[REL] v0.3.0 (#725)

* update changelodg

* use deno validator

* do not validate during tests

* update doc

* update links in changelog

* add release protocol

* fix links

* fix

.github/workflows/run_tests_matlab.yml

@@ -46,9 +46,12 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install unzip wget
 
+    - name: Install Deno
+      uses: denoland/setup-deno@v1
+      with:
+        deno-version: v1.x
     - name: Install bids validator
-      run: npm install -g bids-validator
-
+      run: deno install -Agf -n bids-validator jsr:@bids/validator
 
     - name: Install bids example
       run: |

.github/workflows/run_tests_octave.yml

@@ -40,8 +40,12 @@ jobs:
         sudo apt-get -y -qq update
         sudo apt-get -y install unzip wget
 
+    - name: Install Deno
+      uses: denoland/setup-deno@v1
+      with:
+        deno-version: v1.x
     - name: Install bids validator
-      run: npm install -g bids-validator
+      run: deno install -Agf -n bids-validator jsr:@bids/validator
 
     - name: Install bids-example
       run: |

CITATION.cff

@@ -4,7 +4,7 @@ cff-version: 1.2.0
 
 title: bids-matlab
 
-version: 0.2.0
+version: 0.3.0
 
 license: MIT
 

CONTRIBUTING.md

@@ -413,3 +413,25 @@ make update_schema
 A new version of the schema is fetched automatically regularly via continuous integration
 (see the [github action](.github/workflows/update_schema.yml)) when pushing to the repo
 or opening a pull-request.
+
+## release protocol
+
+- [ ] create a dedicated branch for the release candidate
+- [ ] update version in `citation.cff`
+- [ ] documentation related
+  - [ ] ensure the documentation is up to date
+  - [ ] make sure the doc builds correctly and fix any error
+- [ ] update jupyter books
+- [ ] update binder
+- [ ] update changelog
+  - [ ] change from `[unreleased]` to the version number
+  - [ ] remove unused sections (like `security`)
+- [ ] run `make release`
+- [ ] open a pull request (PR) from this release candidate branch targeting the default branch
+- [ ] fix any remaining failing continuous integration (test, markdown and code linting...)
+- [ ] merge to default branch
+- [ ] create a github tagged release
+- [ ] after release
+  - [ ] set version in `citation.cff` to dev
+  - [ ] update changelog
+    - [ ] add an `[unreleased]` section

Makefile

@@ -1,14 +1,16 @@
- .PHONY: clean manual
+.PHONY: clean manual
+
 clean:
 	rm version.txt
 
 version.txt: clean CITATION.cff
 	grep -w "^version" CITATION.cff | sed "s/version: /v/g" > version.txt
 
-manual:
-	cd docs && sh create_manual.sh
-
 update_schema:
 	wget https://bids-specification.readthedocs.io/en/latest/schema.json -O schema.json
 # get schema from a PR on the spec
 # wget https://bids-specification--1377.org.readthedocs.build/en/1377/schema.json -O schema.json
+
+release: version.txt
+	python docs/generate_doc.py
+	python docs/add_links_to_changelog.py

docs/add_links_to_changelog.py

@@ -0,0 +1,28 @@
+# replace PR numbers and github usernames with links
+from __future__ import annotations
+
+import re
+
+from utils import root_dir
+
+change_log = root_dir() / "docs" / "source" / "changelog.md"
+
+with open(change_log) as f:
+    lines = f.readlines()
+
+with open(change_log, "w") as f:
+    for line in lines:
+        if match := re.search(r" @([a-zA-Z0-9_\-]+)", line):
+            username = match[1]
+            line = line.replace(
+                match[0], f" by [{username}](https://github.com/{username}) "
+            )
+
+        if match := re.search(r"\#([0-9]+)", line):
+            pr_number = match[1]
+            line = line.replace(
+                match[0],
+                f"[{pr_number}](https://github.com/bids-standard/bids-matlab/pull/{pr_number})",
+            )
+
+        f.write(line)

docs/source/dev_doc.rst

@@ -44,8 +44,12 @@ developer documentation
 .. autofunction:: +bids.+internal.keep_file_for_query
 .. _list_all_trial_types:
 .. autofunction:: +bids.+internal.list_all_trial_types
+.. _list_events:
+.. autofunction:: +bids.+internal.list_events
 .. _match_structure_fields:
 .. autofunction:: +bids.+internal.match_structure_fields
+.. _nansum:
+.. autofunction:: +bids.+internal.nansum
 .. _parse_filename:
 .. autofunction:: +bids.+internal.parse_filename
 .. _plot_diagnostic_table:
@@ -54,6 +58,8 @@ developer documentation
 .. autofunction:: +bids.+internal.regexify
 .. _replace_placeholders:
 .. autofunction:: +bids.+internal.replace_placeholders
+.. _resolve_bids_uri:
+.. autofunction:: +bids.+internal.resolve_bids_uri
 .. _return_file_index:
 .. autofunction:: +bids.+internal.return_file_index
 .. _return_file_info:

docs/utils.py

@@ -0,0 +1,8 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+
+def root_dir() -> Path:
+    """Return path to root directory."""
+    return Path(__file__).parent.parent

tests/tests_utils/test_create_participants_tsv.m

@@ -16,15 +16,11 @@ function test_create_participants_tsv_basic()
     bids_path = fullfile(bids_path, 'asl001');
   end
 
-  validate_dataset(bids_path);
-
   output_filename = bids.util.create_participants_tsv(bids_path, 'verbose', false);
 
   participants = bids.util.tsvread(output_filename);
   assertEqual(participants.participant_id, {'sub-Sub103'});
 
