📦 Update variant bases

[rebuild Ubuntu.bionic-non-free]
[rebuild Ubuntu.xenial-20200114]

Ref #1911

Author: shnizzedy

.github/Dockerfiles/Ubuntu.bionic-non-free.Dockerfile

@@ -121,18 +121,18 @@ RUN groupadd -r c-pac && \
 ENV PATH=/usr/bin/nvm/versions/node/v12.12.0/bin:/usr/local/miniconda/bin:$PATH
 
 # Installing conda dependencies, torch & Python dependencies
-COPY requirements.txt /opt/requirements.txt
-RUN conda update conda -y && \
-    conda install nomkl && \
-    conda install -y  \
+COPY dev/docker_data/unpinned_requirements.txt /opt/requirements.txt
+RUN conda install -n base conda-forge::mamba conda-forge::libarchive==3.5.2 -y && \
+    mamba update conda -y && \
+    mamba install nomkl -y && \
+    mamba  install -y  \
       blas \
       cython \
       matplotlib==3.1.3 \
       networkx==2.4 \
       nose==1.3.7 \
       numpy==1.16.4 \
       pandas==1.0.5 \
-      scipy==1.6.3 \
       traits==4.6.0 \
       pip && \
     pip install \

.github/Dockerfiles/Ubuntu.xenial-20200114.Dockerfile

@@ -133,25 +133,25 @@ ENV PATH="/usr/local/miniconda/bin:$PATH" \
     PYTHONNOUSERSITE=1
 
 # install conda dependencies
-RUN conda update conda -y && \
-    conda install nomkl && \
-    conda install -y  \
+RUN conda install -n base conda-forge::mamba conda-forge::libarchive==3.5.2 -y && \
+    mamba update conda -y && \
+    mamba install nomkl -y && \
+    mamba  install -y  \
         blas \
         cython \
         matplotlib==2.2.2 \
         networkx==2.4 \
         nose==1.3.7 \
         numpy==1.15.4 \
         pandas==1.0.5 \
-        scipy==1.6.3 \
         traits==4.6.0 \
         pip
 
 # install torch
 RUN pip install torch==1.2.0 torchvision==0.4.0 -f https://download.pytorch.org/whl/torch_stable.html
 
 # install python dependencies
-COPY requirements.txt /opt/requirements.txt
+COPY dev/docker_data/unpinned_requirements.txt /opt/requirements.txt
 RUN pip install --upgrade setuptools
 RUN pip install --upgrade pip
 RUN pip install -r /opt/requirements.txt

dev/docker_data/unpinned_requirements.txt

@@ -0,0 +1,33 @@
+boto3
+ciftify
+click
+configparser
+future
+INDI-Tools @ git+https://[email protected]/FCP-INDI/INDI-Tools.git@998c246c597209f06f8d5c5b92ddc2c9c1942f46
+joblib
+lockfile
+matplotlib
+networkx
+nibabel
+nilearn
+nipype
+nose
+numpy
+pandas
+pathvalidate
+patsy
+prov
+psutil
+PyBASC
+pybids
+PyPEER @ git+https://[email protected]/ChildMindInstitute/PyPEER.git@6965d2b2bea0fef824e885fec33a8e0e6bd50a97
+python-dateutil
+PyYAML
+requests
+scikit-learn
+scipy
+sdcflows
+torch
+torchvision
+traits
+voluptuous