[REL] 4.0.0 (#1313)

* prepare release

* use deno validator

* fix

* use jammy

Author: Remi-Gau

.github/workflows/run_tests_cli.yml

@@ -25,9 +25,10 @@ jobs:
                 sudo apt-get -y install octave liboctave-dev
         -   name: Info
             run: octave --version
-        -   uses: actions/setup-node@v4
+        -   name: Install Deno
+            uses: denoland/setup-deno@v1
             with:
-                node-version: 18
+                deno-version: v1.x
         -   uses: actions/setup-python@v5
             name: Set up Python ${{ matrix.python-version }}
             with:
@@ -63,10 +64,10 @@ jobs:
             with:
                 submodules: recursive
                 fetch-depth: 0
-
-        -   uses: actions/setup-node@v4
+        -   name: Install Deno
+            uses: denoland/setup-deno@v1
             with:
-                node-version: 18
+                deno-version: v1.x
         -   uses: actions/setup-python@v5
             name: Set up Python
             with:

.github/workflows/run_tests_notebooks.yml

@@ -11,7 +11,7 @@ on:
         -   .github/workflows/*system*
         -   lib
 
-  # Allows you to run this workflow manually from the Actions tab
+    # Allows you to run this workflow manually from the Actions tab
     workflow_dispatch:
 
 jobs:

.github/workflows/tests.yml

@@ -46,10 +46,10 @@ jobs:
 
         steps:
 
-        -   name: Install Node
-            uses: actions/setup-node@v4
+        -   name: Install Deno
+            uses: denoland/setup-deno@v1
             with:
-                node-version: 18
+                deno-version: v1.x
 
         -   name: Install python
             uses: actions/setup-python@v5
@@ -136,10 +136,10 @@ jobs:
 
         steps:
 
-        -   name: Install Node
-            uses: actions/setup-node@v4
+        -   name: Install Deno
+            uses: denoland/setup-deno@v1
             with:
-                node-version: 18
+                deno-version: v1.x
 
         -   name: Install python
             uses: actions/setup-python@v5
@@ -235,10 +235,10 @@ jobs:
         -   name: test ${{ matrix.script }}
             run: test ${{ matrix.script }}
 
-        -   name: Install Node
-            uses: actions/setup-node@v4
+        -   name: Install Deno
+            uses: denoland/setup-deno@v1
             with:
-                node-version: 18
+                deno-version: v1.x
 
         -   name: Install python
             uses: actions/setup-python@v5

.github/workflows/tests_octave.yml

@@ -63,10 +63,10 @@ jobs:
                 sudo apt-get -y -qq update
                 sudo apt-get -y install unzip wget git-annex
 
-        -   name: Install Node
-            uses: actions/setup-node@v4
+        -   name: Install Deno
+            uses: denoland/setup-deno@v1
             with:
-                node-version: 18
+                deno-version: v1.x
 
         -   name: Install python
             uses: actions/setup-python@v5

.github/workflows/tests_windows.yml

@@ -61,10 +61,10 @@ jobs:
             if: matrix.test_type == 'system'
             run: echo ${{ matrix.test_type }} test ${{ matrix.script }}
 
-        -   name: Install Node
-            uses: actions/setup-node@v4
+        -   name: Install Deno
+            uses: denoland/setup-deno@v1
             with:
-                node-version: 18
+                deno-version: v1.x
 
