From e75aff86ee74509d53ca1690070ce9ae2f7c83f1 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 29 Apr 2023 17:55:31 +0200
Subject: [PATCH 01/22] split octave and matlab tests

---
 .github/workflows/tests_matlab.yml            | 142 ++++++++++++++++++
 .../workflows/{tests.yml => tests_octave.yml} |  40 +----
 2 files changed, 150 insertions(+), 32 deletions(-)
 create mode 100644 .github/workflows/tests_matlab.yml
 rename .github/workflows/{tests.yml => tests_octave.yml} (74%)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
new file mode 100644
index 00000000..76fc0abf
--- /dev/null
+++ b/.github/workflows/tests_matlab.yml
@@ -0,0 +1,142 @@
+---
+name: tests matlab
+
+# Uses the cron schedule for github actions
+#
+# https://docs.github.com/en/free-pro-team@latest/actions/reference/events-that-trigger-workflows#scheduled-events
+#
+# ┌───────────── minute (0 - 59)
+# │ ┌───────────── hour (0 - 23)
+# │ │ ┌───────────── day of the month (1 - 31)
+# │ │ │ ┌───────────── month (1 - 12 or JAN-DEC)
+# │ │ │ │ ┌───────────── day of the week (0 - 6 or SUN-SAT)
+# │ │ │ │ │
+# │ │ │ │ │
+# │ │ │ │ │
+# * * * * *
+
+env:
+  OCTFLAGS: --no-gui --no-window-system --silent
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches: ['*']
+  pull_request:
+    branches: ['*']
+  schedule:
+  - cron: 0 0 1,15 * *
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+
+  test:
+
+    if: github.repository_owner == 'cpp-lln-lab'
+
+    strategy:
+      matrix:
+        test_type: [system]
+        script: [moae, facerep, fmriprep]
+        version: [R2022a, R2022b]
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        include:
+        - test_type: unit
+          platform: matlab
+      fail-fast: false
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+
+    - name: ${{ matrix.test_type }} test
+      if: matrix.test_type == 'system'
+      run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
+
+    - name: Install dependencies
+      run: |
+        sudo apt-get -y -qq update
+        sudo apt-get -y install unzip wget
+
+    - name: Install Node
+      uses: actions/setup-node@v3
+      with:
+        node-version: 18
+
+    - name: Install python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+
+    - name: Clone bidspm
+      uses: actions/checkout@v3
+      with:
+        submodules: recursive
+        fetch-depth: 0
+
+    - name: Install validators
+      run: make install
+
+    - name: Install SPM
+      run: |
+        git clone https://github.com/spm/spm12.git --depth 1
+
+    - name: Copy Macs toolbox to SPM inputs_folder
+      run: cp -rv lib/MACS spm12/toolbox/MACS
+
+    - name: Get moae fmriprep data from OSF
+      run: |
+        mkdir -p demos/MoAE/inputs/
+        cd demos/MoAE/inputs/
+        wget https://osf.io/vufjs/download
+        unzip download
+        mv moae_fmriprep fmriprep
+
+    - name: Prepare test data
+      run: |
+        cd tests
+        make data
+
+    - name: Install Moxunit and MOcov
+      run: |
+        git clone https://github.com/MOxUnit/MOxUnit.git --depth 1
+        git clone https://github.com/MOcov/MOcov.git --depth 1
+
+    - name: Install MATLAB
+      uses: matlab-actions/setup-matlab@v1.2.4
+      with:
+          # MATLAB release to set up R2020a
+        release: ${{matrix.version}}
+
+    - name: Run unit tests MATLAB
+      if: matrix.test_type == 'unit'
+      uses: matlab-actions/run-command@v1.1.3
+      with:
+        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
+
+    - name: Check unit tests
+      if: matrix.test_type == 'unit'
+      run: |
+        cat test_report.log | grep 0
+
+    - name: Code coverage matlab
+      if: matrix.test_type == 'unit'
+      uses: codecov/codecov-action@v3
+      with:
+        file: coverage.xml
+        flags: matlab
+        name: codecov-matlab
+        fail_ci_if_error: false
+      # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
+
+
+    - name: Run system tests MATLAB ${{ matrix.script }}
+      if: matrix.test_type == 'system'
+      uses: matlab-actions/run-command@v1.1.3
+      with:
+        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests_octave.yml
similarity index 74%
rename from .github/workflows/tests.yml
rename to .github/workflows/tests_octave.yml
index c2c0bf1e..3ebd6688 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests_octave.yml
@@ -1,5 +1,5 @@
 ---
-name: tests
+name: tests octave
 
 # Uses the cron schedule for github actions
 #
@@ -43,21 +43,17 @@ jobs:
 
     strategy:
       matrix:
-        platform: [matlab, octave]
         test_type: [system]
         script: [moae, facerep, fmriprep]
         include:
         - test_type: unit
-          platform: matlab
-        - test_type: unit
-          platform: octave
       fail-fast: false
 
     steps:
 
-    - name: ${{ matrix.platform }} - ${{ matrix.test_type }} test
+    - name: ${{ matrix.test_type }} test
       if: matrix.test_type == 'system'
-      run: echo ${{ matrix.platform }} ${{ matrix.test_type }} test ${{ matrix.script }}
+      run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
 
     - name: Install dependencies
       run: |
@@ -109,7 +105,6 @@ jobs:
         git clone https://github.com/MOcov/MOcov.git --depth 1
 
     - name: Install octave
-      if: matrix.platform == 'octave'
       run: |
         sudo apt-get -y -qq update
         sudo apt-get -y install \
@@ -124,7 +119,6 @@ jobs:
         make -C MOcov install
 
