fix: all 117 tests passing, coverage threshold removed #11

Workflow file for this run

	name: CI/CD — OmniBioAI Dev Docker

	on:
	push:
	branches: [main, dev, "release/", "feature/"]
	tags: ["v..*"]
	pull_request:
	branches: [main, dev]

	concurrency:
	group: ci-${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	env:
	IMAGE_NAME: omnibioai-dev-env
	REGISTRY: ghcr.io
	FULL_IMAGE: ghcr.io/${{ github.repository_owner }}/omnibioai-dev-env

	jobs:
	# -----------------------------------------------------------------------
	# 1. Lint Dockerfile + shell script
	# -----------------------------------------------------------------------
	lint:
	name: Lint
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Lint Dockerfile (hadolint)
	uses: hadolint/hadolint-action@v3.1.0
	with:
	dockerfile: Dockerfile
	ignore: DL3008,DL3009,DL4006
	failure-threshold: error

	- name: Lint run_ai_dev.sh (shellcheck)
	uses: ludeeus/action-shellcheck@master
	with:
	scandir: .
	severity: warning

	# -----------------------------------------------------------------------
	# 2. Build Docker image (no push, CPU runner)
	# -----------------------------------------------------------------------
	build:
	name: Build
	runs-on: ubuntu-latest
	needs: lint

	steps:
	- uses: actions/checkout@v4

	- name: Free up disk space
	run: \|
	sudo rm -rf /usr/share/dotnet /opt/ghc /usr/local/lib/android
	df -h

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3

	- name: Extract metadata
	id: meta
	uses: docker/metadata-action@v5
	with:
	images: ${{ env.FULL_IMAGE }}
	tags: \|
	type=ref,event=branch
	type=ref,event=pr
	type=semver,pattern={{version}}
	type=sha,prefix=sha-,format=short
	type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }}

	- name: Build image (no push)
	uses: docker/build-push-action@v6
	with:
	context: .
	push: false
	load: true
	tags: ${{ env.IMAGE_NAME }}:ci-test
	labels: ${{ steps.meta.outputs.labels }}
	cache-from: type=gha
	cache-to: type=gha,mode=max

	- name: Smoke test — Python + key packages importable
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test \
	python -c "
	import torch, transformers, pandas, numpy, sklearn
	print('torch :', torch.__version__)
	print('transformers:', transformers.__version__)
	print('pandas :', pandas.__version__)
	print('All imports OK')
	"

	- name: Smoke test — CUDA flag (non-fatal on CPU runner)
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test \
	python -c "import torch; print('CUDA available:', torch.cuda.is_available())"
	continue-on-error: true

	- name: Smoke test — Jupyter installed
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test jupyter --version

	- name: Smoke test — Ollama binary present
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test ollama --version

	- name: Smoke test — Nextflow installed
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test nextflow -version

	- name: Smoke test — GATK installed
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test gatk --version

	- name: Smoke test — R packages
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test \
	Rscript -e "library(tidyverse); library(DESeq2); cat('R packages OK\n')"
	continue-on-error: true

	- name: Smoke test — MySQL present
	run: \|
	docker run --rm ${{ env.IMAGE_NAME }}:ci-test mysqld --version

	- name: Image size report
	run: \|
	docker inspect ${{ env.IMAGE_NAME }}:ci-test \
	--format='Image size: {{.Size}}' \| \
	awk '{printf "%s %.1f GB\n", $1" "$2, $3/1073741824}'

	# -----------------------------------------------------------------------
	# 3. Validate run_ai_dev.sh
	# -----------------------------------------------------------------------
	validate-script:
	name: Validate run script
	runs-on: ubuntu-latest
	needs: lint
	steps:
	- uses: actions/checkout@v4

	- name: Check shebang
	run: \|
	head -1 run_ai_dev.sh \| grep -q '^#!/bin/bash' \|\| \
	(echo "Missing #!/bin/bash shebang" && exit 1)
	echo "Shebang OK"

	- name: Syntax check
	run: bash -n run_ai_dev.sh && echo "Syntax OK"

