use Matlab package layout for robustness

scivision · scivision · commit 2af657aa615f · 2020-08-14T12:23:35.000-04:00
diff --git a/+hdf5nc/+tests/test_hdf5.m b/+hdf5nc/+tests/test_hdf5.m
@@ -8,36 +8,36 @@
 A4(:,:,:,5) = A3;
 
 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)
 %% test_auto_chunk_size
-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_write_basic
-h5save(basic, '/A0', A0)
-h5save(basic, '/A1', A1)
-h5save(basic, '/A2', A2)
-h5save(basic, '/A3', A3)
-h5save(basic, '/A4', A4)
+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')
 %% test_get_variables
-vars = h5variables(basic);
+vars = hdf5nc.h5variables(basic);
 assert(isequal(sort(vars),{'A0', 'A1', 'A2', 'A3', 'A4'}), 'missing variables')
 %% test_exists
-assert(h5exists(basic, '/A3'), 'A3 exists')
-assert(~h5exists(basic, '/oops'), 'oops not exist')
+assert(hdf5nc.h5exists(basic, '/A3'), 'A3 exists')
+assert(~hdf5nc.h5exists(basic, '/oops'), 'oops not exist')
 %% test_size
-s = h5size(basic, '/A0');
+s = hdf5nc.h5size(basic, '/A0');
 assert(isscalar(s) && s==1, 'A0 shape')
 
-s = h5size(basic, '/A1');
+s = hdf5nc.h5size(basic, '/A1');
 assert(isscalar(s) && s==2, 'A1 shape')
 
-s = h5size(basic, '/A2');
+s = hdf5nc.h5size(basic, '/A2');
 assert(isvector(s) && isequal(s, [4,4]), 'A2 shape')
 
-s = h5size(basic, '/A3');
+s = hdf5nc.h5size(basic, '/A3');
 assert(isvector(s) && isequal(s, [4,3,2]), 'A3 shape')
 
-s = h5size(basic, '/A4');
+s = hdf5nc.h5size(basic, '/A4');
 assert(isvector(s) && isequal(s, [4,3,2,5]), 'A4 shape')
 %% test_read
 s = h5read(basic, '/A0');
@@ -55,13 +55,13 @@
 s = h5read(basic, '/A4');
 assert(ndims(s)==4 && isequal(s, A4), 'A4 read')
 %% test_coerce
-h5save(basic, '/int32', A0, [], 'int32')
-h5save(basic, '/int64', A0, [], 'int64')
-h5save(basic, '/float32', A0, [], 'float32')
+hdf5nc.h5save(basic, '/int32', A0, [], 'int32')
+hdf5nc.h5save(basic, '/int64', A0, [], 'int64')
+hdf5nc.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
-h5save(basic, '/A2', 3*magic(4))
+hdf5nc.h5save(basic, '/A2', 3*magic(4))
 assert(isequal(h5read(basic, '/A2'), 3*magic(4)), 'rewrite 2D fail')
diff --git a/+hdf5nc/+tests/test_netcdf.m b/+hdf5nc/+tests/test_netcdf.m
@@ -9,35 +9,35 @@
 
 basic = [tempname, '.nc'];
 
-if isoctave
+if hdf5nc.isoctave
   pkg('load','netcdf')
 end
-%% test_write_basic
-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)})
+% 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)})
 %% test_get_variables
-vars = ncvariables(basic);
+vars = hdf5nc.ncvariables(basic);
 assert(isequal(sort(vars),{'A0', 'A1', 'A2', 'A3', 'A4'}), 'missing variables')
 %% test_exists
-assert(ncexists(basic, 'A3'), 'A3 exists')
-assert(~ncexists(basic, 'oops'), 'oops not exist')
+assert(hdf5nc.ncexists(basic, 'A3'), 'A3 exists')
+assert(~hdf5nc.ncexists(basic, 'oops'), 'oops not exist')
 %% test_size
-s = ncsize(basic, 'A0');
+s = hdf5nc.ncsize(basic, 'A0');
 assert(isscalar(s) && s==1, 'A0 shape')
 
-s = ncsize(basic, 'A1');
+s = hdf5nc.ncsize(basic, 'A1');
 assert(isscalar(s) && s==2, 'A1 shape')
 
-s = ncsize(basic, 'A2');
+s = hdf5nc.ncsize(basic, 'A2');
 assert(isvector(s) && isequal(s, [4,4]), 'A2 shape')
 
-s = ncsize(basic, 'A3');
+s = hdf5nc.ncsize(basic, 'A3');
 assert(isvector(s) && isequal(s, [4,3,2]), 'A3 shape')
 