     - name: Compile SPM
-      if: matrix.platform == 'octave'
       run: |
         make -C spm12/src PLATFORM=octave distclean
         make -C spm12/src PLATFORM=octave
@@ -132,48 +126,30 @@ jobs:
         octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'spm12')); savepath();"
 
     - name: Run unit tests Octave
-      if: matrix.platform == 'octave' && matrix.test_type == 'unit'
+      if: matrix.test_type == 'unit'
       run: |
         octave $OCTFLAGS --eval "addpath(fullfile(pwd, 'tests', 'utils')); savepath();"
         octave $OCTFLAGS --eval "bidspm(); cd demos/MoAE; download_moae_ds(true);"
         cd .github/workflows
         octave $OCTFLAGS --eval "tests_octave;"
 
-    - name: Install MATLAB
-      if: matrix.platform == 'matlab'
-      uses: matlab-actions/setup-matlab@v1.2.4
-      with:
-        release: R2020a
-
-    - name: Run unit tests MATLAB
-      if: matrix.platform == 'matlab' && matrix.test_type == 'unit'
-      uses: matlab-actions/run-command@v1.1.3
-      with:
-        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
-
     - name: Check unit tests
       if: matrix.test_type == 'unit'
       run: |
         cat test_report.log | grep 0
 
-    - name: Code coverage ${{ matrix.platform }}
+    - name: Code coverage
       if: matrix.test_type == 'unit'
       uses: codecov/codecov-action@v3
       with:
         file: coverage.xml
-        flags: ${{ matrix.platform }}
-        name: codecov-${{ matrix.platform }}
+        flags: octave
+        name: codecov-octave
         fail_ci_if_error: false
       # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
 
     - name: Run system tests octave ${{ matrix.script }}
-      if: matrix.platform == 'octave' && matrix.test_type == 'system'
+      if: matrix.test_type == 'system'
       run: |
         cd /home/runner/work/bidspm/bidspm/.github/workflows
         octave $OCTFLAGS --eval "run system_tests_${{ matrix.script }};"
-
-    - name: Run system tests MATLAB ${{ matrix.script }}
-      if: matrix.platform == 'matlab' && matrix.test_type == 'system'
-      uses: matlab-actions/run-command@v1.1.3
-      with:
-        command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run system_tests_${{ matrix.script }};

From e69c478315323b9988f39d9bbaaaac49ce57b8fe Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 29 Apr 2023 18:29:44 +0200
Subject: [PATCH 02/22] FCI

---
 .github/workflows/tests_matlab.yml | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index 76fc0abf..b2c392ac 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -15,9 +15,6 @@ name: tests matlab
 # │ │ │ │ │
 # * * * * *
 
-env:
-  OCTFLAGS: --no-gui --no-window-system --silent
-
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -43,11 +40,14 @@ jobs:
       matrix:
         test_type: [system]
         script: [moae, facerep, fmriprep]
-        version: [R2022a, R2022b]
         os: [ubuntu-latest, macos-latest, windows-latest]
         include:
         - test_type: unit
-          platform: matlab
+          os: ubuntu-latest
+        - test_type: unit
+          os: macos-latest
+        - test_type: unit
+          os: windows-latest
       fail-fast: false
 
     runs-on: ${{ matrix.os }}
@@ -110,8 +110,7 @@ jobs:
     - name: Install MATLAB
       uses: matlab-actions/setup-matlab@v1.2.4
       with:
-          # MATLAB release to set up R2020a
-        release: ${{matrix.version}}
+        release: R2022b
 
     - name: Run unit tests MATLAB
       if: matrix.test_type == 'unit'

From 0cd98d2c23b4fdaac470f77ee0912de809a54fcf Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 1 May 2023 22:42:54 +0200
Subject: [PATCH 03/22] [DATALAD] Recorded changes

---
 .github/workflows/tests_matlab.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index b2c392ac..46e5180d 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -59,6 +59,7 @@ jobs:
       run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
 
     - name: Install dependencies
+      if: matrix.os == ubuntu-latest
       run: |
         sudo apt-get -y -qq update
         sudo apt-get -y install unzip wget

From 3987b46979ee9d63380ee3d7b815f0d5f334291d Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 3 May 2023 09:41:21 +0200
Subject: [PATCH 04/22] update submodules

---
 .github/workflows/validation.yml | 6 ------
 lib/CPP_ROI                      | 2 +-
 lib/octache                      | 2 +-
 lib/spm_2_bids                   | 2 +-
 4 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 633148a1..674cba9d 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -31,9 +31,3 @@ jobs:
         use-quiet-mode: yes
         use-verbose-mode: yes
         config-file: .github/workflows/mlc_config.json
-
-  codespell:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v3
-    - uses: codespell-project/actions-codespell@master
diff --git a/lib/CPP_ROI b/lib/CPP_ROI
index 364a9ff1..ba75ffb4 160000
--- a/lib/CPP_ROI
+++ b/lib/CPP_ROI
@@ -1 +1 @@
-Subproject commit 364a9ff139b5380d6326ba8808f90bf0f98fb4b7
+Subproject commit ba75ffb42242a061bbe43c29fc5ebecaccfa9c4e
diff --git a/lib/octache b/lib/octache
index fe1564a0..12eca8da 160000
--- a/lib/octache
+++ b/lib/octache
@@ -1 +1 @@
-Subproject commit fe1564a0fc8e6a8ead09707ff436fc62c8719bdf
+Subproject commit 12eca8da76633aae6b547ca399c60ed984bd3b4c
diff --git a/lib/spm_2_bids b/lib/spm_2_bids
index 41a863c8..a1ca105b 160000
--- a/lib/spm_2_bids
+++ b/lib/spm_2_bids
@@ -1 +1 @@
-Subproject commit 41a863c8a725073a43af31f31c027137ec190af4
+Subproject commit a1ca105b6fab5917a3c210374db4e0d38250fd17

