lavlab-shell 0.2.0__tar.gz → 0.3.1__tar.gz

lavlab_shell-0.3.1/.github/workflows/build.yml

@@ -0,0 +1,54 @@
+name: Build Wheel using Hatch
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  build-wheel:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install "virtualenv==20.23.1"
+          python -m pip install --upgrade hatch
+
+      - name: Build wheel with hatch
+        run: hatch build
+      - name: Upload wheel
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheel
+          path: dist/*.whl
+
+              - uses: actions/checkout@v4
+
+              - name: Build Docker image (hatch stage)
+                uses: docker/build-push-action@v4
+                with:
+                  context: .
+                  file: ./Dockerfile
+                  target: hatch
+                  tags: shell-ci:latest
+
+              - name: Run build inside Docker container
+                run: |
+                  docker run --rm \
+                    -v "${{ github.workspace }}:/app" \
+                    -w /app \
+                    shell-ci:latest build
+
+              - name: Upload wheel
+                uses: actions/upload-artifact@v4
+                with:
+                  name: wheel
+                  path: dist/*.whl

{lavlab_shell-0.2.0 → lavlab_shell-0.3.1}/.github/workflows/publish.yml

@@ -17,17 +17,20 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+      - name: Build Docker image (hatch stage)
+        uses: docker/build-push-action@v4
         with:
-          python-version: "3.12"
+          context: .
+          file: ./Dockerfile
+          target: hatch
+          tags: shell-ci:latest
 
-      - name: Install build tools
+      - name: Build wheel and sdist inside Docker
         run: |
-          python -m pip install --upgrade pip setuptools wheel hatch
-
-      - name: Build wheel and sdist
-        run: hatch build
+          docker run --rm \
+            -v "${{ github.workspace }}:/app" \
+            -w /app \
+            shell-ci:latest build
 
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

{lavlab_shell-0.2.0 → lavlab_shell-0.3.1}/.github/workflows/pytest.yml

@@ -10,11 +10,19 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Build Docker image
-        run: docker build --target hatch -t shell:hatch .
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov coverage[toml]>=6.2
 
       - name: Run pytest and generate coverage report
-        run: docker run --rm -e HATCH_ENV=test -v "${{ github.workspace }}:/app" shell:hatch cov
+        run: |
+          pytest --cov=src --cov-report=xml:coverage.xml
 
       - name: Upload coverage artifact
         uses: actions/upload-artifact@v4

{lavlab_shell-0.2.0 → lavlab_shell-0.3.1}/Dockerfile

@@ -22,7 +22,9 @@ COPY src/ src/
 RUN chown -R vscode:vscode /app
 
 FROM base AS hatch
-RUN pip3 install --no-cache-dir hatch uv
+RUN pip3 install --no-cache-dir --upgrade pip setuptools wheel
+RUN pip3 install --no-cache-dir 'virtualenv<21'
+RUN pip3 install --no-cache-dir --upgrade hatch hatch-uv
 ENV HATCH_ENV=default
 ENTRYPOINT ["hatch", "run"]
 
@@ -32,7 +34,7 @@ COPY requirements.txt ./
 COPY tests/ tests/
 COPY docs/ docs/
 COPY mkdocs.yml ./
-RUN pip3 install --no-cache-dir hatch \
+RUN pip3 install --no-cache-dir hatch hatch-uv \
     && hatch build \
     && pip3 install --no-cache-dir $(find /app -name 'requirement*.txt' -exec echo -n '-r {} ' \;)
 USER vscode

{lavlab_shell-0.2.0 → lavlab_shell-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lavlab-shell
-Version: 0.2.0
+Version: 0.3.1
 Summary: SHELL Highlights Epithelium and Lumen Locations — whole-slide H&E segmentation
 Project-URL: Documentation, https://github.com/laviolette-lab/shell#readme
 Project-URL: Issues, https://github.com/laviolette-lab/shell/issues
@@ -21,6 +21,7 @@ Requires-Dist: monai
 Requires-Dist: numpy
 Requires-Dist: openslide-python
 Requires-Dist: pyvips
+Requires-Dist: scikit-image
 Requires-Dist: scipy
 Requires-Dist: torch
 Provides-Extra: omero

{lavlab_shell-0.2.0 → lavlab_shell-0.3.1}/pyproject.toml

@@ -33,6 +33,7 @@ dependencies = [
     "pyvips",
     "openslide-python",
     "macenko-pca",
+    "scikit-image",
 ]
 
