Merge pull request #124 from dessn/#107

Moved CreateCov over to submit_batch

pippin/cosmofitters/cosmomc.py

@@ -52,7 +52,7 @@ def __init__(self, name, output_dir, config, options, global_config, dependencie
         self.path_to_cosmomc = get_output_loc(self.global_config["CosmoMC"]["location"])
 
         self.create_cov_dep = self.get_dep(CreateCov)
-        self.blind = self.create_cov_dep.output["blind"] if self.create_cov_dep is not None else self.options.get("BLIND", False)
+        self.blind = np.all(self.create_cov_dep.output["blind"]) if self.create_cov_dep is not None else self.options.get("BLIND", False)
         assert isinstance(self.blind, (bool, np.bool_)), "Blind should be set to a boolan value!"
         self.ini_prefix = options.get("INI").replace(".ini", "")
         self.static = self.ini_prefix.replace(".ini", "") in ["cmb_omw", "cmb_omol"]

pippin/cosmofitters/wfit.py

@@ -7,7 +7,6 @@
 
 from pippin.config import mkdirs, get_output_loc, get_data_loc, chown_dir, read_yaml
 from pippin.create_cov import CreateCov
-from pippin.sb_create_cov import SBCreateCov
 from pippin.cosmofitters.cosmofit import CosmoFit
 from pippin.base import ConfigBasedExecutable
 from pippin.task import Task
@@ -94,7 +93,7 @@ def _run(self):
     @staticmethod
     def get_tasks(c, prior_tasks, base_output_dir, stage_number, prefix, global_config):
 
-        create_cov_tasks = Task.get_task_of_type(prior_tasks, CreateCov) + Task.get_task_of_type(prior_tasks, SBCreateCov)
+        create_cov_tasks = Task.get_task_of_type(prior_tasks, CreateCov)
 
         def _get_wfit_dir(base_output_dir, stage_number, name):
             return f"{base_output_dir}/{stage_number}_COSMOFIT/WFIT/{name}"

pippin/manager.py

@@ -11,7 +11,6 @@
 from pippin.config import get_logger, get_config, get_output_dir, mkdirs, chown_dir, chown_file, get_data_loc
 from pippin.cosmofitters.cosmofit import CosmoFit
 from pippin.create_cov import CreateCov
-from pippin.sb_create_cov import SBCreateCov
 from pippin.dataprep import DataPrep
 from pippin.merge import Merger
 from pippin.snana_fit import SNANALightCurveFit
@@ -26,13 +25,6 @@ class Manager:
     def __init__(self, filename, config_path, config_raw, config, message_store):
         self.logger = get_logger()
         self.task_index = {t: i for i, t in enumerate(self.task_order)}
-        debug1 = config["DEBUG1"]
-        if debug1:
-            self.logger.warning("DEBUG1 enabled, replacing CREATE_COV with SB_CREATE_COV")
-            self.task_index[SBCreateCov] = self.task_index.pop(CreateCov)
-            ind = self.task_index[SBCreateCov]
-            Manager.task_order[ind] = SBCreateCov
-            Manager.stages[ind] = "SB_CREATE_COV"
         self.message_store = message_store
         self.filename = filename
         self.filename_path = config_path

run.py

@@ -161,10 +161,6 @@ def run(args):
 
     logging.info(f"Running on: {os.environ.get('HOSTNAME', '$HOSTNAME not set')} login node.")
 
-    if args.debug1:
-        logging.warning("DEBUG1 enabled, this is still experimental. Please let Patrick know if anything goes wrong!")
-    config["DEBUG1"] = args.debug1
-
     manager = Manager(config_filename, yaml_path, config_raw, config, message_store)
 
     # Gracefully hand Ctrl-c
@@ -241,7 +237,6 @@ def get_args(test=False):
     parser.add_argument("-p", "--permission", help="Fix permissions and groups on all output, don't rerun", action="store_true", default=False)
     parser.add_argument("-i", "--ignore", help="Dont rerun tasks with this stage or less. Accepts either the stage number of name (i.e. 1 or SIM)", default=None)
     parser.add_argument("-S", "--syntax", help="Get the syntax of the given stage. Accepts either the stage number or name (i.e. 1 or SIM). If run without argument, will tell you all stage numbers / names.", default=None, const="options", type=str, nargs='?')
-    parser.add_argument("--debug1", help="Enable debug option 1: Move CREATE_COV over to submit_batch", action="store_true", default=False)
     command_group = parser.add_mutually_exclusive_group()
     command_group.add_argument("-C", "--compress", help="Compress pippin output during job. Combine with -c / --check in order to compress completed pippin job.", action="store_true", default=False)
     command_group.add_argument("-U", "--uncompress", help="Do not compress pippin output during job. Combine with -c / --check in order to uncompress completed pippin job.  Mutually exclusive with -C / --compress", action="store_true", default=False)

tests/test_valid_config.py

@@ -198,7 +198,7 @@ def test_createcov_config_valid():
     assert isinstance(tasks[-1], CreateCov)
 
     task = tasks[-1]
-    assert task.output["name"] == "COVTEST_BCOR"
+    assert task.output["name"] == "COVTEST"
     assert len(task.output["covopts"]) == 2
     assert "ALL" in task.output["covopts"]
     assert "NOSYS" in task.output["covopts"]
@@ -215,7 +215,7 @@ def test_cosmomc_config_valid():
     assert isinstance(tasks[-1], CosmoMC)
 
     task = tasks[-1]
-    assert task.output["name"] == "COSMOMC_SN_OMW_COVTEST_BCOR"
+    assert task.output["name"] == "COSMOMC_SN_OMW_COVTEST"
     assert len(task.output["covopts"]) == 2
     assert "ALL" in task.output["covopts"]
     assert "NOSYS" in task.output["covopts"]