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change the pip version
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benmalef committed Jun 26, 2024
1 parent 81e4d66 commit 2d4bbac
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154 changes: 76 additions & 78 deletions .github/workflows/openfl-test.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,35 +5,33 @@ name: OpenFL-Test

on:
push:
branches: [ master ]
branches: [master]
pull_request: {}


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@v41
with:
- 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@v41
with:
files: |
.github/*.md
.github/ISSUE_TEMPLATE/*.md
Expand All @@ -46,59 +44,59 @@ jobs:
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: |
${{ runner.os }}-pip-
- name: Set up Python 3.9
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
uses: actions/setup-python@v4
with:
python-version: 3.9
- name: Install dependencies and package
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
sudo apt-get update
sudo apt-get install libvips libvips-tools -y
python -m pip install --upgrade pip
python -m pip install wheel
pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cpu
pip install -e .
- name: Run generic unit tests to download data and construct CSVs
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
pytest --cov=. --cov-report=xml -k "prepare_data_for_ci"
# openfl tests start here
- name: Run OpenFL tests
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
echo "Removing onnx because of protobuf version conflict"
pip uninstall onnx -y
echo "Installing OpenFL"
git clone --depth=1 https://github.com/securefederatedai/openfl.git
cd openfl
git fetch --tags
# echo "Checkout the latest OpenFL tag"
# latestTag=$(git describe --tags "$(git rev-list --tags --max-count=1)")
# git checkout $latestTag
# sed -i -e 's/protobuf==3.19.6/protobuf/g' setup.py ## this should NOT be there
pip install -e .
cd ..
echo "Copying files to appropriate directories and updated headers"
head -n 1 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
tail -n +9 testing/data/train_2d_rad_segmentation.csv >> /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
head -n 8 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/train.csv
sed -i 's/# n_channels: 3/num_channels: 3/g' testing/config_segmentation.yaml
config_to_use=$(pwd)/testing/config_segmentation.yaml
cd openfl
python -m tests.github.test_gandlf --template gandlf_seg_test --fed_workspace aggregator --col1 one --col2 two --rounds-to-train 1 --gandlf_config $config_to_use
- 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: |
${{ runner.os }}-pip-
- name: Set up Python 3.9
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
uses: actions/setup-python@v4
with:
python-version: 3.9
- name: Install dependencies and package
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
sudo apt-get update
sudo apt-get install libvips libvips-tools -y
python -m pip install --upgrade pip==24.0
python -m pip install wheel
pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cpu
pip install -e .
- name: Run generic unit tests to download data and construct CSVs
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
pytest --cov=. --cov-report=xml -k "prepare_data_for_ci"
# openfl tests start here
- name: Run OpenFL tests
if: steps.changed-files-specific.outputs.only_modified == 'false' # Run on any non-docs change
run: |
echo "Removing onnx because of protobuf version conflict"
pip uninstall onnx -y
echo "Installing OpenFL"
git clone --depth=1 https://github.com/securefederatedai/openfl.git
cd openfl
git fetch --tags
# echo "Checkout the latest OpenFL tag"
# latestTag=$(git describe --tags "$(git rev-list --tags --max-count=1)")
# git checkout $latestTag
# sed -i -e 's/protobuf==3.19.6/protobuf/g' setup.py ## this should NOT be there
pip install -e .
cd ..
echo "Copying files to appropriate directories and updated headers"
head -n 1 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
tail -n +9 testing/data/train_2d_rad_segmentation.csv >> /home/runner/work/GaNDLF/GaNDLF/openfl/valid.csv
head -n 8 testing/data/train_2d_rad_segmentation.csv > /home/runner/work/GaNDLF/GaNDLF/openfl/train.csv
sed -i 's/# n_channels: 3/num_channels: 3/g' testing/config_segmentation.yaml
config_to_use=$(pwd)/testing/config_segmentation.yaml
cd openfl
python -m tests.github.test_gandlf --template gandlf_seg_test --fed_workspace aggregator --col1 one --col2 two --rounds-to-train 1 --gandlf_config $config_to_use
2 changes: 1 addition & 1 deletion Dockerfile-CPU
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ LABEL version=1.0
RUN apt-get update && apt-get install -y software-properties-common
RUN add-apt-repository ppa:deadsnakes/ppa
RUN apt-get update && apt-get install -y python3.9 python3-pip libjpeg8-dev zlib1g-dev python3-dev libpython3.9-dev libffi-dev libgl1
RUN python3.9 -m pip install --upgrade pip
RUN python3.9 -m pip install --upgrade pip==24.0
# EXPLICITLY install cpu versions of torch/torchvision (not all versions have +cpu modes on PyPI...)
RUN python3.9 -m pip install torch==2.2.1 torchvision==0.17.1 torchaudio==2.2.1 --index-url https://download.pytorch.org/whl/cpu
RUN python3.9 -m pip install openvino-dev==2023.0.1 opencv-python-headless mlcube_docker
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