add nobrainer dockerfiles

.github/workflows/docker-image.yml

@@ -1,10 +1,5 @@
-name: Docker Image CI
-
-on:
-  push:
-    branches: [ "main" ]
-  pull_request:
-    branches: [ "main" ]
+name: docker-image
+on: workflow_dispatch
 
 jobs:
 
@@ -26,7 +21,7 @@ jobs:
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
         
     - name: Build the Docker image
-      run: docker build -t hvgazula/pialnn ./docker
+      run: docker build -t hvgazula/nobrainer ./nobrainer-docker/cpu.Dockerfile
 
     # Cleanup steps to free up disk space
 
@@ -35,4 +30,4 @@ jobs:
 #     if: github.event.pull_request.merged == true
       run: |
           docker login -u ${{ secrets.DOCKER_USERNAME }} -p ${{ secrets.DOCKER_PASSWORD }}
-          docker push hvgazula/pialnn
+          docker push hvgazula/nobrainer:cpu

nobrainer-docker/README.md

@@ -0,0 +1,33 @@
+# Nobrainer in a container
+
+The Dockerfiles in this directory can be used to create Docker images to use _Nobrainer_ on CPU or GPU.
+
+## Build images
+
+```bash
+cd /code/nobrainer  # Top-level nobrainer directory
+docker build -t neuronets/nobrainer:master-cpu -f docker/cpu.Dockerfile .
+docker build -t neuronets/nobrainer:master-gpu -f docker/gpu.Dockerfile .
+```
+
+# Convert Docker images to Singularity containers
+
+Using Singularity version 3.x, Docker images can be converted to Singularity containers using the `singularity` command-line tool.
+
+## Pulling from DockerHub
+
+In most cases (e.g., working on a HPC cluster), the _Nobrainer_ singularity container can be created with:
+
+```bash
+singularity pull docker://neuronets/nobrainer:master-gpu
+```
+
+## Building from local Docker cache
+
+If you built a _Nobrainer_ Docker images locally and would like to convert it to a Singularity container, you can do so with:
+
+```bash
+sudo singularity pull docker-daemon://neuronets/nobrainer:master-gpu
+```
+
+Please note the use of `sudo` here. This is necessary for interacting with the Docker daemon.

nobrainer-docker/cpu.Dockerfile

@@ -0,0 +1,23 @@
+FROM tensorflow/tensorflow:2.14.0-jupyter
+RUN curl -sSL http://neuro.debian.net/lists/focal.us-nh.full | tee /etc/apt/sources.list.d/neurodebian.sources.list \
+  && export GNUPGHOME="$(mktemp -d)" \
+  && echo "disable-ipv6" >> ${GNUPGHOME}/dirmngr.conf \
+  && (apt-key adv --homedir $GNUPGHOME --recv-keys --keyserver hkp://pgpkeys.eu 0xA5D32F012649A5A9 \
+  || { curl -sSL http://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add -; } ) \
+  && apt-get update \
+  && apt-get install -y git-annex-standalone git \
+  && rm -rf /tmp/*
+COPY [".", "/opt/nobrainer"]
+RUN cd /opt/nobrainer \
+    && sed -i 's/tensorflow >=/tensorflow-cpu >=/g' setup.cfg
+RUN python3 -m pip install --no-cache-dir /opt/nobrainer datalad datalad-osf
+RUN git config --global user.email "neuronets@example.com" \
+    && git config --global user.name "Neuronets maintainers"
+RUN datalad clone https://github.com/neuronets/trained-models /models \
+  && cd /models && git-annex enableremote osf-storage \
+  && datalad get -s osf-storage .
+ENV LC_ALL=C.UTF-8 \
+    LANG=C.UTF-8
+WORKDIR "/work"
+LABEL maintainer="Satrajit Ghosh <satrajit.ghosh@gmail.com>"
+ENTRYPOINT ["nobrainer"]

nobrainer-docker/gpu.Dockerfile

@@ -0,0 +1,22 @@
+FROM tensorflow/tensorflow:2.14.0-gpu-jupyter
+RUN curl -sSL http://neuro.debian.net/lists/focal.us-nh.full | tee /etc/apt/sources.list.d/neurodebian.sources.list \
+  && export GNUPGHOME="$(mktemp -d)" \
+  && echo "disable-ipv6" >> ${GNUPGHOME}/dirmngr.conf \
+  && (apt-key adv --homedir $GNUPGHOME --recv-keys --keyserver hkp://pgpkeys.eu 0xA5D32F012649A5A9 \
+  || { curl -sSL http://neuro.debian.net/_static/neuro.debian.net.asc | apt-key add -; } ) \
+  && apt-get update \
+  && apt-get install -y git-annex-standalone git \
+  && rm -rf /tmp/*
+COPY [".", "/opt/nobrainer"]
+RUN cd /opt/nobrainer
+RUN python3 -m pip install --no-cache-dir /opt/nobrainer datalad datalad-osf
+RUN git config --global user.email "neuronets@example.com" \
+    && git config --global user.name "Neuronets maintainers"
+RUN datalad clone https://github.com/neuronets/trained-models /models \
+  && cd /models && git-annex enableremote osf-storage \
+  && datalad get -s osf-storage .
+ENV LC_ALL=C.UTF-8 \
+    LANG=C.UTF-8
+WORKDIR "/work"
+LABEL maintainer="Satrajit Ghosh <satrajit.ghosh@gmail.com>"
+ENTRYPOINT ["nobrainer"]