Merge pull request #336 from choosehappy/upgrade-openslide

Upgrade openslide to 4.0

Author: jacksonjacobs1

.devcontainer/devcontainer.json

@@ -0,0 +1,11 @@
+{
+  "name": "HistoQC Development Container",
+  "build": {
+    "dockerfile": "../Dockerfile",
+    "context": ".."
+  },
+  "workspaceFolder": "/opt/HistoQC",
+  "workspaceMount": "source=${localWorkspaceFolder},target=/opt/HistoQC,type=bind",
+  "remoteUser": "root",
+  "postCreateCommand": "python -m venv venv && venv/bin/pip install --no-cache-dir -e . && apt update && apt install -y git"
+}

Dockerfile

@@ -5,7 +5,7 @@
 # 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
+FROM python:3.10 AS builder
 ARG DEBIAN_FRONTEND=noninteractive
 WORKDIR /opt/HistoQC
 COPY . .
@@ -14,15 +14,13 @@ COPY . .
 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 . \
-    # We force this so there is no error even if the dll does not exist.
-    && rm -f libopenslide-0.dll
+    && python -m pip install --no-cache-dir .
 
-FROM python:3.8-slim
+
+FROM python:3.10-slim
 ARG DEBIAN_FRONTEND=noninteractive
 RUN apt-get update \
     && apt-get install -y --no-install-recommends \
-        libopenslide0 \
         libtk8.6 \
         procps \
     && rm -rf /var/lib/apt/lists/*

pyproject.toml

@@ -26,9 +26,10 @@ classifiers = [
     "Operating System :: Unix"
 ]
 
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 dependencies = [
-    "openslide-python==1.1.2",
+    "openslide-bin==4.0.1.2",
+    "openslide-python==1.4.6",
     "scikit-image~=0.19.2",
     "scikit-learn~=1.2.1",
     "numpy~=1.23.5",