Restore green CI (lock, setuptools, UTF-8 reads, Fiji cache)

.github/workflows/tests.yml

@@ -113,6 +113,11 @@ jobs:
           python -m pip install --upgrade pip
           pip install -e ".[bioformats,dev]"
 
+      # Tests forbid downloads (tests/conftest.py), so the bundle cache is
+      # filled here, outside pytest, when actions/cache restores nothing.
+      - name: Prepare the declared Fiji bundle cache
+        run: python -c "from polystore.imagej_runtime import FIJI_IMAGEJ_RUNTIME; print(FIJI_IMAGEJ_RUNTIME.distribution.materialize().imagej_directory)"
+
       - name: Resolve and initialize the declared Fiji runtime
         env:
           POLYSTORE_LIVE_IMAGEJ_TEST: "1"

pyproject.toml

@@ -102,6 +102,7 @@ dev = [
     "pandas>=2.3.1",
     "jpype1>=1.4.0",
     "roifile",
+    "setuptools>=77.0",
     "black>=23.0.0",
     "ruff>=0.1.0",
 ]

src/polystore/atomic.py

@@ -194,7 +194,7 @@ def _read_json_or_default(
         return default_data
 
     try:
-        with open(file_path) as f:
+        with open(file_path, encoding="utf-8") as f:
             return json.load(f)
     except (OSError, json.JSONDecodeError) as e:
         logger.warning(f"Failed to read {file_path}, using default: {e}")

tests/test_bioformats_java.py

@@ -206,7 +206,7 @@ def test_format_probe_closes_failed_reader_and_can_retry(monkeypatch, operation)
 
 
 def test_format_probe_operations_share_the_context_reader_lifetime():
-    tree = ast.parse(Path(bioformats_java.__file__).read_text())
+    tree = ast.parse(Path(bioformats_java.__file__).read_text(encoding="utf-8"))
     context = next(
         node
         for node in tree.body

tests/test_publisher_admission.py

@@ -14,7 +14,7 @@
 
 
 def test_publisher_installs_the_dev_candidate_editably():
-    workflow = (ROOT / ".github/workflows/publish.yml").read_text()
+    workflow = (ROOT / ".github/workflows/publish.yml").read_text(encoding="utf-8")
     commands = [shlex.split(line.strip()) for line in workflow.splitlines()]
     (install,) = [command for command in commands if ".[dev]" in command]
     assert install[:4] == ["python", "-m", "pip", "install"]
@@ -30,7 +30,7 @@ def test_editable_artifact_owns_checkout_path_and_roi_dev_requirement(tmp_path,
         assert Path(archive.read(pth).decode().strip()).resolve() == ROOT / "src"
         (metadata_name,) = [name for name in archive.namelist() if name.endswith("/METADATA")]
         metadata = Parser().parsestr(archive.read(metadata_name).decode())
-    project = tomllib.loads((ROOT / "pyproject.toml").read_text())["project"]
+    project = tomllib.loads((ROOT / "pyproject.toml").read_text(encoding="utf-8"))["project"]
     assert metadata["Name"] == project["name"]
     assert metadata["Version"] == project["version"]
     requirements = [Requirement(value) for value in metadata.get_all("Requires-Dist")]

tests/test_streaming_return_route.py

@@ -12,7 +12,7 @@
 def test_no_consumer_retains_the_deleted_global_ack_alias():
     root = Path(__file__).resolve().parents[1] / "src" / "polystore"
     for source in root.rglob("*.py"):
-        tree = ast.parse(source.read_text(), filename=str(source))
+        tree = ast.parse(source.read_text(encoding="utf-8"), filename=str(source))
         assert not any(
             isinstance(node, ast.Attribute) and node.attr in {"_send_ack", "_setup_ack_socket"}
             for node in ast.walk(tree)