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| Original file line number | Diff line number | Diff line change |
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| name: Tests | ||
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| on: [push] | ||
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| jobs: | ||
| test: | ||
| runs-on: ubuntu-latest | ||
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| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| lfs: true | ||
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| - name: Set up Python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: '3.10' | ||
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| - name: Install Poetry | ||
| uses: snok/install-poetry@v1 | ||
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| - name: Install Poetry Dynamic Versioning | ||
| run: | | ||
| poetry self add "poetry-dynamic-versioning[plugin]" | ||
| - name: Build package | ||
| run: | | ||
| poetry install --extras "cli" | ||
| poetry build | ||
| - name: Test package | ||
| run: | | ||
| poetry run pytest -v | ||
| - name: Lint package | ||
| run: poetry run black --check --diff . | ||
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| - name: Archive test output | ||
| uses: actions/upload-artifact@v3 | ||
| with: | ||
| name: test_curves | ||
| path: | | ||
| test_results.* | ||
| if-no-files-found: error |
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| test_results.* | ||
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| # Compiled python modules. | ||
| *.pyc | ||
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Git LFS file not shown
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@@ -3,7 +3,7 @@ name = "lollipop" | |
| version = "0.0.0" | ||
| description = "tool for Deconvolution for Wastewater Genomics" | ||
| authors = ["David Dreifuss <[email protected]>", "Ivan Blagoev Topolsky <[email protected]>", "Matteo Carrara <[email protected]>"] | ||
| maintainer = ["Ivan Blagoev Topolsky <[email protected]>"] | ||
| maintainers = ["Ivan Blagoev Topolsky <[email protected]>"] | ||
| license = "GPL-3.0-or-later" | ||
| readme = "README.md" | ||
| repository = "https://github.com/cbg-ethz/LolliPop" | ||
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@@ -31,8 +31,8 @@ lollipop = { callable = "lollipop.cli:cli", extras = ["cli"] } | |
| deconvolute = { callable = "lollipop.deconvolute:deconvolute", extras = ["cli"] } | ||
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| [tool.poetry.dev-dependencies] | ||
| black = "^22.1.0" | ||
| #pytest = "^6.2.1" | ||
| black = "^23.3.0" | ||
| pytest = "^6.2.1" | ||
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| [build-system] | ||
| requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"] | ||
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| import subprocess | ||
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| def test_workflow(): | ||
| # data: its handled with LFS | ||
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| # dummy run | ||
| subprocess.check_call(["lollipop", "--version"]) | ||
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| # do fast test from preprint | ||
| subprocess.check_call( | ||
| [ | ||
| "lollipop", | ||
| "deconvolute", | ||
| "--output=test_results.csv", | ||
| "--out-json=test_results.json", | ||
| "--fmt-columns", | ||
| "--variants-config=config_preprint.yaml", | ||
| "--deconv-config=presets/deconv_linear.yaml", | ||
| "--location=Zürich (ZH)", | ||
| "--seed=42", | ||
| "preprint/data/tallymut_line_full.tsv", | ||
| ] | ||
| ) |