commenting out analyzer that's failing because of comps login issues …

…(nothing else has that problem, will investigate), cleaning up calibra folder BEFORE the run, small fixes.
InstituteforDiseaseModeling · Sep 20, 2023 · 089a50e · 089a50e
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commit 089a50e
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Showing 2 changed files with 19 additions and 16 deletions.
diff --git a/examples/Snakefile b/examples/Snakefile
@@ -30,7 +30,7 @@ def get_command(script="run_simulations.py", python_version: str = None):
 # doing it manually because... too complicated otherwise? re
 expected_outputs = [r"monique/calibration/baseline_calibration/01_serialize_transmission_sweep/experiment_id.txt",
                     r"monique/calibration/baseline_calibration/02_run_transmission_sweep/experiment_id.txt",
-                    r"monthly_U5_PfPR.csv",
+                    # r"monthly_U5_PfPR.csv",
                     r"../data/example_files/simulation_output/calibration/baseline_calibration/LL_allxLH_each_admin_run/CC_run3.csv",
                     r"../data/example_files/simulation_inputs/larval_habitats/monthly_habitats_1.csv",
                     r"monique/calibration/seasonality_calibration/01_burnin_for_seasonalityCalib/experiment_id.txt",
@@ -82,17 +82,17 @@ rule run_transmission_sweep:
         shell(get_command(script=baseline_calibration + r"02_run_transmission_sweep/run_simulations.py",
             python_version=config['python_version']))
 
-rule analyze_ssmt_monthy_U5_PfPR:
-    input: baseline_calibration + r"02_run_transmission_sweep/experiment_id.txt",
-           baseline_calibration + r"03_analyze_ssmt_monthly_U5_PfPR.py"
-    output: r"monthly_U5_PfPR.csv"
-    run:
-        with open(input[0]) as exp_id_file:
-            burnin_id = exp_id_file.read()
-            update_parameters_in_file(input[1],
-                {"experiments = ": f"experiments = {{'PfPR_sweep_main_example': '{burnin_id}'}}\n"})
-        shell(get_command(script=baseline_calibration + r"03_analyze_ssmt_monthly_U5_PfPR.py",
-            python_version=config['python_version']))
+# rule analyze_ssmt_monthy_U5_PfPR:
+#     input: baseline_calibration + r"02_run_transmission_sweep/experiment_id.txt",
+#            baseline_calibration + r"03_analyze_ssmt_monthly_U5_PfPR.py"
+#     output: r"monthly_U5_PfPR.csv"
+#     run:
+#         with open(input[0]) as exp_id_file:
+#             burnin_id = exp_id_file.read()
+#             update_parameters_in_file(input[1],
+#                 {"experiments = ": f"experiments = {{'PfPR_sweep_main_example': '{burnin_id}'}}\n"})
+#         shell(get_command(script=baseline_calibration + r"03_analyze_ssmt_monthly_U5_PfPR.py",
+#             python_version=config['python_version']))
 
 rule find_best_xLH_fits:
     output:
@@ -131,11 +131,11 @@ rule seasonality_calibration:
                                             "burnin_years = ": "    burnin_years = 5\n"})
         update_parameters_in_file(input[2],{"USER_PATH = ": f"USER_PATH = r'../data'\n",
                                             "sif_id = None": "sif_id = 'dtk_sif.id'\n"})
-        shell(get_command(script=r"monique/calibration/seasonality_calibration/02_seasonality_calibration/run_calibration.py",
-            python_version=config['python_version']))
         calibra = seasonality_cal + r"02_seasonality_calibration/Calibra_results"
         if os.path.exists(calibra):
             shutil.rmtree(calibra)
+        shell(get_command(script=r"monique/calibration/seasonality_calibration/02_seasonality_calibration/run_calibration.py",
+            python_version=config['python_version']))
 
 rule save_best_seasonality_fit:
     input: seasonality_cal + r"/03_save_best_seasonality_fit.py"
@@ -204,13 +204,15 @@ run_2005_to_2022 = r"ben/example/run_2005-2022/"
 
 rule run_2005_2022:
     input: run_1960_to_2004 + r"experiment_id.txt",
-           run_2005_to_2022 + r"params.py",run_2005_to_2022 + r"manifest.py"
+           run_2005_to_2022 + r"params.py",
+           run_2005_to_2022 + r"manifest.py"
     output: run_2005_to_2022 + r"experiment_id.txt"
     run:
         with open(input[0]) as exp_id_file:
             burnin_id = exp_id_file.read()
         update_parameters_in_file(input[1],{"burnin_id = ": f"burnin_id = '{burnin_id}'\n",
-                                            "iopath = ": "iopath = 'ben/IO' \n"})
+                                            "iopath = ": "iopath = 'ben/IO' \n",
+                                            "ser_date =": "ser_date = 5 * 365\n"})
         update_parameters_in_file(input[2],{"BEN_DIR = ": f"BEN_DIR = r'ben'\n",
                                             "sif_path = ": "sif_path = 'dtk_sif.id'\n"})
         shell(get_command(script=run_2005_to_2022 + r"run_simulations.py",

diff --git a/examples/ben/example/run_2005-2022/set_config.py b/examples/ben/example/run_2005-2022/set_config.py
@@ -17,6 +17,7 @@ def set_config(config):
     config.parameters.Report_Event_Recorder_Events = ['Received_NMF_Treatment', 'Received_Severe_Treatment',
                                                       'Received_Treatment']
     config.parameters.Report_Event_Recorder_Ignore_Events_In_List = 0
+    config.parameters.Custom_Individual_Events = ['Received_NMF_Treatment']
 
     set_species_param(config, 'arabiensis', 'Anthropophily', 0.88, overwrite=True)
     set_species_param(config, 'arabiensis', 'Indoor_Feeding_Fraction', 0.5, overwrite=True)