[WIP][ENH] add Dockerfile for python version og GLM single

Dockerfile

@@ -0,0 +1,127 @@
+# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
+# Latest release: Neurodocker version 0.8.0
+# Timestamp: 2022/04/11 12:55:39 UTC
+# 
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+# 
+#     https://github.com/ReproNim/neurodocker
+
+FROM python:3.9.12-slim-buster
+
+USER root
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    ND_ENTRYPOINT="/neurodocker/startup.sh"
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bzip2 \
+           ca-certificates \
+           curl \
+           locales \
+           unzip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && update-locale LANG="en_US.UTF-8" \
+    && chmod 777 /opt && chmod a+s /opt \
+    && mkdir -p /neurodocker \
+    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
+         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
+    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
+    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
+    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
+    fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           build-essential \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY ["glmsingle", "setup.py", "MANIFEST.in", "README.md", "requirements.txt", "/glmsingle/"]
+
+WORKDIR /glmsingle
+
+RUN pip install .
+
+RUN pip install jupyterlab
+
+EXPOSE 8888
+
+RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
+USER neuro
+
+WORKDIR /home/neuro
+
+COPY ["examples", "/home/neuro/examples"]
+
+RUN echo '{ \
+    \n  "pkg_manager": "apt", \
+    \n  "instructions": [ \
+    \n    [ \
+    \n      "base", \
+    \n      "python:3.9.12-slim-buster" \
+    \n    ], \
+    \n    [ \
+    \n      "install", \
+    \n      [ \
+    \n        "build-essential" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "copy", \
+    \n      [ \
+    \n        "glmsingle", \
+    \n        "setup.py", \
+    \n        "MANIFEST.in", \
+    \n        "README.md", \
+    \n        "requirements.txt", \
+    \n        "/glmsingle/" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "workdir", \
+    \n      "/glmsingle" \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "pip install ." \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "pip install jupyterlab" \
+    \n    ], \
+    \n    [ \
+    \n      "expose", \
+    \n      [ \
+    \n        "8888" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "workdir", \
+    \n      "/home/neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "copy", \
+    \n      [ \
+    \n        "examples", \
+    \n        "/home/neuro/examples" \
+    \n      ] \
+    \n    ] \
+    \n  ] \
+    \n}' > /neurodocker/neurodocker_specs.json

Makefile

@@ -113,4 +113,33 @@ coverage-python: ## check code coverage quickly with the default Python
 install: clean ## install the package to the active Python's site-packages
 	python setup.py install
 
-################################################################################
+################################################################################
+
+################################################################################
+# 	DOCKER
+
+.PHONY: Dockerfile 
+Dockerfile:
+	docker run --rm repronim/neurodocker:0.7.0 generate docker \
+		--base python:3.9.12-slim-buster \
+		--pkg-manager apt \
+		--install "build-essential" \
+		--copy glmsingle setup.py MANIFEST.in README.md requirements.txt /glmsingle/ \
+		--workdir /glmsingle \
+		--run "pip install ." \
+		--run "pip install jupyterlab" \
+		--expose 8888 \
+		--user neuro \
+		--workdir /home/neuro \
+		--copy examples /home/neuro/examples > Dockerfile
+
+docker_build: Dockerfile
+	docker build . -t glmsingle:latest
+
+docker_run: docker_build
+	mkdir -p $$PWD/tmp
+	docker run -it --rm \
+		--publish 8888:8888 \
+		--volume $$PWD/tmp:/home/neuro/tmp \
+		glmsingle:latest \
+			jupyter-lab --no-browser --ip 0.0.0.0

requirements.txt

@@ -1,8 +1,8 @@
-numpy
-scipy
-sklearn
-matplotlib
-tqdm
-fracridge
-nibabel
-h5py
+fracridge>=1.4.3
+h5py>=3.1.0
+matplotlib>=3.3.4
+nibabel>=3.2.2
+numpy>=1.17.0
+scikit-learn>=0.23.2
+scipy>=1.5.4
+tqdm>=4.63.1

setup.py

@@ -28,5 +28,6 @@
     packages=find_packages(),
     include_package_data=True,
     zip_safe=False,
-    install_requires=requires
+    install_requires=requires,
+    python_requires='>=3.6'
 )