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Author SHA1 Message Date
Nicolas Mounet
d76e7a98d5 Removing pre-defined distributions for Activity 2021-05-21 11:03:53 +02:00
Nicolas Mounet
57c7c78117 caching _generate_activity_distribution (for Activity models) 2021-05-14 12:38:35 +02:00
Nicolas Mounet
b6bb878fc2 Adding predefined Activity distributions 2021-05-11 20:00:40 +02:00
Nicolas Mounet
17ffc4f6f8 Vectorisation of Activity 2021-05-11 18:18:19 +02:00
Nicolas Mounet
1564b9ea65 Adding tests on vectorisation of Activity inhalation_rate and exhalation_rate 2021-05-11 18:17:43 +02:00
Philip James Elson
6df4a86670 Merge branch 'feature/about_page' into 'master' 
Introduce About page

Closes #163 and #117

See merge request cara/cara!177
 2021-05-11 10:20:49 +00:00
Gabriella Azzopardi
77f52a8087 Introduce About page 2021-05-11 10:20:47 +00:00
Philip James Elson
60568aab35 Merge branch 'develop/quick_fix_integration' into 'master' 
Minor fix in ConcentrationModel.integrated_concentration

See merge request cara/cara!178
 2021-05-10 18:29:57 +00:00
Nicolas Mounet
bb4bcebe21 Minor fix in ConcentrationModel.integrated_concentration 2021-05-10 20:23:54 +02:00
Gabriella Azzopardi
87c7733bb5 Merge branch 'feature/error-handling-jinja' into 'master' 
Add Jinja error handling details from #117

See merge request cara/cara!167
 2021-05-10 17:29:05 +00:00
Philip James Elson
9d5743c565 Merge branch 'develop/improve_dose_integration' into 'master' 
Improvement of integration method in quanta_exposure

See merge request cara/cara!176
 2021-05-10 17:13:10 +00:00
Nicolas Mounet
feedcc0df1 Add ConcentrationModels.integrated_concentration and provide an analytic solution to the integral. 2021-05-10 17:13:09 +00:00
Philip James Elson
13cf8bafb3 Merge branch 'develop/time_dependence_concentration_model' into 'master' 
Avoid using time-dependence of parameters in concentration computation

See merge request cara/cara!172
 2021-05-06 17:59:56 +00:00
Nicolas Mounet
7d4284e5f9 Correcting test_next_state_change_time 2021-05-06 06:07:33 +02:00
Phil Elson
31a5954a4a Review actions on time handling. 2021-05-05 21:03:36 +02:00
Nicolas Mounet
f613ff80ba Supressing now useless (wrong) tests on time-independence of parameters in ConcentrationModel; adding a test on error handling if time used for concentration computation is beyond the last state change time 2021-05-05 12:46:27 +02:00
Nicolas Mounet
817ca8f3bf ConcentrationModel: _next_state_change used only in concentration function, now; improving docstrings and error handling 2021-05-05 12:45:02 +02:00
Nicolas Mounet
ac866491df Adding docstrings in DummyPopulation and DummyVentilation (test_concentration_model) 2021-05-04 09:03:45 +02:00
Nicolas Mounet
717390377e concentration_limit method not public anymore; providing a docstring 2021-05-04 08:57:40 +02:00
Nicolas Mounet
236a7139f5 Adding a test for next_state_change in ConcentrationModel 2021-05-04 08:49:02 +02:00
Nicolas Mounet
f8b565ea5b Avoid next_state_change to be public in ConcentrationModel; raise an error if time is higher than largest transition time 2021-05-04 07:27:58 +02:00
Nicolas Mounet
94d01104d0 Using concentration_limit method in concentration (ConcentrationModel) 2021-05-04 06:43:27 +02:00
Nicolas Mounet
68893f905f Merge branch 'master' of https://gitlab.cern.ch/cara/cara into develop/time_dependence_concentration_model 2021-05-04 06:37:00 +02:00
Philip James Elson
9e3adf30b0 Merge branch 'feature/model_vectorisation_pt3' into 'master' 
Vectorise ExposureModel

