From 94b832b17f104bc16e8056907dc82c37f054582a Mon Sep 17 00:00:00 2001
From: twallema <tijs.alleman@ugent.be>
Date: Tue, 14 May 2024 15:06:52 +0200
Subject: [PATCH 1/6] update env

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index d3f130385..7308b6248 100644
--- a/environment.yml
+++ b/environment.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - defaults
 dependencies:
-  - python=3.11.4
+  - python=3.12
   - pandas  
   - numpy  
   - scipy  

From c07d7fc6909c4c29556914f57642ef3c5df91720 Mon Sep 17 00:00:00 2001
From: twallema <tijs.alleman@ugent.be>
Date: Tue, 14 May 2024 15:29:37 +0200
Subject: [PATCH 2/6] trim dependencies

---
 setup.py | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/setup.py b/setup.py
index a0623b6da..b3268ff5f 100644
--- a/setup.py
+++ b/setup.py
@@ -13,15 +13,9 @@
         'numpy',
         'scipy',
         'pandas',
-        'xlrd',
-	    'openpyxl',
-        'zarr',
-        'emcee',
-        'xarray',
-        'rbfopt',
+        'openpyxl',
         'numba',
-        'SAlib',
-        'h5py'
+        'pySODM',
     ],
     extras_require={
         "develop":  ["pytest",

From 5884450cee12cd769a75892545e963e6eb6ab88b Mon Sep 17 00:00:00 2001
From: twallema <tijs.alleman@ugent.be>
Date: Tue, 14 May 2024 15:29:53 +0200
Subject: [PATCH 3/6] remove warning suppression in spatial model

---
 .../calibrate_BASE-COVID19_SEIQRD_spatial_hybrid_vacc.py      | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_spatial_hybrid_vacc.py b/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_spatial_hybrid_vacc.py
index 4b7d3e84e..4d2264b1d 100644
--- a/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_spatial_hybrid_vacc.py
+++ b/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_spatial_hybrid_vacc.py
@@ -32,8 +32,6 @@
 from pySODM.optimization.mcmc import perturbate_theta, run_EnsembleSampler, emcee_sampler_to_dictionary
 from pySODM.optimization.objective_functions import log_posterior_probability, log_prior_uniform, ll_poisson, ll_negative_binomial
 
-import warnings
-warnings.filterwarnings("ignore")
 
 ####################################
 ## Public or private spatial data ##
@@ -237,7 +235,7 @@
     # Join them together
     pars = pars1 + pars2 + pars3 + pars4
     bounds = bounds1 + bounds2 + bounds3 + bounds4
-    labels = ['$\\Omega$', '$\Psi$', '$k$', '$\Psi_{F}$', '$\Psi_{W}$', '$\Psi_{B}$', '$K_{inf, abc}$', '$K_{inf,\\delta}$', '$A$', '$f_h$']
+    labels = [r'$\Omega$', r'$\Psi$', '$k$', r'$\Psi_{F}$', r'$\Psi_{W}$', r'$\Psi_{B}$', r'$K_{inf, abc}$', r'$K_{inf,\delta}$', '$A$', '$f_h$']
     # Setup objective function with uniform priors
     objective_function = log_posterior_probability(model,pars,bounds,data,states,log_likelihood_fnc,log_likelihood_fnc_args,labels=labels, aggregation_function=aggregate_Brussels_Brabant_DataArray)
 

From d0e15a37f03ceff90c2d2dbb65d98f2bf4b6207b Mon Sep 17 00:00:00 2001
From: twallema <tijs.alleman@ugent.be>
Date: Tue, 14 May 2024 15:30:39 +0200
Subject: [PATCH 4/6] chained assignment warning in VOC parameters

---
 src/covid19_DTM/data/model_parameters.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/covid19_DTM/data/model_parameters.py b/src/covid19_DTM/data/model_parameters.py
index ec844bc11..6cbbce428 100644
--- a/src/covid19_DTM/data/model_parameters.py
+++ b/src/covid19_DTM/data/model_parameters.py
@@ -464,13 +464,13 @@ def get_COVID19_SEIQRD_VOC_parameters(VOCs=['WT', 'abc', 'delta', 'omicron'], pa
         index=['WT', 'abc', 'delta', 'omicron'], columns=pd.MultiIndex.from_tuples(columns))
 
