Merge pull request #712 from bioimage-io/dev

pre release fixes for 0.5.5.0

Author: FynnBe

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 repos:
   - repo: https://github.com/ambv/black
-    rev: 24.2.0
+    rev: 25.1.0
     hooks:
       - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.2
+    rev: v0.12.8
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix, --show-fixes]
   - repo: local
     hooks:

bioimageio/spec/_internal/io.py

@@ -705,23 +705,19 @@ def _open_url(
         or hashlib.sha256(str(source).encode(encoding="utf-8")).hexdigest()
     )
 
-    try:
-        reader = cache.fetch(
-            source,
-            fetcher=partial(_fetch_url, progressbar=progressbar),
-            force_refetch=digest,
-        )
-    except Exception as e:
-        raise ValueError(f"Failed to fetch {source}.") from e
-    else:
-        return BytesReader(
-            reader,
-            suffix=source_path.suffix,
-            sha256=sha,
-            original_file_name=source_path.name,
-            original_root=source.parent,
-            is_zipfile=None,
-        )
+    reader = cache.fetch(
+        source,
+        fetcher=partial(_fetch_url, progressbar=progressbar),
+        force_refetch=digest,
+    )
+    return BytesReader(
+        reader,
+        suffix=source_path.suffix,
+        sha256=sha,
+        original_file_name=source_path.name,
+        original_root=source.parent,
+        is_zipfile=None,
+    )
 
 
 def _fetch_url(

bioimageio/spec/_internal/io_utils.py

@@ -167,7 +167,7 @@ def open_bioimageio_yaml(
                 )
 
             try:
-                r = httpx.get(url)
+                r = httpx.get(url, follow_redirects=True)
                 _ = r.raise_for_status()
                 unparsed_content = r.content.decode(encoding="utf-8")
                 content = _sanitize_bioimageio_yaml(read_yaml(unparsed_content))
@@ -232,7 +232,7 @@ def _get_id_map_impl(url: str) -> Dict[str, LightHttpFileDescr]:
     if not isinstance(url, str) or "/" not in url:
         logger.opt(depth=1).error("invalid id map url: {}", url)
     try:
-        id_map_raw: Any = httpx.get(url, timeout=10).json()
+        id_map_raw: Any = httpx.get(url, timeout=10, follow_redirects=True).json()
     except Exception as e:
         logger.opt(depth=1).error("failed to get {}: {}", url, e)
         return {}

bioimageio/spec/_internal/url.py

@@ -58,10 +58,17 @@ def _validate_url_impl(
     try:
         if request_mode in ("head", "get"):
             request_ctxt = nullcontext(
-                httpx.request(request_mode.upper(), val_url, timeout=timeout)
+                httpx.request(
+                    request_mode.upper(),
+                    val_url,
+                    timeout=timeout,
+                    follow_redirects=True,
+                )
             )
         elif request_mode == "get_stream":
-            request_ctxt = httpx.stream("GET", val_url, timeout=timeout)
+            request_ctxt = httpx.stream(
+                "GET", val_url, timeout=timeout, follow_redirects=True
+            )
         else:
             assert_never(request_mode)
 

bioimageio/spec/_upload.py

@@ -124,6 +124,7 @@ def upload(
                 "file_path": file_name,
             },
             headers=headers,
+            follow_redirects=True,
         )
         upload_url = response.raise_for_status().json()
 
@@ -140,6 +141,7 @@ def upload(
             files=files,  # pyright: ignore[reportArgumentType]
             # TODO: follow up on https://github.com/encode/httpx/discussions/3611
             headers={"Content-Type": ""},  # Important for S3 uploads
+            follow_redirects=True,
         )
         logger.info("Uploaded '{}' successfully", file_name)
 
@@ -153,6 +155,7 @@ def upload(
             "manifest": manifest,
         },
         headers=headers,
+        follow_redirects=True,
     )
     logger.info(
         "Updated status of {}/{} to 'request-review'", artifact_id, artifact_version

changelog.md

@@ -12,8 +12,6 @@ This changelog includes implementation details and my reference the [changes to
 
 #### bioimageio.spec 0.5.5.0
 
-note: Not yet released
-
 - added programmatic `uplaod` (alpha stage)
 - [generic format 0.3.2 and model format 0.5.5](#generic-032-and-model-055)
 
@@ -304,8 +302,6 @@ If the changes also apply to `type` model, the coresponding model format version
 
 #### generic 0.3.2 and model 0.5.5
 
-note: not yet released
-
 - Non-breaking changes:
   - New optional `version_comment` field
   - Many FAIR fields are optional now to make it easier to tinker with resources not ready for publishing yet.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.black]
 line-length = 88
-target-version = ["py38", "py39", "py310", "py311", "py312"]
+target-version = ["py38", "py39", "py310", "py311", "py312", "py313"]
 preview = true
 
 [tool.pyright]
@@ -14,7 +14,7 @@ exclude = [
 ]
 include = ["bioimageio", "scripts", "tests"]
 pythonPlatform = "All"
-pythonVersion = "3.12"
+pythonVersion = "3.8"
 reportDuplicateImport = "error"
 reportImplicitStringConcatenation = "error"
 reportImportCycles = true
@@ -48,7 +48,7 @@ testpaths = ["bioimageio/spec", "tests"]
 
 [tool.ruff]
 line-length = 88
-target-version = "py312"
+target-version = "py38"
 exclude = [
     "bioimageio_cache",
     "scripts/pdoc/original.py",

scripts/update_spdx_licenses_zenodo.py

@@ -32,7 +32,7 @@ def main(recheck: bool = False):
                 "https://zenodo.org/api/vocabularies/licenses/"
                 + lic["licenseId"].lower()
             )
-            r = httpx.get(url, timeout=5)
+            r = httpx.get(url, timeout=5, follow_redirects=True)
 
             if 200 <= r.status_code < 300:
                 known = True

setup.py

@@ -31,7 +31,7 @@
     install_requires=[
         "annotated-types>=0.5.0,<1",
         "email_validator",
-        "genericache==0.4.1",
+        "genericache==0.5.2",
         "imageio",
         "loguru",
         "markdown",
@@ -47,6 +47,7 @@
         "tifffile>=2020.7.4",
         "tqdm",
         "typing-extensions",
+        "exceptiongroup",  # TODO: remove when py3.11 is lowest supported version
         "zipp",
     ],
     extras_require={

tests/test_internal/test_io.py

@@ -255,5 +255,7 @@ def test_open_url_with_wrong_sha():
     url = "https://example.com/file.txt"
     sha = Sha256("0" * 64)  # invalid sha256 for testing
 
-    with pytest.raises(ValueError, match=f"Failed to fetch {url}."):
+    with pytest.raises(
+        httpx.HTTPStatusError, match=f"Client error '404 Not Found' for url '{url}'"
+    ):
         _ = _open_url(HttpUrl(url), sha256=sha)