diff --git a/Dockerfile b/Dockerfile index 183366b..d7a0563 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,11 +1,11 @@ -FROM ghcr.io/imageomics/dataverse-access:1 as model_fetcher -ARG DATAVERSE_API_TOKEN -ENV DATAVERSE_URL=https://datacommons.tdai.osu.edu/ -ENV MODEL_DV_DOI=doi:10.5072/FK2/MMX6FY +FROM alpine/git:2.40.1 as model_fetcher +ENV MODEL_REPO_URL=https://huggingface.co/imageomics/Drexel-metadata-generator # Download model_final.pth RUN mkdir -p /model \ - && dva download $MODEL_DV_DOI /model + && cd /model \ + && git clone --depth=1 ${MODEL_REPO_URL} +RUN ls /model FROM python:3.8.10-slim-buster LABEL "org.opencontainers.image.authors"="John Bradley " @@ -27,11 +27,14 @@ ENV PATH="/pipeline:${PATH}" COPY Pipfile /pipeline/. +# Fix issue installing pycallgraph related to use_2to3 being removed from setuptools +RUN pip install setuptools==57.0.0 + # Install requirements RUN pipenv install --skip-lock --system && pipenv --clear COPY config /pipeline/config -COPY --from=model_fetcher /model/model_final.pth \ +COPY --from=model_fetcher /model/Drexel-metadata-generator/model_final.pth \ /pipeline/output/enhanced/model_final.pth COPY gen_metadata.py /pipeline diff --git a/Pipfile b/Pipfile index dc86b76..5cbc786 100644 --- a/Pipfile +++ b/Pipfile @@ -11,10 +11,10 @@ verify_ssl = false [packages] numpy = "*" pynrrd = "*" -pillow = "*" +pillow = "==9.4.0" opencv-python = "*" ipython = "*" -scikit-image = "*" +scikit-image = "==0.19.3" pandas = "*" iopath = "*" imutils = "*"