change relative include to include from (.). Subs - for _ in tests

pfb/parser/schemas.py

@@ -3,7 +3,7 @@
 import glob
 from typing import *
 from scabha import configuratt
-from scabha.cargo import Parameter
+from scabha.cargo import Parameter, _UNSET_DEFAULT
 from omegaconf.omegaconf import OmegaConf
 
 
@@ -28,14 +28,14 @@ class _CabInputsOutputs(object):
                                   config_class="PfbCleanCabs",
                                   use_cache=False)
 
-    # this is required since upgrade of scabha to caching branch
     # tmp is a tuple containing the config object as the first element
     # and a set containing locations of .yaml configs for pfb workers
     schema = OmegaConf.create(tmp[0])
 
+    # is this still necessary?
     for worker in schema.keys():
         for param in schema[worker]['inputs']:
-            if schema[worker]['inputs'][param]['default'] == '<UNSET DEFAULT VALUE>':
+            if schema[worker]['inputs'][param]['default'] == _UNSET_DEFAULT:
                 schema[worker]['inputs'][param]['default'] = None
 
 

pfb/parser/uncabbedcabs.yml

@@ -5,7 +5,7 @@ pfb.init:
     pass_missing_as_none: true
 
   _include:
-    - init.yaml
+    - (.)init.yaml
 
 pfb.grid:
   command: pfb.workers.grid.grid
@@ -14,7 +14,7 @@ pfb.grid:
     pass_missing_as_none: true
 
   _include:
-    - grid.yaml
+    - (.)grid.yaml
 
 pfb.degrid:
   command: pfb.workers.degrid.degrid
@@ -23,7 +23,7 @@ pfb.degrid:
     pass_missing_as_none: true
 
   _include:
-    - degrid.yaml
+    - (.)degrid.yaml
 
 pfb.clean:
   command: pfb.workers.clean.clean
@@ -32,7 +32,7 @@ pfb.clean:
     pass_missing_as_none: true
 
   _include:
-    - clean.yaml
+    - (.)clean.yaml
 
 pfb.restore:
   command: pfb.workers.restore.restore
@@ -41,7 +41,7 @@ pfb.restore:
     pass_missing_as_none: true
 
   _include:
-    - restore.yaml
+    - (.)restore.yaml
 
 pfb.fwdbwd:
   command: pfb.workers.fwdbwd.fwdbwd
@@ -50,7 +50,7 @@ pfb.fwdbwd:
     pass_missing_as_none: true
 
   _include:
-    - fwdbwd.yaml
+    - (.)fwdbwd.yaml
 
 pfb.forward:
   command: pfb.workers.forward.forward
@@ -59,7 +59,7 @@ pfb.forward:
     pass_missing_as_none: true
 
   _include:
-    - forward.yaml
+    - (.)forward.yaml
 
 pfb.spotless:
   command: pfb.workers.spotless.spotless
@@ -68,7 +68,7 @@ pfb.spotless:
     pass_missing_as_none: true
 
   _include:
-    - spotless.yaml
+    - (.)spotless.yaml
 
 pfb.model2comps:
   command: pfb.workers.model2comps.model2comps
@@ -77,4 +77,4 @@ pfb.model2comps:
     pass_missing_as_none: true
 
   _include:
-    - model2comps.yaml
+    - (.)model2comps.yaml

pfb/workers/init.py

@@ -23,8 +23,8 @@ def init(**kw):
     '''
     Initialise data products for imaging
     '''
-    defaults.update(kw)
-    opts = OmegaConf.create(defaults)
+    defaults.update(kw)  # is this still necessary?
+    opts = OmegaConf.create(kw)
     import time
     timestamp = time.strftime("%Y%m%d-%H%M%S")
     ldir = Path(opts.log_directory).resolve()

tests/test_clean.py

@@ -182,7 +182,7 @@ def test_clean(do_gains, ms_name):
     from pfb.parser.schemas import schema
     init_args = {}
     for key in schema.init["inputs"].keys():
-        init_args[key] = schema.init["inputs"][key]["default"]
+        init_args[key.replace("-", "_")] = schema.init["inputs"][key]["default"]
     # overwrite defaults
     init_args["ms"] = str(test_dir / 'test_ascii_1h60.0s.MS')
     init_args["output_filename"] = outname
@@ -198,7 +198,7 @@ def test_clean(do_gains, ms_name):
     # grid data to produce dirty image
     grid_args = {}
     for key in schema.grid["inputs"].keys():
-        grid_args[key] = schema.grid["inputs"][key]["default"]
+        grid_args[key.replace("-", "_")] = schema.grid["inputs"][key]["default"]
     # overwrite defaults
     grid_args["output_filename"] = outname
     grid_args["postfix"] = postfix
@@ -218,7 +218,7 @@ def test_clean(do_gains, ms_name):
     # run clean
     clean_args = {}
     for key in schema.clean["inputs"].keys():
-        clean_args[key] = schema.clean["inputs"][key]["default"]
+        clean_args[key.replace("-", "_")] = schema.clean["inputs"][key]["default"]
     clean_args["output_filename"] = outname
     clean_args["postfix"] = postfix
     clean_args["nband"] = nchan