-  validate_dataset(bids_path);
-
   delete(output_filename);
 
 end
@@ -34,20 +30,14 @@ function test_create_participants_tsv_already_exist()
   skip_if_octave('mixed-string-concat warning thrown');
 
   bids_path = temp_dir();
-
   copyfile(fullfile(get_test_data_dir(), 'ds210'), bids_path);
-
   if bids.internal.is_octave
     bids_path = fullfile(bids_path, 'ds210');
   end
 
   output_filename = bids.util.create_participants_tsv(bids_path);
 
-  validate_dataset(bids_path);
-
   assertWarning(@()bids.util.create_participants_tsv(bids_path, 'verbose', true), ...
                 'create_participants_tsv:participantFileExist');
 
-  delete(output_filename);
-
 end

tests/tests_utils/test_create_readme.m

@@ -8,20 +8,21 @@
 
 function test_create_readme_basic()
 
-  bids_path = fullfile(get_test_data_dir(), 'ds210');
-
-  validate_dataset(bids_path);
+  source_ds = fullfile(get_test_data_dir(), 'ds210');
+  tmp_path = temp_dir();
+  copyfile(source_ds, tmp_path);
+  if bids.internal.is_octave()
+    bids_path = fullfile(tmp_path, 'ds210');
+  else
+    bids_path = tmp_path;
+  end
 
   bids.util.create_readme(bids_path, false, ...
                           'tolerant', true, ...
                           'verbose', false);
 
   assertEqual(exist(fullfile(bids_path, 'README.md'), 'file'), 2);
 
-  validate_dataset(bids_path);
-
-  delete(fullfile(bids_path, 'README.md'));
-
 end
 
 function test_create_readme_warning_already_present()

tests/tests_utils/test_create_scans_tsv.m

@@ -17,17 +17,13 @@ function test_create_scans_tsv_basic_no_session()
     bids_path = tmp_path;
   end
 
-  validate_dataset(bids_path);
-
   output_filenames = bids.util.create_scans_tsv(bids_path, 'verbose', false);
 
   assertEqual(numel(output_filenames), 1);
   assertEqual(exist(fullfile(bids_path, output_filenames{1}), 'file'), 2);
   content = bids.util.tsvread(fullfile(bids_path, output_filenames{1}));
   assertEqual(fieldnames(content), {'filename'; 'acq_time'; 'comments'});
 
-  validate_dataset(bids_path);
-
 end
 
 function test_create_scans_tsv_basic()
@@ -41,15 +37,11 @@ function test_create_scans_tsv_basic()
     bids_path = tmp_path;
   end
 
-  validate_dataset(bids_path);
-
   output_filenames = bids.util.create_scans_tsv(bids_path, 'verbose', false);
 
   assertEqual(numel(output_filenames), 28);
   assertEqual(exist(fullfile(bids_path, output_filenames{1}), 'file'), 2);
   content = bids.util.tsvread(fullfile(bids_path, output_filenames{1}));
   assertEqual(fieldnames(content), {'filename'; 'acq_time'; 'comments'});
 
-  validate_dataset(bids_path);
-
 end

tests/tests_utils/test_create_sessions_tsv.m

@@ -16,14 +16,10 @@ function test_create_sessions_tsv_no_session()
     bids_path = fullfile(bids_path, 'ds210');
   end
 
-  validate_dataset(bids_path);
-
   output_filenames = bids.util.create_sessions_tsv(bids_path, 'verbose', false);
 
   assert(isempty(output_filenames));
 
-  validate_dataset(bids_path);
-
   skip_if_octave('mixed-string-concat warning thrown');
 
   assertWarning(@() bids.util.create_sessions_tsv(bids_path, 'verbose', true), ...
@@ -35,21 +31,21 @@ function test_create_sessions_tsv_basic()
 
   bids_path = temp_dir();
 
-  copyfile(fullfile(get_test_data_dir(), 'ieeg_epilepsy'), bids_path);
+  copyfile(fullfile(get_test_data_dir(), 'synthetic'), bids_path);
 
   if bids.internal.is_octave
-    bids_path = fullfile(bids_path, 'ieeg_epilepsy');
+    bids_path = fullfile(bids_path, 'synthetic');
   end
 
   validate_dataset(bids_path);
 
   output_filenames = bids.util.create_sessions_tsv(bids_path, 'verbose', false);
 
-  assertEqual(numel(output_filenames), 1);
+  assertEqual(numel(output_filenames), 5);
   assertEqual(exist(fullfile(bids_path, output_filenames{1}), 'file'), 2);
   content = bids.util.tsvread(fullfile(bids_path, output_filenames{1}));
   assertEqual(fieldnames(content), {'session_id'; 'acq_time'; 'comments'});
-  assertEqual(content.session_id, {'ses-postimp'; 'ses-preimp'});
+  assertEqual(content.session_id, {'ses-01'; 'ses-02'});
 
   validate_dataset(bids_path);
 

tests/utils/validate_dataset.m

@@ -1,10 +1,6 @@
 function validate_dataset(bids_path)
 
-  if ispc
-    return
-  end
-
-  [sts, msg] = bids.validate(bids_path,  '--config.ignore=99 --ignoreNiftiHeaders');
+  [sts, msg] = bids.validate(bids_path,  '--ignoreNiftiHeaders');
   assert(sts == 0, msg);
 
 end

version.txt

@@ -1 +1 @@
-v0.2.0
+v0.3.0