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@github-actions github-actions released this 15 Apr 15:20
· 518 commits to master since this release
v1.4.0
0e614fa

This is a large release that incorporates a number of changes made including but not restricted to:

  • Removal of data from git-lfs and migrated to Azure
  • Removal of old quant_api code
  • Updated defaults.yml

Commits

  • [8cc167e]: removed proportion_asymptomatic (this is no longer used in the opencl model) (Nick Malleson) #215
  • [6a9e22e]: trying to get ABC working (Nick Malleson) #215
  • [eaaa428]: figured out that ABC needs a stochastic model otherwise it doest sample from the prior properly so added a new argument to run_opencl_model_multi that randomises the ids (Nick Malleson) #215
  • [a7e9172]: bump version number 1.3.0 (Alex Coleman) #212
  • [e5022f7]: fixing the long branch names created by the GHA issue brancher (Alex Coleman) #213
  • [1893b33]: minor (Nick Malleson) #215
  • [9b3ddf9]: continuing with ABC (Nick Malleson) #215
  • [e43c461]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #215
  • [02caf94]: got abc working with 1 parameter (Nick Malleson) #215
  • [c33cb90]: got abc working with 1 parameter (Nick Malleson) #215
  • [dce6663]: Removed junk from the test file (Nick Malleson) #215
  • [ad83829]: updating github actions to fix #166 (Alex Coleman) #216
  • [2fbeb37]: minor (Nick Malleson) #217
  • [c5287ec]: Merge branch 'nm_sensitivity_testing' of https://github.com/Urban-Analytics/RAMP-UA into nm_sensitivity_testing (Nick Malleson) #217
  • [133b53c]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #217
  • [f8e8ab0]: minor (Nick Malleson) #217
  • [5507df6]: fixed incorrect error calculation (Nick Malleson) #223
  • [50445b6]: fixed problem about not comparing cumulative cases (Nick Malleson) #223
  • [0f26d83]: fixed bug that meant the daily cases rather than cumulative cases were being compared to the (cumulative) observations (Nick Malleson) #223
  • [7d07ef9]: got simplex method (multiple parameters) and ABC working (with one parameter) (Nick Malleson) #223
  • [52e5f33]: got abc working with multiple parameters (Nick Malleson) #223
  • [485d057]: fixed bug in dictionary iteration (Nick Malleson) #223
  • [4d4ffd3]: Add files via upload (Fiona Spooner) #222
  • [2b00ed1]: Add files via upload (Fiona Spooner) #222
  • [421b88e]: Update default.yml (Fiona Spooner) #222
  • working on plotting abc with multiple parameters #223 (Nick Malleson)
  • [aba45fb]: Update default.yml (Nick Malleson) #223
  • [6ecf4c8]: minor:working on multi-paramet abc (Nick Malleson) #227
  • [3ec5451]: Merge branch 'nm_sensitivity_testing' of https://github.com/Urban-Analytics/RAMP-UA into nm_sensitivity_testing (Nick Malleson) #227
  • [4848a59]: tried sampling from the posterior to make new model predictions (Nick Malleson) #227
  • [8ec0021]: added pickled abc multi-param results (Nick Malleson) #227
  • [24a262d]: removing proportion asymptomatic - current master gui doesn't run as this parameter no longer exists (Fiona Spooner) #224
  • [cfa0c3f]: matching with the R/Python model (Fiona Spooner) #225
  • [757208a]: Merge branch 'master' into symptomatic_multi (Fiona Spooner) #225
  • [1def62a]: updateing gui to include the updated number of age mortality rates (Fiona Spooner) #226
  • [24e11cf]: sorry keep branching from branches (Fiona Spooner) #226
  • [f8f9158]: ran multi-parameter ABC for more iterations and the results improved a lot (Nick Malleson) #227
  • [30568ac]: fix test by setting param explicitly (Rory) #225
  • [23698f5]: finished ABC for now (Nick Malleson) #227