tests/test_polproducts.py

@@ -225,7 +225,7 @@ def test_polproducts(do_gains, ms_name):
         # set defaults from schema
         init_args = {}
         for key in schema.init["inputs"].keys():
-            init_args[key] = schema.init["inputs"][key]["default"]
+            init_args[key.replace("-", "_")] = schema.init["inputs"][key]["default"]
         # overwrite defaults
         init_args["ms"] = str(test_dir / 'test_ascii_1h60.0s.MS')
         init_args["output_filename"] = outname
@@ -242,7 +242,7 @@ def test_polproducts(do_gains, ms_name):
         # grid data to produce dirty image
         grid_args = {}
         for key in schema.grid["inputs"].keys():
-            grid_args[key] = schema.grid["inputs"][key]["default"]
+            grid_args[key.replace("-", "_")] = schema.grid["inputs"][key]["default"]
         # overwrite defaults
         grid_args["output_filename"] = outname
         grid_args["postfix"] = postfix

tests/test_spotless.py

@@ -134,7 +134,7 @@ def test_spotless(ms_name):
     # set defaults from schema
     init_args = {}
     for key in schema.init["inputs"].keys():
-        init_args[key] = schema.init["inputs"][key]["default"]
+        init_args[key.replace("-", "_")] = schema.init["inputs"][key]["default"]
     # overwrite defaults
     outname = str(test_dir / 'test')
     init_args["ms"] = str(test_dir / 'test_ascii_1h60.0s.MS')
@@ -151,7 +151,7 @@ def test_spotless(ms_name):
     # grid data to produce dirty image
     grid_args = {}
     for key in schema.grid["inputs"].keys():
-        grid_args[key] = schema.grid["inputs"][key]["default"]
+        grid_args[key.replace("-", "_")] = schema.grid["inputs"][key]["default"]
     # overwrite defaults
     grid_args["output_filename"] = outname
     grid_args["nband"] = nchan
@@ -175,7 +175,7 @@ def test_spotless(ms_name):
     # run clean
     spotless_args = {}
     for key in schema.spotless["inputs"].keys():
-        spotless_args[key] = schema.spotless["inputs"][key]["default"]
+        spotless_args[key.replace("-", "_")] = schema.spotless["inputs"][key]["default"]
     spotless_args["output_filename"] = outname
     spotless_args["nband"] = nchan
     spotless_args["niter"] = 2
@@ -217,7 +217,7 @@ def test_spotless(ms_name):
 
     model2comps_args = {}
     for key in schema.model2comps["inputs"].keys():
-        model2comps_args[key] = schema.model2comps["inputs"][key]["default"]
+        model2comps_args[key.replace("-", "_")] = schema.model2comps["inputs"][key]["default"]
     model2comps_args["output_filename"] = outname
     model2comps_args["nbasisf"] = nchan
     model2comps_args["fit_mode"] = 'Legendre'
@@ -266,7 +266,7 @@ def test_spotless(ms_name):
     # degrid from coeffs populating MODEL_DATA
     degrid_args = {}
     for key in schema.degrid["inputs"].keys():
-        degrid_args[key] = schema.degrid["inputs"][key]["default"]
+        degrid_args[key.replace("-", "_")] = schema.degrid["inputs"][key]["default"]
     degrid_args["ms"] = str(test_dir / 'test_ascii_1h60.0s.MS')
     degrid_args["mds"] = f'{outname}_I_main_model.mds'
     degrid_args["channels_per_image"] = 1
@@ -284,7 +284,7 @@ def test_spotless(ms_name):
     # gridding CORRECTED_DATA should return identical residuals
     init_args = {}
     for key in schema.init["inputs"].keys():
-        init_args[key] = schema.init["inputs"][key]["default"]
+        init_args[key.replace("-", "_")] = schema.init["inputs"][key]["default"]
     # overwrite defaults
     outname = str(test_dir / 'test2')
     init_args["ms"] = str(test_dir / 'test_ascii_1h60.0s.MS')
@@ -301,7 +301,7 @@ def test_spotless(ms_name):
     # grid data to produce dirty image
     grid_args = {}
     for key in schema.grid["inputs"].keys():
-        grid_args[key] = schema.grid["inputs"][key]["default"]
+        grid_args[key.replace("-", "_")] = schema.grid["inputs"][key]["default"]
     # overwrite defaults
     grid_args["output_filename"] = outname
     grid_args["nband"] = nchan