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feat: integrate dev branch and update software environments (#25) #29

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17 changes: 7 additions & 10 deletions .github/workflows/benchmark.yml
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@imallona imallona Jun 11, 2025

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we switch to clustering_[conda|apptainer|envmodules].yaml only, and they're short, all others are out
we test on PR and nightly (short and long), perhaps with timeout
we don't write artifacts
we don't test reduced-imallona branch because it's not relevant anymore
we switch to the new run_omnibenchmark action

Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@ jobs:
run-benchmark:
name: Run Benchmark
runs-on: ubuntu-latest
## runs-on: self-hosted
steps:
- name: Check out repository
uses: actions/checkout@v4
Expand Down Expand Up @@ -48,27 +47,26 @@ jobs:
shell: bash -l {0}
run: |
mamba install -y pip
pip install git+https://github.com/omnibenchmark/omnibenchmark.git@reduce_install_scope
pip install git+https://github.com/omnibenchmark/omnibenchmark.git@main

- name: Load benchmark cache
id: cache-benchmark
uses: actions/cache@v3
with:
path: out/
key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}
key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering_conda_short.yml') }}

- name: Run benchmark
shell: bash -l {0}
continue-on-error: true
continue-on-error: false
run: |
echo "y" | ob run benchmark -b Clustering.yaml --local --cores 3 --continue-on-error
ob run benchmark -b Clustering_conda_short.yml --local --cores 3 --continue-on-error --yes

upload-artifact:
name: Benchmark Artifact
runs-on: ubuntu-latest
## runs-on: self-hosted
needs: run-benchmark
if: always()
if: github.ref == 'refs/heads/main' && github.repository_owner == 'omnibenchmark'
steps:
- name: Check out repository
uses: actions/checkout@v4
Expand All @@ -77,7 +75,7 @@ jobs:
uses: actions/cache@v3
with:
path: out/
key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}
key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering_conda_short.yaml') }}

- name: Prepare output
run: |
Expand All @@ -99,12 +97,11 @@ jobs:

- name: Deploy to GitHub Pages
uses: actions/deploy-pages@v4

- name: Create Job Summary
if: always()
run: |
echo "### Reports" >> $GITHUB_STEP_SUMMARY
echo "- [Plotting Report](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }})" >> $GITHUB_STEP_SUMMARY
echo "### All Outputs" >> $GITHUB_STEP_SUMMARY
echo "- [Complete Benchmark Output](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}#artifacts)" >> $GITHUB_STEP_SUMMARY

74 changes: 2 additions & 72 deletions .github/workflows/micromamba.yml
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@imallona imallona Jun 11, 2025

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same as above, and replace by the run_ob action

Original file line number Diff line number Diff line change
Expand Up @@ -7,21 +7,15 @@ on:
pull_request:
workflow_dispatch:
schedule:
# - cron: "*/30 * * * *" # Runs every 30 minutes for testing
- cron: "30 1 * * *" # at 1.30am
## these permissions are only for deployment to gh pages
# permissions:
# id-token: write
# pages: write

jobs:
run-benchmark-micromamba:
name: run_clustbench_micromamba
## runs-on: ubuntu-latest
runs-on: self-hosted
strategy:
matrix:
ob_branch: [dev, reduce_install_scope, main]
ob_branch: [main]
micromamba-version: ['2.1.1-0', '2.0.5-0', '1.5.12-0', '1.5.8-0']
fail-fast: false
concurrency:
Expand Down Expand Up @@ -50,81 +44,17 @@ jobs:
micromamba --version
pip install git+https://github.com/omnibenchmark/omnibenchmark.git@${{ matrix.ob_branch }}

# - name: Enable a benchmarking `out` cache
# id: cache-benchmark
# uses: actions/cache@v3
# with:
# path: out/
# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}

- name: Run benchmark
shell: bash -l {0}
run: |
env
output=$( echo "y" | ob run benchmark -b Clustering.yaml --local --cores 10 2>&1 )
output=$( ob run benchmark -b Clustering_conda_short.yaml --local --cores 10 2>&1 )
status=$?
if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
status=0
fi
echo -e $output
sh -c "exit $status"
if: matrix.ob_branch == 'dev' || matrix.ob_branch == 'reduce_install_scope'

- name: Run benchmark
shell: bash -l {0}
run: |
env
output=$( ob run benchmark -b Clustering.yaml --local --threads 10 2>&1 )
status=$?
if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
status=0
fi
echo -e $output
sh -c "exit $status"
if: matrix.ob_branch == 'main'

# upload-artifact:
# name: Benchmark Artifact
# runs-on: ubuntu-latest
# ## runs-on: self-hosted
# needs: run-benchmark
# if: always()
# steps:
# - name: Check out repository
# uses: actions/checkout@v4

