this runs please run

InstituteforDiseaseModeling · Sep 22, 2023 · 38de13c · 38de13c
1 parent 77330e3
commit 38de13c
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/examples/Snakefile b/examples/Snakefile
@@ -65,22 +65,24 @@ rule all:
 baseline_calibration = r"monique/calibration/baseline_calibration/"
 rule serialize_transmission_sweep:
     input: baseline_calibration + r"01_serialize_transmission_sweep/params.py",
-           baseline_calibration + r"01_serialize_transmission_sweep/manifest.py"
+           baseline_calibration + r"01_serialize_transmission_sweep/manifest.py",
+           baseline_calibration+ r"01_serialize_transmission_sweep/config_sweep_builders.py"
     output: touch(baseline_calibration + r"01_serialize_transmission_sweep/experiment_id.txt")
     run:
         update_parameters_in_file(input[0],{"years = 30": f"years = 10\n",
                                             "num_seeds = ": "num_seeds = 1\n",
                                             "population_size =": "population_size = 2000\n"})
         update_parameters_in_file(input[1],{"USER_PATH = ": f"USER_PATH = r'../data'\n",
                                             "sif_id = None": "sif_id = 'dtk_sif.id'\n"})
+        update_parameters_in_file(input[2],{"rep_admin:": f"        rep_admin: [np.logspace(-1.6, 2, 25)[ii] for ii in [0, 4]] for rep_admin in\n"})
         shell(get_command(script=baseline_calibration + r"01_serialize_transmission_sweep/run_simulations.py",
             python_version=config['python_version']))
 
 rule run_transmission_sweep:
     input: baseline_calibration + r"01_serialize_transmission_sweep/experiment_id.txt",
            baseline_calibration + r"02_run_transmission_sweep/params.py",
            baseline_calibration + r"02_run_transmission_sweep/manifest.py",
-           baseline_calibration + r"02_run_transmission_sweep/config_sweep_builders.py",
+           baseline_calibration + r"02_run_transmission_sweep/config_sweep_builders.py"
     output: touch(baseline_calibration + r"02_run_transmission_sweep/experiment_id.txt")
     run:
         with open(input[0]) as exp_id_file:
@@ -91,7 +93,7 @@ rule run_transmission_sweep:
                                             "population_size =": "population_size = 2000\n"})
         update_parameters_in_file(input[2],{"USER_PATH = ": f"USER_PATH = r'../data'\n",
                                             "sif_id = None": "sif_id = 'dtk_sif.id'\n"})
-        update_parameters_in_file(input[3],{"rep_admin:": f"        rep_admin: [np.logspace(-1.6, 25)[ii] for ii in [0, 8, 20]] for rep_admin in\n"})
+        update_parameters_in_file(input[3],{"rep_admin:": f"        rep_admin: [np.logspace(-1.6, 2, 25)[ii] for ii in [0, 4]] for rep_admin in\n"})
         shell(get_command(script=baseline_calibration + r"02_run_transmission_sweep/run_simulations.py",
             python_version=config['python_version']))
 

diff --git a/...calibration/baseline_calibration/01_serialize_transmission_sweep/config_sweep_builders.py b/...calibration/baseline_calibration/01_serialize_transmission_sweep/config_sweep_builders.py
@@ -118,7 +118,6 @@ def get_sweep_builders(**kwargs):
                                     f'monthly_habitats_1_{params.population_size}.csv'))
 
     sweepspace = {
-        # rep_admin: np.logspace(-1.6, 2, 25) for rep_admin in lhdf['archetype'].values
         rep_admin: [np.logspace(-1.6, 2, 25)[ii] for ii in [0, 4, 8, 12, 16, 20]] for rep_admin in
         lhdf['archetype'].values  # make sure this matches the values used in the next step
     }