Update Polus-autocropping-plugin (PolusAI#596)

* add project.toml, update pachages for cp313,update bfio, helpers.py (Generator)

* fix autocrop.py and crrate a local utils

* add .bumpversion.cfg and bump2 new version

* update gitignore

* update Dockerfile, pyproject.toml

Author: vanlam2308

transforms/images/polus-autocropping-plugin/.bumpversion.cfg

@@ -0,0 +1,12 @@
+[bumpversion]
+current_version = 1.0.3
+commit = False
+tag = False
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"

transforms/images/polus-autocropping-plugin/.gitignore

@@ -0,0 +1 @@
+uv.lock

transforms/images/polus-autocropping-plugin/Dockerfile

@@ -1,12 +1,14 @@
-FROM polusai/bfio:2.1.9
-
-COPY requirements.txt .
-
-RUN pip3 install -r requirements.txt --no-cache-dir
-
-COPY VERSION /
-COPY src ${EXEC_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}
-
-ENTRYPOINT ["python3", "/opt/executables/main.py"]
+ENV TOOL_DIR="transforms/images/polus-autocropping-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-autocropping-plugin/VERSION

@@ -1 +1 @@
-1.0.2
+1.0.3

transforms/images/polus-autocropping-plugin/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "Autocropping",
-  "version": "1.0.2",
+  "version": "1.0.3",
   "title": "Autocropping",
   "description": "Automatically remove noise and other useless sections from images.",
   "author": "Najib Ishaq (najib.ishaq@axleinfo.com)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/polus-plugins/transforms/images/polus-autocropping-plugin",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/autocropping-plugin:1.0.2",
+  "containerId": "polusai/autocropping-plugin:1.0.3",
   "inputs": [
     {
       "name": "inputDir",

transforms/images/polus-autocropping-plugin/pyproject.toml

@@ -0,0 +1,23 @@
+[project]
+name = "polus-autocropping-plugin"
+version = "1.0.3"
+requires-python = ">=3.11"
+dependencies = [
+    "bfio>=2.5.0",
+    "filepattern>=2.2.1",
+    "scipy>=1.11.0",
+]
+
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.mypy]
+python_version = "3.11"
+# Package lives under src/ (autocrop_utils avoids clash with repo-root utils/)
+mypy_path = "src"
+explicit_package_bases = true
+namespace_packages = true

transforms/images/polus-autocropping-plugin/requirements.txt

@@ -1,2 +1,2 @@
 filepattern==1.4.7
-scipy>=1.7.1
+scipy>=1.7.1

transforms/images/polus-autocropping-plugin/src/__init__.py

@@ -1,2 +1,3 @@
-from . import utils
+"""Polus autocropping plugin."""
 from . import autocrop
+from . import autocrop_utils