Add batch and uep plot tests #48

.gitignore

@@ -43,6 +43,7 @@ htmlcov/
 .cache
 nosetests.xml
 coverage.xml
+coverage
 *.cover
 .hypothesis/
 .pytest_cache/

pymuonsuite/muairss.py

@@ -230,14 +230,12 @@ def muairss_batch_io(args, global_params, save=False):
 
     for path in structure_files:
         name = parse_structure_name(path)
-        parameter_file = os.path.join(structures_path, "{}.yaml".format(name))
-        if not os.path.isfile(parameter_file):
-            parameter_file = None
         with silence_stdio():
             struct = io.read(path)
         params = dict(global_params)  # Copy
         params["name"] = name
-        if parameter_file is not None:
+        parameter_file = os.path.join(structures_path, "{}.yaml".format(name))
+        if os.path.isfile(parameter_file):
             params = load_input_file(parameter_file, MuAirssSchema, merge=params)
         params["out_folder"] = params["name"]
 

pymuonsuite/schemas.py

@@ -88,21 +88,22 @@ def validate_save_min(value):
     return isinstance(value, bool)
 
 
-def load_input_file(fname, param_schema, merge=None):
+def load_input_file(fname, param_schema: Schema, merge: dict = None):
     """Load a given input YAML file and validate it with a schema."""
 
     if merge is None:
         with open(fname, "r") as params_file:
             params = yaml.safe_load(params_file)
     else:
         try:
-            param_schema.validate(merge)
+            existing_params = {k: v for k, v in merge.items() if v is not None}
+            param_schema.validate(existing_params)
         except SchemaError as e:
-            message = "Invalid merge params passed to" " load_input_file\n{0}".format(e)
-            raise RuntimeError(message)
+            message = "Invalid merge params passed to load_input_file"
+            raise RuntimeError(message) from e
         with open(fname, "r") as params_file:
             new_params = yaml.safe_load(params_file)
-        params = dict(merge)
+        params = dict(existing_params)
         params.update(new_params)
 
     if params is None:

pymuonsuite/test/test_data/Si2/Si2-muairss-all.yaml

@@ -0,0 +1,16 @@
+poisson_r: 1.0
+name: Si2
+charged: true
+geom_steps: 300
+vdw_scale: 0.25
+calculator: all
+uep_gw_factor: 4.0
+uep_chden: Si2.den_fmt
+geom_force_tol: 0.05
+clustering_method: kmeans
+clustering_kmeans_k: 2
+dftb_set: pbc-0-3
+out_folder: muon-airss-out-all
+castep_param: Si2.param
+script_file: submit.sh
+uep_save_structs: False

pymuonsuite/test/test_data/Si2/batch/Si2.yaml

@@ -0,0 +1,16 @@
+poisson_r: 1.0
+name: Si2
+charged: true
+geom_steps: 300
+vdw_scale: 0.25
+calculator: all
+uep_gw_factor: 4.0
+uep_chden: Si2.den_fmt
+geom_force_tol: 0.05
+clustering_method: kmeans
+clustering_kmeans_k: 2
+dftb_set: pbc-0-3
+out_folder: muon-airss-out-all
+castep_param: Si2.param
+script_file: submit.sh
+uep_save_structs: true

pymuonsuite/test/test_data/Si2/script-dftb

@@ -1,6 +1,5 @@
 #!/bin/bash
-target="muon-airss-out-dftb/dftb+/"
-for folder in "$target"*
+for folder in "$1"/*
 do
 	cd $folder
 	dftb+

pymuonsuite/test/test_data/Si2/script-uep

@@ -1,6 +1,5 @@
 #!/bin/bash
-target=$1
-for folder in "$target"*
+for folder in "$1"/*
 do
 	pm-uep-opt $folder/$(basename $folder).yaml
 done

pymuonsuite/test/test_data/Si2/script-uep-windows.ps1

@@ -1,4 +1,4 @@
-$Target="muon-airss-out-uep/uep"
+$Target=$args[0]
 
 $SubFolders = Get-ChildItem -Path $Target -Directory
 

pymuonsuite/test/test_data/Si8/Si8-invalid-line.yaml

@@ -0,0 +1,2 @@
+chden_seed: Si8
+line_plots: [[0, 1, 5, 0]]

pymuonsuite/test/test_data/Si8/Si8-invalid-plane.yaml

@@ -0,0 +1,2 @@
+chden_seed: Si8
+plane_plots: [[0, 1, 2, 5, 5, 0]]