Merge pull request #227 from HopkinsIDD/add-examples

add the flepiMoP sample repository and run integrations against it

.github/workflows/ci.yml

@@ -43,6 +43,12 @@ jobs:
           cd flepimop/gempyor_pkg
           pytest -s
         shell: bash
+      - name: Run gempyor-cli integration tests from examples
+        run: |
+          source /var/python/3.10/virtualenv/bin/activate
+          cd examples
+          pytest -s
+        shell: bash
       - name: Run flepicommon tests
         run: |
           setwd("flepimop/R_packages/flepicommon")

.gitignore

@@ -17,6 +17,9 @@ model_output/
 .Rhistory
 .Rapp.history
 
+*.pdf
+*.h5
+
 # Session Data files
 .RData
 

batch/SLURM_inference_job.run

@@ -110,8 +110,8 @@ if [[ $FLEPI_CONTINUATION == "TRUE" ]]; then
                                                                                                         extension='$extension'))")
     # in filename is always a seir file
     export IN_FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name(run_id='$FLEPI_CONTINUATION_RUN_ID',
-                                                                                                        prefix='$FLEPI_PREFIX/$FLEPI_CONTINUATION_RUN_ID'
-                                                                                                        inference_filepath_suffix='/global/final',
+                                                                                                        prefix='$FLEPI_PREFIX/$FLEPI_CONTINUATION_RUN_ID',
+                                                                                                        inference_filepath_suffix='global/final',
                                                                                                         index=$FLEPI_SLOT_INDEX,
                                                                                                         ftype='seir',
                                                                                                         extension='$extension'))")
@@ -128,6 +128,7 @@ if [[ $FLEPI_CONTINUATION == "TRUE" ]]; then
     else
         echo "CONTINUATION: Could not copy file of type $filetype ($IN_FILENAME -> $INIT_FILENAME)"
     fi
+    #Rscript R/scripts/init_R18_resume_highrisk.R --config $CONFIG_PATH --init_filename_raw $INIT_FILENAME --init_filename_post $INIT_FILENAME
     #Rscript $FLEPI_PATH/flepimop/main_scripts/seir_init_immuneladder.R --res_config config_SMH_R17_noBoo_lowIE_phase2_blk2.yml
     #Rscript $FLEPI_PATH/preprocessing/seir_init_immuneladder_r17phase3_preOm.R --res_config config_SMH_R17_noBoo_lowIE_phase2_blk2.yml
 fi

batch/inference_job_launcher.py

@@ -12,6 +12,7 @@
 from datetime import datetime, timezone, date
 import yaml
 from gempyor import file_paths
+import gempyor.utils
 
 
 def user_confirmation(question="Continue?", default=False):
@@ -36,7 +37,7 @@ def user_confirmation(question="Continue?", default=False):
 @click.option(
     "-c",
     "--config",
-    "config_file",
+    "config_filepath",
     envvar="CONFIG_PATH",
     type=click.Path(exists=True),
     required=True,
@@ -272,7 +273,7 @@ def user_confirmation(question="Continue?", default=False):
 )
 def launch_batch(
     batch_system,
-    config_file,
+    config_filepath,
     flepi_path,
     data_path,
     run_id,
@@ -301,7 +302,7 @@ def launch_batch(
     continuation_run_id,
 ):
     config = None
-    with open(config_file) as f:
+    with open(config_filepath) as f:
         config = yaml.full_load(f)
 
     # A unique name for this job run, based on the config name and current time
@@ -327,7 +328,7 @@ def launch_batch(
             )
             return 1
     else:
-        print(f"WARNING: no inference section found in {config_file}!")
+        print(f"WARNING: no inference section found in {config_filepath}!")
 
     if "s3://" in str(restart_from_location):  # ugly hack: str because it might be None
         restart_from_run_id = aws_countfiles_autodetect_runid(
@@ -402,7 +403,7 @@ def launch_batch(
         if "scenarios" in config["outcome_modifiers"]:
             outcome_modifiers_scenarios = config["outcome_modifiers"]["scenarios"]
 
