Merge branch 'main' into fixing-issue-labels

batch/inference_job_launcher.py

@@ -806,7 +806,7 @@ def launch(self, job_name, config_filepath, seir_modifiers_scenarios, outcome_mo
                 slurm_job_id = stdout.decode().split(" ")[-1][:-1]
                 print(f">>> SUCCESS SCHEDULING JOB. Slurm job id is {slurm_job_id}")
 
-                postprod_command = f"""sbatch {export_str} --dependency=afterany:{slurm_job_id} --mem={12000}M --time={60} --job-name=post-{cur_job_name} --output=log_postprod_{self.run_id}_{cur_job_name}.txt {os.path.dirname(os.path.realpath(__file__))}/SLURM_postprocess_runner.run"""
+                postprod_command = f"""sbatch {export_str} --dependency=afterany:{slurm_job_id} --mem={12000}M --time={240} --job-name=post-{cur_job_name} --output=log_postprod_{self.run_id}_{cur_job_name}.txt {os.path.dirname(os.path.realpath(__file__))}/SLURM_postprocess_runner.run"""
                 print("post-processing command to be run >>>>>>>> ")
                 print(postprod_command)
                 print(" <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< ")

build/local_install.R

@@ -6,13 +6,14 @@ local({r <- getOption("repos")
 
 # Installs the custom-made packages in this repository
 
-library(devtools)
 
-install.packages(c("covidcast","data.table","vroom","dplyr"), quiet=TRUE)
+install.packages(c("data.table","vroom","dplyr"), quiet=TRUE) # removed "covidcast"
 # devtools::install_github("hrbrmstr/cdcfluview")
 
 # To run if operating in the container -----
 
+# library(devtools)
+
 initial.options <- commandArgs(trailingOnly = FALSE)
 file.arg.name <- "--file="
 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)]) # get the name of this file, by looking for the option "--file" in the arguments that were used to start this R instance and getting the term that comes after