# - name: Load cached output
# uses: actions/cache@v3
# with:
# path: out/
# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}

# - name: Prepare output
# run: |
# zip -r benchmark_output.zip out/
# mkdir -p gh-pages
# cp out/plotting/plotting_report.html gh-pages/index.html

# - name: Upload zipped output
# uses: actions/upload-artifact@v4
# with:
# name: benchmark-output
# path: benchmark_output.zip
# retention-days: 7

# - name: Upload Pages Artifact
# uses: actions/upload-pages-artifact@v3
# with:
# path: gh-pages

# - name: Deploy to GitHub Pages
# uses: actions/deploy-pages@v4

# - name: Create Job Summary
# if: always()
# run: |
# echo "### Reports" >> $GITHUB_STEP_SUMMARY
# echo "- [Plotting Report](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }})" >> $GITHUB_STEP_SUMMARY
# echo "### All Outputs" >> $GITHUB_STEP_SUMMARY
# echo "- [Complete Benchmark Output](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}#artifacts)" >> $GITHUB_STEP_SUMMARY

84 changes: 2 additions & 82 deletions .github/workflows/miniconda_miniforge.yml
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@imallona imallona Jun 11, 2025

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same as above, and replace by the run_ob action

Original file line number Diff line number Diff line change
Expand Up @@ -7,22 +7,16 @@ on:
pull_request:
workflow_dispatch:
schedule:
# - cron: "*/30 * * * *" # Runs every 30 minutes for testing
- cron: "30 1 * * *" # at 1.30am

## these permissions are only for deployment to gh pages
# permissions:
# id-token: write
# pages: write

jobs:
run-benchmark-miniforge:
name: run_clustbench_miniforge
## runs-on: ubuntu-latest
runs-on: self-hosted
strategy:
matrix:
ob_branch: [dev, reduce_install_scope, main]
ob_branch: [main]
fail-fast: false
concurrency:
group: mambaforge-${{ matrix.ob_branch }}
Expand Down Expand Up @@ -59,81 +53,7 @@ jobs:
mamba install -y pip
pip install git+https://github.com/omnibenchmark/omnibenchmark.git@${{ matrix.ob_branch }}

# - name: Enable a benchmarking `out` cache
# id: cache-benchmark
# uses: actions/cache@v3
# with:
# path: out/
# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}

- name: Run benchmark
shell: bash -l {0}
run: |
env
output=$( echo "y" | ob run benchmark -b Clustering.yaml --local --cores 10 2>&1 )
status=$?
if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
status=0
fi
echo -e $output
sh -c "exit $status"
if: matrix.ob_branch == 'dev' || matrix.ob_branch == 'reduce_install_scope'

- name: Run benchmark
shell: bash -l {0}
run: |
env
output=$( ob run benchmark -b Clustering.yaml --local --threads 10 2>&1 )
status=$?
if echo "$output" | grep -i 'Benchmark run has finished successfully'; then
status=0
fi
echo -e $output
sh -c "exit $status"
if: matrix.ob_branch == 'main'

# upload-artifact:
# name: Benchmark Artifact
# runs-on: ubuntu-latest
# ## runs-on: self-hosted
# needs: run-benchmark
# if: always()
# steps:
# - name: Check out repository
# uses: actions/checkout@v4

# - name: Load cached output
# uses: actions/cache@v3
# with:
# path: out/
# key: benchmark-${{ runner.os }}-${{ hashFiles('Clustering.yaml') }}

# - name: Prepare output
# run: |
# zip -r benchmark_output.zip out/
# mkdir -p gh-pages
# cp out/plotting/plotting_report.html gh-pages/index.html

# - name: Upload zipped output
# uses: actions/upload-artifact@v4
# with:
# name: benchmark-output
# path: benchmark_output.zip
# retention-days: 7

# - name: Upload Pages Artifact
# uses: actions/upload-pages-artifact@v3
# with:
# path: gh-pages

# - name: Deploy to GitHub Pages
# uses: actions/deploy-pages@v4

# - name: Create Job Summary
# if: always()
# run: |
# echo "### Reports" >> $GITHUB_STEP_SUMMARY
# echo "- [Plotting Report](https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }})" >> $GITHUB_STEP_SUMMARY
# echo "### All Outputs" >> $GITHUB_STEP_SUMMARY
# echo "- [Complete Benchmark Output](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}#artifacts)" >> $GITHUB_STEP_SUMMARY

ob run benchmark -b Clustering_conda_short.yml --local --cores 3 --continue-on-error --yes
10 changes: 10 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
# image build artifacts
envs/*.sif

# snakemake
snakemake.log
.snakemake/

# vim swaps
*.swp
*.swo
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