phylogicNDT

Dockerfile

FROM mambaorg/micromamba:latest

SHELL ["/bin/bash", "-lc"]
WORKDIR /phylogicndt

USER root
RUN apt-get update && apt-get install -y --no-install-recommends \
    graphviz graphviz-dev pkg-config \
 && rm -rf /var/lib/apt/lists/*
USER mambauser

RUN micromamba create -y -n phylogic -c conda-forge \
    python=3.8 \
    pip git compilers make \
    numpy scipy matplotlib pandas scikit-learn \
    r-base tk graphviz pygraphviz \
 && micromamba clean -a -y

ENV MAMBA_DOCKERFILE_ACTIVATE=1
ENV PATH=/opt/conda/envs/phylogic/bin:/opt/conda/bin:$PATH

COPY req /tmp/req
RUN micromamba run -n phylogic pip install -U "pip<25.1" "setuptools<81" wheel \
 && grep -vE '^(intervaltree==|networkx==|scikit-learn==)' /tmp/req > /tmp/req.fixed \
 && micromamba run -n phylogic pip install --prefer-binary -r /tmp/req.fixed \
 && micromamba run -n phylogic pip install -U intervaltree sortedcontainers "networkx>=2.8" \
 && micromamba run -n phylogic pip install --no-build-isolation \
    git+https://github.com/rmcgibbo/logsumexp.git#egg=sselogsumexp

COPY . /phylogicndt/

ENV PYTHONPATH=/phylogicndt:/phylogicndt/data:/phylogicndt/PhylogicSim:/phylogicndt/Cluster:/phylogicndt/BuildTree:/phylogicndt/GrowthKinetics:/phylogicndt/SinglePatientTiming:/phylogicndt/LeagueModel:/phylogicndt/utils

WORKDIR /phylogicndt
ENTRYPOINT ["micromamba", "run", "-n", "phylogic"]
CMD ["bash"]