsonca

  authored and

  TimothyWillard

  committed
  d0ba0f1

• update scenario parsing, test files

  

  pearsonca

  authored and

  TimothyWillard

  committed
  7fcf9e2

• incorporate backwards compat

  

  pearsonca

  authored and

  TimothyWillard

  committed
  1da4613

• deal with None cases

  

  pearsonca

  authored and

  TimothyWillard

  committed
  349af52

• addressing some tw comments

  

  pearsonca

  authored and

  TimothyWillard

  committed
  c06b475

• add back in commented out

  

  pearsonca

  authored and

  TimothyWillard

  committed
  4da0748

• add back in commented out + whitespace

  

  pearsonca

  authored and

  TimothyWillard

  committed
  77215ba

• reorder imports in shared cli

  

  pearsonca

  authored and

  TimothyWillard

  committed
  95bdcc9

• fix scenario parsing issues, re-route gempyor-simulate calls

  

  pearsonca

  authored and

  TimothyWillard

  committed
  8cc838a

• re-add trailing comma

  

  pearsonca

  authored and

  TimothyWillard

  committed
  93ab641

• revert tutorial pruning

  

  pearsonca

  authored and

  TimothyWillard

  committed
  e937413

• revert more tutorial pruning

  

  pearsonca

  authored and

  TimothyWillard

  committed
  c785100

• maybe fix CI?

  

  pearsonca

  authored and

  TimothyWillard

  committed
  d4a0f12

• another attempt to fix dispatch

  

  pearsonca

  authored and

  TimothyWillard

  committed
  736616e

• address cli testing issue

  

  pearsonca

  authored and

  TimothyWillard

  committed
  bf3c8d8

• update examples and cli testing

  

  pearsonca

  authored and

  TimothyWillard

  committed
  e98396e

• prune deprecated, some shared_cli reorg

  

  pearsonca

  authored and

  TimothyWillard

  committed
  04a8b3e

• WIP on kwargs approach to cli [skip ci]

  

  pearsonca

  authored and

  TimothyWillard

  committed
  44d3d34

• dynamically generated docstrings

  

  pearsonca

  authored and

  TimothyWillard

  committed
  3f15fb0

• kwargs-ify parse_config_files

  

  pearsonca

  authored and

  TimothyWillard

  committed
  34672aa

• Update flepimop/gempyor_pkg/src/gempyor/shared_cli.py

  Show description for 53fda99
  

  pearsonca

  and

  TimothyWillard

  committed
  53fda99

• kwargs-ify simulate

  

  pearsonca

  authored and

  TimothyWillard

  committed
  fc30bf7

• adding gempyor-simulate deprecation

  

  pearsonca

  authored and

  TimothyWillard

  committed
  04b6660

• deprecate gempyor-simulate

  

  pearsonca

  authored and

  TimothyWillard

  committed
  b83f178

• stub in parse config [skip ci]

  

  pearsonca

  authored and

  TimothyWillard

  committed
  ef10edf

• leverage click.Parameter typecasting / validation

  

  pearsonca

  authored and

  TimothyWillard

  committed
  cca888c

• introduce passing click context if available

  

  pearsonca

  authored and

  TimothyWillard

  committed
  9b69cc6

• add unit testing for parse config

  

  pearsonca

  authored and

  TimothyWillard

  committed
  e198517

• handle tuple case in shared_cli

  

  pearsonca

  authored and

  TimothyWillard

  committed
  6f685ba

• full option testing

  

  pearsonca

  authored and

  TimothyWillard

  committed
  728a000

• apply black formatting [skip ci]

  

  pearsonca

  authored and

  TimothyWillard

  committed
  4adc388

• WIP test patch [skip ci]

  

  pearsonca

  authored and

  TimothyWillard

  committed
  54d9ac6

• working patch test

  

  pearsonca

  authored and

  TimothyWillard

  committed
  f999b56

• Update flepimop/gempyor_pkg/src/gempyor/shared_cli.py

  Show description for d761c5a
  

  pearsonca

  and

  TimothyWillard

  committed
  d761c5a

• Update flepimop/gempyor_pkg/src/gempyor/shared_cli.py

  

  pearsonca

  authored and

  TimothyWillard

  committed
  fe4f289

• prune yaml import from test

  

  pearsonca

  authored and

  TimothyWillard

  committed
  605fb64

• docstring generation tweaking

  

  pearsonca

  authored and

  TimothyWillard

  committed
  986aafa

• reconstitute simulate interface [skip ci]

  

  pearsonca

  authored and

  TimothyWillard

  committed
  a1bb715

• issue warnings for config files with duplicate keys

  

  pearsonca

  authored and

  TimothyWillard

  committed
  80023ec

• clarify click version requirement and remove string filtering

  

  pearsonca

  authored and

  TimothyWillard

  committed
  158a2bc

• correct click version

  

  pearsonca

  authored and

  TimothyWillard

  committed
  48eca06

• update documentation to remove reference to gempyor-simulate [skip ci]