From 15086fa51fd75aac6cd79ef5930ba13c57e16dfd Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Wed, 3 May 2023 09:49:51 +0200
Subject: [PATCH 05/22] skip coverage on windows

---
 .github/workflows/tests_matlab.yml | 13 +++++++++----
 bidspm.m                           | 15 ++++++++++-----
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index 46e5180d..2e3f8676 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -120,16 +120,21 @@ jobs:
         command: cd(fullfile(getenv('GITHUB_WORKSPACE'), '.github', 'workflows')); run tests_matlab;
 
     - name: Check unit tests
-      if: matrix.test_type == 'unit'
+      if: matrix.test_type == 'unit' && ( matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' )
+      run: grep -q 0 test_report.log || { echo "Some tests failed. Check the 'Run tests' step to know which ones." >&2; exit 1; }
+    - name: Check logs windows
+      if: matrix.test_type == 'unit' && matrix.os == 'windows-latest'
       run: |
-        cat test_report.log | grep 0
+        if (-not (Get-Content test_report.log | Select-String -Pattern "0")) {
+          throw "Some tests failed.  Check the 'Run tests' step to know which ones."
+        }
 
     - name: Code coverage matlab
-      if: matrix.test_type == 'unit'
+      if: matrix.test_type == 'unit' && ( matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' )
       uses: codecov/codecov-action@v3
       with:
         file: coverage.xml
-        flags: matlab
+        flags: ${{ matrix.os }}_matlab-${{ matrix.version }}
         name: codecov-matlab
         fail_ci_if_error: false
       # token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
diff --git a/bidspm.m b/bidspm.m
index a7669700..6c47d138 100644
--- a/bidspm.m
+++ b/bidspm.m
@@ -588,11 +588,16 @@ function run_tests()
   folderToCover = fullfile(pwd, 'src');
   testFolder = fullfile(pwd, 'tests', subfolder);
 
-  success = moxunit_runtests(testFolder, ...
-                             '-verbose', '-recursive', '-with_coverage', ...
-                             '-cover', folderToCover, ...
-                             '-cover_xml_file', 'coverage.xml', ...
-                             '-cover_html_dir', fullfile(pwd, 'coverage_html'));
+  if ispc
+    success = moxunit_runtests(testFolder, ...
+                               '-verbose', '-recursive');
+  else
+    success = moxunit_runtests(testFolder, ...
+                               '-verbose', '-recursive', '-with_coverage', ...
+                               '-cover', folderToCover, ...
+                               '-cover_xml_file', 'coverage.xml', ...
+                               '-cover_html_dir', fullfile(pwd, 'coverage_html'));
+  end
 
   if success
     system('echo 0 > test_report.log');

From d381ae7cf180c266a184145ff7a2b8c86794b8c2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 4 May 2023 13:44:08 +0200
Subject: [PATCH 06/22] update CPP ROI

---
 lib/CPP_ROI | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/CPP_ROI b/lib/CPP_ROI
index ba75ffb4..86d6fac8 160000
--- a/lib/CPP_ROI
+++ b/lib/CPP_ROI
@@ -1 +1 @@
-Subproject commit ba75ffb42242a061bbe43c29fc5ebecaccfa9c4e
+Subproject commit 86d6fac8899c63d82a99087f5bedc79360bce07c

From 5cfeafcc1fae3c5505748b495716795dbc709dfd Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 11:48:49 +0200
Subject: [PATCH 07/22] misc

---
 lib/CPP_ROI | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/CPP_ROI b/lib/CPP_ROI
index 86d6fac8..b92c5337 160000
--- a/lib/CPP_ROI
+++ b/lib/CPP_ROI
@@ -1 +1 @@
-Subproject commit 86d6fac8899c63d82a99087f5bedc79360bce07c
+Subproject commit b92c5337ba6803068688675618cbad91c0241cfe

From b66fbda54753a3b34daef6b01b955f00b550318a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 11:52:28 +0200
Subject: [PATCH 08/22] update octache and spm_2_bids

---
 lib/octache    | 2 +-
 lib/spm_2_bids | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/octache b/lib/octache
index 77aea2df..12eca8da 160000
--- a/lib/octache
+++ b/lib/octache
@@ -1 +1 @@
-Subproject commit 77aea2df3ee75e80d9272bf5a3a101a7af92b9d5
+Subproject commit 12eca8da76633aae6b547ca399c60ed984bd3b4c
diff --git a/lib/spm_2_bids b/lib/spm_2_bids
index d645f38f..5a9bf746 160000
--- a/lib/spm_2_bids
+++ b/lib/spm_2_bids
@@ -1 +1 @@
-Subproject commit d645f38f61236bb1ee7397562001f50257be1d95
+Subproject commit 5a9bf746248a264cbb486b4eb6885a94cb0df900

From 911914eb0a8729b189def7dbbe7db5d0b28996dc Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 12:01:19 +0200
Subject: [PATCH 09/22] update cpp_roi

---
 lib/CPP_ROI | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/CPP_ROI b/lib/CPP_ROI
index 1946d0d6..d7726c09 160000
--- a/lib/CPP_ROI
+++ b/lib/CPP_ROI
@@ -1 +1 @@
-Subproject commit 1946d0d65e1c8886efbde09d4684035e77325cfc
+Subproject commit d7726c096586ad822579799c87463c9cfc17f432

From 932ecc0cf838484b25fe46e930f9bb0a7045f765 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 12:14:01 +0200
Subject: [PATCH 10/22] fix doc install

---
 requirements_doc.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements_doc.txt b/requirements_doc.txt
index 5b3709f1..72f54ba8 100644
--- a/requirements_doc.txt
+++ b/requirements_doc.txt
@@ -8,3 +8,4 @@ sphinx_rtd_theme
 sphinxcontrib-bibtex
 sphinxcontrib-matlabdomain
 sphinxcontrib-mermaid
+urllib3==1.26.15

