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Try seg and upload artefacts #3

Try seg and upload artefacts

Try seg and upload artefacts #3

Workflow file for this run

name: Reconstruct and evaluate
on:
workflow_call:
inputs:
algo_list:
required: true
type: string
runner:
required: true
type: string
jobs:
# Defining matrix for OS and Python
recon_and_evaluate:
name: Matrix Test
if: ${{ inputs.algo_list != '[]' }}
runs-on: ${{ fromJSON(inputs.runner) }}
# Default shell for ALL subsequent steps.
defaults:
run:
shell: bash -l {0}
# Defining matrix for OS and Python
strategy:
fail-fast: false
matrix:
algo: ${{ fromJSON(inputs.algo_list) }}
steps:
- uses: actions/checkout@v3
- name: Get modified algorithms
id: getfile
run: |
shell: bash
# Step 2: Install environment.
- name: Install Conda Env All OS
uses: conda-incubator/setup-miniconda@v2
with:
python-version: 3.9
activate-environment: venv
auto-update-conda: true
environment-file: environment.yml
# Step 3: List conda info, conda packages
- name: Conda info and list
# List
run: |
conda info
conda list
- name: Reconstruct and evaluate
run: |
#sudo apt-get update
#sudo apt-get install python3.10 python3.10-venv python-is-python3 -y
#pip install osfclient argparse numpy scikit-learn scikit-image scipy
export PATH=$PATH:/home/runnerx/.local/bin
export PIPELINE_NAME="$(basename "${{ matrix.algo }}")"
bash run.sh algos/${PIPELINE_NAME}

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You have an error in your yaml syntax on line 64
- name: Reconstruct and evaluate
run: |
#sudo apt-get update
#sudo apt-get install python3.10 python3.10-venv python-is-python3 -y
#pip install osfclient argparse numpy scikit-learn scikit-image scipy
export PATH=$PATH:/home/runnerx/.local/bin
export PIPELINE_NAME="$(basename "${{ matrix.algo }}")"
bash run.sh algos/${PIPELINE_NAME}
- name: Archive production artifacts
uses: actions/upload-artifact@v4
with:
name: Segmentation files
path: |
output/${PIPELINE_NAME}/output.tar.gz