Add model from huggingface in container

Updates Dockerfile to download the model file from huggingface
instead of datacommons.

Some fixes were needed to install requirements due to changes
to the upstream container and various packages:
- setuptools is manually installed with support for use_2to3
  - pipenv needs use_2to3 to install pycallgraph
- pillow is now pinned
   - PIL.Image.LINEAR is missing in later versions
- scikit-image is now pinned
  - measure.perimeter() neighbourhood param has been renamed

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 <[email protected]>"
@@ -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

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 = "*"