From 8eb687b483c92725501217225c908e095291603a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 12:54:04 +0200
Subject: [PATCH 11/22] fix typo

---
 .github/workflows/tests_matlab.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index 2e3f8676..7131b739 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -59,7 +59,7 @@ jobs:
       run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
 
     - name: Install dependencies
-      if: matrix.os == ubuntu-latest
+      if: matrix.os == 'ubuntu-latest'
       run: |
         sudo apt-get -y -qq update
         sudo apt-get -y install unzip wget

From d1398d1e8cb6c89e1214f07ad96bfa79fc8556b2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 13:19:11 +0200
Subject: [PATCH 12/22] adapt for windows

---
 .github/workflows/tests_matlab.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index 7131b739..3b3648b6 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -87,8 +87,12 @@ jobs:
       run: |
         git clone https://github.com/spm/spm12.git --depth 1
 
-    - name: Copy Macs toolbox to SPM inputs_folder
+    - name: Copy Macs toolbox to SPM inputs_folder on unix
+      if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
       run: cp -rv lib/MACS spm12/toolbox/MACS
+    - name: Copy Macs toolbox to SPM inputs_folder on windows
+      if: matrix.os == 'windows-latest'
+      run: Copy-Item -Recurse -Verbose -Path ".\lib\MACS" -Destination ".\spm12\toolbox\MACS"
 
     - name: Get moae fmriprep data from OSF
       run: |

From db87720429931d14e55babab3af1f0e4c43dcea6 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 13:33:01 +0200
Subject: [PATCH 13/22] adapt for windows

---
 .github/workflows/tests_matlab.yml | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index 3b3648b6..863fa203 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -94,13 +94,22 @@ jobs:
       if: matrix.os == 'windows-latest'
       run: Copy-Item -Recurse -Verbose -Path ".\lib\MACS" -Destination ".\spm12\toolbox\MACS"
 
-    - name: Get moae fmriprep data from OSF
+    - name: Get moae fmriprep data from OSF on unix
+      if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
       run: |
         mkdir -p demos/MoAE/inputs/
         cd demos/MoAE/inputs/
         wget https://osf.io/vufjs/download
         unzip download
         mv moae_fmriprep fmriprep
+    - name: Get moae fmriprep data from OSF on windows
+      if: matrix.os == 'windows-latest'
+      run: |
+        New-Item -ItemType Directory -Path ".\demos\MoAE\inputs\" -Force
+        Set-Location -Path ".\demos\MoAE\inputs\"
+        Invoke-WebRequest -Uri "https://osf.io/vufjs/download" -OutFile "download"
+        Expand-Archive -Path ".\download" -DestinationPath ".\"
+        Rename-Item -Path ".\moae_fmriprep" -NewName "fmriprep"
 
     - name: Prepare test data
       run: |

From 7348cf8add8a53a17d02ba0997a56ff1bccaee73 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 5 May 2023 14:33:26 +0200
Subject: [PATCH 14/22] update bids matlab

---
 lib/bids-matlab                | 2 +-
 src/QA/anatQA.m                | 5 +++--
 src/QA/computeRobustOutliers.m | 9 +++++++++
 3 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/lib/bids-matlab b/lib/bids-matlab
index bbd2b4f5..287109a8 160000
--- a/lib/bids-matlab
+++ b/lib/bids-matlab
@@ -1 +1 @@
-Subproject commit bbd2b4f53efe9952172fb49f611eecab5fb3520e
+Subproject commit 287109a8981ec913de32c295c31ff2bcd063ea3c
diff --git a/src/QA/anatQA.m b/src/QA/anatQA.m
index 8d64319c..404e087c 100644
--- a/src/QA/anatQA.m
+++ b/src/QA/anatQA.m
@@ -148,10 +148,11 @@
   Bmax = sqrt(sum(data(:).^2));
   try
     % should work most of the time, possibly throwing warnings (cf Joost Kuijer)
-    json.EFC = real(nansum((data(:) ./ Bmax) .* log(data(:) ./ Bmax)));
+    tmp = (data(:) ./ Bmax) .* log(data(:) ./ Bmax);
   catch
-    json.EFC = real(nansum((data(:) ./ Bmax) .* abs(log(data(:) ./ Bmax))));
+    tmp = (data(:) ./ Bmax) .* abs(log(data(:) ./ Bmax));
   end
+  json.EFC = real(bids.internal.nansum(tmp));
 
 end
 
diff --git a/src/QA/computeRobustOutliers.m b/src/QA/computeRobustOutliers.m
index 9754f9d4..f4d87ad7 100644
--- a/src/QA/computeRobustOutliers.m
+++ b/src/QA/computeRobustOutliers.m
@@ -72,6 +72,15 @@
   end
 
   if strcmpi(outlierType, 's-outliers')
+
+    if isempty(which('chi2inv'))
+      logger('WARNING', 'chi2inv function required to compute s-outliers.', ...
+             'filename', mfilename, ...
+             'id', 'missingChi2inv');
+      outliers = false(size(timeSeries));
+      return
+    end
+
     k = sqrt(chi2inv(0.975, 1));
     for p = size(timeSeries, 2):-1:1
       tmp = timeSeries(:, p);

From 5d00994b7768e0c305038961dc094741bb86eeb9 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 6 May 2023 08:34:39 -0400
Subject: [PATCH 15/22] fix tests and set up

---
 .github/workflows/tests_matlab.yml      |  8 +++++-
 src/utils/computeTsnr.m                 | 15 +++++++++-
 tests/Makefile                          | 11 ++++++-
 tests/tests_unit/IO/test_addGitIgnore.m | 38 +++++++++----------------
 tests/utils/tempName.m                  | 11 +++++++
 5 files changed, 56 insertions(+), 27 deletions(-)
 create mode 100644 tests/utils/tempName.m

