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Remi-GauRemi-Gau
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Merge pull request #42 from bids-apps/lint
[ENH] reformat, refactor and implement some bids app 2.0 features
2 parents 37b2e3d + 32d679c commit a648781

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-99
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‎.circleci/config.yml

+8-16
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@@ -50,42 +50,34 @@ jobs:
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- run: mkdir -p ${HOME}/outputs<< parameters.dataset >>
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- run: sudo apt-get install tree
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- run:
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name: print version
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command: |
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docker run -ti --rm --read-only \
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-v /tmp/workspace/data/ds114_test1:/bids_dataset \
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bids/${CIRCLE_PROJECT_REPONAME,,} --version
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# participant level tests for single session dataset
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- run:
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command: |
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docker run -ti --rm --read-only \
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-v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
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-v ${HOME}/outputs<< parameters.dataset >>:/outputs \
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bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01
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no_output_timeout: 6h
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- run:
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name: participant level test
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command: |
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docker run -ti --rm --read-only \
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-v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
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-v ${HOME}/outputs<< parameters.dataset >>:/outputs \
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bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02
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no_output_timeout: 6h
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bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant
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tree ${HOME}/outputs<< parameters.dataset >>
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- run:
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name: group level test
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command: |
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docker run -ti --rm --read-only \
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-v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
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-v ${HOME}/outputs1:/outputs \
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-v ${HOME}/outputs<< parameters.dataset >>:/outputs \
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bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group
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no_output_timeout: 6h
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- store_artifacts:
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path: ~/output<< parameters.dataset >>
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tree ${HOME}/outputs<< parameters.dataset >>
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deploy:
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machine:
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image: ubuntu-2204:2022.10.2
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‎.github/workflows/validate.yml

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

‎.pre-commit-config.yaml

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

‎Dockerfile

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

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

‎boutiques/bids-app-example.json renamed to ‎boutiques/descriptor.json

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{
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"author": "chrisfilo and others",
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"custom": {
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"BIDSApplicationVersion": "2.0"
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},
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"command-line": "mkdir -p OUTPUT_DIR; /run.py BIDS_DIR OUTPUT_DIR ANALYSIS_LEVEL PARTICIPANT_LABEL SESSION_LABEL",
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"container-image": {
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"image": "bids/example",
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"type": "docker"
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},
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"description": "See https://github.com/BIDS-Apps/example",
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"descriptor-url": "https://github.com/BIDS-Apps/example/blob/master/boutiques/bids-app-example.json",
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"descriptor-url": "https://github.com/BIDS-Apps/example/blob/master/boutiques/descriptor.json",
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"groups": [
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{
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"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. ",
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"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.",
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"id": "output_directory",
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"members": [
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"output_dir_name",
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"participant",
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"group"
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],
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"value-key": "ANALYSIS_LEVEL"
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"value-key": "ANALYSIS_LEVEL",
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"optional": false
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},
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{
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"command-line-flag": "--participant_label",

‎pyproject.toml

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[tool.black]
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line-length = 79
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[tool.codespell]
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[tool.isort]
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combine_as_imports = true
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line_length = 79
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profile = "black"
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skip_gitignore = true

‎requirements.in

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nibabel

‎requirements.txt

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

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