 [project.optional-dependencies]
@@ -53,27 +54,25 @@ path = "src/shell/__about__.py"
 [tool.hatch.build.targets.wheel]
 packages = ["src/shell"]
 
-[tool.hatch.env]
-requires = ["hatch-pip-compile"]
-
 [tool.hatch.envs.default]
-type = "pip-compile"
-pip-compile-resolver = "uv"
-pip-compile-hashes = false
-pip-compile-args = ["--allow-unsafe", "--universal"]
-dependencies = ["setuptools==82.0.0"]
+dependencies = ["setuptools>=82.0.0"]
 
 [tool.hatch.envs.default.scripts]
 build = "hatch build && chmod -R 777 dist/*"
 
 [tool.hatch.envs.test]
-dependencies = ["pytest", "pytest-cov", "coverage[toml]>=6.2", "setuptools==82.0.0"]
+dependencies = [
+    "pytest",
+    "pytest-cov",
+    "coverage[toml]>=6.2",
+    "setuptools>=82.0.0",
+]
 [tool.hatch.envs.test.scripts]
 test = "pytest {args:tests}"
 cov = "pytest --cov=src --cov-report=term-missing --cov-report=xml {args:tests}"
 
 [tool.hatch.envs.lint]
-dependencies = ["ruff>=0.4.0", "setuptools==82.0.0"]
+dependencies = ["ruff>=0.4.0", "setuptools>=82.0.0"]
 [tool.hatch.envs.lint.scripts]
 check = "ruff check src tests"
 format = "ruff format src tests"
@@ -82,7 +81,7 @@ fix = "ruff check --fix src tests"
 all = ["format", "fix", "check"]
 
 [tool.hatch.envs.types]
-dependencies = ["mypy>=1.0.0", "setuptools==82.0.0"]
+dependencies = ["mypy>=1.0.0", "setuptools>=82.0.0"]
 [tool.hatch.envs.types.scripts]
 check = "mypy --install-types --non-interactive {args:src/shell tests}"
 
@@ -95,7 +94,7 @@ dependencies = [
     "mkdocs-minify-plugin",
     "mkdocs-material-extensions",
     "mkdocs-git-revision-date-localized-plugin",
-    "setuptools==82.0.0",
+    "setuptools>=82.0.0",
 ]
 [tool.hatch.envs.docs.scripts]
 build-docs = "mkdocs build"

{lavlab_shell-0.2.0 → lavlab_shell-0.3.1}/src/shell/__about__.py

@@ -3,4 +3,4 @@
 # SPDX-License-Identifier: MIT
 """Version information for shell."""
 
-__version__ = "0.2.0"
+__version__ = "0.3.1"

{lavlab_shell-0.2.0 → lavlab_shell-0.3.1}/src/shell/cli.py

@@ -12,6 +12,30 @@ Provides two subcommands:
 
 from __future__ import annotations
 
+import os
+
+# Ensure PyTorch initialises its runtime and threads before other native
+# libraries (pyvips, Ice/OMERO) to avoid macOS-level races that can lead
+# to segmentation faults when different C extensions compete for thread
+# runtime ownership.  Set conservative thread counts before importing torch.
+os.environ.setdefault("OMP_NUM_THREADS", "1")
+os.environ.setdefault("OPENBLAS_NUM_THREADS", "1")
+os.environ.setdefault("MKL_NUM_THREADS", "1")
+os.environ.setdefault("VECLIB_MAXIMUM_THREADS", "1")
+
+try:
+    # Import torch early so it initialises its native runtime in the main
+    # thread. This is intentional — we only probe __version__ to force
+    # initialisation without performing heavy work here.
+    import torch  # type: ignore
+
+    _ = torch.__version__  # ensure attribute access triggers initialisation
+    TORCH_AVAILABLE = True
+except Exception:
+    # If torch is unavailable we still continue — the program will emit
+    # a clearer error later when trying to build/load the model.
+    TORCH_AVAILABLE = False
+
 import argparse
 import getpass
 import logging
@@ -19,6 +43,9 @@ import sys
 
 from shell.__about__ import __version__
 
+# Module logger — used for diagnostic messages instead of printing directly.
+log = logging.getLogger(__name__)
+
 