-s = ncsize(basic, 'A4');
+s = hdf5nc.ncsize(basic, 'A4');
 assert(isvector(s) && isequal(s, [4,3,2,5]), 'A4 shape')
 %% test_read
 s = ncread(basic, '/A0');
@@ -55,13 +55,13 @@
 s = ncread(basic, '/A4');
 assert(ndims(s)==4 && isequal(s, A4), 'A4 read')
 %% test_coerce
-ncsave(basic, 'int32', A0, [], 'int32')
-ncsave(basic, 'int64', A0, [], 'int64')
-ncsave(basic, 'float32', A0, [], 'float32')
+hdf5nc.ncsave(basic, 'int32', A0, [], 'int32')
+hdf5nc.ncsave(basic, 'int64', A0, [], 'int64')
+hdf5nc.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
-ncsave(basic, 'A2', 3*magic(4))
+hdf5nc.ncsave(basic, 'A2', 3*magic(4))
 assert(isequal(ncread(basic, 'A2'), 3*magic(4)), 'rewrite 2D fail')
diff --git a/+hdf5nc/auto_chunk_size.m b/+hdf5nc/auto_chunk_size.m
diff --git a/+hdf5nc/coerce_ds.m b/+hdf5nc/coerce_ds.m
diff --git a/+hdf5nc/expanduser.m b/+hdf5nc/expanduser.m
@@ -1,4 +1,3 @@
-%!assert(ischar(expanduser('~')))
 function expanded = expanduser(p)
 % expanded = expanduser(path)
 %
@@ -27,14 +26,8 @@
   return
 end
 
-validateattributes(p, {'char'}, {'vector'})
-%% GNU Octave
-if isoctave
-  expanded = tilde_expand(p);
-  return
-end
+validateattributes(p, {'char'}, {'vector'}, 1)
 
-%% Matlab
 expanded = p;
 
 if strcmp(expanded(1), '~')
diff --git a/+hdf5nc/h5exists.m b/+hdf5nc/h5exists.m
@@ -10,6 +10,6 @@
 validateattributes(filename, {'char'}, {'vector'}, 1)
 validateattributes(varname, {'char'}, {'vector'}, 2)
 
-exists = any(strcmp(h5variables(filename), varname(2:end)));
+exists = any(strcmp(hdf5nc.h5variables(filename), varname(2:end)));
 
 end % function
diff --git a/+hdf5nc/h5save.m b/+hdf5nc/h5save.m
@@ -5,8 +5,7 @@ function h5save(filename, varname, A, sizeA, dtype)
 
 narginchk(3, 5)
 
-% Matlab can't cope with tilde in many cases, especially on Windows
-filename = expanduser(filename);
+filename = hdf5nc.expanduser(filename);
 
 if nargin < 4 || isempty(sizeA)
   if isvector(A)
@@ -17,14 +16,14 @@ function h5save(filename, varname, A, sizeA, dtype)
 end
 
 if nargin >= 5 && ~isempty(dtype)
-  A = coerce_ds(A, dtype);
+  A = hdf5nc.coerce_ds(A, dtype);
 end
 if ischar(A)
   A = string(A);
   sizeA = size(A);
 end
 
-if isfile(filename) && h5exists(filename, varname)
+if isfile(filename) && hdf5nc.h5exists(filename, varname)
   exist_file(filename, varname, A, sizeA)
 else
   new_file(filename, varname, A, sizeA)
@@ -34,9 +33,10 @@ function h5save(filename, varname, A, sizeA, dtype)
 
 
 function exist_file(filename, varname, A, sizeA)
+
 narginchk(4,4)
 
-diskshape = h5size(filename, varname);
+diskshape = hdf5nc.h5size(filename, varname);
 if length(diskshape) >= 2
   % start is always a row vector, regardless of shape of array
   start = ones(1,ndims(A));
@@ -69,7 +69,8 @@ function new_file(filename, varname, A, sizeA)
   % enable Gzip compression--remember Matlab's dim order is flipped from
   % C / Python
   h5create(filename, varname, sizeA, 'DataType', class(A), ...
-    'Deflate', 1, 'Fletcher32', true, 'Shuffle', true, 'ChunkSize', auto_chunk_size(sizeA))
+    'Deflate', 1, 'Fletcher32', true, 'Shuffle', true, ...
+    'ChunkSize', hdf5nc.auto_chunk_size(sizeA))
 end % if
 
 h5write(filename, varname, A)
diff --git a/+hdf5nc/h5size.m b/+hdf5nc/h5size.m
@@ -10,7 +10,7 @@
 validateattributes(filename, {'char'}, {'vector'}, 1)
 validateattributes(variable, {'char'}, {'vector'}, 2)
 
-finf = h5info(expanduser(filename), variable);
+finf = h5info(hdf5nc.expanduser(filename), variable);
 fsize = finf.Dataspace.Size;
 
 end % function
diff --git a/+hdf5nc/h5variables.m b/+hdf5nc/h5variables.m
@@ -1,12 +1,13 @@
 function [names, groups] = h5variables(filename, group)
 % get dataset names and groups in an HDF5 file
+
 narginchk(1,2)
 
 names = [];
 groups = [];
 
