feat(AutoML): dockerized AUCMEDI AutoML - closes #150

Dockerfile

@@ -0,0 +1,59 @@
+#==============================================================================#
+#  Author:       Dominik Müller                                                #
+#  Copyright:    2022 IT-Infrastructure for Translational Medical Research,    #
+#                University of Augsburg                                        #
+#                                                                              #
+#  This program is free software: you can redistribute it and/or modify        #
+#  it under the terms of the GNU General Public License as published by        #
+#  the Free Software Foundation, either version 3 of the License, or           #
+#  (at your option) any later version.                                         #
+#                                                                              #
+#  This program is distributed in the hope that it will be useful,             #
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of              #
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               #
+#  GNU General Public License for more details.                                #
+#                                                                              #
+#  You should have received a copy of the GNU General Public License           #
+#  along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
+#==============================================================================#
+#-----------------------------------------------------#
+#              Information & System Base              #
+#-----------------------------------------------------#
+# Base image
+FROM tensorflow/tensorflow:latest-gpu
+
+# Meta information
+LABEL authors="Dominik Müller"
+LABEL contact="dominik.mueller@informatik.uni-augsburg.de"
+LABEL repository="https://github.com/frankkramer-lab/aucmedi"
+LABEL license="GNU General Public License v3.0"
+
+#-----------------------------------------------------#
+#                        Setup                        #
+#-----------------------------------------------------#
+# Setup system environment variables
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PIP_ROOT_USER_ACTION=ignore
+
+# Copy git repository into container
+ADD . /root/aucmedi
+
+# Install required software dependencies (cv2)
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends python3-opencv && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Update Python pip
+RUN python -m pip install pip --upgrade
+
+# Install AUCMEDI from local git repo
+RUN python -m pip install /root/aucmedi
+
+# Create working directory
+VOLUME ["/data"]
+WORKDIR /data
+
+#-----------------------------------------------------#
+#                       Startup                       #
+#-----------------------------------------------------#
+ENTRYPOINT ["aucmedi"]

aucmedi/automl/cli.py

@@ -67,11 +67,6 @@ def cli_core():
 #                     "--help",
 #                     action="help",
 #                     help="show this help message and exit")
-#
-#     # Help page hook for passing no parameters
-#     if len(sys.argv)==2 and sys.argv[1] == "yaml":
-#         parser_yaml.print_help(sys.stderr)
-#         sys.exit(1)
 
 #-----------------------------------------------------#
 #                    CLI - Training                   #
@@ -192,11 +187,6 @@ def cli_training(subparsers):
                     action="help",
                     help="show this help message and exit")
 
-    # Help page hook for passing no parameters
-    if len(sys.argv)==2 and sys.argv[1] == "training":
-        parser_train.print_help(sys.stderr)
-        sys.exit(1)
-
 #-----------------------------------------------------#
 #                   CLI - Prediction                  #
 #-----------------------------------------------------#
@@ -273,11 +263,6 @@ def cli_prediction(subparsers):
                     action="help",
                     help="show this help message and exit")
 
-    # Help page hook for passing no parameters
-    if len(sys.argv)==2 and sys.argv[1] == "prediction":
-        parser_predict.print_help(sys.stderr)
-        sys.exit(1)
-
 #-----------------------------------------------------#
 #                   CLI - Evaluation                  #
 #-----------------------------------------------------#
@@ -339,8 +324,3 @@ def cli_evaluation(subparsers):
                     "--help",
                     action="help",
                     help="show this help message and exit")
-
-    # Help page hook for passing no parameters
-    if len(sys.argv)==2 and sys.argv[1] == "evaluation":
-        parser_evaluate.print_help(sys.stderr)
-        sys.exit(1)

docs/automl/docker/usage.md

@@ -0,0 +1,12 @@
+
+
+docker run ghcr.io/frankkramer-lab/aucmedi:latest training
+
+Volumes:
+If you intended to pass a host directory, use absolute path.!!!
+
+Be aware of user changes due to docker volume
+-> created files will have user and group root
+
+
+docker run -v /home/mudomini/projects/testing_area/aucmedi.automl:/data --rm -it domi:latest prediction