Merge branch 'ray_cluster_functionality' of https://github.com/choose…

…happy/HistoQC into ray_cluster_functionality

Dockerfile

@@ -1,23 +1,4 @@
 # Dockerfile for HistoQC.
-# This Dockerfile uses two stages. In the first, the project's python dependencies are
-# installed. This requires a C compiler. In the second stage, the HistoQC directory and
-# the python environment are copied over. We do not require a C compiler in the second
-# stage, and so we can use a slimmer base image.
-
-FROM python:3.8 AS builder
-ARG DEBIAN_FRONTEND=noninteractive
-WORKDIR /opt/HistoQC
-COPY . .
-# Create virtual environment for this project. This makes it easier to copy the Python
-# installation into the second stage of the build.
-ENV PATH="/opt/HistoQC/venv/bin:$PATH"
-RUN python -m venv venv \
-    && python -m pip install --no-cache-dir setuptools wheel \
-    && python -m pip install --no-cache-dir -r requirements.txt \
-    && python -m pip install --no-cache-dir . \
-    # We force this so there is no error even if the dll does not exist.
-    && rm -f libopenslide-0.dll
-
 FROM rayproject/ray-ml:latest-gpu
 ARG DEBIAN_FRONTEND=noninteractive
 USER root
@@ -29,12 +10,14 @@ RUN apt-get update \
     && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /opt/HistoQC
-COPY --from=builder /opt/HistoQC/ .
-
-RUN pip install .
+COPY . .
+# install
+RUN pip install --no-cache-dir setuptools wheel \
+    && pip install --no-cache-dir -r requirements.txt \
+    && pip install --no-cache-dir . \
+    && rm -f libopenslide-0.dll
 
-USER ray
 WORKDIR /data
 
-# CMD ["bash"]
-CMD [ "python", "-m", "histoqc", "--help" ]
+CMD ["bash"]
+

histoqc/BaseImage.py

@@ -1,5 +1,5 @@
 import logging
-import os
+import os, re
 import numpy as np
 import zlib, dill
 from distutils.util import strtobool

histoqc/import_wrapper/__init__.py

@@ -0,0 +1 @@
+from .openslide import openslide

setup.py

@@ -16,7 +16,11 @@
     for f in glob.iglob(f"histoqc/data/{folder}/**/*", recursive=True)
     if os.path.isfile(f)
 ]
-
+import_wrapper_files = [
+    os.path.relpath(f, "histoqc/import_wrapper_files/")
+    for f in glob.iglob(f"histoqc/import_wrapper_files/**/*", recursive=True)
+    if os.path.isfile(f)
+]
 setup(
     use_scm_version={
         # duplicated config from pyproject.toml; keep in sync
@@ -28,5 +32,6 @@
         'histoqc.config': ['*.ini'],
         'histoqc.data': data_files,
         'histoqc.ui': ui_files,
+        'histoqc.import_wrapper': import_wrapper_files
     }
 )