Revert "Add calibration uncertainty model"

bin/gwin

@@ -34,7 +34,6 @@ import gwin
 from gwin import (__version__, burn_in, option_utils)
 from gwin.io.hdf import InferenceFile
 from gwin.option_utils import validate_checkpoint_files
-from gwin.calibration import Recalibrate
 
 # command line usage
 parser = argparse.ArgumentParser(usage=__file__ + " [--options]",
@@ -199,9 +198,9 @@ with ctx:
     # get ifo-specific instances of calibration model
     if cp.has_section('calibration'):
         logging.info("Initializing calibration model")
-        recalibration = {ifo: Recalibrate.from_config(cp, ifo, section='calibration') for
-                         ifo in opts.instruments}
-        model_args['recalibration'] = recalibration
+        recalib = {ifo : strain.read_model_from_config(cp, ifo) for
+                   ifo in opts.instruments}
+        model_args['recalib'] = recalib
 
     # get gates for templates
     gates = strain.gates_from_cli(opts)

bin/gwin_make_workflow

@@ -94,9 +94,9 @@ parser.add_argument("--gps-end-time", type=float, nargs="+", default=None,
                          "this option is ignored.")
 
 # input configuration file options
-parser.add_argument("--inference-config-file", type=str, nargs='+', required=True,
+parser.add_argument("--inference-config-file", type=str, required=True,
                     help="workflow.WorkflowConfigParser parsable file with "
-                         "prior information.")
+                         "proir information.")
 parser.add_argument("--prior-section", type=str, default="prior",
                     help="Name of the section in inference configuration file "
                          "that contains priors.")
@@ -154,6 +154,9 @@ workflow_options = opts.bank_file != None \
 if not workflow_options and not (opts.gps_end_time != None):
     raise ValueError("Must use either workflow options or --gps-end-time")
 
+# typecast str from command line to File instances
+config_file = to_file(opts.inference_config_file)
+
 # sections for output HTML pages
 rdir = layout.SectionNumber("results",
                             ["detector_sensitivity", "priors", "posteriors",
@@ -191,6 +194,9 @@ workflow_options = opts.bank_file != None \
 if not workflow_options and not (opts.gps_end_time != None):
     raise ValueError("Must use either workflow options or --gps-end-time")
 
+# typecast str from command line to File instances
+config_file = to_file(opts.inference_config_file)
+
 # if using workflow files to find analysis times
 if workflow_options:
 
@@ -233,11 +239,7 @@ inference_exe = wf.Executable(workflow.cp, "inference", ifos=workflow.ifos,
                               out_dir=opts.output_dir)
 
 # read inference configuration file
-# typecast str from command line to File instances
-cp = WorkflowConfigParser(opts.inference_config_file)
-with open('inference.ini', 'w') as ff:
-    cp.write(ff)
-config_file = to_file('inference.ini')
+cp = WorkflowConfigParser([opts.inference_config_file])
 
 # get channel names
 channel_names = {}

docs/command-line/gwin_make_workflow.rst

@@ -78,19 +78,11 @@ A simple configuration file for parameter estimation on the ringdown is::
 
 If you want to use another variable parameter in the inference sampler then add its name to ``[variable_params]`` and add a prior section like shown above.
 
-When working on real data, it is necessary to marginalise over calibration uncertainty.
-The model and parameters describing the calibration uncertainty can be passed in another ini file, e.g.:
-
-.. literalinclude:: ../../examples/workflow/GW150914_example/calibration.ini
-:language: ini
-
 =====================
 Generate the workflow
 =====================
 
-To generate a workflow you will need your configuration files.
-The workflow creates a single config file ``inference.ini`` from all the files specified in ``INFERENCE_CONFIG_PATH``.
-We set the following enviroment variables for this example::
+To generate a workflow you will need your configuration files. We set the following enviroment variables for this example::
 
     # name of the workflow
     WORKFLOW_NAME="r1"
@@ -100,7 +92,7 @@ We set the following enviroment variables for this example::
 
     # input configuration files
     CONFIG_PATH=workflow.ini
-    INFERENCE_CONFIG_PATH="gwin.ini calibration.ini"
+    INFERENCE_CONFIG_PATH=gwin.ini
 
 Specify a directory to save the HTML pages::