  • [c163a1a]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #227
  • moved calibration stuff into a dir called "calibration" and made new ipynb for abc stuff #227 (Nick Malleson)
  • [bb7448b]: minor (Nick Malleson) #227
  • [3951a54]: now propery drawing from posterior (Nick Malleson) #227
  • [92f75b5]: ABC completed for four parameters (Nick Malleson) #227
  • [87c15a6]: started looking at spatial variation (Nick Malleson) #228
  • [691191f]: imported new ABC results and added a density plot for posterior (Nick Malleson) #228
  • [b9ed051]: renamed databases so that naming is consistent with the notebook that uses them and took out the multi-parameter ABC stuff from calibration.ipync (it is all in abc1.ipynb) (Nick Malleson) #228
  • [5860d78]: minor (Nick Malleson) #228
  • [c6448dc]: added new notebook for calibration on the location multipliers (Nick Malleson) #228
  • [a302dd3]: added info about asymptomatic priors (Nick Malleson) #228
  • [1f2a356]: raise a warning if default (hard-coded) parameters are used (Nick Malleson) #249
  • [e28f013]: added ability to set place hazard multipliers and partly-finished tests (Nick Malleson) #249
  • [faf41db]: fixed ability to set place hazard multipliers (current_risk_beta multiplication was bypassed if manual place multipliers were set) and finished tests (Nick Malleson) #249
  • [4de4689]: implemented abc2 for running ABC on place parameters (Nick Malleson) #249
  • [5b8697f]: added ability to add constant parameters at the class level (Nick Malleson) #249
  • [b1397e8]: ABC on location hazard multipliers (Nick Malleson) #249
  • [54bc6b9]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #249
  • [fb7468a]: corrected doc build to install package (Alex Coleman) #235
  • [4e29261]: initial work on a download util function (Alex Coleman) #236
  • [d4eaa52]: corrected tests for download_data (Alex Coleman) #236
  • [f2aa15e]: added doc string and corrected mock.patch (Alex Coleman) #236
  • [3fec9f5]: unpack data function and test (Alex Coleman) #236
  • [418c905]: migrated urls to new ramp storage url (Alex Coleman) #236
  • [b4a6ae4]: added a wrapper function for downloading and unpacking (Alex Coleman) #236
  • [00c042e]: removed all devon data updated gitignore (Alex Coleman) #236
  • [0f9beb9]: added tests for data_setup wrapper (Alex Coleman) #236
  • [dcdf9ca]: refactored download_data (Alex Coleman) #236
  • [f3285cf]: adjusted data_setup given refactor of download_data (Alex Coleman) #236
  • [952a6a0]: added section for data_setup function (Alex Coleman) #236
  • [1ada023]: Update covid_run.R (Fiona Spooner) #238
  • [df8a61c]: adding code and data used to identify high risk MSOAs (Fiona Spooner) #240
  • [d5b0af0]: adding README for population data (Fiona Spooner) #240
  • [01aeb07]: more comments (Fiona Spooner) #240
  • [9ee1cf2]: commiting to merge (Fiona Spooner) #240
  • [459bee0]: updating comments and code to select high risk MSOAs (Fiona Spooner) #240
  • [a78f064]: complete code for getting high risk MSOAs, still devon focussed but easy to change (Fiona Spooner) #240
  • [066d11f]: created README for seeding COVID process (Fiona Spooner) #240
  • [243d5f7]: removing income' (Fiona Spooner) #240
  • [a5b5cf8]: updating title (Fiona Spooner) #240
  • [f4c89a1]: adding comments (Fiona Spooner) #240
  • [6af4d24]: updating readme links (Fiona Spooner) #240
  • [d974b6c]: updating md (Fiona Spooner) #240
  • [cdc328c]: updating md (Fiona Spooner) #240
  • [8beaac8]: update version of rpy2 (Alex Coleman) #241
  • [4816a82]: Update default.yml (Fiona Spooner) #242
  • [7743572]: removed data files readded to devon_data folder (Alex Coleman) #243
