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@github-actions github-actions released this 02 Nov 10:27
· 751 commits to master since this release
v1.2.0
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Learn about vigilant mode.

Commits

  • [c8d0db9]: new directory for experiments (Nick Malleson) #169
  • [f321584]: moved notebook to experiments dir (Nick Malleson) #169
  • [906dcc0]: read parameters in from the parameters file (Nick Malleson) #169
  • [0e1ed7e]: trying to get multiprocess version workin in notebook (Nick Malleson) #169
  • [b5fd4c9]: trying to implement multiprocess model running but processes still hanging, I think to do with the notebook server (Nick Malleson) #169
  • [5e741c1]: still trying to get multiprocessing working (Nick Malleson) #169
  • [891fa1a]: trying to get multiprocess working in the notebook (Nick Malleson) #169
  • [0f1deeb]: slight changes to allow for the new infection_prob function (Fiona Spooner) #167
  • [6ff451a]: updating to run new infection_prob function (Fiona Spooner) #167
  • [f8c3506]: Delete covid_run.R (Fiona Spooner) #167
  • [21e8510]: replace hard-coded number of diseases (7) with a count from the DiseaseStatus enum (Nick Malleson) #169
  • [5352e23]: making graphs showing variability (Nick Malleson) #169
  • [79e44c8]: Introduced a str representaiton of DiseaseStatus to prevent need for use of disease_status.name.lower() in dicts and also use a dictionary comprehension to cut down some code repetition (Nick Malleson) #169
  • [7991453]: added error bars to plots, now will start sensitivity testing (Nick Malleson) #169
  • [300043b]: added error bars to plots, now will start sensitivity testing (Nick Malleson) #169
  • [ece3e8f]: updated results analysis to include error bars (Nick Malleson) #169
  • [dc3ab30]: updated results analysis to include error bars (Nick Malleson) #169
  • [9523a32]: recreating no lockdown issue (Fiona Spooner) #170
  • [755f31f]: Merge branch 'master' of https://github.com/Urban-Analytics/RAMP-UA into charlie_probability (Fiona Spooner) #170
  • [2113e6a]: removed the do_lockdown variable fro population_initialisation, it was redundant now that most of the model logic is in microsim_model.py (Nick Malleson) #170
  • [e59cca9]: moved the reading of the lockdown file and creation of the time_activity_multiplier into main.py. Now it is not part of the population caches so if the lockdown file changes the old caches can still be used. (Nick Malleson) #170
  • [cf5a369]: exposed store_detailed_counts so that model can run faster if required (Nick Malleson) #169
  • [fd48d2d]: removed temp file (Nick Malleson) #169
  • [99ea756]: updated test to read lockdown file separately from population initialisation (Nick Malleson) #170
  • [df34f35]: updated test to read lockdown file separately from population initialisation (Nick Malleson) #170
  • [bf45135]: Merge branch 'master' into spoonerf-issue-168-No_lockdown_not_working (Nick Malleson) #170
  • [93d196c]: updated hazard kernel function (cshenton) #171
  • [21caa7e]: symptomatic risk function working (Fiona Spooner) #174
  • [c12a90c]: make the repetition number (reprn) an object level variable so that it can be passed to the R code (Nick Malleson) #178
  • [e0d1975]: pass the repetition number to the calculate_disease_status function (Nick Malleson) #178
  • [d5bd103]: moved random number generator into the microsim model (Nick Malleson) #176
  • [75525a8]: updated tests now that random number generator has moved from population initialisation to microsim model (Nick Malleson) #176
  • [a081b38]: adding in seed logic (Fiona Spooner) #179
  • [5b3cadc]: taking in the repnr from python (Fiona Spooner) #178
  • [73eda3b]: Merge branch 'nickmalleson-issue-173-Send_Python_repetition_number_to_R' of https://github.com/Urban-Analytics/RAMP-UA into set_seed (Fiona Spooner) #179
  • [5e54811]: setting seed as default and printing the see (Fiona Spooner) #179
  • [28a1ed5]: removing some infection_length() vars that are no longer needed (Fiona Spooner) #178
  • [10d7683]: Merge branch 'master' into nickmalleson-issue-173-Send_Python_repetition_number_to_R (Fiona Spooner) #178
  • [042b7da]: Merge branch 'nickmalleson-issue-173-Send_Python_repetition_number_to_R' of https://github.com/Urban-Analytics/RAMP-UA into set_seed (Fiona Spooner) #179
  • [f9087c9]: adding seed to the necessary functions (Fiona Spooner) #179
  • [143073e]: seeding repetitions seems to be working (Fiona Spooner) #179
  • [fbfa48f]: adding set seed parameter - default as false (Fiona Spooner) #179
  • [2ea8528]: adding withr package to environment as this is used in the seed setting (Fiona Spooner) #179
  • [c1e13f8]: initial sphinx docs (Alex Coleman) #181
  • [b38397a]: updated environment yml for sphinx docs (Alex Coleman) #181
  • [2b7120b]: auto generated docs rst files and updated gitignore and readme (Alex Coleman) #181
  • [ec4a8a5]: added microsim to index rst (Alex Coleman) #181
  • [8a8da3c]: moved microsim_model up in the order of rst (Alex Coleman) #181
  • [3c78bc0]: added autodoc typehints (Alex Coleman) #181
  • [1b65895]: neatifying docs structure (Alex Coleman) #181
  • [2f61a72]: added usage and setup sections (Alex Coleman) #181
