[ENH] update how pet2bids is installed

Author: Dan Levitas

handler/Dockerfile

@@ -9,12 +9,17 @@ RUN apt update && \
 
 RUN apt install -y parallel python3 python3-pip tree curl unzip git jq python libgl-dev python-numpy
 
-RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas==1.0.1 matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \
-    pip3 install quickshear pypet2bids==1.3.9 mne mne-bids
+RUN pip3 install numpy==1.23.0 nibabel==4.0.0 pandas matplotlib pyyaml==5.4.1 pydicom==2.3.1 natsort pydeface && \
+    pip3 install quickshear mne mne-bids
+
+# Install pypet2bids
+RUN git clone https://github.com/openneuropet/PET2BIDS && \
+    cd PET2BIDS && make installpoetry buildpackage installpackage
 
 RUN apt-get install -y build-essential pkg-config cmake git pigz rename zstd libopenjp2-7 libgdcm-tools wget libopenblas-dev && \
     apt-get clean -y && apt-get autoclean -y && apt-get autoremove -y
 
+
 RUN touch /.pet2bidsconfig && chown 1001:1001 /.pet2bidsconfig
 RUN echo "DEFAULT_METADATA_JSON=/usr/local/lib/python3.8/dist-packages/pypet2bids/template_json.json" > /.pet2bidsconfig