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sr_bench.yml
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name: SRBench
on:
workflow_dispatch:
inputs:
repository:
required: true
type: choice
options:
- https://github.com/janoPig/HROCH.git
commit:
required: true
type: string
regressor:
required: true
type: choice
options:
- HROCH_1s
- HROCH_10s
- HROCH_1m
- HROCH_5m
env:
CACHE_NUMBER: 0
defaults:
run:
shell: bash
working-directory: /home/runner/work/
jobs:
cache_env:
runs-on: ubuntu-latest
steps:
- name: Cache conda
uses: actions/cache@v2
with:
path: /usr/share/miniconda/envs/srbench
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: cache
- name: Cache srbench
uses: actions/cache@v2
with:
path: /home/runner/work/srbench
key: ${{ runner.os }}-srbench-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: srbench
- name: Cache pmlb
uses: actions/cache@v2
with:
path: /home/runner/work/pmlb
key: ${{ runner.os }}-pmlb-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: pmlb
- name: Install SRBench
env:
REPO: ${{ github.event.inputs.repository }}@${{ github.event.inputs.commit }}
if: steps.cache.outputs.cache-hit != 'true'
run: |
echo "Install SRBench"
pwd
# clone pmlb
#git clone https://github.com/janoPig/pmlb.git
#cd pmlb
#git lfs pull
#cd ..
wget https://github.com/janoPig/pmlb/archive/refs/heads/master.zip
unzip master.zip
mv pmlb-master pmlb
# clone srbench
mkdir srbench
cd srbench
git clone --branch git_workflow --depth 1 https://github.com/janoPig/srbench.git
cd srbench
# current branch
line_old='git+https://github.com/BRANCH_PLACEHOLDER'
line_new=$(echo "git+$REPO")
sed -i "s%$line_old%$line_new%g" environment.yml
# install enviroment
# source /usr/share/miniconda/bin/activate
conda env create -f environment.yml
bbox_matrix:
needs: cache_env
strategy:
matrix:
seed: [0, 1, 2, 3, 4, 5, 6, 7 , 8, 9]
env:
SEED: ${{ matrix.seed }}
runs-on: ubuntu-latest
steps:
- name: Cache conda
uses: actions/cache@v2
with:
path: /usr/share/miniconda/envs/srbench
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: cache
- name: Cache srbench
uses: actions/cache@v2
with:
path: /home/runner/work/srbench
key: ${{ runner.os }}-srbench-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: srbench
- name: Cache pmlb
uses: actions/cache@v2
with:
path: /home/runner/work/pmlb
key: ${{ runner.os }}-pmlb-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: pmlb
- name: BBox experiment
run: |
echo "BBox experiment"
pwd
mkdir -p output/output
# install enviroment
source /usr/share/miniconda/bin/activate
conda activate srbench
cd srbench/srbench/experiment
# black-box experiment
python analyze.py ../../../pmlb/datasets -n_trials 1 -starting_seed $SEED -ml ${{ github.event.inputs.regressor }} -results ../results_blackbox -skip_tuning --local -n_jobs 2 -job_limit 100000
mv ../results_blackbox ../../../output/output/
- name: Archive production artifacts
uses: actions/upload-artifact@v3
with:
name: bbox_experiment
path: |
/home/runner/work/output
bbox_postprocessing:
needs: bbox_matrix
runs-on: ubuntu-latest
steps:
- name: Cache conda
uses: actions/cache@v2
with:
path: /usr/share/miniconda/envs/srbench
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: cache
- name: Cache srbench
uses: actions/cache@v2
with:
path: /home/runner/work/srbench
key: ${{ runner.os }}-srbench-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: srbench
- name: Cache pmlb
uses: actions/cache@v2
with:
path: /home/runner/work/pmlb
key: ${{ runner.os }}-pmlb-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: pmlb
- name: Download result
uses: actions/download-artifact@v3
with:
name: bbox_experiment
- name: BBox postprocess
run: |
echo "BBox postprocess"
pwd
ls
mkdir -p output2/output
# install enviroment
source /usr/share/miniconda/bin/activate
conda activate srbench
cd srbench/srbench
mv $GITHUB_WORKSPACE/output/results_blackbox .
