Merge pull request #473 from bioimage-io/dev

avoid 'conda activate' and update xarray pin

Author: FynnBe

.github/workflows/build.yaml

@@ -82,7 +82,7 @@ jobs:
       - name: Install dependencies
         run: |
           pip install --upgrade pip
-          pip install -e .[dev] numpy==${{matrix.numpy-version}}.*
+          pip install -e .[dev,partners] numpy==${{matrix.numpy-version}}.*
       - name: Pyright
         if: matrix.run-expensive-tests # pyright is not expensive, but we only want to run it once due to otherwise inconsistent typing
         run: |
@@ -165,7 +165,7 @@ jobs:
         with:
           python-version: '3.12'
           cache: 'pip'
-      - run: pip install -e .[dev]
+      - run: pip install -e .[dev,partners]
       - name: Generate developer docs
         run: ./scripts/pdoc/run.sh
       - run: cp README.md ./dist/README.md

README.md

@@ -361,108 +361,15 @@ There are different environment files available that only install tensorflow or
 
 `bioimageio.spec` and `bioimageio.core` use [loguru](https://github.com/Delgan/loguru) for logging, hence the logging level
 may be controlled with the `LOGURU_LEVEL` environment variable.
+The `bioimageio` CLI has logging enabled by default.
+To activate logging when using bioimageio.spec/bioimageio.core as a library, add
 
-## Changelog
-
-### 0.9.3
-
-- bump bioimageio.spec library version to 0.5.5.5
-- more robust test model reporting
-- improved user input axis intepretation
-- fixed conda subprocess calls
-
-### 0.9.2
-
-- fix model inference tolerance reporting
-
-### 0.9.1
-
-- fixes:
-  - CLI
-    - improved handling of summary argument to not create a path with brackets when given a list of paths.
-    - improved backward compatibility when runnig tests for models specifying an older bioimageio.core version in their environment.
-    This is relevant when using `runtime_env="as-described"`.
-    It works by simply trying option `--summary` (new option name) and `--summary-path` (outdated option name)
-
-### 0.9.0
-
-- update to [bioimageio.spec 0.5.4.3](https://github.com/bioimage-io/spec-bioimage-io/blob/main/changelog.md#bioimageiospec-0543)
-
-### 0.8.0
-
-- breaking: removed `decimals` argument from bioimageio CLI and `bioimageio.core.commands.test()`
-- New feature: `bioimageio.core.test_description` accepts **runtime_env** and **run_command** to test a resource
-  using the conda environment described by that resource (or another specified conda env)
-- new CLI command: `bioimageio add-weights` (and utility function: bioimageio.core.add_weights)
-- removed `bioimageio.core.proc_ops.get_proc_class` in favor of `bioimageio.core.proc_ops.get_proc`
-- new CLI command: `bioimageio update-format`
-- new CLI command: `bioimageio update-hashes`
-
-### 0.7.0
-
-- breaking:
-  - bioimageio CLI now has implicit boolean flags
-- non-breaking:
-  - use new `ValidationDetail.recommended_env` in `ValidationSummary`
-  - improve `get_io_sample_block_metas()`
-    - now works for sufficiently large, but not exactly shaped inputs
-  - update to support `zipfile.ZipFile` object with bioimageio.spec==0.5.3.5
-  - add io helpers `resolve` and `resolve_and_extract`
-  - added `enable_determinism` function and **determinism** input argument for testing with seeded
-    random generators and optionally (determinsim=="full") instructing DL frameworks to use
-    deterministic algorithms.
-
-### 0.6.10
-
-- fix #423
-
-### 0.6.9
-
-- improve bioimageio command line interface (details in #157)
-  - add `predict` command
-  - package command input `path` is now required
-
-### 0.6.8
+```python
+from loguru import logger
 
