Add scatter CI #350
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Add scatter CI #350
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sateeshperi
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Oct 29, 2023
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edmundmiller
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sateeshperi
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Nov 6, 2023
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November 7, 2023 03:08
Pull Request is not mergeable
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Sounds good, once I get the tests passing in this PR at least 😆 |
sateeshperi
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Dec 22, 2023
adamrtalbot
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Dec 22, 2023
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| - name: Cache Nextflow installation | ||
| id: cache-software | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: test-datasets/ | ||
| key: ${{ steps.hash_workspace.outputs.digest }} | ||
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| - name: Check out test data | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| repository: nf-core/test-datasets | ||
| ref: methylseq | ||
| path: test-datasets/ | ||
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| - name: Replace remote paths in samplesheets | ||
| run: | | ||
| for f in ./test-datasets/samplesheet/*csv; do | ||
| sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f | ||
| sed -i 's=https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/=./test-datasets/=g' $f | ||
| echo "========== $f ============" | ||
| cat $f | ||
| echo "========================================" | ||
| done; | ||
| path: | | ||
| /usr/local/bin/nf-test | ||
| /home/runner/.nf-test/nf-test.jar | ||
| key: methylseq-${{ runner.os }}-${{ matrix.NXF_VER }} |
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Let's add Nextflow to this cache as well.
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| - name: Setup Nextflow | ||
| uses: nf-core/setup-nextflow@v1 |
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We're going to hit the API limits again, I think we should add Nextflow to the software cache (see other comment).
| - name: List nf-test | ||
| id: list | ||
| run: | | ||
| echo "tests=$(nf-test list --silent --format=json)" >> "$GITHUB_OUTPUT" |
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I didn't know about this...
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Could you run this at dev time instead of in the action? It seems wasteful to create an entire job that runs this every single time when it only changes when you run the test.
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We could create an nf-test pre-commit...
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That's an option. But how is this worse than checking for changes in modules?
We'll also be adding the check for changes to this job as well to run only CI jobs on changed code.
| - name: Run nf-test | ||
| run: | | ||
| nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml | ||
| nf-test test \ | ||
| --profile="test,${{ matrix.profile }}" \ |
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I'm still tempted to group up conda, singularity and docker onto the same job to make things more efficient. Sure, they will run sequentially which will slow things down but we will reduce our load on GHA by 1/3rd. Food for thought, not necessary right now.
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Here's my arguement against that. I don't think efficiency is the only thing to optomize for here.
It's a developer tool, and I think that will confuse the pipeline developers and new contributors.
It's also the same amount of wall time, if you don't include the setup. I'd rather spend our time optimizing the setup and cacheing properly to cut down on that.
The other thing splitting up the jobs allow us to do is to fail fast. Instead of getting through docker and singularity and then condad failing a checksum, we then have to rerun all three, instead of just conda. So we end up using 3x the walltime anyways if the CI doesn't work perfectly the first time.
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You don't seem to have any check that could be used for branch protection?
Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
sateeshperi
reviewed
Dec 22, 2023
Again Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: sateeshperi <sateeshperi@users.noreply.github.com>
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Uses a GitHub runner per test to significantly speed up CI times.
It does break the flaky index tests.