See merge request cara/cara!163
 2021-05-04 04:31:46 +00:00
Nicolas Mounet
99c0e4e1f8 Extending vectorised tests to expected_new_cases 2021-05-04 05:57:21 +02:00
Andre Henriques
54ad996d0b Merge branch 'feature/docker-calculator' into 'master' 
Add a dockerfile and details of how to run it

See merge request cara/cara!171
 2021-05-03 21:03:02 +00:00
Nicolas Mounet
c3cf37d3da Simplifying test_exposure_model (towards unit tests rather than integration tests) 2021-05-03 22:22:25 +02:00
Phil Elson
178ee72fe3 Add a dockerfile and details of how to run it. 2021-05-03 20:10:44 +02:00
Andre Henriques
0422132d65 Merge branch 'readme_citation_style' into 'master' 
typo in heading style

See merge request cara/cara!170
 2021-05-03 15:13:50 +00:00
Andre Henriques
a3ad121f71 typo in heading style 2021-05-03 15:11:45 +00:00
Nicolas Mounet
2e928b5fef Merge branch 'master' of https://gitlab.cern.ch/cara/cara into feature/model_vectorisation_pt3 2021-05-03 17:09:54 +02:00
Philip James Elson
f0d8da7361 Merge branch 'author_citation' into 'master' 
Add authorship and citation to README.md

See merge request cara/cara!169
 2021-05-03 14:28:24 +00:00
Philip James Elson
e02396514e Merge branch 'develop/hours2time_in_concentration_plot' into 'master' 
Better xtick labels in concentration plots

See merge request cara/cara!165
 2021-05-03 14:27:30 +00:00
Nicolas Mounet
26d7ef9f5d Replacing the use of hours2timestring by datetimes, in the x-axis of the plots generated in report_generator 2021-05-03 14:27:29 +00:00
Andre Henriques
54b2fc96ef add NTNU for Markus 2021-05-03 13:03:49 +00:00
Nicolas Mounet
8b1571dcf1 Exposing concentration_limit in ConcentrationModel 2021-05-03 15:01:42 +02:00
Nicolas Mounet
d0ef2f13c9 Adding test on concentration limit in concentration model 2021-05-03 15:01:02 +02:00
Andre Henriques
7abd6dd65b Add authorship and citation to README.md 2021-05-03 12:57:47 +00:00
Andre Henriques
99152f7e44 Merge branch 'fix/license_headers' into 'master' 
Compromise on the header information added to key files

See merge request cara/cara!168
 2021-05-03 12:46:21 +00:00
Phil Elson
05dffa3f50 Compromise on the header information added to key files, ensuring that the details are correct, but are canonically defined in one place. 2021-05-03 13:46:03 +02:00
Phil Elson
d1f22a03a7 Re-instate all error handling details from #117. 2021-05-03 13:40:15 +02:00
Andre Henriques
58006ebe5f Merge branch 'feature/OSS_license' into 'master' 
Prepare the repository for an Apache 2.0 license

See merge request cara/cara!161
 2021-05-03 11:38:43 +00:00
Gabriella Azzopardi
5a6711be3e Merge branch 'feature/md_text_blocks' into 'master' 
Implement common markdown blocks infrastructure

See merge request cara/cara!166
 2021-05-03 11:33:18 +00:00
Philip James Elson
49c28aaa98 Implement common markdown blocks infrastructure 2021-05-03 11:33:17 +00:00
Nicolas Mounet
b622283206 In concentration model, compute infectious virus removal rate only at time of next state change, to make sure it stays constant 2021-05-03 12:35:10 +02:00
Nicolas Mounet
307cf13bfa Adding a test to check that infectious virus removal rate is computed only at the time of a state change 2021-05-03 12:30:00 +02:00
Nicolas Mounet
6511ac1c4f Merge branch 'master' of https://gitlab.cern.ch/cara/cara into feature/model_vectorisation_pt3 2021-04-30 11:57:54 +02:00
Andre Henriques
bef6602cc1 Merge branch 'link-cara-parameters' into 'master' 
Update userguide with link to existing cara parameters

Closes #158

See merge request cara/cara!164
 2021-04-29 22:05:22 +00:00
Andre Henriques
b79440512d Update userguide with link to existing cara parameters 2021-04-29 22:05:21 +00:00
Phil Elson
93d91e0d4d Review actions. 2021-04-29 23:56:33 +02:00