[ENH] reformat, refactor and implement some bids app 2.0 features

.circleci/config.yml

@@ -50,42 +50,34 @@ jobs:
 
     - run: mkdir -p ${HOME}/outputs<< parameters.dataset >>
 
+    - run: sudo apt-get install tree
+
     - run:
         name: print version
         command: |
           docker run -ti --rm --read-only \
             -v /tmp/workspace/data/ds114_test1:/bids_dataset \
               bids/${CIRCLE_PROJECT_REPONAME,,} --version
 
-        # participant level tests for single session dataset
-    - run:
-        command: |
-          docker run -ti --rm --read-only \
-            -v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
-            -v ${HOME}/outputs<< parameters.dataset >>:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01
-        no_output_timeout: 6h
     - run:
+        name: participant level test
         command: |
           docker run -ti --rm --read-only \
             -v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
             -v ${HOME}/outputs<< parameters.dataset >>:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02
-        no_output_timeout: 6h
+              bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant
+          tree ${HOME}/outputs<< parameters.dataset >>
 
     - run:
+        name: group level test
         command: |
           docker run -ti --rm --read-only \
             -v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
-            -v ${HOME}/outputs1:/outputs \
+            -v ${HOME}/outputs<< parameters.dataset >>:/outputs \
               bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group
-        no_output_timeout: 6h
-
-    - store_artifacts:
-        path: ~/output<< parameters.dataset >>
+          tree ${HOME}/outputs<< parameters.dataset >>
 
   deploy:
-
     machine:
       image: ubuntu-2204:2022.10.2
 

.github/workflows/validate.yml

@@ -0,0 +1,28 @@
+---
+name: validate boutiques descriptor
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: ['*']
+
+jobs:
+  validate:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: 3.12
+    - name: Install
+      run: pip install boutiques
+    - name: Validate
+      run: bosh validate boutiques/descriptor.json

.pre-commit-config.yaml

@@ -14,14 +14,12 @@ repos:
   - id: check-case-conflict
   - id: check-merge-conflict
 
-
 - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
   rev: 0.2.3
   hooks:
   - id: yamlfmt
     args: [--mapping, '2', --sequence, '2', --offset, '0']
 
-
 - repo: https://github.com/hadolint/hadolint
   rev: v2.13.0-beta
   hooks:
@@ -32,5 +30,26 @@ repos:
     types: [dockerfile]
     entry: ghcr.io/hadolint/hadolint hadolint
 
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+
+# Aplly black formatting to python code
+# https://github.com/psf/black
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 24.4.2
+  hooks:
+  - id: black
+    args: [--config, pyproject.toml]
+
+# Checks for spelling errors
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.6
+  hooks:
+  - id: codespell
+    args: [--toml, pyproject.toml]
+    additional_dependencies: [tomli]
+
 ci:
   skip: [hadolint-docker]

Dockerfile

@@ -1,13 +1,14 @@
-FROM bids/base_fsl:6.0.1
+FROM bids/base_fsl:6.0.1@sha256:b92b9b4a0642dfbe011c3827384f781ba7d377686e82edaf14f406d3eb906783
 
 ARG DEBIAN_FRONTEND="noninteractive"
 
+COPY requirements.txt /requirements.txt
 
 RUN apt-get update -qq && \
     apt-get install -q -y --no-install-recommends \
         python3 \
         python3-pip && \
-    pip3 install nibabel==5.1.0 && \
+    pip3 install -r /requirements.txt && \
     apt-get remove -y python3-pip && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 

Singularity

@@ -2,8 +2,8 @@ Bootstrap: docker
 From: bids/example
 
 %help
-You are in the BIDS-example container. To see help run
-singularity run BIDS-example.simg -h
+You are in the BIDS-example container.
+To see help run singularity run: BIDS-example.simg -h
 
 %runscript
     exec /run.py "$@"

boutiques/bids-app-example.json → boutiques/descriptor.json

@@ -1,15 +1,18 @@
 {
     "author": "chrisfilo and others",
+    "custom": {
+      "BIDSApplicationVersion": "2.0"
+    },
     "command-line": "mkdir -p OUTPUT_DIR; /run.py BIDS_DIR OUTPUT_DIR ANALYSIS_LEVEL PARTICIPANT_LABEL SESSION_LABEL",
     "container-image": {
         "image": "bids/example",
         "type": "docker"
     },
     "description": "See https://github.com/BIDS-Apps/example",
-    "descriptor-url": "https://github.com/BIDS-Apps/example/blob/master/boutiques/bids-app-example.json",
+    "descriptor-url": "https://github.com/BIDS-Apps/example/blob/master/boutiques/descriptor.json",
     "groups": [
         {
-            "description": "For a participants analysis, an output directory name must be specified. For a group analysis, a directory containing the output of participant-level analyses must be selected. ",
+            "description": "For a participants analysis, an output directory name must be specified. For a group analysis, a directory containing the output of participant-level analyses must be selected.",
             "id": "output_directory",
             "members": [
                 "output_dir_name",
@@ -54,7 +57,8 @@
                 "participant",
                 "group"
             ],
-            "value-key": "ANALYSIS_LEVEL"
+            "value-key": "ANALYSIS_LEVEL",
+            "optional": false
         },
         {
             "command-line-flag": "--participant_label",

pyproject.toml

@@ -0,0 +1,10 @@
+[tool.black]
+line-length = 79
+
+[tool.codespell]
+
+[tool.isort]
+combine_as_imports = true
+line_length = 79
+profile = "black"
+skip_gitignore = true

requirements.in

@@ -0,0 +1 @@
+nibabel

requirements.txt

@@ -0,0 +1,12 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --strip-extras requirements.in
+#
+nibabel==5.2.1
+    # via -r requirements.in
+numpy==1.26.4
+    # via nibabel
+packaging==24.0
+    # via nibabel