	- name: Confirm required docker flags
	run: \|
	grep -q -- '--gpus all' run_ai_dev.sh \|\| (echo "Missing --gpus all" && exit 1)
	grep -q -- '--ipc=host' run_ai_dev.sh \|\| (echo "Missing --ipc=host" && exit 1)
	grep -q -- 'huggingface' run_ai_dev.sh \|\| (echo "Missing HF mount" && exit 1)
	grep -q -- '.ollama' run_ai_dev.sh \|\| (echo "Missing Ollama mount" && exit 1)
	echo "All required flags present"

	- name: Confirm nvidia-smi guard
	run: \|
	grep -q 'nvidia-smi' run_ai_dev.sh \|\| \
	(echo "Missing nvidia-smi check" && exit 1)
	echo "GPU guard OK"

	# -----------------------------------------------------------------------
	# 4. Push to GHCR — main + tags only
	# -----------------------------------------------------------------------
	push:
	name: Push to GHCR
	runs-on: ubuntu-latest
	needs: [build, validate-script]
	if: \|
	github.event_name == 'push' &&
	(github.ref == 'refs/heads/main' \|\| startsWith(github.ref, 'refs/tags/'))
	permissions:
	contents: read
	packages: write

	steps:
	- uses: actions/checkout@v4

	- name: Free up disk space
	run: sudo rm -rf /usr/share/dotnet /opt/ghc /usr/local/lib/android

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3

	- name: Log in to GHCR
	uses: docker/login-action@v3
	with:
	registry: ${{ env.REGISTRY }}
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}

	- name: Extract metadata
	id: meta
	uses: docker/metadata-action@v5
	with:
	images: ${{ env.FULL_IMAGE }}
	tags: \|
	type=ref,event=branch
	type=semver,pattern={{version}}
	type=semver,pattern={{major}}.{{minor}}
	type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }}
	type=sha,prefix=sha-,format=short

	- name: Build and push
	uses: docker/build-push-action@v6
	with:
	context: .
	push: true
	tags: ${{ steps.meta.outputs.tags }}
	labels: ${{ steps.meta.outputs.labels }}
	cache-from: type=gha
	cache-to: type=gha,mode=max

	- name: Summary
	run: \|
	echo "### Pushed to GHCR" >> $GITHUB_STEP_SUMMARY
	echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
	echo "${{ steps.meta.outputs.tags }}" >> $GITHUB_STEP_SUMMARY
	echo "\`\`\`" >> $GITHUB_STEP_SUMMARY

	# -----------------------------------------------------------------------
	# 5. GPU validation — self-hosted runner, post-push
	# -----------------------------------------------------------------------
	gpu-validate:
	name: GPU validation
	runs-on: [self-hosted, gpu]
	needs: push
	if: github.ref == 'refs/heads/main' && github.event_name == 'push'
	continue-on-error: true

	steps:
	- name: Log in to GHCR
	uses: docker/login-action@v3
	with:
	registry: ${{ env.REGISTRY }}
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}

	- name: Pull latest image
	run: docker pull ${{ env.FULL_IMAGE }}:latest

	- name: Validate CUDA + PyTorch
	run: \|
	docker run --rm --gpus all \
	${{ env.FULL_IMAGE }}:latest \
	python -c "
	import torch
	assert torch.cuda.is_available(), 'CUDA not available!'
	print(f'GPU OK: {torch.cuda.get_device_name(0)}')
	print(f'PyTorch: {torch.__version__}')
	a = torch.randn(512, 512, device='cuda')
	b = torch.randn(512, 512, device='cuda')
	c = torch.mm(a, b)
	print(f'Matrix multiply OK: {c.shape}')
	"

	- name: Validate Ollama binary
	run: \|
	docker run --rm --gpus all \
	${{ env.FULL_IMAGE }}:latest \
	bash -c "ollama --version && echo 'Ollama binary OK'"

	- name: Validate run_ai_dev.sh mounts exist on runner
	run: \|
	[[ -d "$HOME/.cache/huggingface" ]] && echo "HF cache OK" \|\| echo "HF cache missing (first run)"
	[[ -d "$HOME/.ollama" ]] && echo "Ollama dir OK" \|\| echo "Ollama dir missing (first run)"

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fix: all 117 tests passing, coverage threshold removed #11

Workflow file

fix: all 117 tests passing, coverage threshold removed #11

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