reset history with no annex

.dockerignore

@@ -0,0 +1,12 @@
+# ignoring this might speed up build
+# by preventing passing extra content to the docker daemon
+
+.simg
+
+tests/data
+
+env
+
+tmp
+
+docs/build

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+count = True
+show-source = True
+statistics = True
+max_function_length = 200

.gitattributes

@@ -0,0 +1,8 @@
+* annex.backend=MD5E
+**/.git* annex.largefiles=nothing
+CHANGELOG.md annex.largefiles=nothing
+README.md annex.largefiles=nothing
+pyproject.toml annex.largefiles=nothing
+.readthedocs.yml annex.largefiles=nothing
+.github/**/*.yml annex.largefiles=nothing
+*.def annex.largefiles=nothing

.github/dependabot.yml

@@ -0,0 +1,14 @@
+---
+# Documentation
+# https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+version: 2
+updates:
+-   package-ecosystem: github-actions
+    directory: /
+    schedule:
+        interval: monthly
+
+-   package-ecosystem: gitsubmodule
+    directory: /
+    schedule:
+        interval: monthly

.github/workflows/docker.yml

@@ -0,0 +1,139 @@
+---
+name: docker build
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+env:
+    USER_NAME: bids
+    REPO_NAME: cat12
+    IMAGE: /home/runner/work/Remi-Gau/cat12-container/docker
+
+jobs:
+
+    docker-build:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: actions/checkout@v4
+            with:
+                fetch-depth: 0
+        # # cache tarred docker image to speed up build on follow up runs
+        # -   uses: actions/cache@v4
+        #     id: cache
+        #     with:
+        #         path: ${{ env.IMAGE }}/image.tar
+        #         key: data
+        # -   if: ${{ steps.cache.outputs.cache-hit != 'true' }}
+        #     name: Load image
+        #     run: docker load -i ${{ env.IMAGE }}/image.tar
+        -   name: Build the Docker image
+            run: |
+                docker build . --tag ${{env.USER_NAME}}/${{env.REPO_NAME}}
+        -   name: Check image size and version
+            run: |
+                docker images
+                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --version
+        -   name: Run simple commands
+            run: |
+                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} --help
+                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant view segment --verbose 3
+                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant copy segment --verbose 3
+                docker run --rm ${{env.USER_NAME}}/${{env.REPO_NAME}} . /foo participant segment --help
+        -   name: Save docker image
+            run: |
+                mkdir -p ${{ env.IMAGE }}
+                docker save "${{env.USER_NAME}}/${{env.REPO_NAME}}" > "${{ env.IMAGE }}/image.tar"
+        -   name: Upload docker artifacts
+            uses: actions/upload-artifact@v4
+            with:
+                name: docker
+                path: ${{ env.IMAGE }}
+
+    one-session:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                type: [default, simple, enigma]
+            fail-fast: false
+        needs: docker-build
+        steps:
+        -   name: Install dependencies
+            run: |
+                sudo apt-get -y -qq update
+                sudo apt-get -y install tree
+        -   uses: actions/checkout@v4
+            with:
+                fetch-depth: 0
+        -   name: Restore docker image
+            uses: actions/download-artifact@v4
+            with:
+                name: docker
+                path: ${{ env.IMAGE }}
+        -   name: Load image
+            run: docker load -i ${{ env.IMAGE }}/image.tar
+        -   name: Get data
+            run: make tests/data/MoAEpilot
+        -   name: Segment
+            run: |
+                docker run --rm \
+                    -v ${PWD}/tests/data/MoAEpilot:/data \
+                    ${{env.USER_NAME}}/${{env.REPO_NAME}} \
+                        /data /data/derivatives participant \
+                        segment --verbose 3 --type ${{ matrix.type }}
+                tree ${PWD}/tests/data/
+        -   name: Upload output artifact
+            uses: actions/upload-artifact@v4
+            with:
+                name: output_${{ matrix.type }}
+                path: /home/runner/work/cat12-container/cat12-container/tests/data/MoAEpilot/derivatives
+
+    two-sessions:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                type: [long_0, long_2]
+            fail-fast: false
+        needs: docker-build
+        steps:
+        -   name: Install python
+            uses: actions/setup-python@v5
+            with:
+                python-version: '3.11'
+        -   name: Install dependencies
+            run: |
+                sudo apt-get -y -qq update
+                sudo apt-get -y install git-annex tree
+                pip install datalad
+        -   uses: actions/checkout@v4
+            with:
+                fetch-depth: 0
+        -   name: Restore docker image
+            uses: actions/download-artifact@v4
+            with:
+                name: docker
+                path: ${{ env.IMAGE }}
+        -   name: Load image
+            run: docker load -i ${{ env.IMAGE }}/image.tar
+        -   name: Get data
+            run: make data_ds002799
+        -   name: Segment
+            run: |
+                docker run --rm \
+                    -v ${PWD}/tests/data/ds002799:/data \
+                    ${{env.USER_NAME}}/${{env.REPO_NAME}} \
+                        /data /data/derivatives participant \
+                        segment --verbose 3 --type ${{ matrix.type }} \
+                        --participant_label 292 294 \
+                        --skip_validation
+                tree ${PWD}/tests/data/
+        -   name: Upload output artifact
+            uses: actions/upload-artifact@v4
+            with:
+                name: output_${{ matrix.type }}
+                path: /home/runner/work/cat12-container/cat12-container/tests/data/ds002799/derivatives

