Refactor varargin to arguments blocks

src/did/+did/+datastructures/emptystruct.m

@@ -19,6 +19,9 @@
     %       end;
     %
     % See also: VAR2STRUCT
+    arguments (Repeating)
+        varargin
+    end
 
     if isempty(varargin)
         s = struct([]);
@@ -37,5 +40,5 @@
         end
         s = s([]);
         %}
-        s = cell2struct(cell(numel(fields),0), fields');
+        s = cell2struct(cell(numel(fields),0), fields(:));
     end

src/did/+did/+file/fileobj.m

@@ -329,20 +329,27 @@ function frewind(fileobj_obj)
             end
         end % fscanf()
 
-        function count = fprintf(fileobj_obj, varargin)
+        function count = fprintf(fileobj_obj, format, varargin)
             % FPRINTF - print data to a FILEOBJ_OBJ
             %
             % [COUNT] = FPRINTF(FID,FORMAT,A, ...)
             %
             % Call FPRINTF (see FPRINTF for inputs) for the file associated with
             % FILEOBJ_OBJ.
+            arguments
+                fileobj_obj
+                format (1,:) char
+            end
+            arguments (Repeating)
+                varargin
+            end
 
             if strcmpi(fileobj_obj.permission,'r')
                 error('DID:File:Fileobj','Cannot use fprintf() method with read-only file');
             end
             count = 0;
             if fileobj_obj.fid >= 0
-                count = fprintf(fileobj_obj.fid,varargin{:});
+                count = fprintf(fileobj_obj.fid,format,varargin{:});
             end
         end % fprintf()
 
@@ -370,4 +377,4 @@ function delete(fileobj_obj)
         end % delete()
     end % methods
 
-end % classdef
+end % classdef

src/did/+did/+file/readonly_fileobj.m

@@ -9,16 +9,23 @@
     % See also: FILEOBJ
 
     methods
-        function fileobj_obj = readonly_fileobj(varargin)
+        function fileobj_obj = readonly_fileobj(options)
             % READONLY_FILEOBJ - create a new read-only binary file object
             %
             % FILEOBJ_OBJ = READONLY_FILEOBJ(...)
             %
             % Creates an empty FILEOBJ object. If FILENAME is provided,
             % then the filename is stored.
+            arguments
+                options.machineformat (1,1) string {did.file.mustBeValidMachineFormat} = 'n'; % native machine format
+                options.permission (1,1) string {did.file.mustBeValidPermission} = "r"
+                options.fid (1,1) int64 = -1
+                options.fullpathfilename = '';
+            end
 
             % Call the super-class constructor
-            fileobj_obj@did.file.fileobj(varargin{:});
+            super_options = namedargs2cell(options);
+            fileobj_obj@did.file.fileobj(super_options{:});
 
             % Ensure that the default 'r' permission was not modified
             if ~strcmpi(fileobj_obj.permission(1),'r')

src/did/+did/+fun/findalldependencies.m

@@ -1,4 +1,4 @@
-function [d] = findalldependencies(DB, visited, varargin)
+function [d] = findalldependencies(DB, visited, docs)
     % FINDALLDEPENDENCIES- find documents that have dependencies on documents that do not exist
     %
     % [D] = FINDALLDEPENDENCIES(DB, VISITED, DOC1, DOC2, ...)
@@ -10,19 +10,27 @@
     %
     % D is always a cell array of DID.DOCUMENT objects (perhaps empty, {}).
     %
+    arguments
+        DB did.database
+        visited cell
+    end
+    arguments (Repeating)
+        docs
+    end
+
 
     d = {};
 
     if isempty(visited)
         visited = {};
     end
 
-    for i=1:numel(varargin)
-        visited = cat(1,visited,{varargin{i}.id()});
+    for i=1:numel(docs)
+        visited = cat(1,visited,{docs{i}.id()});
     end
 
-    for i=1:numel(varargin)
-        q_v = ndi_query('','depends_on','*',varargin{i}.id());
+    for i=1:numel(docs)
+        q_v = ndi_query('','depends_on','*',docs{i}.id());
         bb = DB.database_search(q_v);
 
         for j=1:numel(bb)

src/did/+did/+fun/finddocs_missing_dependencies.m

@@ -1,4 +1,4 @@
-function d = finddocs_missing_dependencies(DB, varargin)
+function d = finddocs_missing_dependencies(DB, names)
     % FINDDOCS_MISSING_DEPENDENCIES - find documents that have dependencies on documents that do not exist
     %
     % D = FINDDOCS_MISSING_DEPENDENCIES(DB)
@@ -14,6 +14,12 @@
     % works similarly except that it only examines variables with depends_on
     % fields with names NAME1, NAME2, etc.
     %
+    arguments
+        DB did.database
+    end
+    arguments (Repeating)
+        names
+    end
 
     documents_observed = {}; % keep track of what we have seen so we don't have to search multiple times
 