-- testing model inference will now check all weight formats
-  (previously only the first one for which model adapter creation succeeded had been checked)
-- fix predict with blocking (Thanks @thodkatz)
-
-### 0.6.7
-
-- `predict()` argument `inputs` may be sample
-
-### 0.6.6
-
-- add aliases to match previous API more closely
-
-### 0.6.5
-
-- improve adapter error messages
-
-### 0.6.4
-
-- add `bioimageio validate-format` command
-- improve error messages and display of command results
-
-### 0.6.3
-
-- Fix [#386](https://github.com/bioimage-io/core-bioimage-io-python/issues/386)
-- (in model inference testing) stop assuming model inputs are tileable
-
-### 0.6.2
-
-- Fix [#384](https://github.com/bioimage-io/core-bioimage-io-python/issues/384)
-
-### 0.6.1
-
-- Fix [#378](https://github.com/bioimage-io/core-bioimage-io-python/pull/378) (with [#379](https://github.com/bioimage-io/core-bioimage-io-python/pull/379))*
-
-### 0.6.0
-
-- add compatibility with new bioimageio.spec 0.5 (0.5.2post1)
-- improve interfaces
+logger.enable("bioimageio")
+```
 
-### 0.5.10
+## Changelog
 
-- [Fix critical bug in predict with tiling](https://github.com/bioimage-io/core-bioimage-io-python/pull/359)
+See [changelog.md](changelog.md)

changelog.md

@@ -0,0 +1,109 @@
+### 0.9.4
+
+- bump bioimageio.spec library version to 0.5.5.6
+- Replace `conda activate <env name>` with `conda run -n <env name> python --version` when checking if a conda environment exists
+  (This is closer to the actual `conda run` command we need and avoids requests by conda to rerun `conda init` (in CI).)
+- remove upper xarray pin (use ops from xarray.computation.ops, fallback to xarray.core.ops for older xarray versions)
+
+### 0.9.3
+
+- bump bioimageio.spec library version to 0.5.5.5
+- more robust test model reporting
+- improved user input axis intepretation
+- fixed conda subprocess calls
+
+### 0.9.2
+
+- fix model inference tolerance reporting
+
+### 0.9.1
+
+- fixes:
+  - CLI
+    - improved handling of summary argument to not create a path with brackets when given a list of paths.
+    - improved backward compatibility when runnig tests for models specifying an older bioimageio.core version in their environment.
+    This is relevant when using `runtime_env="as-described"`.
+    It works by simply trying option `--summary` (new option name) and `--summary-path` (outdated option name)
+
+### 0.9.0
+
+- update to [bioimageio.spec 0.5.4.3](https://github.com/bioimage-io/spec-bioimage-io/blob/main/changelog.md#bioimageiospec-0543)
+
+### 0.8.0
+
+- breaking: removed `decimals` argument from bioimageio CLI and `bioimageio.core.commands.test()`
+- New feature: `bioimageio.core.test_description` accepts **runtime_env** and **run_command** to test a resource
+  using the conda environment described by that resource (or another specified conda env)
+- new CLI command: `bioimageio add-weights` (and utility function: bioimageio.core.add_weights)
+- removed `bioimageio.core.proc_ops.get_proc_class` in favor of `bioimageio.core.proc_ops.get_proc`
+- new CLI command: `bioimageio update-format`
+- new CLI command: `bioimageio update-hashes`
+
+### 0.7.0
+
+- breaking:
+  - bioimageio CLI now has implicit boolean flags
+- non-breaking:
+  - use new `ValidationDetail.recommended_env` in `ValidationSummary`
+  - improve `get_io_sample_block_metas()`
+    - now works for sufficiently large, but not exactly shaped inputs
+  - update to support `zipfile.ZipFile` object with bioimageio.spec==0.5.3.5
+  - add io helpers `resolve` and `resolve_and_extract`
+  - added `enable_determinism` function and **determinism** input argument for testing with seeded
+    random generators and optionally (determinsim=="full") instructing DL frameworks to use
+    deterministic algorithms.
+
+### 0.6.10
+
+- fix #423
+
+### 0.6.9
+
+- improve bioimageio command line interface (details in #157)
+  - add `predict` command
+  - package command input `path` is now required
+
+### 0.6.8
+
+- testing model inference will now check all weight formats
+  (previously only the first one for which model adapter creation succeeded had been checked)
+- fix predict with blocking (Thanks @thodkatz)
+
+### 0.6.7
+
+- `predict()` argument `inputs` may be sample
+
+### 0.6.6
+
+- add aliases to match previous API more closely
+
+### 0.6.5
+
+- improve adapter error messages
+
+### 0.6.4
+
+- add `bioimageio validate-format` command
+- improve error messages and display of command results
+
+### 0.6.3
+
+- Fix [#386](https://github.com/bioimage-io/core-bioimage-io-python/issues/386)
+- (in model inference testing) stop assuming model inputs are tileable
+
+### 0.6.2
+
+- Fix [#384](https://github.com/bioimage-io/core-bioimage-io-python/issues/384)
+
+### 0.6.1
+
+- Fix [#378](https://github.com/bioimage-io/core-bioimage-io-python/pull/378) (with [#379](https://github.com/bioimage-io/core-bioimage-io-python/pull/379))*
+
+### 0.6.0
+
+- add compatibility with new bioimageio.spec 0.5 (0.5.2post1)
+- improve interfaces
+
+### 0.5.10
+
+- [Fix critical bug in predict with tiling](https://github.com/bioimage-io/core-bioimage-io-python/pull/359)

