FIX: Docker build

[effigies]

Bumps neurodocker to 0.5.0 and sets the workdir to ~neuro so that conda can throw temporary .cph_tmp* directories into the CWD with impunity.

conda/conda-package-handling#34

[effigies]

@kaczmarj Just a note that it looks like Neurodocker 0.5.0 puts single quotes around conda packages, disabling python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}.

CondaValueError: invalid package specification: python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}

The command '/bin/sh -c export PATH="/opt/miniconda-latest/bin:$PATH"     && echo "Downloading Miniconda installer ..."     && conda_installer="/tmp/miniconda.sh"     && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh     && bash "$conda_installer" -b -p /opt/miniconda-latest     && rm -f "$conda_installer"     && conda update -yq -nbase conda     && conda config --system --prepend channels conda-forge     && conda config --system --set auto_update_conda false     && conda config --system --set show_channel_urls true     && sync && conda clean --all && sync     && conda create -y -q --name neuro     && conda install -y -q --name neuro            'python=${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}'            'libxml2'            'libxslt'            'matplotlib'            'mkl'            '"numpy!=1.16.0"'            'paramiko'            'pandas'            'psutil'            'scikit-learn'            'scipy'            'traits'     && sync && conda clean --all && sync     && bash -c "source activate neuro     &&   pip install --no-cache-dir               'pytest-xdist'"     && rm -rf ~/.cache/pip/*     && sync     && sed -i '$isource activate neuro' $ND_ENTRYPOINT' returned a non-zero code: 1

[effigies]

Looks like it was introduced in ReproNim/neurodocker#239. I think switching to double-quotes will probably fix things up.

[codecov-io]

Codecov Report

Merging #2963 into master will increase coverage by 2.67%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #2963      +/-   ##
==========================================
+ Coverage   64.24%   66.91%   +2.67%     
==========================================
  Files         342      344       +2     
  Lines       43692    43747      +55     
  Branches     5453     5456       +3     
==========================================
+ Hits        28068    29275    +1207     
+ Misses      14545    13725     -820     
+ Partials     1079      747     -332

Flag	Coverage Δ
#smoketests	48.53% <ø> (?)
#unittests	65.03% <ø> (+0.79%)	⬆️

Impacted Files	Coverage Δ
nipype/pipeline/plugins/legacymultiproc.py	66.5% <0%> (-1%)	⬇️
nipype/__init__.py	59.45% <0%> (ø)
nipype/testing/__init__.py	88.88% <0%> (ø)
nipype/utils/profiler.py	19.42% <0%> (+0.57%)	⬆️
nipype/interfaces/spm/preprocess.py	52.88% <0%> (+0.65%)	⬆️
nipype/pipeline/plugins/base.py	60.32% <0%> (+1.08%)	⬆️
nipype/interfaces/freesurfer/model.py	64.25% <0%> (+1.12%)	⬆️
nipype/interfaces/utility/base.py	87.5% <0%> (+1.13%)	⬆️
nipype/interfaces/fsl/maths.py	99.42% <0%> (+1.15%)	⬆️
nipype/interfaces/utility/wrappers.py	86.41% <0%> (+1.23%)	⬆️
... and 39 more

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[oesteban]

thx!

[kaczmarj]

Thank you! I will change the single quotes to double quotes in conda and pip installs.

…

On Jul 17, 2019, at 2:39 AM, Oscar Esteban ***@***.***> wrote: thx! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[kaczmarj]

@effigies @oesteban - i updated neurodocker to use double quotes in all conda and pip installs. this behavior is available in the current docker image kaczmarj/neurodocker:master.