[ENH] Update boutiques descriptor and example invocation (#225)

* update boutiques descriptor

* update boutiques descriptor

* use matrix in ci

* fix

.github/workflows/system_tests.yml

@@ -17,41 +17,33 @@ env:
 
 jobs:
     system_test:
-
         runs-on: ubuntu-latest
-
         strategy:
             matrix:
                 python-version: ['3.11']
-
+                cmd: [demo, demo_boutiques]
+            fail-fast: false
         steps:
-
         -   name: Clone repo
             uses: actions/checkout@v4
-
         -   name: Set up Python ${{ matrix.python-version }}
             uses: actions/setup-python@v5
             with:
                 python-version: ${{ matrix.python-version }}
-
         -   name: Install dependencies
             run: |
                 sudo apt-get update -y
                 sudo apt-get install -y git-annex
                 python -m pip install --upgrade pip setuptools
-                pip install datalad
-
+                pip install datalad boutiques
         -   name: Install bidsmreye
             run: |
                 pip install .
-
         -   name: Datalad WTF
             run: |
                 datalad wtf
-
-        -   name: Run demo
-            run: make demo
-
+        -   name: Run ${{ matrix.cmd }}
+            run: make ${{ matrix.cmd }}
         -   name: Re run demo (should be faster)
             run: |
                 make prepare

Makefile

@@ -139,6 +139,9 @@ generalize: ## demo: predicts labels of MOAE dataset
 				--model 1_guided_fixations \
 				-vv
 
+# run demo via boutiques
+demo_boutiques: tests/data/moae_fmriprep
+	bosh exec launch --no-container boutiques/bidsmreye_0.4.0.json boutiques/invocation.json
 
 ## ds002799
 .PHONY: get_ds002799_dat

README.md

@@ -100,19 +100,6 @@ Note that you might need to install cudnn first
 conda install -c conda-forge cudnn
 ```
 
-#### ANTsPy installation issues
-
-If installation of [ANTsPy](https://github.com/ANTsX/ANTsPy) fails try to manually install it via:
-
-<!-- may help on windows ? -->
-
-```bash
-git clone https://github.com/ANTsX/ANTsPy
-cd ANTsPy
-pip install CMake
-python3 setup.py install
-```
-
 ### Dev install
 
 Clone this repository.

boutiques/README.md

@@ -7,6 +7,4 @@ BIDS app and an example of invocation.
 ## How to use
 
 * Install Boutiques: `pip install boutiques`
-* Run the example: `bosh ./bids-app-example.json -i ./invocation.json -e -d`
-  (assumes `ds001` is a valid dataset in the current working
-  directory.)
+* Run the example: `bosh boutiques/bidsmreye_0.4.0.json -i boutiques/invocation.json -e -d`