[FIX] add "USER root" to top of every Dockerfile (#306)

* add "USER root" to top of every Dockerfile * being singularity `%post` with root user * update cache version In #306, the circleci tests were failing for minc. This commit is an attempt to fix that, because the problem was not reproducible on jakub's local installation. * try switching the order instructions are added * switch back commands * select working version of miniconda installer * add missing comma * change placement of miniconda version to singularity * change if syntax Co-authored-by: Jakub Kaczmarzyk <jakubk@mit.edu>
ReproNim · Jan 9, 2020 · d890e05 · d890e05
1 parent 11f80f6
commit d890e05
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Showing 5 changed files with 18 additions and 14 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -34,9 +34,9 @@ jobs:
           *setup_kwds
       - restore_cache:
           keys:
-            - dfs-v0-{{ .Branch }}-{{ .Revision }}
-            - dfs-v0-{{ .Branch }}
-            - dfs-v0
+            - dfs-v1-{{ .Branch }}-{{ .Revision }}
+            - dfs-v1-{{ .Branch }}
+            - dfs-v1
       - run:
           name: Test docker image builds
           no_output_timeout: 360m
@@ -45,8 +45,7 @@ jobs:
             pytest --cov -k 'test_docker' neurodocker
             codecov
       - save_cache:
-          key: dfs-v0-{{ .Branch }}-{{ .Revision }}
-          when: always
+          key: dfs-v1-{{ .Branch }}-{{ .Revision }}
           paths:
             - /tmp/cache
 
@@ -61,9 +60,9 @@ jobs:
           *setup_kwds
       - restore_cache:
           keys:
-            - srs-v0-{{ .Branch }}-{{ .Revision }}
-            - srs-v0-{{ .Branch }}
-            - srs-v0
+            - srs-v1-{{ .Branch }}-{{ .Revision }}
+            - srs-v1-{{ .Branch }}
+            - srs-v1
       - run:
           name: Install singularity
           command: |
@@ -82,8 +81,7 @@ jobs:
             pytest --cov -k 'test_singularity' neurodocker
             codecov
       - save_cache:
-          key: srs-v0-{{ .Branch }}-{{ .Revision }}
-          when: always
+          key: srs-v1-{{ .Branch }}-{{ .Revision }}
           paths:
             - ~/tmp/cache
 

diff --git a/neurodocker/generators/docker.py b/neurodocker/generators/docker.py
@@ -306,13 +306,16 @@ def _add_header(self):
         # base, arg noninteractive frontend, ndfreeze, header, entrypoint.
         offset = 1 if self._specs['instructions'][1][0] == 'ndfreeze' else 0
         self._specs['instructions'].insert(
-            1, ('arg', {
+            1, ('user', 'root')
+        )
+        self._specs['instructions'].insert(
+            2, ('arg', {
                 'DEBIAN_FRONTEND': 'noninteractive'
             }))
         kwds = {'version': 'generic', 'method': 'custom'}
-        self._specs['instructions'].insert(2 + offset, ('_header', kwds))
+        self._specs['instructions'].insert(3 + offset, ('_header', kwds))
         self._specs['instructions'].insert(
-            3 + offset, ('entrypoint', "/neurodocker/startup.sh"))
+            4 + offset, ('entrypoint', "/neurodocker/startup.sh"))
 
     def _ispecs_to_dockerfile_str(self):
         pkg_man = self._specs['pkg_manager']

diff --git a/neurodocker/generators/singularity.py b/neurodocker/generators/singularity.py
@@ -157,6 +157,8 @@ def _add_neurodocker_header(self):
             if self._specs['instructions'][1][0] == 'ndfreeze':
                 offset = 1
         self._specs['instructions'].insert(1 + offset, ('_header', kwds))
+        self._specs['instructions'].insert(1 + offset, ('user', 'root'))
+
 
     def _fill_parts(self):
         pkg_man = self._specs['pkg_manager']

diff --git a/neurodocker/interfaces/tests/test_miniconda.py b/neurodocker/interfaces/tests/test_miniconda.py
@@ -45,6 +45,7 @@ def test_singularity(self):
                 (
                     'miniconda',
                     {
+                        'version': '4.6.14',
                         'create_env': 'default',
                         'conda_install': ['python=3.6.5', 'traits'],
                         'pip_install': ['nipype'],

diff --git a/neurodocker/templates/miniconda.yaml b/neurodocker/templates/miniconda.yaml
@@ -17,7 +17,7 @@ generic:
       curl {{ miniconda.curl_opts }} -o "$conda_installer" {{ miniconda.binaries_url }}
       bash "$conda_installer" -b -p {{ miniconda.install_path }}
       rm -f "$conda_installer"
-      {%- if miniconda.version == "latest" %}
+      {% if miniconda.version == "latest" -%}
       conda update -yq -nbase conda
       {% endif -%}
       conda config --system --prepend channels conda-forge