rm libmng1 apt dependency (#247)

* rm libmng1 apt dependency

* fix error with bare generate singularity

* test r7219 on ubuntu 16.04

* use debian stretch base image

* change test script to a=1

Author: Jakub Kaczmarzyk

neurodocker/generators/singularity.py

@@ -147,7 +147,10 @@ def _render_labels(self):
     def _add_neurodocker_header(self):
         kwds = {'version': 'generic', 'method': 'custom'}
         # If ndfreeze is requested, put it before the neurodocker header.
-        offset = 1 if self._specs['instructions'][1][0] == 'ndfreeze' else 0
+        offset = 0
+        if len(self._specs['instructions']) > 1:
+            if self._specs['instructions'][1][0] == 'ndfreeze':
+                offset = 1
         self._specs['instructions'].insert(1 + offset, ('_header', kwds))
 
     def _fill_parts(self):

neurodocker/interfaces/tests/test_spm12.py

@@ -9,8 +9,8 @@ def test_docker(self):
         specs = {
             'pkg_manager': 'apt',
             'instructions': [
-                ('base', 'ubuntu:18.04'),
-                ('spm12', {'version': 'dev'}),
+                ('base', 'debian:stretch'),
+                ('spm12', {'version': 'r7219'}),
                 ('user', 'neuro'),
             ],
         }
@@ -23,7 +23,7 @@ def test_singularity(self):
         specs = {
             'pkg_manager': 'apt',
             'instructions': [
-                ('base', 'docker://ubuntu:16.04'),
+                ('base', 'docker://debian:stretch'),
                 ('spm12', {'version': 'r7219'}),
                 ('user', 'neuro'),
             ],

neurodocker/interfaces/tests/test_spm12.sh

@@ -2,7 +2,7 @@
 
 set -exu
 
-echo 'fprintf("testing")' > /tmp/test.m
-$SPMMCRCMD /tmp/test.m
+echo "a = 1" > ~/test.m
+$SPMMCRCMD ~/test.m
 
 printf 'passed'

neurodocker/templates/fsl.yaml

@@ -16,7 +16,7 @@ generic:
       "5.0.9": https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-5.0.9-centos6_64.tar.gz
       "5.0.8": https://fsl.fmrib.ox.ac.uk/fsldownloads/oldversions/fsl-5.0.8-centos6_64.tar.gz
     dependencies:
-      apt: bc dc file libfontconfig1 libfreetype6 libgl1-mesa-dev libglu1-mesa-dev libgomp1 libice6 libmng1 libxcursor1 libxft2 libxinerama1 libxrandr2 libxrender1 libxt6 wget
+      apt: bc dc file libfontconfig1 libfreetype6 libgl1-mesa-dev libglu1-mesa-dev libgomp1 libice6 libxcursor1 libxft2 libxinerama1 libxrandr2 libxrender1 libxt6 wget
       yum: bc file libGL libGLU libgomp libICE libjpeg libmng libpng12 libSM libX11 libXcursor libXext libXft libXinerama libXrandr libXt wget
     env:
       FSLDIR: "{{ fsl.install_path }}"