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Add error handling for brain age model #539

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Add error handling for brain age model

Add error handling for brain age model #539

Workflow file for this run

.github/workflows/openfl-test.yml at 13b0cc0
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: OpenFL-Test
on:
push:
branches: [ master ]
pull_request:
branches: [ master ]
jobs:
openfl-test:
runs-on: ubuntu-latest
steps:
- name: Free space
run: |
df -h
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
sudo rm -rf "$ANDROID_SDK_ROOT"
df -h
- name: Checkout
uses: actions/checkout@v3
# Use changed-files-specific action to collect file changes.
# The following commented condition applied to a step will run that step only if non-docs files have changed.
# It should be applied to all functionality-related steps.
# if: steps.changed-files-specific.outputs.only_modified == 'false'
- name: Detect and screen file changes
id: changed-files-specific
uses: tj-actions/changed-files@v34
with:
files: |
.github/*.md
.github/ISSUE_TEMPLATE/*.md
.github/workflows/devcontainer.yml
.github/workflows/docker-image.yml
.devcontainer/**
docs/**
mlcube/**
*.md
LICENSE
Dockerfile-*
- name: Summarize docs and non-docs modifications
run: |
echo "List of docs files that have changed: ${{ steps.changed-files-specific.outputs.all_modified_files }}"
echo "Changed non-docs files: ${{ steps.changed-files-specific.outputs.other_modified_files }}"
# This second step is unnecessary but highly recommended because
# It will cache database and saves time re-downloading it if database isn't stale.
- name: Cache pip
uses: actions/cache@v3
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Set up Python 3.8
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
uses: actions/setup-python@v4
with:
python-version: 3.8
- name: Install dependencies and package
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
sudo apt-get update
sudo apt-get install libvips libvips-tools -y
python -m pip install --upgrade pip
python -m pip install wheel
pip install torch==1.13.1+cpu torchvision==0.14.1+cpu torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cpu
pip install -e .
- name: Run generic unit tests to download data and construct CSVs
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
pytest --cov=. --cov-report=xml -k "generic_download"
pytest --cov=. --cov-report=xml -k "generic_constructTrainingCSV"
# openfl tests start here
- name: Run OpenFL tests
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
echo "Removing onnx because of protobuf version conflict"
pip uninstall onnx -y
echo "Installing OpenFL"
git clone https://github.com/securefederatedai/openfl.git
cd openfl
git fetch --tags
git checkout $(git describe --tags --abbrev=0)
sed -i -e 's/protobuf==3.19.6/protobuf/g' setup.py ## this should NOT be there
pip install -e .
cd ..
echo "Copying files to appropriate directories"
head -n 1 testing/data/train_3d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/seg_test_val.csv
tail -n +9 testing/data/train_3d_rad_segmentation.csv >> /home/runner/work/GaNDLF/GaNDLF/openfl/seg_test_val.csv
head -n 8 testing/data/train_3d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/seg_test_train.csv
cd openfl
python -m tests.github.test_fets_challenge --template fets_challenge_seg_test --fed_workspace aggregator --col1 col1 --col2 col2 --rounds-to-train 1