Updated container files to 0.9.16 (Scanpy 1.4.4.post1)

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.6.8-slim
+FROM python:3.7.4-slim
 
 ENV DEBIAN_FRONTEND=noninteractive
 RUN BUILDPKGS="build-essential apt-utils \
@@ -9,7 +9,7 @@ RUN BUILDPKGS="build-essential apt-utils \
     apt-get install -y debconf locales && dpkg-reconfigure locales && \
     apt-get install -y $BUILDPKGS && \
     ### run time:
-    apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++ musl \
+    apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++6 musl \
         libopenblas-base tcl tk libxml2 libffi6 less procps
 
 # install dependencies:
@@ -18,9 +18,9 @@ RUN pip install --no-cache-dir --upgrade pip && \
     pip install --no-cache-dir -r /tmp/requirements_docker.txt
 
 # use version from argument (--build-arg version=0.9.7), or a default:
-ARG version="0.9.15"
+ARG version="0.9.16"
 RUN pip install --no-cache-dir pyscenic==$version && \
-    pip install --no-cache-dir scanpy==1.4.4
+    pip install --no-cache-dir scanpy==1.4.4.post1
 
 RUN apt-get remove --purge -y $BUILDPKGS && \
     rm -rf /var/lib/apt/lists/*

Singularity

@@ -1,5 +1,5 @@
 BootStrap: docker
-From: python:3.6.8-slim
+From: python:3.7.4-slim
 
 %files
     ./requirements_docker.txt /tmp/
@@ -11,13 +11,13 @@ From: python:3.6.8-slim
         tcl-dev tk-dev libxml2-dev zlib1g-dev libffi-dev cmake"
     apt-get update
     apt-get install -y debconf locales && dpkg-reconfigure locales
-    apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++ musl \
+    apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++6 musl \
         libopenblas-base tcl tk libxml2 libffi6 less procps
     apt-get install -y $BUILDPKGS
 
     pip install --no-cache-dir -r /tmp/requirements_docker.txt
-    pip install --no-cache-dir --upgrade pyscenic==0.9.15
-    pip install --no-cache-dir scanpy==1.4.4
+    pip install --no-cache-dir --upgrade pyscenic==0.9.16
+    pip install --no-cache-dir scanpy==1.4.4.post1
 
     apt-get remove --purge -y $BUILDPKGS && \
     rm -rf /var/lib/apt/lists/*

Singularity.0.9.16

@@ -0,0 +1,24 @@
+BootStrap: docker
+From: python:3.7.4-slim
+
+%files
+    ./requirements_docker.txt /tmp/
+
+%post
+    BUILDPKGS="build-essential apt-utils \
+        python3-dev libhdf5-dev libfreetype6-dev libtool \
+        m4 autoconf automake patch bison flex libpng-dev libopenblas-dev \
+        tcl-dev tk-dev libxml2-dev zlib1g-dev libffi-dev cmake"
+    apt-get update
+    apt-get install -y debconf locales && dpkg-reconfigure locales
+    apt-get install -y zlib1g hdf5-tools gfortran libgcc1 libstdc++6 musl \
+        libopenblas-base tcl tk libxml2 libffi6 less procps
+    apt-get install -y $BUILDPKGS
+
+    pip install --no-cache-dir -r /tmp/requirements_docker.txt
+    pip install --no-cache-dir --upgrade pyscenic==0.9.16
+    pip install --no-cache-dir scanpy==1.4.4.post1
+
+    apt-get remove --purge -y $BUILDPKGS && \
+    rm -rf /var/lib/apt/lists/*
+

requirements_docker.txt

@@ -28,7 +28,7 @@ kiwisolver==1.1.0
 llvmlite==0.29.0
 loompy==2.0.17
 louvain==0.6.1
-matplotlib==3.0.2
+matplotlib==3.1.1
 mock==3.0.5
 msgpack==0.6.1
 MulticoreTSNE==0.1