  • [2023ed1]: added new file for programming overview and linked to it (Nick Malleson) #247
  • [df4f369]: wrote draft overview of the main python files (Nick Malleson) #247
  • [d56c1f3]: added readme and removed old test file (Nick Malleson) #249
  • [e2c76f8]: updated explanation of the calibration files (Nick Malleson) #249
  • [5c2f75a]: Update README.md (Nick Malleson)
  • [1bf5ada]: initial draft of updating contributing page on docs (Alex Coleman) #256
  • [f83b3c5]: updated docs structure to avoid duplication between (Alex Coleman) #256
  • [92fb808]: Update index.rst (Nick Malleson) #247
  • [ffef36a]: Merge branch 'master' into nickmalleson-issue-246 (Nick Malleson) #247
  • [ce47ee9]: renamed "overview" to "developers guide" (Nick Malleson) #261
  • [d906f73]: added links to function and class documentation (Nick Malleson) #261
  • [9d46ae1]: removed all non-quant references and removed parameter that allowed the specification of quant directory (Nick Malleson) #263
  • spelling #263 (Nick Malleson)
  • [3393e3e]: removed old retail and schools dummy data from tests and updated the test data so that the areas matched those in the quant api (Nick Malleson) #263
  • [7a6b5e1]: updated hard-coded tests and removed the old Devon-specific tests (Nick Malleson) #263
  • [9a8c3fa]: Update README.md (initialisation timing) (annazan) #266
  • [a7700d7]: Merge branch 'master' into nickmalleson-issue-255 (Nick Malleson) #263
  • [d769ee1]: removed redundant quant api for #268 (Nick Malleson) #263
  • [656dfa7]: added progress bar (Nick Malleson) #270
  • [1950d38]: standardized docstrings to sphinx format (Alex Coleman) #272
  • [8d687d5]: updated docstring for getProbableHospitalByMOSAIZ (Alex Coleman) #272
  • [e19856d]: corrected typo in getProbableHospitalByMSOAIZ (Alex Coleman) #272
  • [a233905]: added docstring for get_flows (Alex Coleman) #272
  • [71de021]: tidied up docstrings (Alex Coleman) #272
  • [5851529]: Merge branch 'master' into nickmalleson-issue-255 (Nick Malleson) #263
  • [fa69eec]: changed references in tests to look for quant data in dummy data folder (Nick Malleson) #263
  • [a181651]: added test_mode to quant api that generates a very small flow matrix rather than reading in the full national one (Nick Malleson) #263
  • [11914a2]: (forgot t include generating temporary hospital flows) (Nick Malleson) #263
  • [7c1e7b2]: added dummy QUANT data (Nick Malleson) #263
  • [d4d123b]: Created dummy quant flow matrices so that the test_mode option can be removed from QUant (nicer without it) (Nick Malleson) #263
  • [5220809]: Updated docstrings as per suggestions from Richard (Nick Malleson) #272
  • [12e1535]: Update tests/dummy_data/QUANT_RAMP/filter_data.py (Nick Malleson) #263
  • [4133513]: Removed old comments (Nick Malleson) #263
  • [6d992fd]: Update tests/dummy_data/QUANT_RAMP/filter_data2.py (Nick Malleson) #263
  • [05e4c41]: Removed old, commented code (Nick Malleson) #263
  • [a6934c4]: Removed redundant warning check (Nick Malleson) #263
  • [17db587]: removing python-version in python testing workflow (Alex Coleman) #274
  • [3410894]: removing duplicate reference to usage section (Alex Coleman) #275
  • [669ab37]: Create README.md (Nick Malleson) #263
  • [327db93]: Delete add_msoa_to_venue.py (Nick Malleson) #263
  • [6369eb0]: Merge branch 'master' into nickmalleson-issue-255 (Nick Malleson) #263
  • [83bc943]: bump version number for v1.4.0 (Alex Coleman) #277
  • [0e614fa]: removed python version specification from tagged releas github action due to errors (Alex Coleman) #277
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