 def build_parser() -> argparse.ArgumentParser:
     """Build and return the argument parser."""
@@ -98,12 +125,6 @@ def build_parser() -> argparse.ArgumentParser:
         default=None,
         help="Optional: also save the intermediate EHO image.",
     )
-    infer_p.add_argument(
-        "--stain-downsample",
-        type=int,
-        default=4,
-        help="Downsample factor for stain parameter estimation.",
-    )
     infer_p.add_argument(
         "--device",
         type=str,
@@ -138,7 +159,6 @@ def build_parser() -> argparse.ArgumentParser:
         default=1.0,
         help="Desired output resolution (um/pixel)",
     )
-    omero_p.add_argument("--max-dim", type=int, default=None)
     omero_p.add_argument(
         "--model-path",
         type=str,
@@ -283,7 +303,6 @@ def main(argv: list[str] | None = None) -> int:
             target_mpp=args.target_mpp,
             mpp=args.mpp,
             save_eho=args.save_eho,
-            stain_downsample=args.stain_downsample,
             device=args.device,
         )
 
@@ -295,36 +314,57 @@ def main(argv: list[str] | None = None) -> int:
         return 0
 
     if args.command == "infer-omero":
+        # Diagnostic prints added to help narrow where a macOS segfault occurs.
+        # These prints are intentionally lightweight and flushed so they appear
+        # even if the process crashes in a C extension later on.
+        log.debug("DIAG: infer-omero selected")
+        log.debug("DIAG: about to import infer_omero_wsi")
         from shell.infer_omero_wsi import infer_omero_wsi
 
+        log.debug("DIAG: imported infer_omero_wsi")
+
         if args.password is None:
             args.password = getpass.getpass("OMERO password: ")
 
-        print(f"Connecting to {args.host}:{args.port} …")
-        infer_omero_wsi(
-            host=args.host,
-            port=args.port,
-            username=args.username,
-            password=args.password,
-            image_id=args.image_id,
-            model_path=args.model_path,
-            model_version=args.model_version,
-            output_path=args.output,
-            target_mpp=args.target_mpp,
-            max_dim=args.max_dim,
-            group_id=args.group_id,
-            save_eho=args.save_eho,
-            no_tissue_crop=args.no_tissue_crop,
-            device=args.device,
-            inference_tile_size=args.inference_tile_size,
-            tile_overlap=args.tile_overlap,
-            sw_overlap=args.sw_overlap,
-            num_bg_tiles=args.num_bg_tiles,
-            min_thumb_size=args.min_thumb_size,
-            min_tissue_frac=args.min_tissue_frac,
-            prefetch_depth=args.prefetch_depth,
-            num_fetch_workers=args.fetch_workers,
-        )
+        print(f"Connecting to {args.host}:{args.port} …", flush=True)
+        log.debug("DIAG: about to call infer_omero_wsi")
+        try:
+            infer_omero_wsi(
+                host=args.host,
+                port=args.port,
+                username=args.username,
+                password=args.password,
+                image_id=args.image_id,
+                model_path=args.model_path,
+                model_version=args.model_version,
+                output_path=args.output,
+                target_mpp=args.target_mpp,
+                group_id=args.group_id,
+                save_eho=args.save_eho,
+                no_tissue_crop=args.no_tissue_crop,
+                device=args.device,
+                inference_tile_size=args.inference_tile_size,
+                tile_overlap=args.tile_overlap,
+                sw_overlap=args.sw_overlap,
+                num_bg_tiles=args.num_bg_tiles,
+                min_thumb_size=args.min_thumb_size,
+                min_tissue_frac=args.min_tissue_frac,
+                prefetch_depth=args.prefetch_depth,
+                num_fetch_workers=args.fetch_workers,
+            )
+            log.debug("DIAG: infer_omero_wsi returned normally")
+        except BaseException as e:
+            # Catch and print Python-level exceptions; note segfaults (native crashes)
+            # will not be caught here, but these diagnostics will show progress up to
+            # the crash point.
+            import sys
+            import traceback
+
+            log.debug("DIAG: infer_omero_wsi raised an exception:")
+            traceback.print_exc()
+            # Re-raise so existing behaviour (non-zero exit) remains.
+            raise
+        log.debug("DIAG: after infer_omero_wsi (should have saved output)")
         print(f"Saved prediction to {args.output}")
         return 0