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Author SHA1 Message Date
Phil Elson
c81bdeb21e Include the expert app in the public docker image. 2021-08-25 13:20:59 +02:00
Nicolas Mounet
6491ac17ed Merge branch 'feature/better_plot_sampling' into 'master' 
Choose the times to sample in the report more wisely

See merge request cara/cara!242
 2021-08-25 11:04:43 +02:00
Phil Elson
208ffc20e3 Strengthen the handling of float values for fill_big_gaps 2021-08-25 10:25:48 +02:00
Phil Elson
0861abcdba Add a test for interesting_times which covers a model containing temperatures. 2021-08-25 09:58:45 +02:00
Philip James Elson
fe04e201f1 Merge branch 'update/d3plot' into 'master' 
Update d3 plot units and title - missing from previous MRs

See merge request cara/cara!244
 2021-08-12 07:52:35 +00:00
Andre Henriques
277044473c Update the plots in the report to show virons / m³, following on from !236. 2021-08-12 07:52:34 +00:00
Phil Elson
d1833955dd Choose the times to sample in the report more wisely. 2021-08-10 16:59:47 +02:00
Nicolas Mounet
559ac2723f Merge branch 'feature/higher_resolution_temperature' into 'master' 
Restore the outside temperature data to a 6 minute resolution

See merge request cara/cara!212
 2021-08-06 17:04:03 +00:00
Philip James Elson
eafa8331bc Merge branch 'feature/plotting_d3' into 'master' 
Correct the yrange calculation in the report concentration plot

Closes #183 and #187

See merge request cara/cara!240
 2021-08-06 15:21:49 +00:00
Luis Aleixo
825216c983 Correct the yrange calculation in the report concentration plot 2021-08-06 15:21:48 +00:00
Nicolas Mounet
feef402674 Merge branch 'optimisation/tactical-caching' into 'master' 
Introduce some further caching for performance gains

See merge request cara/cara!241
 2021-08-06 13:38:37 +00:00
Phil Elson
3206a069a0 After review under snakeviz, introduce some further caching for performance gains. 2021-08-06 15:32:01 +02:00
Nicolas Mounet
c745823768 Merge branch 'optimisation/last_state_change_bisection' into 'master' 
Use bisection method to compute the last state change for improved performance

See merge request cara/cara!239
 2021-08-06 13:25:16 +00:00
Phil Elson
f22ba928e0 Ensure that 0 is always one of the state change times. 2021-08-06 15:17:37 +02:00
Phil Elson
eaefa515eb Restore the outside temperature data to a 6 minute resolution for improved smoothness of the presented results. 2021-08-06 12:01:58 +02:00
Phil Elson
06b606f3fa Remove the unused _is_interval_between_state_changes method. 2021-08-06 11:57:00 +02:00
Nicolas Mounet
ad97a6b18c Merge branch 'optimisation/better_concentration_caching' into 'master' 
Optimisation: Improve the caching of concentration(time) calls by ensuring that floats are used throughout the cara codebase when representing time

See merge request cara/cara!238
 2021-08-06 09:53:50 +00:00
Phil Elson
0e71ace0d9 Implement bisection algorithm for finding the most recent state change. 2021-08-06 11:52:14 +02:00
Phil Elson
43b9b864af Improve the testing of ConcentrationModel.last_state_change 2021-08-06 11:52:14 +02:00
Phil Elson
9546c1966c Rename _concentration_at_state_change to _concentration_cached. 2021-08-06 11:50:06 +02:00
Phil Elson
aa269aaf6e Use floats throughout the cara codebase to represent time. 2021-08-06 10:39:41 +02:00
Philip James Elson
e1d8b3a2c8 Merge branch 'feature/virology_parameters' into 'master' 
ER and P(I) formulas update according to qID parameter

Closes #184

See merge request cara/cara!236
 2021-08-06 08:24:28 +00:00
Luis Aleixo
acbf676a28 Remove the concept of quanta in the model, focusing instead on virons. 2021-08-06 08:24:25 +00:00
Philip James Elson
e3e49b5de7 Merge branch 'feature/plotting_d3' into 'master' 
Feature/plotting time vs concentration using d3 library