     # Define logistic growth properties
-    VOC_parameters.loc['WT']['logistic_growth'] = [
+    VOC_parameters.loc['WT', 'logistic_growth'] = [
         datetime(2019, 1, 1), datetime(2019, 2, 1), 0.20]
-    VOC_parameters.loc['abc']['logistic_growth'] = [
+    VOC_parameters.loc['abc', 'logistic_growth'] = [
         datetime(2020, 12, 1), datetime(2021, 2, 14), 0.07]
-    VOC_parameters.loc['delta']['logistic_growth'] = [
+    VOC_parameters.loc['delta', 'logistic_growth'] = [
         datetime(2021, 5, 1), datetime(2021, 6, 25), 0.11]
-    VOC_parameters.loc['omicron']['logistic_growth'] = [
+    VOC_parameters.loc['omicron', 'logistic_growth'] = [
         datetime(2021, 11, 26), datetime(2021, 12, 24), 0.19]
 
     # Define variant properties

From 5f02fae847779b04bcda2df2395f5a6e7002d82a Mon Sep 17 00:00:00 2001
From: twallema <tijs.alleman@ugent.be>
Date: Tue, 14 May 2024 15:30:52 +0200
Subject: [PATCH 5/6] unsuppress warnings in national model calibration

---
 .../calibrate_BASE-COVID19_SEIQRD_hybrid_vacc.py            | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_hybrid_vacc.py b/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_hybrid_vacc.py
index 4ff3bdc52..7f7ecdeaf 100644
--- a/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_hybrid_vacc.py
+++ b/notebooks/calibration/calibrate_BASE-COVID19_SEIQRD_hybrid_vacc.py
@@ -35,10 +35,6 @@
 from pySODM.optimization.mcmc import perturbate_theta, run_EnsembleSampler, emcee_sampler_to_dictionary
 from pySODM.optimization.objective_functions import log_posterior_probability, log_prior_uniform, ll_negative_binomial, ll_poisson
 
-# Suppress warnings
-import warnings
-warnings.filterwarnings("ignore")
-
 #############################
 ## Handle script arguments ##
 #############################
@@ -192,7 +188,7 @@
     pars = pars1 + pars2 + pars3 + pars4
     bounds =  bounds1 + bounds2 + bounds3 + bounds4
     # Define labels
-    labels = ['$\Omega$', '$\Psi$', 'k', '$K_{inf, abc}$', '$K_{inf, \\delta}$', '$A$', '$f_h$']
+    labels = [r'$\Omega$', r'$\Psi$', r'k', r'$K_{inf, abc}$', r'$K_{inf, \delta}$', r'$A$', r'$f_h$']
     # Setup objective function without priors and with negative weights 
     objective_function = log_posterior_probability(model,pars,bounds,data,states,log_likelihood_fnc,log_likelihood_fnc_args,labels=labels)
 

From b53f23626031dabd0248cb1089abbbea08a68947 Mon Sep 17 00:00:00 2001
From: twallema <tijs.alleman@ugent.be>
Date: Tue, 14 May 2024 15:31:00 +0200
Subject: [PATCH 6/6] update vaccination incidences

---
 .../sciensano/vacc_incidence_national.pkl     | Bin 438008 -> 438008 bytes
 .../interim/sciensano/vacc_incidence_prov.pkl | Bin 3894823 -> 3894829 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/data/covid19_DTM/interim/sciensano/vacc_incidence_national.pkl b/data/covid19_DTM/interim/sciensano/vacc_incidence_national.pkl
index 08a3219770066839119c3d0250be415c7cdea6f2..fd6eaabeb681bf15853aed5cb2f4a1b55e30e7c0 100644
GIT binary patch
delta 43
scmexySL(-IsSPt2S>)M1vNX?OY@fpj!c0KS48$xz%({IJBU{W`0DY7Xi~s-t

delta 43
scmexySL(-IsSPt2S$4#P@;1+5Y@fpj!c0KS48$xz%({IJBU{W`0E#yc=l}o!

diff --git a/data/covid19_DTM/interim/sciensano/vacc_incidence_prov.pkl b/data/covid19_DTM/interim/sciensano/vacc_incidence_prov.pkl
index 091b0ec78d5d5ee1653e0203ff8545db420172b6..9a8ed5c4e7e7c9dab90ed358cbf7557b17d15f4d 100644
GIT binary patch
delta 295
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g!!tLEFHaUz?==Xwo;lQZzUsJ^^J2S}9lXu-fA8XA8UO$Q

delta 289
zcmWl|w+=yJ0D#f_dhfmW-aB{1AQGF+WRi%{6BsN;3B%n@5+)wT6G+4>_?+ZiUmtPd
z?JQK!#oWA;#a<Tw3M#3hni^`Uqn-vDX`-1HT4|%54m#<gn;v@Uqn`l=8Df|bMj2zA
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PWHy|P#<Su0xLsC${pep_