Update Polus-stack-z-slice-plugin

transforms/images/polus-stack-z-slice-plugin/bumpversion.cfg → transforms/images/polus-stack-z-slice-plugin/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.4
+current_version = 1.2.6
 commit = True
 tag = False
 

transforms/images/polus-stack-z-slice-plugin/Dockerfile

@@ -1,22 +1,14 @@
-# Get image containing bfio
-FROM polusai/bfio:2.1.9
-
-COPY VERSION /
-
-ARG EXEC_DIR="/opt/executables"
-ARG DATA_DIR="/data"
-
-#Create folders
-RUN mkdir -p ${EXEC_DIR} \
-    && mkdir -p ${DATA_DIR}/inputs \
-    && mkdir ${DATA_DIR}/outputs
-
-#Copy executable
-COPY src ${EXEC_DIR}/
-
-RUN pip3 install -r ${EXEC_DIR}/requirements.txt --no-cache-dir
-
+# Build from repo root (monorepo) or from this tool directory — both work.
+FROM polusai/bfio:2.5.0
+ENV EXEC_DIR="/opt/executables" POLUS_IMG_EXT=".ome.tif" POLUS_TAB_EXT=".csv" POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
-
-# Default command. Additional arguments are provided through the command line
-ENTRYPOINT ["python3", "/opt/executables/main.py"]
+ENV TOOL_DIR="transforms/images/polus-stack-z-slice-plugin"
+RUN mkdir -p image-tools
+COPY . ${EXEC_DIR}/image-tools
+RUN pip3 install -U pip setuptools wheel \
+  && python3 -c 'import sys; assert sys.version_info>=(3,11)' \
+  && R="${EXEC_DIR}/image-tools" && M="$R/$TOOL_DIR" \
+  && if [ -f "$M/pyproject.toml" ]; then pip3 install --no-cache-dir "$M"; \
+     else pip3 install --no-cache-dir "$R"; fi
+ENTRYPOINT ["python3", "-m", "main"]
+CMD ["--help"]

transforms/images/polus-stack-z-slice-plugin/README.md

@@ -18,7 +18,7 @@ To build the Docker image for the conversion plugin, run
 
 ## Input Filename Pattern
 
-This plugin uses the 
+This plugin uses the
 [filepattern](https://github.com/LabShare/polus-plugins/tree/master/utils/polus-filepattern-util)
 utility to indicate which files to stack. In particular, defining a filename
 variable is surrounded by `{}`, and the variable name and number of spaces

transforms/images/polus-stack-z-slice-plugin/VERSION

@@ -1 +1 @@
-1.2.4
+1.2.6

transforms/images/polus-stack-z-slice-plugin/build-docker.sh

@@ -1,4 +1,4 @@
 #!/bin/bash
 
 version=$(<VERSION)
-docker build . -t polusai/stack-z-slice-plugin:${version}
+docker build . -t polusai/stack-z-slice-plugin:${version}

transforms/images/polus-stack-z-slice-plugin/plugin.json

@@ -1,16 +1,15 @@
 {
   "name": "Stack Z-slices",
-  "version": "1.2.4",
+  "version": "1.2.6",
   "title": "Stack Z-slices into a single tiled tiff file",
   "description": "Use a file name pattern to stack individual z-slices into a single image.",
   "author": "Nick Schaub (nick.schaub@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/labshare/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/stack-z-slice-plugin:1.2.4",
+  "containerId": "polusai/stack-z-slice-plugin:1.2.6",
   "inputs": [
-
     {
       "name": "inpDir",
       "type": "collection",

transforms/images/polus-stack-z-slice-plugin/pyproject.toml

@@ -0,0 +1,18 @@
+[project]
+name = "polus-stack-z-slice-plugin"
+version = "1.2.4"
+requires-python = ">=3.11"
+dependencies = [
+    "bfio>=2.5.0",
+    "filepattern>=2.2.1",
+]
+
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.setuptools]
+py-modules = ["main"]

transforms/images/polus-stack-z-slice-plugin/run-plugin.sh

@@ -15,4 +15,4 @@ docker run --mount type=bind,source=${datapath},target=/data/ \
             polusai/stack-z-slice-plugin:${version} \
             --filePattern ${filePattern} \
             --inpDir ${inpDir} \
-            --outDir ${outDir} 
+            --outDir ${outDir}

transforms/images/polus-stack-z-slice-plugin/src/__init__.py

@@ -0,0 +1 @@
+"""Polus stack Z-slice plugin package."""