enh: use base conda env + conda install numpy and scipy

Author: Jakub Kaczmarzyk

Dockerfile

@@ -1,5 +1,5 @@
-# Generated by Neurodocker version 0.4.1
-# Timestamp: 2018-11-01 18:20:45 UTC
+# Generated by Neurodocker version 0.4.1-28-g83dbc15
+# Timestamp: 2018-11-01 21:17:58 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -88,19 +88,20 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
     && conda config --system --set auto_update_conda false \
     && conda config --system --set show_channel_urls true \
     && sync && conda clean -tipsy && sync \
-    && conda create -y -q --name neuro \
-    && conda install -y -q --name neuro \
+    && conda install -y -q --name base \
            python=3.6 \
            traits>=4.6.0 \
+           scipy \
+           numpy \
+           nomkl \
     && sync && conda clean -tipsy && sync \
-    && bash -c "source activate neuro \
-    &&   pip install  --no-cache-dir \
+    && bash -c "source activate base \
+    &&   pip install --no-cache-dir  \
              /src/heudiconv[all]" \
     && rm -rf ~/.cache/pip/* \
-    && sync \
-    && sed -i '$isource activate neuro' $ND_ENTRYPOINT
+    && sync
 
-ENTRYPOINT ["/neurodocker/startup.sh", "heudiconv"]
+ENTRYPOINT ["heudiconv"]
 
 RUN echo '{ \
     \n  "pkg_manager": "apt", \
@@ -137,20 +138,22 @@ RUN echo '{ \
     \n    [ \
     \n      "miniconda", \
     \n      { \
-    \n        "create_env": "neuro", \
+    \n        "use_env": "base", \
     \n        "conda_install": [ \
     \n          "python=3.6", \
-    \n          "traits>=4.6.0" \
+    \n          "traits>=4.6.0", \
+    \n          "scipy", \
+    \n          "numpy", \
+    \n          "nomkl" \
     \n        ], \
-    \n        "activate": true, \
     \n        "pip_install": [ \
     \n          "/src/heudiconv[all]" \
     \n        ] \
     \n      } \
     \n    ], \
     \n    [ \
     \n      "entrypoint", \
-    \n      "/neurodocker/startup.sh heudiconv" \
+    \n      "heudiconv" \
     \n    ] \
     \n  ] \
     \n}' > /neurodocker/neurodocker_specs.json

utils/gen-docker-image.sh

@@ -4,11 +4,13 @@ set -eu
 
 VER=$(grep -Po '(?<=^__version__ = ).*' ../heudiconv/info.py | sed 's/"//g')
 
-docker run --rm kaczmarj/neurodocker:0.4.1 generate docker -b neurodebian:stretch -p apt \
+image="kaczmarj/neurodocker:master@sha256:9f7d58f6977cfcd4dd5d1a2e70be4124417206b716d51b7d9a182820157f1bd3"
+
+docker run --rm $image generate docker -b neurodebian:stretch -p apt \
     --dcm2niix version=v1.0.20180622 method=source \
     --install git gcc pigz liblzma-dev libc-dev git-annex-standalone \
     --copy . /src/heudiconv \
-    --miniconda create_env=neuro conda_install="python=3.6 traits>=4.6.0" activate=True \
+    --miniconda use_env=base conda_install="python=3.6 traits>=4.6.0 scipy numpy nomkl" \
       pip_install="/src/heudiconv[all]" \
-    --entrypoint "/neurodocker/startup.sh heudiconv" \
+    --entrypoint "heudiconv" \
 > ../Dockerfile