From cbe4ea2dec7da2e5bfb5f99c9707062b4b216290 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 3 Jul 2024 15:13:56 +0200
Subject: [PATCH] [FIX] ignore 'na' as trial types when creating default models
 (#709)

* ignore na as trial types when creating default models

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* lint

* rm checks perfomed by pre-commit

* fix octave

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 +bids/+internal/list_all_trial_types.m |  6 ++++++
 .github/workflows/validate.yml         | 29 -------------------------
 .pre-commit-config.yaml                |  1 -
 tests/test_bids_model.m                | 30 ++++++++++++++++++++++++--
 4 files changed, 34 insertions(+), 32 deletions(-)

diff --git a/+bids/+internal/list_all_trial_types.m b/+bids/+internal/list_all_trial_types.m
index cfba2bd5..92434e58 100644
--- a/+bids/+internal/list_all_trial_types.m
+++ b/+bids/+internal/list_all_trial_types.m
@@ -111,4 +111,10 @@
     trial_type_list{idx} = [];
   end
 
+  % n/a not included as trial type
+  idx = ismember(trial_type_list, 'n/a');
+  if any(idx)
+    trial_type_list(idx) = [];
+  end
+
 end
diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml
index 7c300a8c..f432ff58 100644
--- a/.github/workflows/validate.yml
+++ b/.github/workflows/validate.yml
@@ -22,12 +22,6 @@ jobs:
       with:
         args: --validate
 
-  codespell:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: codespell-project/actions-codespell@master
-
   markdown_link_check:
     runs-on: ubuntu-latest
     steps:
@@ -37,26 +31,3 @@ jobs:
         use-quiet-mode: yes
         use-verbose-mode: yes
         config-file: .github/workflows/mlc_config.json
-
-  miss_hit:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        command: [mh_style, mh_metric --ci, mh_lint]
-      fail-fast: false
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        submodules: true
-        fetch-depth: 1
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3.11
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools
-        pip3 install -r requirements.txt
-    - name: ${{ matrix.command }}
-      run: |
-        ${{ matrix.command }}
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f1dfb9fd..2f0770f3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -46,4 +46,3 @@ repos:
   rev: v2.3.0
   hooks:
   - id: codespell
-    args: [--config=setup.cfg]
diff --git a/tests/test_bids_model.m b/tests/test_bids_model.m
index 1f987ca3..fd20e23a 100644
--- a/tests/test_bids_model.m
+++ b/tests/test_bids_model.m
@@ -152,8 +152,7 @@ function test_model_basic()
 
 function test_model_default_model()
 
-  pth_bids_example = get_test_data_dir();
-  BIDS = bids.layout(fullfile(pth_bids_example, 'ds003'));
+  BIDS = bids.layout(fullfile(get_test_data_dir(), 'ds003'));
 
   bm = bids.Model();
   bm = bm.default(BIDS);
@@ -167,6 +166,33 @@ function test_model_default_model()
 
 end
 
+function test_model_default_model_with_nan_trial_type()
+
+  bids_tmp = temp_dir();
+  copyfile(fullfile(get_test_data_dir(), 'ds003'), bids_tmp);
+  if bids.internal.is_octave
+    bids_tmp = fullfile(bids_tmp,  'ds003');
+  end
+
+  BIDS = bids.layout(bids_tmp);
+  tsv_files = bids.query(BIDS, 'data', 'suffix', 'events');
+  content = bids.util.tsvread(tsv_files{1});
+  content.trial_type{1} = 'n/a';
+  bids.util.tsvwrite(tsv_files{1}, content);
+
+  BIDS = bids.layout(bids_tmp);
+
+  bm = bids.Model();
+  bm = bm.default(BIDS);
+
+  %   design matrix should not include n/a
+  assertEqual(bm.Nodes{1}.Model.X, ...
+              {'trial_type.pseudoword'
+               'trial_type.word'
+               '1'                    });
+
+end
+
 function test_model_default_no_events()
 
   pth_bids_example = get_test_data_dir();