Merge pull request #111 from ap--/fix-qet_qupath-0.5.0

Adjust for QuPath 0.5.0

.github/workflows/run_pytests.yaml

@@ -8,27 +8,29 @@ on:
   pull_request: {}
 
 env:
-  QUPATH_VERSION: 0.4.3
+  QUPATH_VERSION: 0.5.0
 
 jobs:
   # RUN PYTEST ON PAQUO SOURCE
   tests:
     name: pytest ${{ matrix.os }}::py${{ matrix.python-version }}
     runs-on: ${{ matrix.os }}
     strategy:
-      max-parallel: 7
+      max-parallel: 8
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         include:
           # we'll test the python support on ubuntu
           - os: ubuntu-latest
-            python-version: '3.10'
+            python-version: '3.11'
           - os: ubuntu-latest
-            python-version: 3.9
+            python-version: '3.12'
           - os: ubuntu-latest
-            python-version: 3.8
+            python-version: '3.9'
+          - os: ubuntu-latest
+            python-version: '3.8'
     steps:
     - uses: actions/checkout@v3
       with:

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: trailing-whitespace
   - id: end-of-file-fixer
   - id: check-added-large-files
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.9.0
+  rev: v3.15.1
   hooks:
   - id: pyupgrade
     args: [--py38-plus]
 - repo: https://github.com/pycqa/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
     exclude: ^examples|^extras|^docs|tests.*|setup.py
@@ -21,21 +21,21 @@ repos:
 #   - id: black
 #     language_version: python3
 - repo: https://github.com/pre-commit/mirrors-mypy
-  rev: 'v1.4.1'
+  rev: 'v1.8.0'
   hooks:
   - id: mypy
     exclude: ^examples|^extras|^docs|tests.*
     additional_dependencies: [packaging, ome-types]
 - repo: https://github.com/PyCQA/flake8
-  rev: '6.0.0'
+  rev: '7.0.0'
   hooks:
   - id: flake8
     additional_dependencies:
-    - flake8-typing-imports==1.12.0
+    - flake8-typing-imports==1.15.0
     language_version: python3
     exclude: "^(build|docs|examples|extras|setup.py)|tests[/]"
 - repo: https://github.com/PyCQA/bandit
-  rev: '1.7.5'
+  rev: '1.7.7'
   hooks:
   - id: bandit
     args: ["-lll", "--ini", ".bandit"]

README.md

@@ -21,7 +21,7 @@ unintuitive, slow or if its documentation is confusing, it's a bug in
 tracker!
 
 Development
-[happens on github](https://github.com/bayer-science-for-a-better-life/paquo)
+[happens on GitHub](https://github.com/bayer-science-for-a-better-life/paquo)
 :octocat:
 
 ## Documentation
@@ -54,18 +54,18 @@ paquo to use that version. Currently, paquo supports every version of QuPath fro
 `0.2.0` to the most recent. _(We even support older `0.2.0-mX` versions but no guarantees)._
 
 ```shell
-> paquo get_qupath --install-path "/some/path/on/your/machine" 0.4.3
-# downloading: https://github.com/qupath/qupath/releases/download/v0.4.3/QuPath-0.4.3-Linux.tar.xz
+> paquo get_qupath --install-path "/some/path/on/your/machine" 0.5.0
+# downloading: https://github.com/qupath/qupath/releases/download/v0.5.0/QuPath-0.4.3-Linux.tar.xz
 # progress ................... OK
-# extracting: [...]/QuPath-0.4.3-Linux.tar.xz
-# available at: /some/path/on/your/machine/QuPath-0.4.3
+# extracting: [...]/QuPath-0.5.0-Linux.tar.xz
+# available at: /some/path/on/your/machine/QuPath-0.5.0
 #
 # use via environment variable:
-#   $ export PAQUO_QUPATH_DIR=/some/path/on/your/machine/QuPath-0.4.3
+#   $ export PAQUO_QUPATH_DIR=/some/path/on/your/machine/QuPath-0.5.0
 #
 # use via .paquo.toml config file:
-#   qupath_dir="/some/path/on/your/machine/QuPath-0.4.3"
-/some/path/on/your/machine/QuPath-0.4.3
+#   qupath_dir="/some/path/on/your/machine/QuPath-0.5.0"
+/some/path/on/your/machine/QuPath-0.5.0
 ```
 
 
@@ -88,9 +88,9 @@ so go ahead and hack.
 - When contributing code, please try to use Pull Requests.
 - tests go hand in hand with modules on ```tests``` packages at the same level. We use ```pytest```.
 