cd postprocessing
python collate_blackbox_results.py ../results_blackbox
mv ../results/black-box_results.feather ../../../output2/output/
- name: Archive production artifacts
uses: actions/upload-artifact@v3
with:
name: bbox_result
path: |
/home/runner/work/output2
gt_matrix:
needs: cache_env
strategy:
matrix:
seed: [0, 1, 2, 3, 4, 5, 6, 7 , 8, 9]
noise: [0, 0.001, 0.01, 0.1]
env:
SEED: ${{ matrix.seed }}
TN: ${{ matrix.noise }}
runs-on: ubuntu-latest
steps:
- name: Cache conda
uses: actions/cache@v2
with:
path: /usr/share/miniconda/envs/srbench
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: cache
- name: Cache srbench
uses: actions/cache@v2
with:
path: /home/runner/work/srbench
key: ${{ runner.os }}-srbench-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: srbench
- name: Cache pmlb
uses: actions/cache@v2
with:
path: /home/runner/work/pmlb
key: ${{ runner.os }}-pmlb-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: pmlb
- name: GT experiment
run: |
echo "GT experiment"
pwd
mkdir -p output/output
# install enviroment
source /usr/share/miniconda/bin/activate
conda activate srbench
cd srbench/srbench/experiment
# submit the ground-truth dataset experiment.
for data in "../../../pmlb/datasets/strogatz_" "../../../pmlb/datasets/feynman_" ; do # feynman and strogatz datasets
python analyze.py \
$data"*" \
-results ../results_sym_data \
-n_trials 1 \
-starting_seed $SEED \
-ml ${{ github.event.inputs.regressor }} \
--local \
-target_noise $TN \
-sym_data \
-job_limit 100000 \
-skip_tuning \
-n_jobs 2
if [ $? -gt 0 ] ; then
break
fi
done
mv ../results_sym_data ../../../output/output/
- name: Archive production artifacts
uses: actions/upload-artifact@v3
with:
name: gt_experiment_${{ matrix.seed }}
path: |
/home/runner/work/output
gt_sympy:
needs: gt_matrix
strategy:
matrix:
seed: [0, 1, 2, 3, 4, 5, 6, 7 , 8, 9]
env:
SEED: ${{ matrix.seed }}
runs-on: ubuntu-latest
steps:
- name: Cache conda
uses: actions/cache@v2
with:
path: /usr/share/miniconda/envs/srbench
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: cache
- name: Cache srbench
uses: actions/cache@v2
with:
path: /home/runner/work/srbench
key: ${{ runner.os }}-srbench-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: srbench
- name: Cache pmlb
uses: actions/cache@v2
with:
path: /home/runner/work/pmlb
key: ${{ runner.os }}-pmlb-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: pmlb
- name: Download result
uses: actions/download-artifact@v3
with:
name: gt_experiment_${{ matrix.seed }}
- name: GT sympy
run: |
echo "GT sympy"
pwd
ls
mkdir -p output2/output
cd srbench/srbench
mv $GITHUB_WORKSPACE/output/results_sym_data .
# install enviroment
source /usr/share/miniconda/bin/activate
conda activate srbench
cd experiment
# assess the ground-truth models that were produced using sympy
for data in "../../../pmlb/datasets/strogatz_" "../../../pmlb/datasets/feynman_" ; do # feynman and strogatz datasets
for TN in 0 0.001 0.01 0.1; do # noise levels
python analyze.py \
-script assess_symbolic_model \
$data"*" \
-results ../results_sym_data \
-target_noise $TN \
-ml ${{ github.event.inputs.regressor }} \
--local \
-sym_data \
-n_trials 1 \
-starting_seed $SEED \
-job_limit 100000 \
-n_jobs 2
if [ $? -gt 0 ] ; then
break
fi
done
done
mv ../results_sym_data ../../../output2/output/
- name: Archive production artifacts
uses: actions/upload-artifact@v3
with:
name: gt_sympy
path: |
/home/runner/work/output2
gt_postprocessing:
needs: gt_sympy
runs-on: ubuntu-latest
steps:
- name: Cache conda
uses: actions/cache@v2
with:
path: /usr/share/miniconda/envs/srbench
key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: cache
- name: Cache srbench
uses: actions/cache@v2
with:
path: /home/runner/work/srbench
key: ${{ runner.os }}-srbench-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: srbench
- name: Cache pmlb
uses: actions/cache@v2
with:
path: /home/runner/work/pmlb
key: ${{ runner.os }}-pmlb-${{ env.CACHE_NUMBER }}-${{ github.sha }}
id: pmlb
- name: Download result
uses: actions/download-artifact@v3
with:
name: gt_sympy
- name: GT postprocess
run: |
echo "GT postprocess"
pwd
ls
mkdir -p output2/output
cd srbench/srbench
mv $GITHUB_WORKSPACE/output/results_sym_data .
# install enviroment
source /usr/share/miniconda/bin/activate
conda activate srbench
cd postprocessing
python collate_groundtruth_results.py ../results_sym_data
mv ../results/ground-truth_results.feather ../../../output2/output/
- name: Archive production artifacts
uses: actions/upload-artifact@v3
with:
name: gt_result
path: |
/home/runner/work/output2