test updates wrt container behavior

This PR removes the generation of a Singularity recipe given problems wrt the `--copy` argument in `neurodocker`. Furthermore, it adds a new branch that aims to host tests for future updates concerning the container behavior, as well as adds  the printing the list of meta-data files that will be evaluated.

Dockerfile

@@ -1,5 +1,6 @@
-# Generated by Neurodocker version 0.5.0
-# Timestamp: 2020-09-16 16:07:32 UTC
+# Your version: 0.6.0 Latest version: 0.7.0
+# Generated by Neurodocker version 0.6.0
+# Timestamp: 2021-04-13 14:10:53 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -72,17 +73,17 @@ RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
     && sync && conda clean --all && sync \
     && conda create -y -q --name bidsonym \
     && conda install -y -q --name bidsonym \
-           'python=3.6' \
-           'numpy' \
-           'nipype' \
-           'nibabel' \
-           'pandas' \
+           "python=3.6" \
+           "numpy" \
+           "nipype" \
+           "nibabel" \
+           "pandas" \
     && sync && conda clean --all && sync \
     && bash -c "source activate bidsonym \
     &&   pip install --no-cache-dir  \
-             'deepdefacer' \
-             'tensorflow' \
-             'scikit-image'" \
+             "deepdefacer" \
+             "tensorflow" \
+             "scikit-image"" \
     && rm -rf ~/.cache/pip/* \
     && sync \
     && sed -i '$isource activate bidsonym' $ND_ENTRYPOINT

bidsonym/utils.py

@@ -113,6 +113,9 @@ def check_meta_data(bids_dir, subject_label, prob_fields=None):
                                       '_desc-headerinfo.csv'),
                          index=False)
 
+    print('the following meta-data files will be checked:')
+    print(*list_meta_files, sep='\n')
+
     for meta_file in list_meta_files:
 
         with open(meta_file, 'r') as json_file:

generate_images.sh

@@ -5,7 +5,7 @@
  set -e
 
 generate_docker() {
-  docker run --rm kaczmarj/neurodocker:0.5.0 generate docker \
+  docker run --rm kaczmarj/neurodocker:0.6.0 generate docker \
              --base neurodebian:stretch-non-free \
              --pkg-manager apt \
              --install fsl-core git num-utils gcc g++ curl build-essential nano\
@@ -34,7 +34,7 @@ generate_docker() {
 }
 
 generate_singularity() {
-  docker run --rm kaczmarj/neurodocker:0.5.0 generate singularity \
+  docker run --rm kaczmarj/neurodocker:0.6.0 generate singularity \
              --base neurodebian:stretch-non-free \
              --pkg-manager apt \
              --install fsl-complete git num-utils gcc g++ curl build-essential\