-You can setup your IDE to help you adhering to these guidelines.
+You can set up your IDE to help you to adhere to these guidelines.
 <br>
-_([Santi](https://github.com/sdvillal) is happy to help you setting up pycharm in 5 minutes)_
+_([Santi](https://github.com/sdvillal) is happy to help you to set up pycharm in 5 minutes)_
 
 
 ## Acknowledgements

paquo/__main__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import argparse
 import functools
 import os
@@ -8,6 +10,7 @@
 from itertools import repeat
 from logging.config import dictConfig
 from pathlib import Path
+from typing import Callable
 
 from paquo._cli import DirectoryType
 from paquo._cli import argument
@@ -270,14 +273,14 @@ def quickview(args, subparser):
 
     f_annotations = None
     if args.annotations:
-        def f_annotations(name):
+        def f_annotations(name):  # noqa
             if name != image.name:
                 return []
             return list(args.annotations)
 
     f_annotations_cmd = None
     if args.annotations_cmd:
-        def f_annotations_cmd(name):
+        def f_annotations_cmd(name):  # noqa
             import shlex
             _cmd = shlex.split(f"{args.annotations_cmd} {name}")
             print("annotations", _cmd)
@@ -286,7 +289,7 @@ def f_annotations_cmd(name):
 
     cmd = None
     if f_annotations_cmd or f_annotations:
-        def cmd(name):
+        def cmd(name):  # noqa
             names = []
             if f_annotations:
                 names.extend(f_annotations(name))
@@ -332,13 +335,16 @@ def _download_cb(it, name):
         finally:
             print("")
 
-    file = download_qupath(
-        args.version,
-        path=args.download_path,
-        callback=_download_cb,
-        system=system,
-        ssl_verify=not args.no_ssl_verify
-    )
+    try:
+        file = download_qupath(
+            args.version,
+            path=args.download_path,
+            callback=_download_cb,
+            system=system,
+            ssl_verify=not args.no_ssl_verify
+        )
+    except Exception:
+        raise SystemExit(1)
     print("# extracting:", file)
     app = extract_qupath(file, args.install_path, system=system)
     print("# available at:", app)

paquo/_utils.py

@@ -126,12 +126,23 @@ def download_qupath(
     else:
         raise ValueError(f"unsupported platform.system() == {system!r}")
 
-    if "rc" not in version:
+    if not version.startswith("v"):
+        version = f"v{version}"
+
+    if Version(version) > Version("0.4.4"):
+        if system == "Darwin":
+            if platform.machine() == "arm64":
+                _sys = "Mac-arm64"
+            else:
+                _sys = "Mac-x64"
         name = f"QuPath-{version}-{_sys}"
     else:
-        name = f"QuPath-{version}"
+        if "rc" not in version:
+            name = f"QuPath-{version[1:]}-{_sys}"
+        else:
+            name = f"QuPath-{version[1:]}"
 
-    url = f"https://github.com/qupath/qupath/releases/download/v{version}/{name}.{ext}"
+    url = f"https://github.com/qupath/qupath/releases/download/{version}/{name}.{ext}"
 
     chunk_size = 10 * 1024 * 1024
 
@@ -153,6 +164,7 @@ def download_qupath(
             for chunk in callback(iter(lambda: f.read(chunk_size), b""), name=url):
                 tmp.write(chunk)
     except Exception:
+        print("# error requesting:", url, file=sys.stderr)
         try:
             os.unlink(out_fn)
         except OSError:
@@ -168,7 +180,7 @@ def extract_qupath(file, destination, system=None):
 
     # normalize QuPath App dirname
     m = re.match(
-        r"QuPath-(?P<version>[0-9]+[.][0-9]+[.][0-9]+(-rc[0-9]+|-m[0-9]+)?)",
+        r"QuPath-v?(?P<version>[0-9]+[.][0-9]+[.][0-9]+(-rc[0-9]+|-m[0-9]+)?)",
         fn,
     )
 
@@ -236,9 +248,12 @@ def extract_qupath(file, destination, system=None):
                     pth = os.path.join(tmp_dir, name)
                     if name.startswith("QuPath") and os.path.isdir(pth):
                         break
+                    if name.startswith("QuPath") and name.endswith(".exe") and os.path.isfile(pth):
+                        pth = tmp_dir
+                        break
                 else:
                     raise RuntimeError("no qupath extracted?")
-            shutil.move(os.path.join(tmp_dir, name), qp_dst)
+            shutil.move(pth, qp_dst)
         return qp_dst
 
     else:

paquo/images.py

@@ -548,7 +548,8 @@ def downsample_levels(self) -> List[Dict[str, float]]:
         The available downsample levels can differ dependent
         on which image backend is used by QuPath
         """
-        md = self._image_server.getMetadata()
+        with redirect(stdout=True, stderr=True):
+            md = self._image_server.getMetadata()
         levels = []
         for level in range(int(md.nLevels())):
             resolution_level = md.getLevel(level)

paquo/java.py

@@ -119,7 +119,12 @@ def supports_newer_addobject_and_pathclass(self) -> bool:
 
