bugfix: {h5,nc}exists: ensure names exactly match. Improve test coverage

Author: scivision

+hdf5nc/+tests/test_hdf5.m

@@ -1,4 +1,5 @@
 % test our custom high-level HDF5 interface
+import hdf5nc.*
 
 A0 = 42.;
 A1 = [42.; 43.];
@@ -7,37 +8,44 @@
 A3(:,:,2) = 2*A3;
 A4(:,:,:,5) = A3;
 
-basic = [tempname, '.h5'];
+basic = tempname + ".h5";
 % create test data first, so that parallel tests works
-hdf5nc.h5save(basic, '/A0', A0)
-hdf5nc.h5save(basic, '/A1', A1)
-hdf5nc.h5save(basic, '/A2', A2)
-hdf5nc.h5save(basic, '/A3', A3)
-hdf5nc.h5save(basic, '/A4', A4)
+h5save(basic, '/A0', A0)
+h5save(basic, '/A1', A1)
+h5save(basic, '/A2', A2)
+h5save(basic, '/A3', A3)
+h5save(basic, '/A4', A4)
 %% test_auto_chunk_size
-assert(isequal(hdf5nc.auto_chunk_size([1500,2500,1000,500,100]), [12,20,8,8,2]), '5D chunk fail')
-assert(isequal(hdf5nc.auto_chunk_size([15,250,100]), [2,32,25]), '3D chunk fail')
-assert(isequal(hdf5nc.auto_chunk_size([15,250]), [15,250]), '2D small chunk fail')
+assert(isequal(auto_chunk_size([1500,2500,1000,500,100]), [12,20,8,8,2]), '5D chunk fail')
+assert(isequal(auto_chunk_size([15,250,100]), [2,32,25]), '3D chunk fail')
+assert(isequal(auto_chunk_size([15,250]), [15,250]), '2D small chunk fail')
 %% test_get_variables
-vars = hdf5nc.h5variables(basic);
+vars = h5variables(basic);
 assert(isequal(sort(vars),{'A0', 'A1', 'A2', 'A3', 'A4'}), 'missing variables')
 %% test_exists
-assert(hdf5nc.h5exists(basic, '/A3'), 'A3 exists')
-assert(~hdf5nc.h5exists(basic, '/oops'), 'oops not exist')
+e0 = h5exists(basic, '/A3');
+assert(isscalar(e0))
+assert(e0, 'A3 exists')
+
+assert(~h5exists(basic, '/oops'), 'oops not exist')
+
+e1 = h5exists(basic, ["A3", "oops"]);
+assert(isrow(e1))
+assert(all(e1 == [true, false]), 'h5exists array')
 %% test_size
-s = hdf5nc.h5size(basic, '/A0');
+s = h5size(basic, '/A0');
 assert(isscalar(s) && s==1, 'A0 shape')
 
-s = hdf5nc.h5size(basic, '/A1');
+s = h5size(basic, '/A1');
 assert(isscalar(s) && s==2, 'A1 shape')
 
-s = hdf5nc.h5size(basic, '/A2');
+s = h5size(basic, '/A2');
 assert(isvector(s) && isequal(s, [4,4]), 'A2 shape')
 
-s = hdf5nc.h5size(basic, '/A3');
+s = h5size(basic, '/A3');
 assert(isvector(s) && isequal(s, [4,3,2]), 'A3 shape')
 
-s = hdf5nc.h5size(basic, '/A4');
+s = h5size(basic, '/A4');
 assert(isvector(s) && isequal(s, [4,3,2,5]), 'A4 shape')
 %% test_read
 s = h5read(basic, '/A0');
@@ -55,13 +63,13 @@
 s = h5read(basic, '/A4');
 assert(ndims(s)==4 && isequal(s, A4), 'A4 read')
 %% test_coerce
-hdf5nc.h5save(basic, '/int32', A0, [], 'int32')
-hdf5nc.h5save(basic, '/int64', A0, [], 'int64')
-hdf5nc.h5save(basic, '/float32', A0, [], 'float32')
+h5save(basic, '/int32', A0, [], 'int32')
+h5save(basic, '/int64', A0, [], 'int64')
+h5save(basic, '/float32', A0, [], 'float32')
 
 assert(isa(h5read(basic, '/int32'), 'int32'), 'int32')
 assert(isa(h5read(basic, '/int64'), 'int64'), 'int64')
 assert(isa(h5read(basic, '/float32'), 'single'), 'float32')
 %% test_rewrite
-hdf5nc.h5save(basic, '/A2', 3*magic(4))
+h5save(basic, '/A2', 3*magic(4))
 assert(isequal(h5read(basic, '/A2'), 3*magic(4)), 'rewrite 2D fail')

+hdf5nc/+tests/test_netcdf.m

@@ -1,4 +1,5 @@
 % test our custom high-level NetCDF4 interface
+import hdf5nc.*
 
 A0 = 42.;
 A1 = [42.; 43.];
@@ -7,37 +8,41 @@
 A3(:,:,2) = 2*A3;
 A4(:,:,:,5) = A3;
 
-basic = [tempname, '.nc'];
+basic = tempname + ".nc";
 