         -   name: Install python
             uses: actions/setup-python@v5

CHANGELOG.md

@@ -24,55 +24,55 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-* [ENH] add QA workflow `bidsQA` to find outliers in MRIQC output or to view number of outlier timepoints (for a given metric and threshold) in each functional run #1297 by @Remi-Gau
-* [ENH] add support for one-way ANOVA across groups at the group level #1296 by @Remi-Gau
-* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to ne more flexible with respect to what praticipants.tsv column to use to allocate subjects in each group #1296 by @Remi-Gau
-* [ENH] make `addConfoundsToDesignMatrix` a method of `BidsModel` #1294 by @Remi-Gau
-* [ENH] add Apptainer definition #1254 by @Remi-Gau and @monique2208
-* [ENH] allow to copy anat only on raw datasets #1181 by @Remi-Gau
-* [ENH] add option to concatenate runs at subject level to facilite running PPI analysis #1133 by @Remi-Gau
-* [ENH] allow to run substeps of substeps of the bayesian model selection #1145 by @Remi-Gau
-* [ENH] add quality control for GLM using the MACS toolbox to give a goodness of fit and several other information criteria (AIC, BIC) (MATLAB only) #1135  by @Remi-Gau
-* [ENH] add several confound strategies to add to bids stats model and a function to create family of models #1126 by @Remi-Gau
-* [ENH] add CLI to run bayesian model selection #1121 by @Remi-Gau
+* [ENH] add QA workflow `bidsQA` to find outliers in MRIQC output or to view number of outlier timepoints (for a given metric and threshold) in each functional run [1297](https://github.com/cpp-lln-lab/bidspm/pull/1297) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add support for one-way ANOVA across groups at the group level [1296](https://github.com/cpp-lln-lab/bidspm/pull/1296) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] allow for 2 sample T-Test, within group T-Test and one-way ANOVA to ne more flexible with respect to what praticipants.tsv column to use to allocate subjects in each group [1296](https://github.com/cpp-lln-lab/bidspm/pull/1296) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] make `addConfoundsToDesignMatrix` a method of `BidsModel` [1294](https://github.com/cpp-lln-lab/bidspm/pull/1294) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add Apptainer definition [1254](https://github.com/cpp-lln-lab/bidspm/pull/1254) by by [Remi-Gau](https://github.com/Remi-Gau)  and by [monique2208](https://github.com/monique2208)
+* [ENH] allow to copy anat only on raw datasets [1181](https://github.com/cpp-lln-lab/bidspm/pull/1181) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add option to concatenate runs at subject level to facilite running PPI analysis [1133](https://github.com/cpp-lln-lab/bidspm/pull/1133) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] allow to run substeps of substeps of the bayesian model selection [1145](https://github.com/cpp-lln-lab/bidspm/pull/1145) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add quality control for GLM using the MACS toolbox to give a goodness of fit and several other information criteria (AIC, BIC) (MATLAB only) [1135](https://github.com/cpp-lln-lab/bidspm/pull/1135)  by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add several confound strategies to add to bids stats model and a function to create family of models [1126](https://github.com/cpp-lln-lab/bidspm/pull/1126) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] add CLI to run bayesian model selection [1121](https://github.com/cpp-lln-lab/bidspm/pull/1121) by by [Remi-Gau](https://github.com/Remi-Gau)
 * [ENH] support label of activations with all atlases [1100](https://github.com/cpp-lln-lab/bidspm/pull/1100) by [Remi-Gau](https://github.com/Remi-Gau)
-* [ENH] add support for session level models #1116 be @Remi-Gau
+* [ENH] add support for session level models [1116](https://github.com/cpp-lln-lab/bidspm/pull/1116) be by [Remi-Gau](https://github.com/Remi-Gau)
 
   - allow to pass dummy contrasts to session level
   - allow inter session contrasts to be computed at the subject level
   - improve naming of contrast to mention bids ses and run
 
-* [ENH] add Bayesian model selection to the python CLI #1292 @Remi-Gau
+* [ENH] add Bayesian model selection to the python CLI [1292](https://github.com/cpp-lln-lab/bidspm/pull/1292) by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Changed
 
-* [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. #1276 @Remi-Gau
-* [DOC] change theme and structure of the documentation #1256 @Remi-Gau
-* [REF] Refactor and update CLI in #1096 @Remi-Gau
-* [ENH] {func}`getData` only loads anat data when requested #1257 @Remi-Gau
-* [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` #1292 @Remi-Gau
+* [ENH] align specification of F contrasts on the BIDS stats model: they should now be specified as a 2D matrix and not a 1D vector. [1276](https://github.com/cpp-lln-lab/bidspm/pull/1276) by [Remi-Gau](https://github.com/Remi-Gau)
+* [DOC] change theme and structure of the documentation [1256](https://github.com/cpp-lln-lab/bidspm/pull/1256) by [Remi-Gau](https://github.com/Remi-Gau)
+* [REF] Refactor and update CLI in [1096](https://github.com/cpp-lln-lab/bidspm/pull/1096) by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] {func}`getData` only loads anat data when requested [1257](https://github.com/cpp-lln-lab/bidspm/pull/1257) by [Remi-Gau](https://github.com/Remi-Gau)
+* [ENH] the python CLI now uses sub-commands instead of the named parameter `--action` [1292](https://github.com/cpp-lln-lab/bidspm/pull/1292) by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Deprecated
 
 ### Removed
 
-* [REF] Remove old CLI in #1096 @Remi-Gau
+* [REF] Remove old CLI in [1096](https://github.com/cpp-lln-lab/bidspm/pull/1096) by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Fixed
 