@@ -30,7 +36,7 @@
     for i=1:numel(d)
         for j=1:numel(d{i}.document_properties.depends_on)
             if nargin>1
-                match = any(strcmpi(d{i}.document_properties.depends_on(j).name,varargin));
+                match = any(strcmpi(d{i}.document_properties.depends_on(j).name,names));
             else
                 match = 1;
             end

src/did/+did/+fun/plotinteractivedocgraph.m

@@ -1,4 +1,4 @@
-function plotinteractivedocgraph(varargin) %(docs, G, mdigraph, nodes)
+function plotinteractivedocgraph(docs, G, mdigraph, nodes, layout)
     % PLOTINTERACTIVEDOCGRAPH(DOCS, G, MDIGRAPH, NODES, LAYOUT)
     %
     % Given a cell array of NDI_DOCUMENTs DOCS, a connectivity matrix
@@ -23,6 +23,13 @@ function plotinteractivedocgraph(varargin) %(docs, G, mdigraph, nodes)
     %   [G,nodes,mdigraph] = did.fun.docs2graph(docs);
     %   did.fun.plotinteractivedocgraph(docs,G,mdigraph,nodes,'layered');
     %
+    arguments
+        docs cell
+        G
+        mdigraph
+        nodes
+        layout char
+    end
 
     if nargin==0
 
@@ -53,15 +60,13 @@ function plotinteractivedocgraph(varargin) %(docs, G, mdigraph, nodes)
         return;
     end
 
-    layout = varargin{5};
-
     f = figure;
 
     userData = struct();
-    userData.docs =  varargin{1};
-    userData.G = varargin{2};
-    userData.mdigraph = varargin{3};
-    userData.nodes = varargin{4};
+    userData.docs =  docs;
+    userData.G = G;
+    userData.mdigraph = mdigraph;
+    userData.nodes = nodes;
 
     set(f,'userdata',userData);
 

src/did/+did/+implementations/matlabdumbjsondb.m

@@ -6,7 +6,7 @@
 
     methods
 
-        function did_matlabdumbjsondb_obj = matlabdumbjsondb(varargin)
+        function did_matlabdumbjsondb_obj = matlabdumbjsondb(command, path, options)
             % DID_MATLABDUMBJSONDB make a new MATLABDUMBJSONDB object
             %
             % DID_MATLABDUMBJSONDB_OBJ = DID_MATLABDUMBJSONDB(COMMAND, PATHNAME)
@@ -18,13 +18,19 @@
             % should be stored on disk.
             %
             % See also: DUMBJSONDB, DUMBJSONDB/DUMBJSONDB
+            arguments
+                command char
+                path char
+                options.dirname char = 'dumbjsondb'
+                options.unique_object_id_field char = 'base.id'
+            end
             connection = '';
             if nargin>1
-                connection = varargin{2};
+                connection = path;
             end
             did_matlabdumbjsondb_obj = did_matlabdumbjsondb_obj@did.database(connection);
-            did_matlabdumbjsondb_obj.db = did.file.dumbjsondb(varargin{1:end},...
-                'dirname','dumbjsondb','unique_object_id_field','base.id');
+            did_matlabdumbjsondb_obj.db = did.file.dumbjsondb(command, path,...
+                'dirname',options.dirname,'unique_object_id_field',options.unique_object_id_field);
         end % did_matlabdumbjsondb()
     end
 

src/did/+did/+implementations/sqldb.m

@@ -6,7 +6,7 @@
     end
 
     methods % constructor
-        function sqldb_obj = sqldb(varargin)
+        function sqldb_obj = sqldb(command, path)
             % SQLDB create a new SQLDB object
             %
             % SQLDB_OBJ = SQLDB(...)
@@ -17,9 +17,13 @@
             % the full pathname of where the files should be stored on disk.
             %
             % See also: DUMBJSONDB, SQLITEDB, POSTGRESDB
+            arguments
+                command char
+                path char
+            end
             connection = '';
             if nargin>1
-                connection = varargin{2};
+                connection = path;
             end
             sqldb_obj = sqldb_obj@did.database(connection);
         end % sqldb()