-if hdf5nc.isoctave
-  pkg('load','netcdf')
-end
 % create test data first, so that parallel tests works
-hdf5nc.ncsave(basic, 'A0', A0)
-hdf5nc.ncsave(basic, 'A1', A1)
-hdf5nc.ncsave(basic, 'A2', A2, {'x2', size(A2,1), 'y2', size(A2,2)})
-hdf5nc.ncsave(basic, 'A3', A3, {'x3', size(A3,1), 'y3', size(A3,2), 'z3', size(A3,3)})
-hdf5nc.ncsave(basic, 'A4', A4, {'x4', size(A4,1), 'y4', size(A4,2), 'z4', size(A4,3), 'w4', size(A4,4)})
+ncsave(basic, 'A0', A0)
+ncsave(basic, 'A1', A1)
+ncsave(basic, 'A2', A2, {'x2', size(A2,1), 'y2', size(A2,2)})
+ncsave(basic, 'A3', A3, {'x3', size(A3,1), 'y3', size(A3,2), 'z3', size(A3,3)})
+ncsave(basic, 'A4', A4, {'x4', size(A4,1), 'y4', size(A4,2), 'z4', size(A4,3), 'w4', size(A4,4)})
 %% test_get_variables
-vars = hdf5nc.ncvariables(basic);
+vars = ncvariables(basic);
 assert(isequal(sort(vars),{'A0', 'A1', 'A2', 'A3', 'A4'}), 'missing variables')
 %% test_exists
-assert(hdf5nc.ncexists(basic, 'A3'), 'A3 exists')
-assert(~hdf5nc.ncexists(basic, 'oops'), 'oops not exist')
+e0 = ncexists(basic, 'A3');
+assert(isscalar(e0))
+assert(e0, 'A3 exists')
+
+assert(~ncexists(basic, '/oops'), 'oops not exist')
+
+e1 = ncexists(basic, ["A3", "oops"]);
+assert(isrow(e1))
+assert(all(e1 == [true, false]), 'ncexists array')
 %% test_size
-s = hdf5nc.ncsize(basic, 'A0');
+s = ncsize(basic, 'A0');
 assert(isscalar(s) && s==1, 'A0 shape')
 
-s = hdf5nc.ncsize(basic, 'A1');
+s = ncsize(basic, 'A1');
 assert(isscalar(s) && s==2, 'A1 shape')
 
-s = hdf5nc.ncsize(basic, 'A2');
+s = ncsize(basic, 'A2');
 assert(isvector(s) && isequal(s, [4,4]), 'A2 shape')
 
-s = hdf5nc.ncsize(basic, 'A3');
+s = ncsize(basic, 'A3');
 assert(isvector(s) && isequal(s, [4,3,2]), 'A3 shape')
 
-s = hdf5nc.ncsize(basic, 'A4');
+s = ncsize(basic, 'A4');
 assert(isvector(s) && isequal(s, [4,3,2,5]), 'A4 shape')
 %% test_read
 s = ncread(basic, '/A0');
@@ -55,13 +60,13 @@
 s = ncread(basic, '/A4');
 assert(ndims(s)==4 && isequal(s, A4), 'A4 read')
 %% test_coerce
-hdf5nc.ncsave(basic, 'int32', A0, [], 'int32')
-hdf5nc.ncsave(basic, 'int64', A0, [], 'int64')
-hdf5nc.ncsave(basic, 'float32', A0, [], 'float32')
+ncsave(basic, 'int32', A0, [], 'int32')
+ncsave(basic, 'int64', A0, [], 'int64')
+ncsave(basic, 'float32', A0, [], 'float32')
 
 assert(isa(ncread(basic, 'int32'), 'int32'), 'int32')
 assert(isa(ncread(basic, 'int64'), 'int64'), 'int64')
 assert(isa(ncread(basic, 'float32'), 'single'), 'float32')
 %% test_rewrite
-hdf5nc.ncsave(basic, 'A2', 3*magic(4))
+ncsave(basic, 'A2', 3*magic(4))
 assert(isequal(ncread(basic, 'A2'), 3*magic(4)), 'rewrite 2D fail')

+hdf5nc/h5exists.m

@@ -4,7 +4,8 @@
 % filename: HDF5 filename
 % varname: name of variable inside HDF5 file
 %
-% exists: boolean
+% exists: boolean (scalar or vector)
+
 arguments
   filename (1,1) string
   varnames (1,:) string
@@ -13,6 +14,6 @@
 i = startsWith(varnames, "/");
 varnames(i) = extractAfter(varnames(i), 1);
 
-exists = contains(varnames, hdf5nc.h5variables(filename));
+exists = ismember(varnames, hdf5nc.h5variables(filename));
 
 end % function

+hdf5nc/h5variables.m

@@ -16,7 +16,7 @@
 
 if group ~= ""
   gs = finf.Groups;
-  i = contains({gs(:).Name}, group);
+  i = string({gs(:).Name}) == group;
   if ~any(i)
     return
   end

+hdf5nc/ncexists.m

@@ -4,12 +4,14 @@
 % filename: NetCDF4 filename
 % varname: name of variable inside file
 %
-% exists: boolean
+% exists: boolean (scalar or vector)
+
 arguments
   filename (1,1) string
   varnames (1,:) string
 end
 
-exists = contains(varnames, hdf5nc.ncvariables(filename));
+% NOT contains because we want exact string match
+exists = ismember(varnames, hdf5nc.ncvariables(filename));
 
 end % function