-* [FIX] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter #1295 by @d-ni374
-* [FIX] update {func}`createDefaultStatsModel` to use proper `GroupBy` at the dataset level #1248 by @d-ni374
-* [FIX] make {func}`getAcquisitionTime` less brittle #1248 by @d-ni374
-* [FIX] fix regular expression in {func}`bidsResults` to identify contrasts #1248 by @d-ni374 and #1275 by @Remi-Gau
-* [FIX] pass analysis level to stats actions when using python CLI #1258 @Remi-Gau
-* [FIX] remove goodness of fit from dataset level analysis as it is not supported by the MACS toolbox #1265 by @Remi-Gau
-* [FIX] add java and zip to container recipes to allow using nidm results with octave #1265 by @Remi-Gau
-* [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation #1203 by @Remi-Gau
-* [FIX] save `onsets.mat` directly in subject stats folder #1187 by @Remi-Gau
-* [FIX] do not compute subject level contrast when running dataset level #1102 by @Remi-Gau
-* [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in #1099 by @Remi-Gau
-* [FIX] rename results files (csv, tsv, png, nii) of each contrasts #1104 by @Remi-Gau
-* [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in #1110 by @Remi-Gau
+* [FIX] ensure that {func}`setBatchCoregistrationFuncToAnat` takes into account bids_filter [1295](https://github.com/cpp-lln-lab/bidspm/pull/1295) by by [d-ni374](https://github.com/d-ni374)
+* [FIX] update {func}`createDefaultStatsModel` to use proper `GroupBy` at the dataset level [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374)
+* [FIX] make {func}`getAcquisitionTime` less brittle [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374)
+* [FIX] fix regular expression in {func}`bidsResults` to identify contrasts [1248](https://github.com/cpp-lln-lab/bidspm/pull/1248) by by [d-ni374](https://github.com/d-ni374)  and [1275](https://github.com/cpp-lln-lab/bidspm/pull/1275) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] pass analysis level to stats actions when using python CLI [1258](https://github.com/cpp-lln-lab/bidspm/pull/1258) by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] remove goodness of fit from dataset level analysis as it is not supported by the MACS toolbox [1265](https://github.com/cpp-lln-lab/bidspm/pull/1265) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] add java and zip to container recipes to allow using nidm results with octave [1265](https://github.com/cpp-lln-lab/bidspm/pull/1265) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] copy the MACS toolbox to the SPM toolbox folder during the initialisation [1203](https://github.com/cpp-lln-lab/bidspm/pull/1203) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] save `onsets.mat` directly in subject stats folder [1187](https://github.com/cpp-lln-lab/bidspm/pull/1187) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] do not compute subject level contrast when running dataset level [1102](https://github.com/cpp-lln-lab/bidspm/pull/1102) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] copy `RepetitionTime` in sidecar JSON after running smoothing in [1099](https://github.com/cpp-lln-lab/bidspm/pull/1099) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] rename results files (csv, tsv, png, nii) of each contrasts [1104](https://github.com/cpp-lln-lab/bidspm/pull/1104) by by [Remi-Gau](https://github.com/Remi-Gau)
+* [FIX] reslice ROIS before running ROI based analysis to make sure they are at the resolution of the BOLD images in [1110](https://github.com/cpp-lln-lab/bidspm/pull/1110) by by [Remi-Gau](https://github.com/Remi-Gau)
 
 ### Security
 
@@ -252,7 +252,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [FIX] various bug fixes in [694](https://github.com/cpp-lln-lab/bidspm/pull/694) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] add some warnings to handle several bugs with empty ROIs in [693](https://github.com/cpp-lln-lab/bidspm/pull/693) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] re enable octave tests CI in [686](https://github.com/cpp-lln-lab/bidspm/pull/686) by [Remi-Gau](https://github.com/Remi-Gau)
-* [FIX] patches for [682](https://github.com/cpp-lln-lab/bidspm/pull/682) and  [683](https://github.com/cpp-lln-lab/bidspm/pull/683) (#687) by [mwmaclean](https://github.com/mwmaclean)
+* [FIX] patches for [682](https://github.com/cpp-lln-lab/bidspm/pull/682) and  [683](https://github.com/cpp-lln-lab/bidspm/pull/683) ([687](https://github.com/cpp-lln-lab/bidspm/pull/687)) by [mwmaclean](https://github.com/mwmaclean)
 * [FIX] ensure that bidsResults does not run if we don't have the proper options in [679](https://github.com/cpp-lln-lab/bidspm/pull/679) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] returnRootDir only relies on fullpaths in [676](https://github.com/cpp-lln-lab/bidspm/pull/676) by [Remi-Gau](https://github.com/Remi-Gau)
 * [FIX] set minimum compatible fmriprep version in [675](https://github.com/cpp-lln-lab/bidspm/pull/675) by [Remi-Gau](https://github.com/Remi-Gau)