Update README.md #80
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name: Algorithm Analysis | |
on: | |
push: | |
branches: | |
- 'main' | |
- 'analysis/**' | |
jobs: | |
algorithms: | |
runs-on: ubuntu-latest | |
outputs: # here we use the outputs from steps, and set outputs for the job `configure` | |
algorithms: ${{ steps.algorithms.outputs.algorithms }} | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
id: setup_python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
- name: Cache pip | |
uses: actions/cache@v3 | |
id: pip-cache | |
with: | |
key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }} | |
path: ${{ env.pythonLocation }} | |
if: steps.pip-cache.outputs.cache-hit != 'true' | |
- name: Install dependencies | |
run: | | |
pip install -r requirements.txt | |
- name: Read algorithms | |
id: algorithms | |
run: | | |
echo 'algorithms<<EOF' >> $GITHUB_OUTPUT | |
cat ./tests/IVIMmodels/unit_tests/algorithms.json >> $GITHUB_OUTPUT | |
echo 'EOF' >> $GITHUB_OUTPUT | |
- name: Log algorithms | |
run: | | |
echo "${{fromJson(steps.algorithms.outputs.algorithms)}}" | |
echo "${{fromJson(steps.algorithms.outputs.algorithms).algorithms}}" | |
- name: Log algorithms file | |
run: cat ./tests/IVIMmodels/unit_tests/algorithms.json | |
build: | |
runs-on: ubuntu-latest | |
needs: algorithms | |
continue-on-error: false | |
strategy: | |
fail-fast: false | |
matrix: | |
algorithm: ${{fromJson(needs.algorithms.outputs.algorithms).algorithms}} | |
SNR: [10, 30, 50, 100, 200] | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up Python | |
uses: actions/setup-python@v5 | |
with: | |
python-version: "3.11" | |
if: steps.pip-cache.outputs.cache-hit != 'true' | |
- name: Restore cache | |
id: python-cache | |
uses: actions/cache@v3 | |
with: | |
key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }} | |
path: ${{ env.pythonLocation }} | |
- name: Generate fitting data | |
run: | | |
python -m pytest -m slow --selectAlgorithm ${{ matrix.algorithm }} --saveFileName test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv --SNR ${{ matrix.SNR }} --fitCount 300 --saveDurationFileName test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv | |
- name: Upload raw data | |
uses: actions/upload-artifact@v3 | |
with: | |
name: Working_Data | |
retention-days: 1 | |
path: | | |
test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv | |
test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv | |
merge: | |
runs-on: ubuntu-latest | |
needs: build | |
steps: | |
- name: Download artifacts | |
uses: actions/download-artifact@v3 | |
with: | |
path: artifacts | |
- name: Merge fitting results | |
run: | | |
head -n 1 $(ls artifacts/Working_Data/test_output_*.csv | head -n 1) > test_output.csv | |
tail -q -n +2 artifacts/Working_Data/test_output_*.csv >> test_output.csv | |
- name: Merge timing results | |
run: | | |
head -n 1 $(ls artifacts/Working_Data/test_duration_*.csv | head -n 1) > test_duration.csv | |
tail -q -n +2 artifacts/Working_Data/test_duration_*.csv >> test_duration.csv | |
- name: Upload merged artifacts | |
uses: actions/upload-artifact@v3 | |
with: | |
name: Data | |
path: | | |
test_output.csv | |
test_duration.csv | |
analyze: | |
runs-on: ubuntu-latest | |
needs: merge | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up R | |
uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
- name: Install R dependencies | |
uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
packages: | | |
any::plyr | |
any::dplyr | |
any::tidyverse | |
any::data.table | |
any::ggplot2 | |
- name: Download artifacts | |
uses: actions/download-artifact@v3 | |
with: | |
name: Data | |
- name: Generate figures | |
run: Rscript --vanilla tests/IVIMmodels/unit_tests/analyze.r test_output.csv test_duration.csv | |
- name: Upload figures | |
uses: actions/upload-artifact@v3 | |
if: always() | |
with: | |
name: Figures | |
path: | | |
D.pdf | |
f.pdf | |
Dp.pdf | |
D_limited.pdf | |
f_limited.pdf | |
Dp_limited.pdf | |
durations.pdf | |
curve_plot.pdf | |
fitted_curves.pdf | |
compare: | |
runs-on: ubuntu-latest | |
needs: merge | |
steps: | |
- uses: actions/checkout@v4 | |
- name: Set up R | |
uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
- name: Install R dependencies | |
uses: r-lib/actions/setup-r-dependencies@v2 | |
with: | |
packages: | | |
any::tidyverse | |
any::assertr | |
- name: Download artifacts | |
uses: actions/download-artifact@v3 | |
with: | |
name: Data | |
- name: Test against previous results | |
run: Rscript --vanilla tests/IVIMmodels/unit_tests/compare.r test_output.csv test_reference.csv tests/IVIMmodels/unit_tests/reference_output.csv test_results.csv | |
- name: Upload data | |
uses: actions/upload-artifact@v3 | |
if: always() | |
with: | |
name: Comparison | |
path: | | |
test_reference.csv | |
test_results.csv |