MAINT: Docker - Update base Ubuntu image & ANTs, makefile

.circleci/config.yml

@@ -156,7 +156,7 @@ jobs:
 
   build_n_pytest:
     machine:
-      image: circleci/classic:201808-01
+      image: ubuntu-2004:202010-01
     working_directory: /tmp/tests
     environment:
       TZ: "/usr/share/zoneinfo/America/Los_Angeles"
@@ -183,14 +183,14 @@ jobs:
             set -e
             if [[ "$success" = "0" ]]; then
                 echo "Pulling from local registry"
-                docker tag localhost:5000/ubuntu ubuntu:xenial-20191010
+                docker tag localhost:5000/ubuntu ubuntu:xenial-20201030
                 docker pull localhost:5000/sdcflows
                 docker tag localhost:5000/sdcflows nipreps/sdcflows:latest
                 docker tag localhost:5000/sdcflows nipreps/sdcflows
             else
                 echo "Pulling from Docker Hub"
-                docker pull ubuntu:xenial-20191010
-                docker tag ubuntu:xenial-20191010 localhost:5000/ubuntu
+                docker pull ubuntu:xenial-20201030
+                docker tag ubuntu:xenial-20201030 localhost:5000/ubuntu
                 docker push localhost:5000/ubuntu
                 docker pull nipreps/sdcflows:latest
             fi
@@ -201,7 +201,9 @@ jobs:
           no_output_timeout: 60m
           command: |
             cd /tmp/src/sdcflows
-            pyenv local 3.7.0
+            export PY3=$(pyenv versions | grep '3\.' |
+                         sed -e 's/.* 3\./3./' -e 's/ .*//')
+            pyenv local $PY3
             python3 -m pip install "setuptools ~= 42.0" "setuptools_scm[toml] >= 3.4" "pip>=10.0.1"
 
             # Get version, update files.
@@ -320,7 +322,9 @@ jobs:
       - run:
           name: Submit unit test coverage
           command: |
-            pyenv local 3.7.0
+            export PY3=$(pyenv versions | grep '3\.' |
+                         sed -e 's/.* 3\./3./' -e 's/ .*//')
+            pyenv local $PY3
             python3 -m pip install codecov
             cd /tmp/src/sdcflows
             python3 -m codecov --file /tmp/tests/unittests.xml \
@@ -390,7 +394,7 @@ jobs:
 
   deploy_docker:
     machine:
-      image: circleci/classic:201711-01
+      image: ubuntu-2004:202010-01
     working_directory: /tmp/src/
     steps:
       - restore_cache:

Dockerfile

@@ -1,5 +1,5 @@
 # Use Ubuntu 16.04 LTS
-FROM ubuntu:xenial-20191010
+FROM ubuntu:xenial-20201030
 
 # Pre-cache neurodebian key
 COPY .docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg
@@ -60,10 +60,11 @@ ENV FSLDIR="/usr/share/fsl/5.0" \
     AFNI_PLUGINPATH="/usr/lib/afni/plugins"
 ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH"
 
-# Installing ANTs 2.2.0 (NeuroDocker build)
+# Installing ANTs 2.3.3 (NeuroDocker build)
+# Note: the URL says 2.3.4 but it is actually 2.3.3
 ENV ANTSPATH=/usr/lib/ants
 RUN mkdir -p $ANTSPATH && \
-    curl -sSL "https://dl.dropbox.com/s/2f4sui1z6lcgyek/ANTs-Linux-centos5_x86_64-v2.2.0-0740f91.tar.gz" \
+    curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
     | tar -xzC $ANTSPATH --strip-components 1
 ENV PATH=$ANTSPATH:$PATH
 

Makefile

@@ -0,0 +1,18 @@
+.PHONY: help docker
+.DEFAULT: help
+
+tag="latest"
+
+help:
+	@echo "Premade recipes"
+	@echo
+	@echo "make docker [tag=TAG]"
+	@echo "\tBuilds a docker image from source. Defaults to 'latest' tag."
+
+
+docker:
+	docker build --rm -t nipreps/sdcflows:$(tag) \
+	--build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \
+	--build-arg VCS_REF=`git rev-parse --short HEAD` \
+	--build-arg VERSION=`python setup.py --version` .
+