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UlthranUlthran
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Merge pull request #17 from sunbeam-labs/16-containerize-and-version
Version and containerize
2 parents 35270d4 + b0c8056 commit a5cd084

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-114
lines changed

15 files changed

+305
-114
lines changed

‎.github/workflows/linter.yml‎

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‎.github/workflows/pr.yml‎

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name: Tests
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on:
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pull_request:
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branches:
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- main
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push:
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branches:
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- main
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jobs:
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run-tests:
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uses: ./.github/workflows/tests.yml
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secrets: inherit
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‎.github/workflows/release.yml‎

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name: Release
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on:
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release:
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types: [published]
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workflow_dispatch:
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jobs:
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run-tests:
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uses: ./.github/workflows/tests.yml
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secrets: inherit
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check-version:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Get sbx version
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shell: bash
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run: |
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SBX_VER=$(cat VERSION)
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echo "SBX_VER=$SBX_VER" >> $GITHUB_ENV
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- id: get_version
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uses: battila7/get-version-action@v2
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- name: Check version
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shell: bash
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run: |
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RELEASE_VERSION=${{ steps.get_version.outputs.version-without-v }}
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echo "Release version: ${RELEASE_VERSION}"
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echo "Sbx version: ${{ env.SBX_VER }}"
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if [[ $RELEASE_VERSION == ${{ env.SBX_VER }} ]]; then
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echo "Versions match, continuing..."
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else
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echo "Versions don't match, exiting..."
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exit 1
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fi
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build-and-push-to-dockerhub:
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name: Push Docker image to Docker Hub
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runs-on: ubuntu-latest
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needs:
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- run-tests
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- check-version
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Log in to Docker Hub
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ctbushman/sbx_mapping
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- name: Build and push Docker image
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uses: docker/build-push-action@v5
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with:
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context: .
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file: envs/sbx_mapping_env.Dockerfile
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push: true
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tags: ${{ steps.meta.outputs.tags }}
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labels: ${{ steps.meta.outputs.labels }}
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test-apptainer:
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name: Apptainer Test
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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- name: Set test env
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run: echo "SUNBEAM_TEST_PROFILE=apptainer" >> $GITHUB_ENV
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- uses: eWaterCycle/setup-apptainer@v2
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with:
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apptainer-version: 1.1.2
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- name: Test with Sunbeam
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uses: sunbeam-labs/sbx_test_action@v1
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with:
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test-directory: ".tests/e2e/"
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- name: Dump Logs
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shell: bash
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if: always()
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run: tail -n +1 logs/*
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- name: Dump Stats
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shell: bash
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if: always()
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run: cat stats/*

‎.github/workflows/tests.yml‎

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branches: [ master, main ]
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push:
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branches: [ master, main ]
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workflow_call:
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workflow_dispatch:
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schedule:
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- cron: "0 13 * * 1"
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jobs:
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jobs:
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lint:
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name: Lint Code
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install Dependencies
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run: pip install black snakefmt
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- name: Run Linter
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run: |
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black --check .
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snakefmt --check *.smk
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test-unit:
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name: Run Extension Unit Tests
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runs-on: ubuntu-latest
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steps:
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- name: Checkout Code
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uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Install Dependencies
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run: pip install pytest pysam
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- name: Run Unit Tests
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run: true #pytest .tests/unit/
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# This'll require having a lib within scripts with internal tests
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test-e2e:
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name: Test Extension with Sunbeam
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runs-on: ubuntu-latest
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needs:
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- test-unit
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- lint
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steps:
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- name: Checkout Code
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Test with Sunbeam
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uses: sunbeam-labs/sbx_test_action@v1

‎.gitignore‎

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.tests/data/hosts/*.fasta.*
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.tests/data/ref/*.fasta.*
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__pycache__
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.snakemake/