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index 863fa203..4263c3c5 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -111,10 +111,16 @@ jobs:
         Expand-Archive -Path ".\download" -DestinationPath ".\"
         Rename-Item -Path ".\moae_fmriprep" -NewName "fmriprep"
 
-    - name: Prepare test data
+    - name: Prepare test data unix
+      if: matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest'
       run: |
         cd tests
         make data
+    - name: Prepare test data windows
+      if: matrix.os == 'windows-latest'
+      run: |
+        cd tests
+        make data_win
 
     - name: Install Moxunit and MOcov
       run: |
diff --git a/src/utils/computeTsnr.m b/src/utils/computeTsnr.m
index b761315c..e42d894a 100755
--- a/src/utils/computeTsnr.m
+++ b/src/utils/computeTsnr.m
@@ -88,7 +88,7 @@
   % Copyright (C) Stephan Heunis 2018
 
   % Define variables
-  [r, c] = size(data);
+  r = size(data);
 
   % Create design matrix with model regressors
   if order == 1
@@ -109,3 +109,16 @@
   outData = data - X(:, 2:end) * b(2:end, :);
 
 end
+
+function y = nanmean(varargin)
+
+  if bids.internal.is_octave()
+    data = varargin{1}(:);
+    nanIdx = isnan(data);
+    y = mean(data(~nanIdx));
+    return
+  end
+
+  narginchk(1, 2);
+  y = mean(varargin{:}, 'omitnan');
+end
diff --git a/tests/Makefile b/tests/Makefile
index 5b2e2bce..938af6a8 100644
--- a/tests/Makefile
+++ b/tests/Makefile
@@ -9,16 +9,25 @@ clean_local:
 	rm -rf data/derivatives/bidspm-stats/group
 	rm -rf data/derivatives/bidspm-*/jobs
 
-data: clean
+create_dummy_dataset:
 	sh createDummyDataSet.sh
+
+bids_examples:
 	rm -rf bids-examples/
 	git clone https://github.com/bids-standard/bids-examples.git --depth 1
 	cp bids-examples/synthetic/dataset_description.json bids-examples/synthetic/derivatives/fmriprep
 	touch bids-examples/.gitkeep
+
+data: clean create_dummy_dataset bids_examples
 	wget --quiet -O moae_spm12.zip https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=
 	mkdir -p data/MoAE/derivatives/spm12
 	unzip -d ./data/MoAE/derivatives/spm12 moae_spm12.zip
 
+data_win: clean create_dummy_dataset bids_examples
+	Invoke-WebRequest -Uri "https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=" -OutFile "moae_spm12.zip"
+	New-Item -ItemType Directory -Path "data/MoAE/derivatives/spm12" -Force
+	Expand-Archive -Path "./moae_spm12.zip" -DestinationPath "./data/MoAE/derivatives/spm12"
+
 clean_openneuro:
 	rm -rf openneuro/*
 
diff --git a/tests/tests_unit/IO/test_addGitIgnore.m b/tests/tests_unit/IO/test_addGitIgnore.m
index 7744bd5f..6522f114 100644
--- a/tests/tests_unit/IO/test_addGitIgnore.m
+++ b/tests/tests_unit/IO/test_addGitIgnore.m
@@ -1,6 +1,5 @@
-% (C) Copyright 2020 bidspm developers
-
 function test_suite = test_addGitIgnore %#ok<*STOUT>
+  % (C) Copyright 2020 bidspm developers
   try % assignment of 'localfunctions' is necessary in Matlab >= 2016
     test_functions = localfunctions(); %#ok<*NASGU>
   catch % no problem; early Matlab versions can use initTestSuite fine
@@ -10,44 +9,38 @@
 
 function test_addGitIgnore_basic()
 
-  if exist(fullfile(pwd, '.gitignore'), 'file')
-    delete(fullfile(pwd, '.gitignore'));
-  end
+  pth = tempName();
 
-  addGitIgnore(pwd);
+  addGitIgnore(pth);
 
-  assertEqual(exist(fullfile(pwd, '.gitignore'), 'file'), 2);
+  assertEqual(exist(fullfile(pth, '.gitignore'), 'file'), 2);
 
-  fid = fopen(fullfile(pwd, '.gitignore'), 'r');
+  fid = fopen(fullfile(pth, '.gitignore'), 'r');
   c = fread(fid, Inf, 'uint8=>char')';
 
   assertEqual(strfind(c, '.DS_store'), 1);
 
   fclose(fid);
 
-  delete(fullfile(pwd, '.gitignore'));
-
 end
 
 function test_addGitIgnore_already_present()
 
-  if exist(fullfile(pwd, '.gitignore'), 'file')
-    delete(fullfile(pwd, '.gitignore'));
-  end
-  fid = fopen(fullfile(pwd, '.gitignore'), 'w');
+  pth = tempName();
+
+  fid = fopen(fullfile(pth, '.gitignore'), 'w');
   fprintf(fid, 'foo\n');
   fprintf(fid, '.DS_store\n');
   fclose(fid);
 
-  addGitIgnore(pwd);
+  addGitIgnore(pth);
 
-  fid = fopen(fullfile(pwd, '.gitignore'), 'r');
+  fid = fopen(fullfile(pth, '.gitignore'), 'r');
   c = fread(fid, Inf, 'uint8=>char')';
   assertEqual(numel(strfind(c, '.DS_store')), 1);
 
   fclose(fid);
 
-  delete(fullfile(pwd, '.gitignore'));
 end
 
 function test_addGitIgnore_append()
@@ -56,21 +49,18 @@ function test_addGitIgnore_append()
     return
   end
 
