update pyproject.toml and Dockerfile

Author: vanlam2308

transforms/images/remove-border-objects-plugin/Dockerfile

@@ -1,15 +1,32 @@
 # Build from repo root (monorepo) or from this tool directory — both work.
 # (Previously used a TensorFlow base image; this matches other tools — rebuild if TF is required.)
 FROM polusai/bfio:2.5.0
-ENV EXEC_DIR="/opt/executables" POLUS_IMG_EXT=".ome.tif" POLUS_TAB_EXT=".csv" POLUS_LOG="INFO"
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
+
+# Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
+# TODO: Change the tool_dir to the tool directory
 ENV TOOL_DIR="transforms/images/remove-border-objects-plugin"
+
+# Copy the repository into the container
 RUN mkdir -p image-tools
 COPY . ${EXEC_DIR}/image-tools
+
+# Install the tool
+# WORKDIR ${EXEC_DIR}/image-tools/${TOOL_DIR}
+# RUN pip3 install . --no-cache-dir
+# WORKDIR ${EXEC_DIR}
+
 RUN pip3 install -U pip setuptools wheel \
   && python3 -c 'import sys; assert sys.version_info>=(3,11)' \
   && R="${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"]
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
+ENTRYPOINT ["python3", "-m", "polus.images.remove_border_objects"]
 CMD ["--help"]

transforms/images/remove-border-objects-plugin/pyproject.toml

@@ -1,20 +1,52 @@
 [project]
 name = "polus-remove-border-objects-plugin"
 version = "0.1.1"
-requires-python = ">=3.11"
+requires-python = ">=3.11,<3.14"
+
 dependencies = [
     "bfio>=2.5.0",
-    "filepattern>=2.2.1",
-    "numpy>=1.26.4",
+    "filepattern>=2.2.4",
+    "typer>=0.24.1,<0.25.0",
+    "numpy>=2.0.0",
+    "tqdm==4.67.3",
+    "basicpy @ git+https://github.com/ndonyapour/BaSiCPy.git@chore/update-supported-python",
     "scikit-image>=0.25",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "bump2version>=1.0.1",
+    "pre-commit>=4.5.1",
+    "black>=26.3.1",
+    "flake8>=6.0.0",
+    "mypy>=1.0.0",
+    "pytest>=7.2.1",
+    "pytest-cov>=7.0.0",
+    "pytest-sugar>=1.1.1,<2.0.0",
+    "pytest-xdist>=3.8.0,<4.0.0",
+]
+
 [build-system]
-requires = ["setuptools>=61.0", "wheel"]
-build-backend = "setuptools.build_meta"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/polus"]
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
+
+#[build-system]
+#requires = ["setuptools>=61.0", "wheel"]
+#build-backend = "setuptools.build_meta"
 
-[tool.setuptools.package-dir]
-"" = "src"
+#[tool.setuptools.package-dir]
+#"" = "src"
 
-[tool.setuptools]
-py-modules = ["main", "functions"]
+#[tool.setuptools]
+#py-modules = ["main", "functions"]