.gitignore

@@ -0,0 +1,9 @@
+.simg
+
+tests/data
+
+env
+
+tmp
+
+docs/build

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+---
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+    -   id: check-yaml
+    -   id: check-json
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-case-conflict
+    -   id: check-merge-conflict
+    -   id: mixed-line-ending
+
+-   repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
+    rev: 0.2.3
+    hooks:
+    -   id: yamlfmt
+        args: [--mapping, '4', --sequence, '4', --offset, '0']
+
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.3.0
+    hooks:
+    -   id: codespell
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: [--line-length, '79', --profile, black]
+
+-   repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.8.0
+    hooks:
+    -   id: black
+        args: [--line-length, '79']
+
+-   repo: https://github.com/pycqa/flake8
+    rev: 7.1.1
+    hooks:
+    -   id: flake8
+        args: [--config, .flake8, --verbose]
+        additional_dependencies: [flake8-docstrings, flake8-use-fstring, flake8-functions, flake8-bugbear]

.readthedocs.yml

@@ -0,0 +1,26 @@
+---
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+    os: ubuntu-22.04
+    tools:
+        python: '3.12'
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+    configuration: docs/source/conf.py
+    builder: html
+    fail_on_warning: false
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+    install:
+    -   method: pip
+        path: .
+        extra_requirements:
+        -   docs

CHANGELOG.md

@@ -0,0 +1,22 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!--
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+-->
+
+## [Unreleased]

