Merge branch 'enable_container'

.dockerignore

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+work
+.nextflow*
+.idea
+.git
+output
+testdata
+dist
+archive/

.github/workflows/docker-image.yml

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+name: Docker Image CI
+
+on:
+  push:
+  pull_request:
+  release:
+    type: [published]
+
+env:
+  TEST_TAG: dessimozlab/fastoma:test
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          # list of Docker images to use as base name for tags
+          images: |
+            dessimozlab/fastoma
+          # generate Docker tags based on the following events/attributes
+          tags: |
+            type=schedule
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=semver,pattern={{major}}
+            type=sha
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Build and export to docker for testing
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          load: true
+          tags: ${{ env.TEST_TAG }}
+
+      #- name: Test
+      #  run: |
+      #    docker run --rm -i -v $PWD/tests:/input -v $PWD/tests/:/reads -v $PWD/output:/out -v $PWD/run:/run ${{ env.TEST_TAG }} --tree --standalone_path /input/marker_genes --dna_reference /input/cds-marker_genes.fasta.gz --reads /reads/sample_1.fastq --output_path /out
+      #    if [ ! -f output/tree_sample_1.nwk ] ; then exit 1; fi
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Build and push
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: true
+          #${{ github.event_name != 'push' && github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.gitignore

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+.nextflow*
+work/
+.idea/
+dist/
+archive
+.git
+.gitignore
+__pycache__

Dockerfile

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+FROM python:3.11-slim as basis
+
+# set environment varibles
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONUNBUFFERED 1
+
+
+FROM basis as builder
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       build-essential \
+       fasttree \
+       libxml2 \
+       mafft \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /src
+RUN pip install --upgrade hatch pip
+COPY pyproject.toml .
+RUN python -m venv /app \
+    && hatch dep show requirements > requirements.txt \
+    && /app/bin/pip install -r requirements.txt
+
+COPY . .
+RUN ls -la \
+    && hatch build \
+    && ls -la dist/ \
+    && /app/bin/pip install dist/*.whl
+
+
+FROM basis as runtime
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       fasttree \
+       libxml2 \
+       mafft \
+       procps \
+    && apt-get -y autoremove \
+    && apt-get -y autoclean \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY --from=builder /app /app
+ENV PATH="/app/bin:$PATH"