  • [0482c34]: added GAH to build and deploy (Alex Coleman) #181
  • [7656b6f]: dont adjust overweight people (Rory) #180
  • [8710e89]: fix test (Rory) #180
  • [9ca53a2]: reorganised documentation (Alex Coleman) #181
  • [0b49596]: added init files and manifest to ensure correct files captured in sdist (sparrow0hawk) #183
  • [1995b24]: init.py caused test errors (sparrow0hawk) #183
  • [93ddd92]: fix bug where default params were created (Rory) #184
  • [37625af]: only show progress bar in quiet mode (Rory) #186
  • [00fb809]: Update ramp_ua.cl (Fiona Spooner) #187
  • [a1b44a8]: Update test_update_statuses_kernel.py (Fiona Spooner) #187
  • [9fdb7d9]: Update ramp_ua.cl (Fiona Spooner) #187
  • [8ae252a]: added -init flag that tells the model to return after creating caches and snapshots (Nick Malleson) #191
  • [2c6e64b]: added quant data using lfs (Nick Malleson) #191
  • [168c4da]: added gitattributes (Nick Malleson) #191
  • [bc63722]: minor tidying (Nick Malleson) #191
  • [3746301]: minor (Nick Malleson) #191
  • [1bc77fc]: minor change to output (Nick Malleson) #191
  • [43e7d82]: added (temporary?) notebook to compare the quant and non-quant results (Nick Malleson) #191
  • [8ba7cab]: added maps to notebook (Nick Malleson) #191
  • [58445cc]: (will remove these parameters files before merging to master (Nick Malleson) #191
  • [1139f47]: scenario directory wast being passed to the microsim object so results directory name was incorrect (Nick Malleson) #191
  • [441fe03]: minor change to print to show if using quant or not (Nick Malleson) #191
  • [778197a]: created larger number of age thresholds (Nick Malleson) #191
  • [5aa8837]: created larger number of age thresholds (Nick Malleson) #191
  • [5420d8d]: created larger number of age thresholds (Nick Malleson) #191
  • [d6735ef]: deleted temp parameter files (Nick Malleson) #191
  • [d629086]: removed redundancy on old (not working) multiprocess code (Nick Malleson) #195
  • [a8b93b3]: new directory for sensitivity testing and code to create calibration data (Nick Malleson) #195
  • [2e96f61]: temporarily adding quant compare scenarios (Nick Malleson) #191
  • [fdc66f6]: temporarily adding quant compare scenarios (Nick Malleson) #191
  • [b3bea14]: Merge branch 'nickmalleson-issue-188-Test_QUANT_data' of https://github.com/Urban-Analytics/RAMP-UA into nickmalleson-issue-188-Test_QUANT_data (Nick Malleson) #191
  • [ba9a03e]: deleted temporary comparison files (Nick Malleson) #191
  • [512ca8d]: changed default behaviour to be to read quant data (Nick Malleson) #191
  • [43ee982]: moved functions.py and created tests for it (Nick Malleson) #195
  • [dc9d7fd]: wrote tests (Nick Malleson) #195
  • [01c044a]: wrote functions to get a fitness value from a model by comparing to observations (Nick Malleson) #195
  • [b6b885f]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #195
  • [69d30db]: reorganised the experiments functions, need to adapt notebook to reflect these changes (Nick Malleson) #195
  • [d16b501]: move initial seeding ffunction to simulator class (Rory) #194
  • [22dd7fc]: Delete gam_fitted_PHE_cases.RDS (Fiona Spooner) #192
  • [69cd3ce]: Add files via upload (Fiona Spooner) #192
  • [9aa0a8d]: added a progress bar when running multiple models (Nick Malleson) #195
  • [462ebf1]: use new hazards array (Rory) #194
  • [cdeffa1]: move test (Rory) #194
  • [815aab3]: remove commented code (Rory) #194
  • [083a172]: change simulator step function (Rory) #194
  • [a63eebf]: Update default.yml (Fiona Spooner) #192
  • [7343311]: adding in symptomatic multipliers by age (Fiona Spooner) #193
  • [eec42ac]: fixing problem with symp_rate (Fiona Spooner) #193
  • [9b89f3f]: all tests pass (Rory) #194
  • [661d6cb]: add test for few high risk individuals (Rory) #194
  • [98fb444]: 0.45 prob for people between 20 and 70 (Fiona Spooner) #193
  • [905ba4f]: update docstrings (Rory) #194
  • [e6e8058]: got calibration (using a simplex algorithm) working. (Nick Malleson) #195
  • [6d80294]: Delete devon_initial_cases.csv (Fiona Spooner) #192
  • [14a5a6b]: pass correct num_seed_days from main (Rory) #194
  • [4d1c554]: Add files via upload (Fiona Spooner) #192
  • [f16142f]: adding in symptomatic_probs to Struct (Fiona Spooner) #193
  • [a894726]: fixing the indexing in the params (Fiona Spooner) #193
  • [696863c]: added a codecov config file (Alex Coleman) #196
  • [10072a5]: adding age component to the test but not acting as expected.. (Fiona Spooner) #193
  • [44eb019]: ensuring order of params same in python and (Fiona Spooner) #193
  • [3edf327]: trying different params index as test_params_to_from_array failing (Fiona Spooner) #193
  • [dbe641d]: updating test_exposed_become_asymptomatic_or_presymptomatic to have age component (Fiona Spooner) #198
  • [0689616]: reverting params (Fiona Spooner) #198
  • [f432345]: switching order of obesity multipliers and symptomatic probs (Fiona Spooner) #198
  • [2599e1f]: updating test_more_overweight_become_symptomatic to match new logic (Fiona Spooner) #198
  • [4524bf4]: merge from master (Rory) #194
  • [a4ff873]: update test to new initial case data (Rory) #194
  • [3a23688]: fixes to jupyter notebook (Rory) #194
Assets 3
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