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Remove t2_sc_seg.nii.gz and t2_lesion_seg.nii.gz. Context: https://gi… #83

Remove t2_sc_seg.nii.gz and t2_lesion_seg.nii.gz. Context: https://gi…

Remove t2_sc_seg.nii.gz and t2_lesion_seg.nii.gz. Context: https://gi… #83

name: "Run batch_single_subject.sh"
# The tl;dr purpose of this workflow is to:
# - A) Run all of the commands in the SCT Course
# - B) If the workflow is run manually, then take the output files and package them into tutorial-specific datasets.
#
# In-depth explanation:
# Most of SCT's tutorials depend on files generated by previous steps. (For example, 'sct_register_to_template'
# depends on the segmented spinal cord image file generated by `sct_deepseg`. This creates a dilemma: If we want
# SCT's tutorials to stand alone, we need to provide these intermediate files. But, if we want to run the tutorials
# start to finish in a sequence (e.g. during the SCT Course), it would be confusing if the intermediate files
# were already there.
#
# The solution is to only store the minimally-necessary files in the repository, then generate the intermediate files
# using this workflow. That way, we can provide 2 different downloads:
# - 'sct_course_data.zip': Files required to run the SCT course from start to finish.
# - 'registration.zip', 'segmentation.zip', etc.: Files required by individual tutorials.
on:
push:
branches:
- master
pull_request:
workflow_dispatch:
inputs:
release_title:
description: 'Release title (e.g. rYYYYMMDD)'
required: true
jobs:
run-course-script:
runs-on: ubuntu-latest
steps:
- name: Checkout spinalcordtoolbox
uses: actions/checkout@v4
with:
repository: spinalcordtoolbox/spinalcordtoolbox
path: spinalcordtoolbox
# install_sct edits ~/.bashrc, but those environment changes don't get passed to subsequent steps in GH Actions.
# So, we filter through the .bashrc and pass the values to $GITHUB_ENV and $GITHUB_PATH.
# Relevant documentation: https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#environment-files
# This workaround should be replaced by https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3198#discussion_r568225392
- name: Install spinalcordtoolbox
run: |
cd spinalcordtoolbox
./install_sct -iy
cat ~/.bashrc | grep "export SCT_DIR" | cut -d " " -f 2 >> $GITHUB_ENV
cat ~/.bashrc | grep "export MPLBACKEND" | cut -d " " -f 2 >> $GITHUB_ENV
cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH
- name: "Checkout '${{ github.event.repository.name }}'"
uses: actions/checkout@v4
with:
ref: ${{ env.GITHUB_SHA }}
path: ${{ github.event.repository.name }}
- name: Run batch_single_subject.sh to generate intermediate files
run: |
cd "${{ github.event.repository.name }}/single_subject"
./batch_single_subject.sh
- name: "Package data into tutorial-specific .zip files"
run: |
cd ${{ github.event.repository.name }}
awk -F, '{ print $1,$2 }' tutorial-datasets.csv | xargs -l zip -ur
- uses: ncipollo/release-action@v1
name: Create release ('${{ github.event.inputs.release_title }}')
id: create_release
with:
tag: ${{ github.event.inputs.release_title }}
commit: ${{ env.GITHUB_SHA }}
token: ${{ secrets.GITHUB_TOKEN }}
# Only create release if workflow is run manually. (This allows the workflow to double as a PR test.)
if: github.event_name == 'workflow_dispatch'
- uses: xresloader/upload-to-github-release@v1
name: Attach .zip files to newly-created release
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
file: "${{ github.event.repository.name }}/*.zip"
draft: false
tag_name: ${{ github.event.inputs.release_title }}
release_id: ${{ steps.create_release.outputs.id }}
# Only attach to release if workflow is run manually. (This allows the workflow to double as a PR test.)
if: github.event_name == 'workflow_dispatch'