  

  pearsonca

  authored and

  TimothyWillard

  committed
  af1566d

• add multi-config documentation

  

  pearsonca

  authored and

  TimothyWillard

  committed
  f4810cf

• update multi-configs gitbook to give caveat example

  

  pearsonca

  authored and

  TimothyWillard

  committed
  65e7fea

• Apply black formatter

  Show description for 2c73f38
  TimothyWillard

  committed
  2c73f38

• Conditional deactivate env, then activate new env

  Show description for d7345dd
  TimothyWillard

  committed
  d7345dd

• Split conda activate into three cases

  Show description for 8da1720
  TimothyWillard

  committed
  8da1720

• Convert setup.cfg to pyproject.toml

  Show description for 24c17ac
  TimothyWillard

  committed
  24c17ac

• Add missing h5py and dask[dataframe] deps

  Show description for 48842f6
  TimothyWillard

  committed
  48842f6

• Restrict max python version

  Show description for 454c664
  TimothyWillard

  committed
  454c664

• Update flepimop/gempyor_pkg/pyproject.toml

  Show description for 50c195e
  

  TimothyWillard

  and

  pearsonca

  committed
  50c195e

• Update home page in pyproject.toml

  Show description for b1cda6e
  TimothyWillard

  committed
  b1cda6e

• added postprocessing for several subpop

  jcblemai

  committed
  0439fcd

Commits on Nov 13, 2024

• Add ModelInfo type hints

  Show description for 7a57dc5
  

  TimothyWillard

  authored and

  pearsonca

  committed
  7a57dc5

• WIP on NPIs

  pearsonca

  committed
  69d1a44

• linting applied

  pearsonca

  committed
  9dd5cb0

• fix npi test

  pearsonca

  committed
  22d8950

• Update flepimop/gempyor_pkg/src/gempyor/NPI/base.py

  pearsonca

  committed
  70f9cd7

Commits on Nov 15, 2024

• Pull HPC init/build from main into emcee_batch

  Show description for ab86912
  TimothyWillard

  committed
  ab86912

Commits on Nov 18, 2024

• Add index to development, init git/github docs

  TimothyWillard

  committed
  c76f83d

• Add more details to git/GitHub dev docs

  TimothyWillard

  committed
  45612b2

• Add development links to SUMMARY.md

  TimothyWillard

  committed
  a095942

• Add description of operations to git/GitHub

  TimothyWillard

  committed
  051a636

• Add branch prefixing to docs

  TimothyWillard

  committed
  0d1ef15

• Remove outdated sections from python guidelines

  TimothyWillard

  committed
  605e068

• Add minor notes about docs in workflow

  TimothyWillard

  committed
  5aea02d

Commits on Nov 19, 2024

• Pull postprocessing from emcee_batch

  TimothyWillard

  committed
  7ae2917

• Pull examples from emcee_batch

  TimothyWillard

  committed
  3977b8d

• Merge emcee_batch into feature/403/emcee_batch

  Show description for 0c67060
  TimothyWillard

  committed
  0c67060

• Apply black formatter post-merge

  TimothyWillard

  committed
  029f8c8

• Update tests for Statistics to pass

  TimothyWillard

  committed
  d58f6d9

• Missing compartments runtime error and tests

  Show description for 0055ed8
  TimothyWillard

  committed
  0055ed8

• Edits to make test_outcome_scenario pass

  Show description for fc23642
  TimothyWillard

  committed
  fc23642

Commits on Nov 21, 2024

• Update test_outcome_modifiers_scenario_with_load

  Show description for 9347849
  TimothyWillard

  committed
  9347849

• Update test_outcomes_npi test

  Show description for aeb3a77
  TimothyWillard

  committed
  aeb3a77

• Update test_outcomes_npi_custom_pname test

  Show description for b65276c
  TimothyWillard

  committed
  b65276c

• Updates to make inference tests pass

  Show description for 413690b
  TimothyWillard

  committed
  413690b

• Fix test_full_npis_read_write test

  Show description for dfc2ae3
  TimothyWillard

  committed
  dfc2ae3

• Update test_spatial_groups test config

  Show description for 0c1bb46
  TimothyWillard

  committed
  0c1bb46

• Bug fix compute_all_multioutcomes

  Show description for e3cb537
  TimothyWillard

  committed
  e3cb537

Commits on Nov 22, 2024

• Update the 'Inference with EMCEE' gitbook docs

  TimothyWillard

  committed
  05b760b

Commits on Nov 26, 2024

• Updated sample/tutorial files

  alsnhll

  committed
  f7d19eb

Commits on Dec 2, 2024

• Remove confusing/unneeded lines

  Show description for 6cbfa5e
  TimothyWillard

  committed
  6cbfa5e

• Use confuse as_str_seq getter for subpop

  Show description for eda84e4
  TimothyWillard

  committed
  eda84e4

Commits on Dec 3, 2024

• Merge pull request #370 from HopkinsIDD/dev-docs

  Show description for f0f5fe7
  TimothyWillard

  authored
  f0f5fe7

• Add test for flepimop modifiers config-plot

  Show description for 481e63f
  TimothyWillard

  committed
  481e63f

• modified to capture stdout and stderr to log in using system2() being applicable in Windows as well in flepimop/main_scripts/inference_main.R