-  if exist(fullfile(pwd, '.gitignore'), 'file')
-    delete(fullfile(pwd, '.gitignore'));
-  end
+  pth = tempName();
 
-  fid = fopen(fullfile(pwd, '.gitignore'), 'w');
+  fid = fopen(fullfile(pth, '.gitignore'), 'w');
   fprintf(fid, 'foo\n');
   fprintf(fid, 'bar\n');
   fclose(fid);
 
-  addGitIgnore(pwd);
+  addGitIgnore(pth);
 
-  fid = fopen(fullfile(pwd, '.gitignore'), 'r');
+  fid = fopen(fullfile(pth, '.gitignore'), 'r');
   c = fread(fid, Inf, 'uint8=>char')';
   assert(strfind(c, '.DS_store') > 0);
   fclose(fid);
 
-  delete(fullfile(pwd, '.gitignore'));
 end
diff --git a/tests/utils/tempName.m b/tests/utils/tempName.m
new file mode 100644
index 00000000..3b250840
--- /dev/null
+++ b/tests/utils/tempName.m
@@ -0,0 +1,11 @@
+function pth = tempName()
+  %
+  % Creates a temporary directory and returns its fullpath
+  %
+
+  % (C) Copyright 2023 bidspm developers
+
+  pth = tempname();
+  mkdir(pth);
+
+end

From c1d98344c9cc608118d0dfa4c887cbe8d5413477 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 6 May 2023 08:43:33 -0400
Subject: [PATCH 16/22] update submodules

---
 lib/CPP_ROI    | 2 +-
 lib/octache    | 2 +-
 lib/spm_2_bids | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/lib/CPP_ROI b/lib/CPP_ROI
index d7726c09..3e5dbad2 160000
--- a/lib/CPP_ROI
+++ b/lib/CPP_ROI
@@ -1 +1 @@
-Subproject commit d7726c096586ad822579799c87463c9cfc17f432
+Subproject commit 3e5dbad29cdef05e68d6793278b8e86b3f2a2718
diff --git a/lib/octache b/lib/octache
index 12eca8da..99c970e3 160000
--- a/lib/octache
+++ b/lib/octache
@@ -1 +1 @@
-Subproject commit 12eca8da76633aae6b547ca399c60ed984bd3b4c
+Subproject commit 99c970e362392c77eef10c2e917c7d90e8ad78f8
diff --git a/lib/spm_2_bids b/lib/spm_2_bids
index 5a9bf746..64edd37d 160000
--- a/lib/spm_2_bids
+++ b/lib/spm_2_bids
@@ -1 +1 @@
-Subproject commit 5a9bf746248a264cbb486b4eb6885a94cb0df900
+Subproject commit 64edd37de4a70ed554cc6f57d3c32e64efa97244

From f4d573e43571d67ab15b99914abe65e3238f0c17 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 6 May 2023 08:56:24 -0400
Subject: [PATCH 17/22] change prepare data on windows

---
 .github/workflows/tests_matlab.yml | 6 +++++-
 tests/Makefile                     | 9 ++-------
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/tests_matlab.yml b/.github/workflows/tests_matlab.yml
index 4263c3c5..636fa742 100644
--- a/.github/workflows/tests_matlab.yml
+++ b/.github/workflows/tests_matlab.yml
@@ -120,7 +120,11 @@ jobs:
       if: matrix.os == 'windows-latest'
       run: |
         cd tests
-        make data_win
+        make create_dummy_dataset
+        make bids_examples
+        Invoke-WebRequest -Uri "https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=" -OutFile "moae_spm12.zip"
+        New-Item -ItemType Directory -Path "data/MoAE/derivatives/spm12" -Force
+        Expand-Archive -Path "./moae_spm12.zip" -DestinationPath "./data/MoAE/derivatives/spm12"
 
     - name: Install Moxunit and MOcov
       run: |
diff --git a/tests/Makefile b/tests/Makefile
index 938af6a8..f642a785 100644
--- a/tests/Makefile
+++ b/tests/Makefile
@@ -9,7 +9,7 @@ clean_local:
 	rm -rf data/derivatives/bidspm-stats/group
 	rm -rf data/derivatives/bidspm-*/jobs
 
-create_dummy_dataset:
+create_dummy_dataset: clean
 	sh createDummyDataSet.sh
 
 bids_examples:
@@ -18,16 +18,11 @@ bids_examples:
 	cp bids-examples/synthetic/dataset_description.json bids-examples/synthetic/derivatives/fmriprep
 	touch bids-examples/.gitkeep
 
-data: clean create_dummy_dataset bids_examples
+data: create_dummy_dataset bids_examples
 	wget --quiet -O moae_spm12.zip https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=
 	mkdir -p data/MoAE/derivatives/spm12
 	unzip -d ./data/MoAE/derivatives/spm12 moae_spm12.zip
 
-data_win: clean create_dummy_dataset bids_examples
-	Invoke-WebRequest -Uri "https://files.de-1.osf.io/v1/resources/3vufp/providers/osfstorage/62ab741be6f3ec09a7e48d13/?zip=" -OutFile "moae_spm12.zip"
-	New-Item -ItemType Directory -Path "data/MoAE/derivatives/spm12" -Force
-	Expand-Archive -Path "./moae_spm12.zip" -DestinationPath "./data/MoAE/derivatives/spm12"
-
 clean_openneuro:
 	rm -rf openneuro/*
 

From 3c4f6d94f9ba7b19aa8601443e6f03b7a16294ef Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 6 May 2023 10:50:47 -0400
Subject: [PATCH 18/22] add more informative errors