-    handler.launch(job_name, config_file, seir_modifiers_scenarios, outcome_modifiers_scenarios)
+    handler.launch(job_name, config_filepath, seir_modifiers_scenarios, outcome_modifiers_scenarios)
 
     # Set job_name as environmental variable so it can be pulled for pushing to git
     os.environ["job_name"] = job_name
@@ -655,7 +656,7 @@ def save_file(self, source, destination, remove_source=False, prefix=""):
         if remove_source:
             os.remove(source)
 
-    def launch(self, job_name, config_file, seir_modifiers_scenarios, outcome_modifiers_scenarios):
+    def launch(self, job_name, config_filepath, seir_modifiers_scenarios, outcome_modifiers_scenarios):
         s3_results_path = f"s3://{self.s3_bucket}/{job_name}"
 
         if self.batch_system == "slurm":
@@ -682,7 +683,7 @@ def launch(self, job_name, config_file, seir_modifiers_scenarios, outcome_modifi
             {"name": "S3_UPLOAD", "value": str(self.s3_upload).lower()},
             {"name": "PROJECT_PATH", "value": str(self.data_path)},
             {"name": "FLEPI_PATH", "value": str(self.flepi_path)},
-            {"name": "CONFIG_PATH", "value": config_file},
+            {"name": "CONFIG_PATH", "value": config_filepath},
             {"name": "FLEPI_NUM_SLOTS", "value": str(self.num_jobs)},
             {
                 "name": "FLEPI_MAX_STACK_SIZE",
@@ -703,7 +704,7 @@ def launch(self, job_name, config_file, seir_modifiers_scenarios, outcome_modifi
             {"name": "FLEPI_MEM_PROF_ITERS", "value": str(os.getenv("FLEPI_MEM_PROF_ITERS", default="50"))},
             {"name": "SLACK_CHANNEL", "value": str(self.slack_channel)},
         ]
-        with open(config_file) as f:
+        with open(config_filepath) as f:
             config = yaml.full_load(f)
 
         for ctr, (s, d) in enumerate(itertools.product(seir_modifiers_scenarios, outcome_modifiers_scenarios)):
@@ -798,31 +799,20 @@ def launch(self, job_name, config_file, seir_modifiers_scenarios, outcome_modifi
                 print("slurm command to be run >>>>>>>> ")
                 print(command)
                 print(" <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< ")
-                import shlex  # using shlex to split the command because it's not obvious https://docs.python.org/3/library/subprocess.html#subprocess.Popen
-
-                sr = subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-                (stdout, stderr) = sr.communicate()
-                if sr.returncode != 0:
-                    print(f"sbatch command failed with returncode {sr.returncode}")
-                    print("sbatch command failed with stdout and stderr:")
-                    print("stdout: ", stdout)
-                    print("stderr: ", stderr)
-                    raise Exception("sbatch command failed")
+
+                returncode, stdout, stderr = gempyor.utils.command_safe_run(
+                    command, command_name="sbatch", fail_on_fail=True
+                )
                 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"""
                 print("post-processing command to be run >>>>>>>> ")
                 print(postprod_command)
                 print(" <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< ")
-                sr = subprocess.Popen(shlex.split(postprod_command), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-                (stdout, stderr) = sr.communicate()
-                if sr.returncode != 0:
-                    print(f"sbatch command failed with returncode {sr.returncode}")
-                    print("sbatch command failed with stdout and stderr:")
-                    print("stdout: ", stdout)
-                    print("stderr: ", stderr)
-                    raise Exception("sbatch command failed")
+                returncode, stdout, stderr = gempyor.utils.command_safe_run(
+                    postprod_command, command_name="sbatch postprod", fail_on_fail=True
+                )
                 postprod_job_id = stdout.decode().split(" ")[-1][:-1]
                 print(f">>> SUCCESS SCHEDULING POST-PROCESSING JOB. Slurm job id is {postprod_job_id}")
 
