checkout repo

.circleci/config.yml

@@ -23,6 +23,7 @@ jobs:
     steps:
     - attach_workspace:
         at: /tmp/workspace
+    - checkout
     - run: docker load -i /tmp/workspace/docker/image.tar
     - run:
         name: push to dockerhub

INSTALL.md

@@ -52,7 +52,7 @@ docker images
 The Dockerfile used to create the image stored on DockerHub is available at the root of the repository ([Dockerfile](Dockerfile)). But you might want to personalize this Dockerfile. To do so, change the command below that will generate a new Dockerfile: 
 
 ```bash
-	docker run --rm repronim/neurodocker:0.9.5 generate docker \
+	neurodocker generate docker \
 			--base-image centos:7 --pkg-manager yum \
 			--yes \
 			--install git \
@@ -61,8 +61,9 @@ The Dockerfile used to create the image stored on DockerHub is available at the
 			--spm12 version=r7771 method=binaries \
 			--miniconda method=binaries \
 						version=latest \
+						mamba=true \
 						conda_install="python=3.10 pip=23.2.1" \
-						pip_install="traits==6.3.0 jupyterlab-4.0.6 graphviz-0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \
+						pip_install="traits==6.3.0 jupyterlab==4.0.6 graphviz==0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \
 			--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile
 ```
 

makefile

@@ -1,20 +1,10 @@
 .PHONY: Dockerfile
 
-Dockerfile:
-	docker run --rm repronim/neurodocker:0.9.5 generate docker \
-			--base-image centos:7 --pkg-manager yum \
-			--yes \
-			--install git \
-			--ants method=binaries version=2.4.3 \
-			--fsl version=6.0.6.4 \
-			--spm12 version=r7771 method=binaries \
-			--miniconda method=binaries \
-						version=latest 
-						conda_install="python=3.10 pip=23.2.1" \
-						pip_install="traits==6.3.0 jupyterlab==4.0.6 graphviz==0.20.1 nipype==1.8.6 scikit-image==0.21.0 matplotlib==3.8.0 nilearn==0.10.1" \
-			--run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile
+# docker run --rm repronim/neurodocker:0.9.5 generate docker 
 
-Dockerfile_mamba:
+# using the mamba option requires to use the version of neurodocker
+# installed from the main branch of the the neurodocker github repo
+Dockerfile:
 	neurodocker generate docker \
 			--base-image centos:7 --pkg-manager yum \
 			--yes \