Rename readYAML to readYAMLfile

Avoid confusion with the existing readYAMLmodel, which reads cobra-
format model YAMLs specifically. The two functions now form a clear
pair: readYAMLfile for arbitrary YAML documents, readYAMLmodel for
the model schema.

Updates the function name, its docstring + error identifiers, and the
single call site in core/applyCondition.m.

Author: edkerk

core/applyCondition.m

@@ -16,7 +16,7 @@
 %   Inputs:
 %       model       RAVEN model struct.
 %       condition   Either a path to a YAML condition file or a struct
-%                   already produced by readYAML. The expected schema
+%                   already produced by readYAMLfile. The expected schema
 %                   (all keys optional):
 %
 %                       prelude:
@@ -46,10 +46,10 @@
 %       model       Modified model.
 %
 % Usage: model = applyCondition(model, 'data/conditions/anaerobic.yml')
-%        model = applyCondition(model, readYAML('data/conditions/anaerobic.yml'))
+%        model = applyCondition(model, readYAMLfile('data/conditions/anaerobic.yml'))
 
 if ischar(condition) || isstring(condition)
-    cond = readYAML(char(condition));
+    cond = readYAMLfile(char(condition));
 elseif isstruct(condition)
     cond = condition;
 else

io/readYAML.m io/readYAMLfile.mio/readYAML.m renamed to io/readYAMLfile.m

@@ -1,5 +1,5 @@
-function out = readYAML(filename)
-% readYAML
+function out = readYAMLfile(filename)
+% readYAMLfile
 %   Read an arbitrary YAML file into a MATLAB struct / cell tree.
 %
 %   Use this for parsing arbitrary YAML configuration / data files
@@ -27,16 +27,16 @@
 %                       py.bool   -> logical
 %                       py.None   -> []
 %
-% Usage: cfg = readYAML('data/conditions/anaerobic.yml')
+% Usage: cfg = readYAMLfile('data/conditions/anaerobic.yml')
 
 if ~isfile(filename)
-    error('readYAML:fileNotFound', 'File not found: %s', filename);
+    error('readYAMLfile:fileNotFound', 'File not found: %s', filename);
 end
 
 try
     py.importlib.import_module('yaml');
 catch ME
-    error('readYAML:pyyamlMissing', ...
+    error('readYAMLfile:pyyamlMissing', ...
         ['pyyaml is required to read arbitrary YAML files. Install it ' ...
          'in your MATLAB-linked Python environment (`pip install pyyaml`).' ...
          '\nUnderlying error: %s'], ME.message);