Update Dockerfile to use Python 3.10 and newer Debian version.

Update Dockerfile to use Python 3.10 and newer Debian version
and don't include optional dependencies in pySCENIC Docker image
by default (scanpy, MulticoreTSNE, papermill, ipykernel) as they
are not needed to pySCENIC in cli mode.

Author: ghuls

.dockerignore

@@ -0,0 +1,5 @@
+*/*/__pycache__
+.github
+.idea
+.pytest_cache
+.tox

Dockerfile

@@ -1,33 +1,34 @@
-FROM python:3.7.9-slim AS compile-image
+FROM python:3.10.6-slim-bullseye AS compile-image
 
 ENV DEBIAN_FRONTEND=noninteractive
-RUN BUILDPKGS="build-essential \
-        python3-dev libhdf5-dev libfreetype6-dev libtool \
-        m4 autoconf automake patch bison flex libpng-dev libopenblas-dev git \
-        tcl-dev tk-dev libxml2-dev zlib1g-dev libffi-dev cmake" && \
-    apt-get update && \
-    apt-get install -y --no-install-recommends apt-utils debconf locales && dpkg-reconfigure locales && \
-    apt-get install -y --no-install-recommends $BUILDPKGS
 
+# Install some dependencies:
+#   - MulticoreTSNE: build-essential cmake
+#   - git: to set the pySCENIC version
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends build-essential cmake git
+
+# Create virtual environment.
 RUN python -m venv /opt/venv
-# Make sure we use the virtualenv:
+
+# Make sure we use the virtual environment.
 ENV PATH="/opt/venv/bin:$PATH"
 
-# install dependencies:
+# Install pySCENIC dependencies with pip.
 COPY requirements_docker.txt /tmp/
-RUN pip install --no-cache-dir --upgrade pip wheel && \
-    pip install --no-cache-dir -r /tmp/requirements_docker.txt
+RUN pip install --no-cache-dir -r /tmp/requirements.txt
 
-# use version from argument (--build-arg version=0.11.0), or a default:
-RUN pip install --no-cache-dir scanpy==1.7.2
+# Install scanpy, MulticoreTSNE and ipykernel.
+#COPY requirements_docker_with_scanpy.txt /tmp/
+#RUN pip install --no-cache-dir -r /tmp/requirements_docker_with_scanpy.txt
 
-# install pySCENIC from local copy:
-COPY pySCENIC /tmp/pySCENIC
+# Install pySCENIC from local copy:
+COPY . /tmp/pySCENIC
 RUN  cd /tmp/pySCENIC && \
      pip install . && \
      cd .. && rm -rf pySCENIC
 
-FROM python:3.7.9-slim AS build-image
+FROM python:3.10.6-slim-bullseye AS build-image
 
 RUN apt-get -y update && \
     apt-get -y --no-install-recommends install \

requirements.doc.txt

@@ -1,3 +1,3 @@
 sphinx
-sphinx_rtd_theme
-restructuredtext_lint
+sphinx-rtd-theme
+restructuredtext-lint

requirements_docker.txt

@@ -0,0 +1,9 @@
+# scanpy
+scanpy[leiden]==1.9.1
+louvain==0.7.1
+# Fastq TSNE implementation.
+MulticoreTSNE==0.1
+# Parameterizing, executing, and analyzing Jupyter Notebooks.
+papermill==2.3.4
+# IPython kernel.
+ipykernel==6.15.1