Draft sMRIPost workflow

.circleci/get_data.py

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+#!/usr/bin/env python3
+"""Download test data."""
+
+import sys
+
+from smripost_linc.tests.utils import download_test_data
+
+if __name__ == '__main__':
+    data_dir = sys.argv[1]
+    dset = sys.argv[2]
+    download_test_data(dset, data_dir)

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.html,dataset_description.json,*.bib
+# te - TE
+# Weill - name
+# reson - Reson. abbreviation in citation
+ignore-words-list = te,weill,reson

.dockerignore

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+# python cache
+__pycache__/**/*
+__pycache__
+*.pyc
+
+# python distribution
+build/**/*
+build
+dist/**/*
+dist
+smripost_linc.egg-info/**/*
+smripost_linc.egg-info
+.eggs/**/*
+.eggs

.git_archival.txt

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+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

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+.git_archival.txt  export-subst

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Something not working as described? Missing/incorrect documentation? This is the place.
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+## Summary
+<!--What is the nature of the bug?-->
+
+## Additional details
+<!--Please fill in the following details-->
+- sMRIPost-LINC version:
+- Docker version:
+- Apptainer version:
+
+### What were you trying to do?
+
+### What did you expect to happen?
+
+### What actually happened?
+
+## Reproducing the bug
+<!--Please share any steps you performed that revealed the bug-->
+<!--Please include any code snippets.
+Enclose them in triple back-ticks (```)
+Like this:
+
+```
+<code>
+```
+-->

.github/ISSUE_TEMPLATE/config.yml

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+contact_links:
+  - name: Usage question
+    url: https://neurostars.org/tags/c/software-support/234/smripost-linc
+    about: Please ask questions about using sMRIPost-LINC on NeuroStars.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Got an idea for a new feature, or changing an existing one? This is the place.
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+## Summary
+<!--What would you like changed/added and why?-->
+
+## Additional details
+<!--What would be the benefit?-->
+
+## Next steps
+<!--Do you have any ideas about the implementation?-->

.github/config.yml

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+# Configuration for new-pr-welcome - https://github.com/behaviorbot/new-pr-welcome
+
+# Comment to be posted to on PRs from first time contributors in your repository
+newPRWelcomeComment: >
+  Thanks for opening this pull request!
+  We have detected this is the first time you have contributed
+  to *sMRIPost-LINC*.
+  We ask you to read through the Contributing Guide:
+  https://github.com/pennlinc/smripost_linc/blob/main/CONTRIBUTING.md
+
+  These are guidelines intended to make communication easier by describing a consistent process, but
+  don't worry if you don't get it everything exactly "right" on the first try.
+
+  To boil it down, here are some highlights:
+
+  1.  Consider starting a conversation in the issues list before submitting a pull request.
+      The discussion might save you a lot of time coding.
+  2.  Any code you submit will be licensed under the same terms (BSD 3-Clause) as the rest of smripost_linc.
+
+  A pull request is a conversation. We may ask you to make some changes before accepting your PR,
+  and likewise, you should feel free to ask us any questions you have.

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    labels: ["maintenance", "ignore-for-release"]
+    assignees: ["tsalo"]
+    schedule:
+      interval: "weekly"
+  - package-ecosystem: pip
+    directory: "/"
+    labels: ["maintenance", "ignore-for-release"]
+    schedule:
+      interval: weekly

.github/pull_request_template.md

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+Closes
+
+## Changes proposed in this pull request
+<!--
+Please describe here the main features / changes proposed for review and integration in smripost_linc
+If this PR addresses some existing problem, please use GitHub's citing tools
+(eg. ref #, closes # or fixes #).
+If there is not an existing issue open describing the problem, please consider opening a new
+issue first and then link it from here (so the *smripost_linc* community has a better understanding
+of ongoing development efforts and possible overlaps between contributions).
+-->
+
+## Documentation that should be reviewed
+<!--
+Please summarize here the main changes to the documentation that the reviewers should be aware of.
+-->

.github/release.yml

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+changelog:
+  exclude:
+    labels:
+      - ignore-for-release
+  categories:
+    - title: 🛠 Breaking Changes
+      labels:
+        - breaking-change
+    - title: 🎉 Exciting New Features
+      labels:
+        - enhancement
+    - title: 👎 Deprecations
+      labels:
+        - deprecation
+    - title: 🐛 Bug Fixes
+      labels:
+        - bug
+    - title: Other Changes
+      labels:
+        - "*"

.github/workflows/contrib.yml

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+name: Contribution checks
+
+on:
+  push:
+    branches:
+      - main
+      - maint/*
+  pull_request:
+    branches:
+      - main
+      - maint/*
+
+defaults:
+  run:
+    shell: bash
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run ruff check .
+      - run: pipx run ruff format --diff .
+
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.gitignore

@@ -1,3 +1,11 @@
+.vscode
+.DS_Store
+.*.swp
+.mypy_cache
+.pytest_cache
+.ruff_cache
+.coverage
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.mailmap

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+Taylor Salo <[email protected]>
+Taylor Salo <[email protected]> <[email protected]>

.pre-commit-config.yaml

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+exclude: ".*/data/.*"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: '.*\.svg'
+      - id: end-of-file-fixer
+        exclude: '.*\.svg'
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+      - id: ruff
+        args: [ --select, ISC001, --fix ]

.readthedocs.yml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  apt_packages:
+    - graphviz
+  tools:
+    python: "3.11"
+  jobs:
+    post_checkout:
+      # Fetch full history, but don't fail if we already have it
+      - git fetch --unshallow || true
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

.versions.json

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+{
+	"flagged": {
+	}
+}

.zenodo.json

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+{
+  "title": "sMRIPost-LINC: a robust preprocessing pipeline for functional MRI",
+  "description": "<p>sMRIPost-LINC is a robust and easy-to-use pipeline for running ICA-AROMA on preprocessed fMRI data organized in BIDS format.</p>",
+  "contributors": [],
+  "creators": [
+    {
+      "affiliation": "University of Pennsylvania",
+      "name": "Salo, Taylor",
+      "orcid": "0000-0001-9813-3167"
+    },
+    {
+      "affiliation": "University of Pennsylvania",
+      "name": "Cieslak, Matthew",
+      "orcid": "0000-0002-1931-4734"
+    },
+    {
+      "affiliation": "University of Pennsylvania",
+      "name": "Satterthwaite, Theodore",
+      "orcid": "0000-0001-7072-9399"
+    }
+  ],
+  "keywords": [
+    "neuroimaging",
+    "workflow",
+    "pipeline",
+    "postprocessing",
+    "sMRI",
+    "BIDS"
+  ],
+  "license": "Apache-2.0",
+  "related_identifiers": [
+    {
+      "identifier": "https://smripost_linc.org",
+      "relation": "documents",
+      "scheme": "url"
+    },
+    {
+      "identifier": "10.1038/s41592-018-0235-4",
+      "relation": "isPartOf",
+      "scheme": "doi"
+    }
+  ],
+  "upload_type": "software"
+}

CHANGES.rst

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+23.0.0 ()
+=========
+
+sMRIPost-LINC's initial release.

CODE_OF_CONDUCT.md

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+# sMRIPost-LINC Code of Conduct
+
+*sMRIPost-LINC* is a project of the
+[*NiPreps* Community, and is under its code of conduct](https://www.pennlinc.org/community/CODE_OF_CONDUCT/).

CONTRIBUTING.md

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+# Contributing to *sMRIPost-LINC*
+
+*sMRIPost-LINC* is a project of the
+[*NiPreps* Community, which specifies the contributing guidelines](https://www.pennlinc.org/community/).