 % use temporary variable to be R2017b OK
-finf = h5info(expanduser(filename));
+finf = h5info(hdf5nc.expanduser(filename));
 ds = finf.Datasets;
 if isempty(ds)
   return
diff --git a/+hdf5nc/isoctave.m b/+hdf5nc/isoctave.m
diff --git a/+hdf5nc/ncexists.m b/+hdf5nc/ncexists.m
@@ -10,6 +10,6 @@
 validateattributes(filename, {'char'}, {'vector'}, 1)
 validateattributes(varname, {'char'}, {'vector'}, 2)
 
-exists = any(strcmp(ncvariables(filename), varname));
+exists = any(strcmp(hdf5nc.ncvariables(filename), varname));
 
 end % function
diff --git a/+hdf5nc/ncsave.m b/+hdf5nc/ncsave.m
@@ -2,7 +2,7 @@ function ncsave(filename, varname, A, ncdims, dtype)
 
 narginchk(3, 5)
 
-filename = expanduser(filename);
+filename = hdf5nc.expanduser(filename);
 
 if nargin >= 4 && ~isempty(ncdims)
   for i = 2:2:length(ncdims)
@@ -29,11 +29,11 @@ function ncsave(filename, varname, A, ncdims, dtype)
 end
 % coerce if needed
 if nargin >= 5 && ~isempty(dtype)
-  A = coerce_ds(A, dtype);
+  A = hdf5nc.coerce_ds(A, dtype);
 end
 
 
-if isfile(filename) && ncexists(filename, varname)
+if isfile(filename) && hdf5nc.ncexists(filename, varname)
   exist_file(filename, varname, A, sizeA)
 else
   new_file(filename, varname, A, sizeA, ncdims)
@@ -43,9 +43,10 @@ function ncsave(filename, varname, A, ncdims, dtype)
 
 
 function exist_file(filename, varname, A, sizeA)
+
 narginchk(4,4)
 
-diskshape = ncsize(filename, varname);
+diskshape = hdf5nc.ncsize(filename, varname);
 
 if all(diskshape == sizeA)
   ncwrite(filename, varname, A)
@@ -59,6 +60,7 @@ function exist_file(filename, varname, A, sizeA)
 
 
 function new_file(filename, varname, A, sizeA, ncdims)
+
 narginchk(5,5)
 
 folder = fileparts(filename);
@@ -75,7 +77,9 @@ function new_file(filename, varname, A, sizeA, ncdims)
   % "Datatype" to be Octave case-sensitive keyword compatible
   nccreate(filename, varname, 'Dimensions', ncdims, ...
     'Datatype', class(A), ...
-    'DeflateLevel', 1, 'Shuffle', true, 'ChunkSize', auto_chunk_size(sizeA), 'Format', 'netcdf4')
+    'DeflateLevel', 1, 'Shuffle', true, ...
+    'ChunkSize', hdf5nc.auto_chunk_size(sizeA), ...
+    'Format', 'netcdf4')
 end
 
 ncwrite(filename, varname, A)
diff --git a/+hdf5nc/ncsize.m b/+hdf5nc/ncsize.m
@@ -10,7 +10,7 @@
 validateattributes(filename, {'char'}, {'vector'}, 1)
 validateattributes(varname, {'char'}, {'vector'}, 2)
 
-vinf = ncinfo(expanduser(filename), varname);
+vinf = ncinfo(hdf5nc.expanduser(filename), varname);
 fsize = vinf.Size;
 
 % Octave compatibility
diff --git a/+hdf5nc/ncvariables.m b/+hdf5nc/ncvariables.m
@@ -3,7 +3,7 @@
 narginchk(1,1)
 
 % use temporary variable to be R2017b OK
-finf = ncinfo(expanduser(filename));
+finf = ncinfo(hdf5nc.expanduser(filename));
 ds = finf.Variables(:);
 names = {ds(:).Name};
 
diff --git a/codemeta.json b/codemeta.json
@@ -0,0 +1,30 @@
+{
+    "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+    "@type": "SoftwareSourceCode",
+    "license": "https://spdx.org/licenses/BSD-3-Clause",
+    "codeRepository": "https://github.com/geospace-code/matlab-hdf5",
+    "contIntegration": "https://github.com/geospace-code/matlab-hdf5/actions",
+    "dateModified": "2020-08-14",
+    "downloadUrl": "https://github.com/geospace-code/matlab-hdf5/releases",
+    "issueTracker": "https://github.com/geospace-code/matlab-hdf5/issues",
+    "name": "matlab-hdf5",
+    "version": "2.0.0",
+    "identifier": "10.5281/zenodo.3964541",
+    "description": "HDF5 / NetCDF4 functions that should be included in Matlab.",
+    "applicationCategory": "compuation",
+    "developmentStatus": "active",
+    "keywords": [
+        "hdf5", "netcdf4"
+    ],
+    "programmingLanguage": [
+        "Matlab"
+    ],
+    "author": [
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0002-1637-6526",
+            "givenName": "Michael",
+            "familyName": "Hirsch"
+        }
+    ]
+}
diff --git a/test_hdf5nc.m b/test_hdf5nc.m
@@ -0,0 +1,3 @@
+% unit test
+suite = matlab.unittest.TestSuite.fromPackage('hdf5nc.tests');
+run(suite);
