download templates into image

bin/pyAFQ

@@ -114,11 +114,32 @@ def parse_cli(arg_dict):
         opts.verbose, opts.dry_run, opts.to_call, opts.generate_json
 
 
+def download_templates():
+    from AFQ.data.fetch import (
+        read_templates,
+        read_pediatric_templates,
+        read_callosum_templates,
+        read_cp_templates,
+        read_or_templates,
+        read_ar_templates)
+
+    read_templates()
+    read_pediatric_templates()
+    read_callosum_templates()
+    read_cp_templates()
+    read_or_templates()
+    read_ar_templates()
+
+
 if __name__ == '__main__':
     arg_dict = afb.func_dict_to_arg_dict(logger=logger)
     config_file, generate_only, overwrite, verbose,\
         dry_run, to_call, generate_json =\
             parse_cli(arg_dict)
+
+    if config_file == "download":
+        download_templates()
+        exit()
 
     if generate_only and generate_json:
         raise ValueError("Can only generate .toml or .json; not both")

gpu_docker/Dockerfile

@@ -48,5 +48,6 @@ RUN cd /opt/GPUStreamlines/build/cuslines && pip install -e .
 
 # Install pyAFQ
 RUN cd /opt/pyAFQ && pip install -e .
+RUN /opt/pyAFQ/bin/pyAFQ download
 
 ENTRYPOINT ["/opt/pyAFQ/bin/pyAFQ"]

gpu_docker/cuda_track_template.def

@@ -57,5 +57,7 @@ From: nvidia/cuda:12.0.1-devel-ubuntu20.04
     # Install pyAFQ
     pip install -e /opt/pyAFQ
 
+    /opt/pyAFQ/bin/pyAFQ download
+
 %runscript
     exec /opt/pyAFQ/bin/pyAFQ "$@"

pyafq_docker/Dockerfile

@@ -10,5 +10,6 @@ ARG COMMIT
 # Install pyAFQ
 RUN pip install --no-cache-dir git+https://github.com/yeatmanlab/pyAFQ.git@${COMMIT}
 RUN pip install fslpy
+RUN pyAFQ download
 
 ENTRYPOINT ["pyAFQ"]