add: cli to generate dockerfiles

Author: jakubk

Makefile

@@ -5,7 +5,7 @@
 PYTHON ?= python
 NOSETESTS=`which nosetests`
 
-.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-coverage test html specs check-before-commit check
+.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-coverage test html specs check-before-commit check gen-base-dockerfile gen-main-dockerfile gen-dockerfiles
 
 zipdoc: html
 	zip documentation.zip doc/_build/html
@@ -61,7 +61,7 @@ test-code: in
 
 test-coverage: clean-tests in
 	py.test --doctest-modules --cov-config .coveragerc --cov=nipype nipype
-	
+
 test: tests # just another name
 tests: clean test-code
 
@@ -79,3 +79,13 @@ check-before-commit: specs trailing-spaces html test
 	@echo "built docs"
 	@echo "ran test"
 	@echo "generated spec tests"
+
+gen-base-dockerfile:
+	@echo "Generating base Dockerfile"
+	bash docker/generate_dockerfiles.sh -b
+
+gen-main-dockerfile:
+	@echo "Generating main Dockerfile"
+	bash docker/generate_dockerfiles.sh -m
+
+gen-dockerfiles: gen-base-dockerfile gen-main-dockerfile

docker/generate_dockerfiles.sh

@@ -1,32 +1,81 @@
- #!/usr/bin/env bash
+#!/usr/bin/env bash
+#
+# Generate base and main Dockerfiles for Nipype.
+
+set -e
+
+USAGE="usage: $(basename $0) [-h] [-b] [-m]"
+
+function Help {
+  cat <<USAGE
+Generate base and/or main Dockerfiles for Nipype.
+
+Usage:
+
+$(basename $0) [-h] [-b] [-m]
+
+Options:
+
+    -h : display this help message and exit
+    -b : generate base Dockerfile
+    -m : generate main Dockerfile
+
+USAGE
+}
+
+# No command-line options passed.
+if [ -z "$1" ]; then
+  echo "$USAGE"
+  exit 1
+fi
+
+# Get command-line options.
+# Used the antsRegistrationSyN.sh as an example.
+# https://github.com/ANTsX/ANTs/blob/master/Scripts/antsRegistrationSyN.sh
+while getopts "hbm" OPT
+do
+  case $OPT in
+    h)
+      Help
+      exit 0
+    ;;
+    b)
+      GENERATE_BASE="1"
+    ;;
+    m)
+      GENERATE_MAIN="1"
+    ;;
+    \?)
+      echo "$USAGE" >&2
+      exit 1
+    ;;
+  esac
+done
+
+
+# neurodocker version 0.3.1-19-g8d02eb4
+NEURODOCKER_IMAGE="kaczmarj/neurodocker@sha256:6b5f92f413b9710b7581e62293a8f74438b14ce7e4ab1ce68db2a09f7c64375a"
+
+# neurodebian:stretch-non-free pulled on November 3, 2017
+BASE_IMAGE="neurodebian@sha256:7590552afd0e7a481a33314724ae27f76ccedd05ffd7ac06ec38638872427b9b"
 
-# kaczmarj/neurodocker:master pulled on September 13, 2017.
-NEURODOCKER_IMAGE="kaczmarj/neurodocker:master"
-# neurodebian/stretch-non-free:latest pulled on September 13, 2017.
-BASE_IMAGE="neurodebian@sha256:b09c09faa34bca0ea096b9360ee5121e048594cb8e2d7744d7d546ade88a2996"
 NIPYPE_BASE_IMAGE="kaczmarj/nipype:base"
 PKG_MANAGER="apt"
-
-# Save Dockerfiles relative to this path so that this script can be run from
-# any directory. https://stackoverflow.com/a/246128/5666087
 DIR="$(dirname "$0")"
 
-
 function generate_base_dockerfile() {
   docker run --rm "$NEURODOCKER_IMAGE" generate \
   --base "$BASE_IMAGE" --pkg-manager "$PKG_MANAGER" \
   --label maintainer="The nipype developers https://github.com/nipy/nipype" \
   --spm version=12 matlab_version=R2017a \
-  --afni version=latest \
+  --afni version=latest install_python2=true \
   --freesurfer version=6.0.0 min=true \
   --run 'echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IC9vcHQvZnJlZXN1cmZlci9saWNlbnNlLnR4dAo=" | base64 -d | sh' \
-  --install ants apt-utils bzip2 file fsl-core fsl-mni152-templates \
+  --install ants apt-utils bzip2 convert3d file fsl-core fsl-mni152-templates \
             fusefat g++ git graphviz make ruby unzip xvfb \
   --add-to-entrypoint "source /etc/fsl/fsl.sh" \
   --env ANTSPATH='/usr/lib/ants' PATH='/usr/lib/ants:$PATH' \
-  --c3d version=1.0.0 \
-  --instruction "RUN gem install fakes3" \
-  --workdir /work \
+  --run "gem install fakes3" \
   --no-check-urls > "$DIR/Dockerfile.base"
 }
 
@@ -45,12 +94,17 @@ function generate_main_dockerfile() {
   --env MKL_NUM_THREADS=1 OMP_NUM_THREADS=1 \
   --user neuro \
   --miniconda env_name=neuro \
-              add_to_path=true \
+              activate=true \
   --copy docker/files/run_builddocs.sh docker/files/run_examples.sh \
          docker/files/run_pytests.sh nipype/external/fsl_imglob.py /usr/bin/ \
   --copy . /src/nipype \
   --user root \
-  --run "chmod 777 -R /src/nipype" \
+  --run 'chown -R neuro /src
+&& chmod +x /usr/bin/fsl_imglob.py /usr/bin/run_*.sh
+&& . /etc/fsl/fsl.sh
+&& ln -sf /usr/bin/fsl_imglob.py ${FSLDIR}/bin/imglob
+&& mkdir /work
+&& chown neuro /work' \
   --user neuro \
   --arg PYTHON_VERSION_MAJOR=3 PYTHON_VERSION_MINOR=6 BUILD_DATE VCS_REF VERSION \
   --miniconda env_name=neuro \
@@ -59,6 +113,12 @@ function generate_main_dockerfile() {
                              pandas psutil scikit-learn scipy traits=4.6.0' \
               pip_opts="-e" \
               pip_install="/src/nipype[all]" \
+  --run-bash "mkdir -p /src/pybids
+         && curl -sSL --retry 5 https://github.com/INCF/pybids/tarball/master
+         | tar -xz -C /src/pybids --strip-components 1
+         && source activate neuro
+         && pip install --no-cache-dir -e /src/pybids" \
+  --workdir /work \
   --label org.label-schema.build-date='$BUILD_DATE' \
           org.label-schema.name="NIPYPE" \
           org.label-schema.description="NIPYPE - Neuroimaging in Python: Pipelines and Interfaces" \
@@ -67,9 +127,13 @@ function generate_main_dockerfile() {
           org.label-schema.vcs-url="https://github.com/nipy/nipype" \
           org.label-schema.version='$VERSION' \
           org.label-schema.schema-version="1.0" \
-  --no-check-urls > "$DIR/../Dockerfile"
+  --no-check-urls
 }
 
 
-generate_base_dockerfile
-generate_main_dockerfile
+if [ "$GENERATE_BASE" == 1 ]; then
+  generate_base_dockerfile > "$DIR/Dockerfile.base"
+fi
+if [ "$GENERATE_MAIN" == 1 ]; then
+  generate_main_dockerfile > "$DIR/../Dockerfile"
+fi