Docker ci

.dockerignore

@@ -0,0 +1,41 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+
+# Unit test / coverage reports
+.pytest_cache/
+coverage_report_html/
+.coverage
+
+# Sphinx documentation
+docs/build/
+
+# data
+data/
+
+# files created by matplotlib testing suite
+result_images/
+
+# distribution / packaging
+*.egg-info
+*.egg
+build/
+dist/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# scratch notebook
+scratch.ipynb
+
+# Mac files
+.DS_Store
+
+# Pycharm
+.idea/
+
+# dask
+dask-worker-space/
+
+# git
+.git
+.gitigore

.github/workflows/publish-to-docker-hub.yml

@@ -0,0 +1,31 @@
+name: Publish PathML Docker image on Docker Hub
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set version number variable
+        run: |
+          VER=$(cat pathml/_version.py | grep -o  '"[^"]\+"' | tr '"' ' ')
+          echo "VERSION=$VER" >> $GITHUB_ENV
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1.2.0
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1.6.0
+      - name: Login to DockerHub
+        uses: docker/login-action@v1.10.0
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2.7.0
+        with:
+          push: true
+          tags:
+            pathml/pathml:latest
+            pathml/pathml:${{ env.VERSION }}

Dockerfile

@@ -0,0 +1,59 @@
+# syntax=docker/dockerfile:1
+
+FROM ubuntu:20.04
+# LABEL about the custom image
+LABEL maintainer="PathML@dfci.harvard.edu"
+LABEL description="This is custom Docker Image for running PathML"
+
+# Disable Prompt During Packages Installation
+ARG DEBIAN_FRONTEND=noninteractive
+
+#Set miniconda path
+ENV PATH="/root/miniconda3/bin:${PATH}"
+ARG PATH="/root/miniconda3/bin:${PATH}"
+
+ENV JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/jre/"
+ARG JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/jre/"
+
+ENV SHELL="/bin/bash"
+
+#install packages on root
+USER root
+
+#download and install miniconda and external dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends  openslide-tools \
+    g++ \
+    gcc \
+    libpixman-1-0 \
+    libblas-dev \
+    liblapack-dev \
+    wget \
+    openjdk-8-jre \
+    openjdk-8-jdk \
+    && wget \
+    https://repo.anaconda.com/miniconda/Miniconda3-py38_4.10.3-Linux-x86_64.sh \
+    && mkdir /root/.conda \
+    && bash Miniconda3-py38_4.10.3-Linux-x86_64.sh -b \
+    && rm -f Miniconda3-py38_4.10.3-Linux-x86_64.sh \
+    && rm -rf /var/lib/apt/lists/*
+
+# copy pathml files into docker
+COPY setup.py README.md /opt/pathml/
+COPY pathml/ /opt/pathml/pathml
+COPY tests/ /opt/pathml/tests
+
+# install pathml and deepcell
+RUN pip3 install --upgrade pip \
+    && pip3 install numpy==1.19.5 \
+    && pip3 install python-bioformats==4.0.0 deepcell /opt/pathml/ pytest
+
+# run tests to verify container
+WORKDIR /opt/pathml
+RUN python3 -m pytest /opt/pathml/tests/ -m "not slow"
+
+WORKDIR /home/pathml
+
+# set up jupyter lab
+RUN pip3 install jupyter -U && pip3 install jupyterlab
+EXPOSE 8888
+ENTRYPOINT ["jupyter", "lab", "--ip=0.0.0.0", "--allow-root", "--no-browser"]

README.md

@@ -26,6 +26,7 @@ There are several ways to install `PathML`:
 
 1. pip install (**recommended for users**)
 2. clone repo to local machine and install from source (recommended for developers/contributors)
+3. Use the PathML Docker container
 
 Options (1) and (2) require that you first install all external dependencies:
 * openslide
@@ -87,6 +88,29 @@ Install `PathML`:
 pip install -e .
 ````
 
+## Installation option 3: docker
+
+Build the PathML docker container:
+````
+docker build -t pathml-analysis .
+````
+
+Connect to the container:
+````
+docker run -it -p 8888:8888 pathml-analysis
+````
+
+The above command runs the container, which is configured to spin up a jupyter lab session and expose it on port 8888. 
+The terminal should display a URL to the jupyter lab session starting with http://127.0.0.1:8888/lab?token=<...>. 
+Navigate to that page and you should connect to the jupyter lab session running on the container with the pathml 
+environment fully configured.
+
+Note that the docker container requires extra configurations to use with GPU.  
+Note that these instructions assume that there are no other processes using port 8888.
+
+Please refer to the `Docker run` [documentation](https://docs.docker.com/engine/reference/run/) for further instructions
+on accessing the container, e.g. for mounting volumes to access files on a local machine from within the container.
+
 ## CUDA
 
 To use GPU acceleration for model training or other tasks, you must install CUDA. 

pathml/_version.py

@@ -3,4 +3,4 @@
 License: GNU GPL 2.0
 """
 
-__version__ = "2.0.1"
+__version__ = "2.0.dev1"

pathml/core/slide_backends.py

@@ -5,12 +5,8 @@
 
 from io import BytesIO
 from typing import Tuple
-
 import numpy as np
 import openslide
-import pathml.core
-import pathml.core.tile
-from pathml.utils import pil_to_rgb
 from PIL import Image
 from pydicom.dataset import Dataset
 from pydicom.encaps import get_frame_offsets
@@ -19,6 +15,11 @@
 from pydicom.tag import SequenceDelimiterTag, TupleTag
 from pydicom.uid import UID
 from scipy.ndimage import zoom
+from javabridge.jutil import JavaException
+
+import pathml.core
+import pathml.core.tile
+from pathml.utils import pil_to_rgb
 
 try:
     import bioformats
@@ -255,7 +256,11 @@ def __init__(self, filename):
         self.filename = filename
         # init java virtual machine
         javabridge.start_vm(class_path=bioformats.JARS, max_heap_size="50G")
-        _init_logger()
+        # disable verbose JVM logging if possible
+        try:
+            _init_logger()
+        except JavaException:
+            pass
         # java maximum array size of 2GB constrains image size
         ImageReader = bioformats.formatreader.make_image_reader_class()
         reader = ImageReader()