  

  kjsato

  authored and

  TimothyWillard

  committed
  df76d3f

• Minor edits to log file construction

  Show description for b3ba872
  TimothyWillard

  committed
  b3ba872

• Move log file to working directory

  TimothyWillard

  committed
  d883bfb

• Use flepimop-inference-slot cmd directly

  Show description for 7f9d3f0
  TimothyWillard

  committed
  7f9d3f0

• Add CLI docs to flepimop modifiers config-plot

  TimothyWillard

  committed
  9ae6bd3

• Merge pull request #289 from HopkinsIDD/main-#169

  Show description for 0ebb08d
  TimothyWillard

  authored
  0ebb08d

• Merge dev into feature/403/emcee_batch

  TimothyWillard

  committed
  73d2a2f

Commits on Dec 4, 2024

• Quick fix for GH-373

  Show description for 980429e
  TimothyWillard

  committed
  980429e

• Initialize GempyorInference.static_sim_arguments

  Show description for 8a83236
  TimothyWillard

  committed
  8a83236

• Improving readability/consistency of errors/exceptions in gempyor (second batch) (#387)

  Show description for 0aca24f
  

  emprzy

  and

  TimothyWillard

  authored
  0aca24f

• Merge dev into feature/403/emcee_batch

  TimothyWillard

  committed
  9ba0c24

• Merge pull request #407 from HopkinsIDD/update_examples

  Show description for 7674af0
  TimothyWillard

  authored
  7674af0

• Update partial configs to match full

  Show description for 7d10aa1
  TimothyWillard

  committed
  7d10aa1

• Merge pull request #404 from HopkinsIDD/feature/403/emcee_batch

  Show description for 5f5f6d6
  TimothyWillard

  authored
  5f5f6d6

Commits on Dec 5, 2024

• Add NEWS.md for release GH-375

  TimothyWillard

  committed
  48c2425

Commits on Dec 6, 2024

• Casting bound values as float in inference_parameter.py to prevent parsing errors (#405)

  Show description for b32cad8
  emprzy

  authored
  b32cad8

Commits on Dec 9, 2024

• Correct formula for poisson log-likelihood

  Show description for 8e5baa3
  TimothyWillard

  committed
  8e5baa3

Commits on Dec 10, 2024

• Add test case with poisson and zeros

  Show description for 10e5d98
  TimothyWillard

  committed
  10e5d98

• Simplify poisson LL tests with only one variable

  TimothyWillard

  committed
  14d9bf3

• flepimop patch unit test for seir::parameters

  Show description for b21cfcc
  TimothyWillard

  committed
  b21cfcc

• Rename dup get_logloss to simulate_proposal

  TimothyWillard

  committed
  a104210

Commits on Dec 11, 2024

• Fix parse_config_files TL key override behavior

  Show description for 02678a3
  TimothyWillard

  committed
  02678a3

• Add --indent option to flepimop patch

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  TimothyWillard

  committed
  fe1dc2b

• Add detailed example to flepimop patch --help

  TimothyWillard

  committed
  ba22f0b

• Force default indent of flepimop patch to 4

  TimothyWillard

  committed
  d3f89d2

• Upgrade TL key collision from warning to error

  TimothyWillard

  committed
  b5142d9

• modify approach to handling help

  

  pearsonca

  authored and

  TimothyWillard

  committed
  b34792d

• Add _dump_formatted_yaml for custom yaml dump

  Show description for 7ae1037
  TimothyWillard

  committed
  7ae1037

• Merge pull request #420 from HopkinsIDD/hotfix/correct-poisson-statistics-pmf

  Show description for b1d8404
  TimothyWillard

  authored
  b1d8404

• flepimop patch --help uses example configs

  Show description for 0fe483e
  TimothyWillard

  committed
  0fe483e

• update multi-configs gitbook

  pearsonca

  committed
  719c23b

• parse_config_files error includes config name

  TimothyWillard

  committed
  11d8a2d

• Resolve seir/outcome modifier scenarios

  TimothyWillard

  committed
  ba9b527

• flepimop patch documenation edits

  Show description for c88c524
  TimothyWillard

  committed
  c88c524

• Merge pull request #423 from HopkinsIDD/hotfix/patching-abilities-documentation

  Show description for c5bde34
  

  TimothyWillard

  and

  pearsonca

  authored
  c5bde34