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Author SHA1 Message Date
Nicolas Mounet
3e9652d012 Removing pre-defined distributions; removing coefficient_of_infectivity 2021-05-25 16:25:30 +02:00
Nicolas Mounet
19d25310dc Merge branch 'master' of https://gitlab.cern.ch/cara/cara into feature/virus_qid_and_viral_loads 2021-05-25 16:12:21 +02:00
Philip James Elson
97330e2316 Merge branch 'feature/activity_vectorisation' into 'master' 
Activity vectorisation

See merge request cara/cara!179
 2021-05-25 09:26:36 +00:00
Nicolas Mounet
e1b9f6ce91 Merge branch 'master' of https://gitlab.cern.ch/cara/cara into feature/activity_vectorisation 2021-05-21 11:07:02 +02:00
Nicolas Mounet
d76e7a98d5 Removing pre-defined distributions for Activity 2021-05-21 11:03:53 +02:00
James Devine
f6c635e359 Merge branch 'jdevine-addclimatetoreadme' into 'master' 
Update README.md with link to climatology tools repo

See merge request cara/cara!175
 2021-05-19 13:04:33 +00:00
James Devine
0d71a5a46d Added comments from MR!175, resolves thread. 2021-05-17 15:13:14 +00:00
Gabriella Azzopardi
d0eb7c709c Merge branch 'feature/responsive_form' into 'master' 
First steps towards making the form reponsive to screensize.

See merge request cara/cara!162
 2021-05-17 13:39:08 +00:00
Nicolas Mounet
de90292338 Correcting viral load distributions (10** was missing) 2021-05-14 12:52:38 +02:00
Nicolas Mounet
2e659da45d caching _generate_virus_distribution and ignoring mypy type checking for KernelDensity 2021-05-14 12:49:17 +02:00
Nicolas Mounet
57c7c78117 caching _generate_activity_distribution (for Activity models) 2021-05-14 12:38:35 +02:00
Nicolas Mounet
64565264ea Draft Virus distributions (from M. Rognlien) - does not pass mypy tests and can't be cached yet 2021-05-14 10:44:37 +02:00
Nicolas Mounet
d5dcfa5a40 Virus class: input is now qID instead of coefficient_of_infectivity (which remains as a property), as in the CERN note 2021-05-14 09:15:08 +02:00
Nicolas Mounet
f07bffaa4a Replacing coefficient_of_infectivity by qID in tests 2021-05-14 09:11:38 +02:00
Phil Elson
d082156d46 Follow-up from Andre's review. 2021-05-12 20:08:38 +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
Phil Elson
9d89ba725e Spacing between the generate button and the userguide. 2021-05-10 07:21:42 +02:00
James Devine
ea5ca699f8 Update README.md with link to climatology tools repo 2021-05-06 18:09:00 +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
Phil Elson
a1000eb3ec First steps towards making the form reponsive to screensize. 2021-05-04 07:08:35 +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