@@ -915,7 +905,7 @@ def launch(self, job_name, config_file, seir_modifiers_scenarios, outcome_modifi
         if self.continuation:
             print(f" >> Continuing from run id is {self.continuation_run_id} located in {self.continuation_location}")
         print(f" >> Run id is {self.run_id}")
-        print(f" >> config is {config_file.split('/')[-1]}")
+        print(f" >> config is {config_filepath.split('/')[-1]}")
         flepimop_branch = subprocess.getoutput(f"cd {self.flepi_path}; git rev-parse --abbrev-ref HEAD")
         data_branch = subprocess.getoutput(f"cd {self.data_path}; git rev-parse --abbrev-ref HEAD")
         data_hash = subprocess.getoutput(f"cd {self.data_path}; git rev-parse HEAD")

batch/scenario_job.py

@@ -15,7 +15,7 @@
 @click.option(
     "-c",
     "--config",
-    "config_file",
+    "config_filepath",
     envvar="CONFIG_PATH",
     type=click.Path(exists=True),
     required=True,
@@ -109,7 +109,7 @@
     help="The amount of RAM in megabytes needed per CPU running simulations",
 )
 def launch_batch(
-    config_file,
+    config_filepath,
     num_jobs,
     slots_per_job,
     dvc_target,
@@ -122,26 +122,26 @@ def launch_batch(
     memory,
 ):
     config = None
-    with open(config_file) as f:
+    with open(config_filepath) as f:
         config = yaml.full_load(f)
 
     # A unique name for this job run, based on the config name and current time
     job_name = f"{config['name']}-{int(time.time())}"
 
     # Update and save the config file with the number of sims to run
-    print(f"Updating {config_file} to run {slots_per_job} slots...")
+    print(f"Updating {config_filepath} to run {slots_per_job} slots...")
     config["nslots"] = slots_per_job
 
     if parallelize_scenarios:
         seir_modifiers_scenarios = config["seir_modifiers"]["scenarios"]
         for s in seir_modifiers_scenarios:
             seir_modifiers_scenario_job_name = f"{job_name}_{s}"
             config["interventions"]["scenarios"] = [s]
-            with open(config_file, "w") as f:
+            with open(config_filepath, "w") as f:
                 yaml.dump(config, f, sort_keys=False)
             launch_job_inner(
                 seir_modifiers_scenario_job_name,
-                config_file,
+                config_filepath,
                 num_jobs,
                 slots_per_job,
                 dvc_target,
@@ -153,14 +153,14 @@ def launch_batch(
                 memory,
             )
         config["interventions"]["scenarios"] = seir_modifiers_scenarios
-        with open(config_file, "w") as f:
+        with open(config_filepath, "w") as f:
             yaml.dump(config, f, sort_keys=False)
     else:
-        with open(config_file, "w") as f:
+        with open(config_filepath, "w") as f:
             yaml.dump(config, f, sort_keys=False)
         launch_job_inner(
             job_name,
-            config_file,
+            config_filepath,
             num_jobs,
             slots_per_job,
             dvc_target,
@@ -179,7 +179,7 @@ def launch_batch(
 
 def launch_job_inner(
     job_name,
-    config_file,
+    config_filepath,
     num_jobs,
     slots_per_job,
     dvc_target,
@@ -212,7 +212,7 @@ def launch_job_inner(
     model_data_path = f"s3://{s3_input_bucket}/{tarfile_name}"
     results_path = f"s3://{s3_output_bucket}/{job_name}"
     env_vars = [
-        {"name": "CONFIG_PATH", "value": config_file},
+        {"name": "CONFIG_PATH", "value": config_filepath},
         {"name": "S3_MODEL_PROJECT_PATH", "value": model_data_path},
         {"name": "DVC_TARGET", "value": dvc_target},
         {"name": "DVC_OUTPUTS", "value": " ".join(dvc_outputs)},

datasetup/build_covid_data.R

@@ -382,6 +382,12 @@ us_data <- us_data %>%
 
 
 
+
+# ~ Manually fix weird MAINE point -------------------------------------------------------------
+
+# if source == ME , dates are between 2023-09-26 and 2023-09-30, set incidH to NA
+us_data <- us_data %>% mutate(incidH = ifelse(source == "ME" & date >= "2023-09-26" & date <= "2023-09-30", NA, incidH))
+
 # ~ Fix non-numeric -------------------------------------------------------------
 #  -- leave NAs so its not assuming an NA is a 0 and fitting to it