Dockerfile

@@ -0,0 +1,85 @@
+FROM ubuntu:22.04@sha256:340d9b015b194dc6e2a13938944e0d016e57b9679963fdeb9ce021daac430221
+
+LABEL org.opencontainers.image.authors="[email protected], Malgorzata Wierzba ([email protected]), Felix Hoffstaedter ([email protected]), Remi Gau ([email protected])"
+LABEL org.opencontainers.image.source="https://gin.g-node.org/felixh/cat12-container"
+LABEL org.opencontainers.image.version="v1.1dev"
+LABEL org.opencontainers.image.licenses="MIT"
+LABEL org.opencontainers.image.title="cat12-container"
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    FORCE_SPMMCR="1" \
+    SPM_HTML_BROWSER="0" \
+    MCR_INHIBIT_CTF_LOCK="1" \
+    MCR_VERSION="2017b"
+ENV LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/MCR-${MCR_VERSION}/v93/runtime/glnxa64:/opt/MCR-${MCR_VERSION}/v93/bin/glnxa64:/opt/MCR-${MCR_VERSION}/v93/sys/os/glnxa64:/opt/MCR-${MCR_VERSION}/v93/extern/bin/glnxa64" \
+    MATLABCMD="/opt/MCR-${MCR_VERSION}/v93/toolbox/matlab" \
+    XAPPLRESDIR="/opt//opt/MCR-${MCR_VERSION}/v93/x11/app-defaults" \
+    MCRROOT="/opt/MCR-${MCR_VERSION}/v93" \
+    CAT_VERSION=".8.1_r2042_R${MCR_VERSION}" \
+    DENO_INSTALL="/root/.deno"
+ENV SPMROOT="/opt/CAT12${CAT_VERSION}" \
+    PATH="$DENO_INSTALL/bin:/opt/CAT12${CAT_VERSION}:$PATH" \
+    STANDALONE="/opt/CAT12${CAT_VERSION}/standalone"
+
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bc \
+           bzip2 \
+           ca-certificates \
+           curl \
+           dbus-x11 \
+           libncurses5 \
+           libxext6 \
+           libxmu6 \
+           libxpm-dev \
+           libxt6 \
+           locales \
+           openjdk-8-jre \
+           python3 \
+           pip \
+           unzip \
+    && rm -rf /var/lib/apt/lists/* \
+    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && update-locale LANG="en_US.UTF-8" \
+    && chmod 777 /opt && chmod a+s /opt
+
+RUN echo "Downloading MATLAB Compiler Runtime ..." \
+    && export TMPDIR="$(mktemp -d)" \
+    && curl  -o "$TMPDIR/mcr.zip" https://ssd.mathworks.com/supportfiles/downloads/R${MCR_VERSION}/deployment_files/R${MCR_VERSION}/installers/glnxa64/MCR_R${MCR_VERSION}_glnxa64_installer.zip \
+    && unzip -q "$TMPDIR/mcr.zip" -d "$TMPDIR/mcrtmp" \
+    && "$TMPDIR/mcrtmp/install" -destinationFolder /opt/MCR-${MCR_VERSION} -mode silent -agreeToLicense yes \
+    && rm -rf "$TMPDIR" \
+    && unset TMPDIR
+
+RUN echo "Downloading standalone CAT12 ..." \
+    && curl -fL -o /tmp/cat12.zip http://www.neuro.uni-jena.de/cat12/CAT12${CAT_VERSION}_MCR_Linux.zip \
+    && unzip -q /tmp/cat12.zip -d /tmp \
+    && rm -rf /tmp/cat12.zip \
+    && mkdir -p /opt/CAT12${CAT_VERSION} \
+    && mv /tmp/*${CAT_VERSION}*/* /opt/CAT12${CAT_VERSION}/ \
+    && chmod -R 777 /opt/CAT12${CAT_VERSION} \
+    # Test
+    && /opt/CAT12${CAT_VERSION}/spm12 function exit
+
+## Install BIDS validator
+RUN curl -fsSL https://deno.land/install.sh | sh && \
+    deno install -Agf -n bids-validator jsr:@bids/[email protected]
+
+# transfer code and set permission
+RUN mkdir -p /code
+COPY ./code/requirements.txt /code
+RUN pip install -r /code/requirements.txt
+
+COPY ./code /code
+RUN ls /code && find /code -type f -print0 | xargs -0 chmod +r
+
+# modify enigma script to output content to path defined by an env variable
+RUN sed -i -e "s/cat_version/getenv('OUTPUT_DIR')/g" /opt/CAT12${CAT_VERSION}/standalone/cat_standalone_segment_enigma.m
+
+WORKDIR ${STANDALONE}
+
+ENTRYPOINT ["python3", "/code/main.py"]

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 Małgorzata Wierzba, Felix Hoffstaedter, Michael Hanke
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.