Closes #183

See merge request cara/cara!233
 2021-08-06 08:18:40 +00:00
Luis Aleixo
acf14c05cd Use d3 for the concentration line plot in the report 2021-08-06 08:18:40 +00:00
Andre Henriques
5e781bbb4b Merge branch 'lrdossan-master-patch-47603' into 'master' 
Attribute Luis' contribution

See merge request cara/cara!237
 2021-08-05 14:24:52 +00:00
Luis Aleixo
077737b2cb Update index.html.j2 with luis' contribution 2021-08-05 14:07:22 +00:00
Luis Aleixo
cc4fb7cd3a Update luis' contribuion on README 2021-08-05 14:06:14 +00:00
Luis Aleixo
9f48be9840 Update README.md 2021-08-04 13:21:16 +00:00
Philip James Elson
2645ff2a43 Merge branch 'feature/check-oc-config-prod' into 'master' 
Align the dev and prod openshift configs, and validate that they remain correct

See merge request cara/cara!230
 2021-07-31 04:04:23 +00:00
Philip James Elson
ec724a5a3f Merge branch 'fix/move-expert-app-into-package' into 'master' 
Fix the expert app, as the new docker image did not support running as non-root

See merge request cara/cara!235
 2021-07-30 15:57:43 +00:00
Phil Elson
af3fe421db Fix the expert app, as the new docker image did not support running as non-root. 2021-07-30 17:53:19 +02:00
Philip James Elson
7855e45676 Merge branch 'fix/move-expert-app-into-package' into 'master' 
Update the public container image to use Python 3.9

See merge request cara/cara!232
 2021-07-30 08:53:32 +00:00
Phil Elson
3ef00c8312 Update the public container image to use Python 3.9 also. 2021-07-30 10:51:30 +02:00
Philip James Elson
67d0281c98 Merge branch 'fix/move-expert-app-into-package' into 'master' 
Move the expert app into the cara package

See merge request cara/cara!231
 2021-07-30 08:48:13 +00:00
Phil Elson
e1392fb8ce Move the expert app into the cara package. Helps with convenient access from the cara-webservice image. 2021-07-30 10:45:24 +02:00
Philip James Elson
ca2bbd8340 Merge branch 'feature/py39-cara-webservice' into 'master' 
Create a Python3.9 based Dockerfile for cara to run on openshift

See merge request cara/cara!229
 2021-07-30 08:17:40 +00:00
Phil Elson
5350845852 Align the dev and prod openshift configs, and validate that they remain correct. 2021-07-30 09:47:32 +02:00
Nicola Tarocco
f7ce8c96f3 Continue to allow a relative path to be specified for the theme directory. 2021-07-30 08:55:19 +02:00
Phil Elson
3103663978 Create a Python3.9 based Dockerfile for cara to run on openshift. 2021-07-30 08:53:06 +02:00
Philip James Elson
234ca99d28 Merge branch 'feature/ci-checking-openshift-config' into 'master' 
Add CI to validate the test-cara openshift configuration

See merge request cara/cara!223
 2021-07-30 06:51:43 +00:00
Phil Elson
a2fd0e7fe5 Update to reflect the resource limit changes in cara-webservice. 2021-07-29 14:49:52 +02:00
Phil Elson
aeeb68cc09 Enable the config checker. 2021-07-29 10:04:53 +02:00
Phil Elson
74ee8b5241 Implement the normalisation and comparison of openshift config items 2021-07-29 09:38:59 +02:00
Phil Elson
b74ffebeb2 Tool to generate the config from the templates. 2021-07-29 09:38:59 +02:00
Phil Elson
91ea826060 Add a CI job to validate the test-cara instance. 2021-07-29 09:38:59 +02:00
Nicolas Mounet
43fd580ac2 Merge branch 'feature/py39' into 'master' 
Add support, and CI for Python 3.9

See merge request cara/cara!228
 2021-07-28 12:31:51 +00:00
Phil Elson
7109c821e8 Add support, and CI for Python 3.9 2021-07-28 11:17:45 +02:00
Nicola Tarocco
145509ba68 Merge branch 'feature/docker-builds' into 'master' 
Build the auth-service through a Dockerfile (and move to py39)

See merge request cara/cara!226
 2021-07-21 15:27:39 +00:00
Phil Elson
2fcadc7952 Add auth-service building to the CI. 2021-07-20 11:14:08 +02:00