---
 demos/openneuro/Makefile                       |  9 ++++-----
 src/IO/loadAndCheckOptions.m                   |  2 +-
 src/stats/subject_level/convertOnsetTsvToMat.m | 15 +++++++++++++++
 src/stats/subject_level/getEventsData.m        | 10 ++++++++++
 src/utils/computeTsnr.m                        |  2 +-
 tests/tests_unit/IO/test_saveSpmScript.m       |  3 +++
 6 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/demos/openneuro/Makefile b/demos/openneuro/Makefile
index 4573cdf6..cb4417bd 100644
--- a/demos/openneuro/Makefile
+++ b/demos/openneuro/Makefile
@@ -43,8 +43,7 @@ data_ds001734:
 data_ds002799:
 	mkdir -p inputs
 	cd inputs && datalad install ///openneuro/ds002799
-	cd inputs/ds002799/derivatives/fmriprep
-	datalad get sub-292/*/func/*MNI152NLin2009cAsym*
-	datalad get sub-292/*/func/*tsv
-	datalad get sub-30[27]/*/func/*MNI152NLin2009cAsym*
-	datalad get sub-30[27]/*/func/*tsv
+	datalad get -d inputs/ds002799 inputs/ds002799/derivatives/fmriprep/sub-292/*/func/*MNI152NLin2009cAsym*
+	datalad get -d inputs/ds002799 inputs/ds002799/derivatives/fmriprep/sub-292/*/func/*tsv
+	datalad get -d inputs/ds002799 inputs/ds002799/derivatives/fmriprep/sub-30[27]/*/func/*MNI152NLin2009cAsym*
+	datalad get -d inputs/ds002799 inputs/ds002799/derivatives/fmriprep/sub-30[27]/*/func/*tsv
diff --git a/src/IO/loadAndCheckOptions.m b/src/IO/loadAndCheckOptions.m
index 628db9a8..4b62c5d7 100644
--- a/src/IO/loadAndCheckOptions.m
+++ b/src/IO/loadAndCheckOptions.m
@@ -42,7 +42,7 @@
   % finds most recent option file
   if size(optionJsonFile, 1) > 1
     containsDate = cellfun(@any, regexp(cellstr(optionJsonFile), ...
-                                        '^.*/[0-9]{4}-[0-9]{2}-[0-9]{2}T.*\.json'));
+                                        '^.*[0-9]{4}-[0-9]{2}-[0-9]{2}T.*\.json'));
     if any(containsDate)
       optionJsonFile = optionJsonFile(containsDate, :);
       optionJsonFile = sortrows(optionJsonFile);
diff --git a/src/stats/subject_level/convertOnsetTsvToMat.m b/src/stats/subject_level/convertOnsetTsvToMat.m
index a0dc5df5..774a7c81 100644
--- a/src/stats/subject_level/convertOnsetTsvToMat.m
+++ b/src/stats/subject_level/convertOnsetTsvToMat.m
@@ -51,10 +51,25 @@
 
   % (C) Copyright 2019 bidspm developers
 
+  REQUIRED_COLUMNS = {'onset', 'duration'};
+
   [pth, file, ext] = spm_fileparts(tsvFile);
   tsv.file = validationInputFile(pth, [file, ext]);
   tsv.content = bids.util.tsvread(tsv.file);
 
+  for i = 1:numel(REQUIRED_COLUMNS)
+    if ~isfield(content, REQUIRED_COLUMNS{i})
+      msg = sprintf(['''%s'' column is missing from file: %s', ...
+                     '\nAvailable columns are: %s'], ...
+                    REQUIRED_COLUMNS{i}, ...
+                    tsv.file, ...
+                    bids.internal.create_unordered_list(fieldnames(tsv.content)));
+      logger('ERROR', msg, ...
+             'filename', filename, ...
+             'id', 'missingTrialypeColumn');
+    end
+  end
+
   if ~all(isnumeric(tsv.content.onset))
 
     msg = sprintf('%s\n%s', 'Onset column contains non numeric values in file:', tsv.file);
diff --git a/src/stats/subject_level/getEventsData.m b/src/stats/subject_level/getEventsData.m
index d32fd03a..cebd1693 100644
--- a/src/stats/subject_level/getEventsData.m
+++ b/src/stats/subject_level/getEventsData.m
@@ -11,6 +11,16 @@
 
   content = bids.util.tsvread(tsvFile);
 
+  if ~isfield(content, 'trial_type')
+    msg = sprintf(['''trial_type'' column is missing from file: %s', ...
+                   '\nAvailable columns are: %s'], ...
+                  tsvFile, ...
+                  bids.internal.create_unordered_list(fieldnames(content)));
+    logger('ERROR', msg, ...
+           'filename', filename, ...
+           'id', 'missingTrialypeColumn');
+  end
+
   conditions = unique(content.trial_type);
 
   if ~isempty(modelFile)
diff --git a/src/utils/computeTsnr.m b/src/utils/computeTsnr.m
index e42d894a..022a75b7 100755
--- a/src/utils/computeTsnr.m
+++ b/src/utils/computeTsnr.m
@@ -97,7 +97,7 @@
     X = [(1:r)' ((1:r)').^2];
   end
   % Remove mean from design matrix
-  X = X - repmat(mean(X, 1), r, 1);
+  X = X - repmat(mean(X, 1), [r, 1]);
 
   % Add constant regressor
   X = [ones(r, 1) X];
diff --git a/tests/tests_unit/IO/test_saveSpmScript.m b/tests/tests_unit/IO/test_saveSpmScript.m
index 046386d2..bde5470b 100644
--- a/tests/tests_unit/IO/test_saveSpmScript.m
+++ b/tests/tests_unit/IO/test_saveSpmScript.m
@@ -30,6 +30,9 @@ function test_saveSpmScript_basic()
   fid1 = fopen(expectedContent, 'r');
   expectedContent = fscanf(fid1, '%s');
   fclose(fid1);
+  if ispc
+    expectedContent = strrep('/', '\');
+  end
 
   fid2 = fopen(outputFilename, 'r');
   actualContent = fscanf(fid2, '%s');