‎.tests/__init__.py‎

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‎.tests/conftest.py‎

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import os
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import pytest
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import shutil
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import subprocess as sp
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import sys
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@pytest.fixture
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def setup(tmpdir):
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reads_fp = os.path.abspath(".tests/data/reads/")
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genomes_fp = os.path.abspath(".tests/data/ref/")
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project_dir = os.path.join(tmpdir, "project/")
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profile = os.environ.get("TEST_PROFILE", "")
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if profile:
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profile_list = ["--profile", profile]
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else:
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profile_list = []
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sp.check_output(
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["sunbeam", "init", "--data_fp", reads_fp, project_dir] + profile_list
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)
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config_fp = os.path.join(project_dir, "sunbeam_config.yml")
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config_str = f"sbx_mapping: {{genomes_fp: {genomes_fp}}}"
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sp.check_output(
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[
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"sunbeam",
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"config",
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"modify",
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"-i",
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"-s",
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f"{config_str}",
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f"{config_fp}",
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]
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)
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yield tmpdir, project_dir
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shutil.rmtree(tmpdir)
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@pytest.fixture
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def run_sunbeam(setup):
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tmpdir, project_dir = setup
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output_fp = os.path.join(project_dir, "sunbeam_output")
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try:
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# Run the test job
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sp.check_output(
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[
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"sunbeam",
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"run",
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"--conda-frontend",
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"conda",
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"--profile",
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project_dir,
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"all_mapping",
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"--directory",
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tmpdir,
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]
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)
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except sp.CalledProcessError as e:
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shutil.copytree(os.path.join(output_fp, "logs/"), "logs/")
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shutil.copytree(os.path.join(project_dir, "stats/"), "stats/")
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sys.exit(e)
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shutil.copytree(os.path.join(output_fp, "logs/"), "logs/")
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shutil.copytree(os.path.join(project_dir, "stats/"), "stats/")
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bfragilis_sliding_cov_fp = os.path.join(
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output_fp, "mapping/filtered/Bfragilis/sliding_coverage.csv"
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)
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ecoli_sliding_cov_fp = os.path.join(
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output_fp, "mapping/filtered/Ecoli/sliding_coverage.csv"
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)
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bfragilis_filtered_cov_fp = os.path.join(
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output_fp, "mapping/filtered/Bfragilis/coverage_filtered.csv"
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)
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ecoli_filtered_cov_fp = os.path.join(
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output_fp, "mapping/filtered/Ecoli/coverage_filtered.csv"
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)
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bfragilis_num_reads_fp = os.path.join(
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output_fp, "mapping/filtered/Bfragilis/numReads.tsv"
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)
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ecoli_num_reads_fp = os.path.join(output_fp, "mapping/filtered/Ecoli/numReads.tsv")
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benchmarks_fp = os.path.join(project_dir, "stats/")
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yield bfragilis_sliding_cov_fp, ecoli_sliding_cov_fp, bfragilis_filtered_cov_fp, ecoli_filtered_cov_fp, bfragilis_num_reads_fp, ecoli_num_reads_fp, benchmarks_fp

‎.tests/e2e/test_full_run.py‎

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import os
2-
import pytest
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import shutil
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import subprocess as sp
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import sys
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import tempfile
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8-
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@pytest.fixture
10-
def setup():
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temp_dir = tempfile.mkdtemp()
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reads_fp = os.path.abspath(".tests/data/reads/")
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genomes_fp = os.path.abspath(".tests/data/ref/")
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project_dir = os.path.join(temp_dir, "project/")
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sp.check_output(["sunbeam", "init", "--data_fp", reads_fp, project_dir])
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config_fp = os.path.join(project_dir, "sunbeam_config.yml")
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config_str = f"sbx_mapping: {{genomes_fp: {genomes_fp}}}"
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sp.check_output(
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["sunbeam", "config", "modify", "-i", "-s", f"{config_str}", f"{config_fp}",]
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)
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yield temp_dir, project_dir
28-
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shutil.rmtree(temp_dir)
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@pytest.fixture
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def run_sunbeam(setup):
34-
temp_dir, project_dir = setup
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output_fp = os.path.join(project_dir, "sunbeam_output")
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try:
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# Run the test job
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sp.check_output(
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[
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"sunbeam",
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"run",
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"--conda-frontend",
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"conda",
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"--profile",
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project_dir,
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"all_mapping",
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"--directory",
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temp_dir,
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]
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)
53-
except sp.CalledProcessError as e:
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shutil.copytree(os.path.join(output_fp, "logs/"), "logs/")
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shutil.copytree(os.path.join(project_dir, "stats/"), "stats/")
56-
sys.exit(e)
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shutil.copytree(os.path.join(output_fp, "logs/"), "logs/")
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shutil.copytree(os.path.join(project_dir, "stats/"), "stats/")
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bfragilis_sliding_cov_fp = os.path.join(
62-
output_fp, "mapping/filtered/Bfragilis/sliding_coverage.csv"
63-
)
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ecoli_sliding_cov_fp = os.path.join(
65-
output_fp, "mapping/filtered/Ecoli/sliding_coverage.csv"
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)
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bfragilis_filtered_cov_fp = os.path.join(
68-
output_fp, "mapping/filtered/Bfragilis/coverage_filtered.csv"
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)
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ecoli_filtered_cov_fp = os.path.join(
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output_fp, "mapping/filtered/Ecoli/coverage_filtered.csv"
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)
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bfragilis_num_reads_fp = os.path.join(
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output_fp, "mapping/filtered/Bfragilis/numReads.tsv"
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)
76-
ecoli_num_reads_fp = os.path.join(output_fp, "mapping/filtered/Ecoli/numReads.tsv")
77-
78-
benchmarks_fp = os.path.join(project_dir, "stats/")
79-
80-
yield bfragilis_sliding_cov_fp, ecoli_sliding_cov_fp, bfragilis_filtered_cov_fp, ecoli_filtered_cov_fp, bfragilis_num_reads_fp, ecoli_num_reads_fp, benchmarks_fp
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def test_full_run(run_sunbeam):

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