 PathAnnotationObject = JClass("qupath.lib.objects.PathAnnotationObject")
 PathClass = JClass('qupath.lib.objects.classes.PathClass')
-PathClassFactory = JClass('qupath.lib.objects.classes.PathClassFactory')
+
+if not compatibility.supports_newer_addobject_and_pathclass():
+    PathClassFactory = JClass('qupath.lib.objects.classes.PathClassFactory')
+else:
+    PathClassFactory = None
+
 PathDetectionObject = JClass("qupath.lib.objects.PathDetectionObject")
 PathIO = JClass("qupath.lib.io.PathIO")
 PathObjectHierarchy = JClass('qupath.lib.objects.hierarchy.PathObjectHierarchy')

paquo/tests/test_images.py

@@ -1,5 +1,6 @@
 import platform
 import shutil
+import sys
 import tempfile
 from contextlib import nullcontext
 from operator import itemgetter
@@ -23,7 +24,11 @@ def image_entry(svs_small):
 
 @pytest.fixture(scope='function')
 def removable_svs_small(svs_small):
-    with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
+    kw = {} if sys.version_info < (3, 10) else {"ignore_cleanup_errors": True}
+    with tempfile.TemporaryDirectory(
+        prefix='paquo-',
+        **kw
+    ) as tmpdir:
         new_path = Path(tmpdir) / svs_small.name
         shutil.copy(svs_small, new_path)
         yield new_path
@@ -32,21 +37,35 @@ def removable_svs_small(svs_small):
 @pytest.fixture(scope='function')
 def project_with_removed_image(removable_svs_small):
     with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
-        qp = QuPathProject(tmpdir, mode='x')
-        _ = qp.add_image(removable_svs_small, image_type=QuPathImageType.BRIGHTFIELD_H_E)
-        qp.save()
-        removable_svs_small.unlink()
-        yield qp.path
+        with QuPathProject(tmpdir, mode='x') as qp:
+            _ = qp.add_image(removable_svs_small, image_type=QuPathImageType.BRIGHTFIELD_H_E)
+            qp.save()
+            path = qp.path
+        try:
+            removable_svs_small.unlink()
+        except PermissionError:
+            if platform.system() == "Windows":
+                pytest.xfail("Windows QuPath==0.5.0 permission issue")
+            else:
+                raise
+        yield path
 
 
 @pytest.fixture(scope='function')
 def project_with_removed_image_without_image_data(removable_svs_small):
     with tempfile.TemporaryDirectory(prefix='paquo-') as tmpdir:
-        qp = QuPathProject(tmpdir, mode='x')
-        _ = qp.add_image(removable_svs_small)
-        qp.save()
-        removable_svs_small.unlink()
-        yield qp.path
+        with QuPathProject(tmpdir, mode='x') as qp:
+            _ = qp.add_image(removable_svs_small)
+            qp.save()
+            path = qp.path
+        try:
+            removable_svs_small.unlink()
+        except PermissionError:
+            if platform.system() == "Windows":
+                pytest.xfail("Windows QuPath==0.5.0 permission issue")
+            else:
+                raise
+        yield path
 
 
 def test_image_entry_return_hierarchy(image_entry):
@@ -74,22 +93,21 @@ def test_image_properties_from_image_server(image_entry):
     assert image_entry.num_z_slices == 1
 
 
-@pytest.mark.xfail(
-    platform.uname().machine == "arm64",
-    reason="QuPath-vendored openslide not working on arm64"
-)
 def test_image_downsample_levels(image_entry):
     levels = [
         {'downsample': 1.0,
          'height': 2967,
          'width': 2220},
         # todo: when openslide can be used by qupath, this downsample level
         #   in the test image disappears. investigate...
-        # {'downsample': 3.865438534407666,
-        #  'height': 768,
-        #  'width': 574},
+        {'downsample': 3.865438534407666,
+         'height': 768,
+         'width': 574},
     ]
-    assert image_entry.downsample_levels == levels
+    assert (
+        image_entry.downsample_levels == levels
+        or image_entry.downsample_levels == levels[:1]
+    )
 
 
 def test_metadata_interface(image_entry):