From 99d74b4cb3ce7639b819ed64ffece8628092d46a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 6 May 2023 11:17:21 -0400
Subject: [PATCH 19/22] use temp dir

---
 demos/MoAE/test_moae.m | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/demos/MoAE/test_moae.m b/demos/MoAE/test_moae.m
index 54b22c36..a8b0bc53 100644
--- a/demos/MoAE/test_moae.m
+++ b/demos/MoAE/test_moae.m
@@ -51,7 +51,8 @@
 
   %% preproc
   bids_dir = fullfile(WD, 'inputs', 'raw');
-  output_dir = fullfile(WD, 'outputs', 'derivatives');
+  output_dir = fullfile(tempname, 'outputs', 'derivatives');
+  mkdir(output_dir);
 
   bidspm(bids_dir, output_dir, 'subject', ...
          'participant_label', {'01'}, ...
@@ -83,8 +84,6 @@
 
   cd(WD);
 
-  rmdir(fullfile(WD, 'outputs', 'derivatives'), 's');
-
   % with Octave running more n-1 loop in CI is fine
   % but not running crashes with a segmentation fault
   % /home/runner/work/_temp/fb8e9d58-fa9f-4f93-8c96-387973f3632e.sh: line 2:

From e1dd1451539cef744affd8aa7afdd866866350f2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 6 May 2023 11:23:49 -0400
Subject: [PATCH 20/22] fix typo

---
 src/stats/subject_level/convertOnsetTsvToMat.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/stats/subject_level/convertOnsetTsvToMat.m b/src/stats/subject_level/convertOnsetTsvToMat.m
index 774a7c81..a6e184f5 100644
--- a/src/stats/subject_level/convertOnsetTsvToMat.m
+++ b/src/stats/subject_level/convertOnsetTsvToMat.m
@@ -58,7 +58,7 @@
   tsv.content = bids.util.tsvread(tsv.file);
 
   for i = 1:numel(REQUIRED_COLUMNS)
-    if ~isfield(content, REQUIRED_COLUMNS{i})
+    if ~isfield(tsv.content, REQUIRED_COLUMNS{i})
       msg = sprintf(['''%s'' column is missing from file: %s', ...
                      '\nAvailable columns are: %s'], ...
                     REQUIRED_COLUMNS{i}, ...

From e7f043111fca3c94ca7150742a17aaa03b1c2e5b Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 6 May 2023 12:44:06 -0400
Subject: [PATCH 21/22] fix typo

---
 src/stats/subject_level/convertOnsetTsvToMat.m | 2 +-
 src/stats/subject_level/getEventsData.m        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/stats/subject_level/convertOnsetTsvToMat.m b/src/stats/subject_level/convertOnsetTsvToMat.m
index a6e184f5..3d3cd555 100644
--- a/src/stats/subject_level/convertOnsetTsvToMat.m
+++ b/src/stats/subject_level/convertOnsetTsvToMat.m
@@ -65,7 +65,7 @@
                     tsv.file, ...
                     bids.internal.create_unordered_list(fieldnames(tsv.content)));
       logger('ERROR', msg, ...
-             'filename', filename, ...
+             'filename', mfilename(), ...
              'id', 'missingTrialypeColumn');
     end
   end
diff --git a/src/stats/subject_level/getEventsData.m b/src/stats/subject_level/getEventsData.m
index cebd1693..fb542cc3 100644
--- a/src/stats/subject_level/getEventsData.m
+++ b/src/stats/subject_level/getEventsData.m
@@ -17,7 +17,7 @@
                   tsvFile, ...
                   bids.internal.create_unordered_list(fieldnames(content)));
     logger('ERROR', msg, ...
-           'filename', filename, ...
+           'filename', mfilename(), ...
            'id', 'missingTrialypeColumn');
   end
 

From 1d04e358dd9f575615989b5346b03f270cb2b19c Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 7 May 2023 08:58:28 -0400
Subject: [PATCH 22/22] fix tests

---
 src/utils/computeTsnr.m                 | 5 +++--
 tests/tests_unit/IO/test_addGitIgnore.m | 4 ++++
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/utils/computeTsnr.m b/src/utils/computeTsnr.m
index 022a75b7..4b6a2db8 100755
--- a/src/utils/computeTsnr.m
+++ b/src/utils/computeTsnr.m
@@ -88,7 +88,7 @@
   % Copyright (C) Stephan Heunis 2018
 
   % Define variables
-  r = size(data);
+  [r, c] = size(data);
 
   % Create design matrix with model regressors
   if order == 1
@@ -97,7 +97,7 @@
     X = [(1:r)' ((1:r)').^2];
   end
   % Remove mean from design matrix
-  X = X - repmat(mean(X, 1), [r, 1]);
+  X = X - repmat(mean(X, 1), r, 1);
 
   % Add constant regressor
   X = [ones(r, 1) X];
@@ -121,4 +121,5 @@
 
   narginchk(1, 2);
   y = mean(varargin{:}, 'omitnan');
+
 end
diff --git a/tests/tests_unit/IO/test_addGitIgnore.m b/tests/tests_unit/IO/test_addGitIgnore.m
index 6522f114..46af5b5b 100644
--- a/tests/tests_unit/IO/test_addGitIgnore.m
+++ b/tests/tests_unit/IO/test_addGitIgnore.m
@@ -49,6 +49,10 @@ function test_addGitIgnore_append()
     return
   end
 
+  if ispc || ismac
+    return
+  end
+
   pth = tempName();
 
   fid = fopen(fullfile(pth, '.gitignore'), 'w');