[MAINT] Update from main (#606)

* docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] * CI: Use PAT to submit pull requests (#534) This will ensure that actions run on the PR. The default `GITHUB_TOKEN` is not enabled to do that to avoid a possible loop of new PRs with actions. * Bump peter-evans/create-pull-request from 4 to 5 (#536) Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 4 to 5. - [Release notes](https://github.com/peter-evans/create-pull-request/releases) - [Commits](peter-evans/create-pull-request@v4...v5) --- updated-dependencies: - dependency-name: peter-evans/create-pull-request dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#548) * update schema * readd token$ * update ci (#558) * [FIX] remove byte order mark from tsv file (#556) * fix bom * add data * octave fix * Bump matlab-actions/run-command from 1.1.3 to 1.2.0 (#570) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.1.3 to 1.2.0. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.1.3...v1.2.0) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] update schema (#577) * update schema * rm token * docs: add coxroy as a contributor for bug, ideas, and userTesting (#585) * docs: update README.md [skip ci] * docs: update .all-contributorsrc [skip ci] --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> * BIDS schema update (#587) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#592) Co-authored-by: Remi-Gau <[email protected]> * BIDS schema update (#594) Co-authored-by: Remi-Gau <[email protected]> * Bump matlab-actions/run-command from 1.2.0 to 1.2.1 (#602) Bumps [matlab-actions/run-command](https://github.com/matlab-actions/run-command) from 1.2.0 to 1.2.1. - [Release notes](https://github.com/matlab-actions/run-command/releases) - [Commits](matlab-actions/run-command@v1.2.0...v1.2.1) --- updated-dependencies: - dependency-name: matlab-actions/run-command dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [FIX] handle nan and and datetimes when printing tables (#605) * fix bugs in tables and datetimes * skip on windows * update schema --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Chris Markiewicz <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Remi-Gau <[email protected]>
bids-standard · Jul 31, 2023 · d2b1c9c · d2b1c9c
1 parent 3dbfed5
commit d2b1c9c
Show file tree

Hide file tree

Showing 6 changed files with 69 additions and 9 deletions.
diff --git a/+bids/+util/tsvwrite.m b/+bids/+util/tsvwrite.m
@@ -14,11 +14,8 @@ function tsvwrite(filename, var)
   %
   % Based on spm_save.m from SPM12.
   %
-  %
 
   % (C) Copyright 2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
-  %
-
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   delim = sprintf('\t');
@@ -57,6 +54,7 @@ function tsvwrite(filename, var)
         var = num2cell(var);
       end
 
+      var = convert_datetimes(var);
       var = cellfun(@(x) num2str(x, 16), var, 'UniformOutput', false);
       var = strtrim(var);
       var(cellfun(@(x) strcmp(x, 'NaN'), var)) = {'n/a'};
@@ -66,9 +64,10 @@ function tsvwrite(filename, var)
     write_to_file(filename, var, delim);
 
   elseif isa(var, 'table')
-    writetable(var, filename, ...
-               'FileType', 'text', ...
-               'Delimiter', delim);
+    header = var.Properties.VariableNames;
+    var = table2cell(var);
+    var = cat(1, header, var);
+    bids.util.tsvwrite(filename, var);
 
   else
     error('Unknown data type.');
@@ -77,6 +76,17 @@ function tsvwrite(filename, var)
 
 end
 
+function var = convert_datetimes(var)
+  if bids.internal.is_octave
+    return
+  end
+  is_datetime = find(cellfun(@(x) isdatetime(x), var(:)));
+  for i = 1:numel(is_datetime)
+    idx = is_datetime(i);
+    var{idx} = char(var{idx}, 'yyyy-MM-dd''T''HH:mm:ss.SSS'); % bids-compliant datetime
+  end
+end
+
 function write_to_file(filename, var, delim)
 
   fid = fopen(filename, 'Wt');

diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -236,6 +236,17 @@
       "contributions": [
         "bug"
       ]
+    },
+    {
+      "login": "coxroy",
+      "name": "coxroy",
+      "avatar_url": "https://avatars.githubusercontent.com/u/26691793?v=4",
+      "profile": "https://github.com/coxroy",
+      "contributions": [
+        "bug",
+        "ideas",
+        "userTesting"
+      ]
     }
   ],
   "contributorsPerLine": 7,
@@ -244,5 +255,6 @@
   "repoType": "github",
   "repoHost": "https://github.com",
   "skipCi": true,
-  "commitConvention": "angular"
+  "commitConvention": "angular",
+  "commitType": "docs"
 }
diff --git a/.github/workflows/run_tests_matlab.yml b/.github/workflows/run_tests_matlab.yml
@@ -22,9 +22,11 @@ jobs:
         version: [R2021a, R2021b, R2022a, R2022b]
         os: [ubuntu-latest, macos-latest, windows-latest]
 
+
     runs-on: ${{matrix.os}}
 
     steps:
+
     - name: Install MATLAB
       uses: matlab-actions/[email protected]
       with:

diff --git a/README.md b/README.md
@@ -268,6 +268,7 @@ Thanks goes to these wonderful people
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/avanaudenhaege"><img src="https://avatars.githubusercontent.com/u/75271651?v=4?s=100" width="100px;" alt="avanaudenhaege"/><br /><sub><b>avanaudenhaege</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/issues?q=author%3Aavanaudenhaege" title="Bug reports">🐛</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/coxroy"><img src="https://avatars.githubusercontent.com/u/26691793?v=4?s=100" width="100px;" alt="coxroy"/><br /><sub><b>coxroy</b></sub></a><br /><a href="https://github.com/bids-standard/bids-matlab/issues?q=author%3Acoxroy" title="Bug reports">🐛</a> <a href="#ideas-coxroy" title="Ideas, Planning, & Feedback">🤔</a> <a href="#userTesting-coxroy" title="User Testing">📓</a></td>
     </tr>
   </tbody>
 </table>

diff --git a/schema.json b/schema.json
diff --git a/tests/tests_utils/test_tsvwrite.m b/tests/tests_utils/test_tsvwrite.m
@@ -6,6 +6,41 @@
   initTestSuite;
 end
 
+function test_datetime_in_table()
+  % TODO fix line issue on windows
+  if bids.internal.is_octave() || ispc()
+    moxunit_throw_test_skipped_exception('no datetime in Octave and line issue in windows');
+  end
+  x = '201401010000';
+  acq_time = datetime(x, 'InputFormat', 'yyyyMMddHHmm');
+  sub_id = {'foo'};
+  patients = table(sub_id, acq_time);
+  file = fullfile(tempname(), 'foo.tsv');
+  bids.util.mkdir(fileparts(file));
+  bids.util.tsvwrite(file, patients);
+
+  FID = fopen(file, 'r');
+  C = textscan(FID, '%s%s', 'Delimiter', '\t', 'EndOfLine', '\n');
+  assertEqual(C{2}{2}, '2014-01-01T00:00:00.000');
+end
+
+function test_nan_in_table()
+  % TODO fix line issue on windows
+  if bids.internal.is_octave()  || ispc()
+    moxunit_throw_test_skipped_exception('no table in Octave and line issue in windows');
+  end
+  sub_id = {'foo'; 'bar'};
+  age = [25; nan];
+  patients = table(sub_id, age);
+  file = fullfile(tempname(), 'foo.tsv');
+  bids.util.mkdir(fileparts(file));
+  bids.util.tsvwrite(file, patients);
+
+  FID = fopen(file, 'r');
+  C = textscan(FID, '%s%s', 'Delimiter', '\t', 'EndOfLine', '\n');
+  assertEqual(C{2}{3}, 'n/a');
+end
+
 function test_tsvwrite_basic()
 
   pth = fileparts(mfilename('fullpath'));
@@ -67,7 +102,7 @@ function test_tsvwrite_basic()
 
   FID = fopen(tsv_file, 'r');
   C = textscan(FID, '%s%s', 'Delimiter', '\t', 'EndOfLine', '\n');
-  assertEqual(C{1}{2}, 'n/a'); %
+  assertEqual(C{1}{2}, 'n/a');
 
   delete(tsv_file);