pyproject.toml

@@ -6,7 +6,7 @@ requires-python = ">=3.9"
 readme = "README.md"
 dynamic = ["version"]
 dependencies = [
-    "bioimageio.spec ==0.5.5.5",
+    "bioimageio.spec ==0.5.5.6",
     "h5py",
     "imagecodecs",
     "imageio>=2.10",
@@ -18,7 +18,7 @@ dependencies = [
     "scipy",
     "tqdm",
     "typing-extensions",
-    "xarray>=2023.01,<2025.3.0",
+    "xarray>=2023.01",
 ]
 classifiers = [
     "Development Status :: 3 - Alpha",
@@ -43,16 +43,19 @@ Source = "https://github.com/bioimage-io/core-bioimage-io-python"
 onnx = ["onnxruntime"]
 pytorch = ["torch>=1.6,<3", "torchvision>=0.21", "keras>=3.0,<4"]
 tensorflow = ["tensorflow", "keras>=2.15,<4"]
-dev = [
+partners = [
     # "biapy",          # pins core exactly
     "careamics",
-    "cellpose",         # for model testing
+    # "stardist",         # for model testing and stardist postprocessing  # TODO: add updated stardist to partners env
+]
+dev = [
+    "cellpose",          # for model testing
     "crick",
     "httpx",
     "jupyter",
     "keras>=3.0,<4",
     "matplotlib",
-    "monai",            # for model testing
+    "monai",             # for model testing
     "numpy",
     "onnx",
     "onnxruntime",
@@ -63,8 +66,7 @@ dev = [
     "pytest-cov",
     "pytest",
     "python-dotenv",
-    "segment-anything", # for model testing
-    # "stardist",          # for model testing and stardist postprocessing  # TODO: add updated stardist to dev env
+    "segment-anything",  # for model testing
     "tensorflow",
     "timm",              # for model testing
     "torch>=1.6,<3",

src/bioimageio/core/__init__.py

@@ -3,7 +3,7 @@
 """
 # ruff: noqa: E402
 
-__version__ = "0.9.3"
+__version__ = "0.9.4"
 from loguru import logger
 
 logger.disable("bioimageio.core")

src/bioimageio/core/_magic_tensor_ops.py

@@ -6,7 +6,14 @@
 from typing import Any, Callable
 
 from typing_extensions import Self
-from xarray.core import nputils, ops
+from xarray.core import nputils
+
+try:
+    # xarray >= 2025.03
+    from xarray.computation import ops
+except ImportError:
+    # xarray < 2025.03
+    from xarray.core import ops  # type: ignore
 
 
 class MagicTensorOpsMixin:

src/bioimageio/core/_resource_tests.py

@@ -260,6 +260,15 @@ def test_description(
     else:
         assert_never(runtime_env)
 
+    try:
+        run_command(["thiscommandshouldalwaysfail", "please"])
+    except Exception:
+        pass
+    else:
+        raise RuntimeError(
+            "given run_command does not raise an exception for a failing command"
+        )
+
     td_kwargs: Dict[str, Any] = (
         dict(ignore_cleanup_errors=True) if sys.version_info >= (3, 10) else {}
     )
@@ -387,8 +396,8 @@ def _test_in_env(
         raise RuntimeError("Conda not available") from e
 
     try:
-        run_command([CONDA_CMD, "activate", env_name])
-    except Exception:
+        run_command([CONDA_CMD, "run", "-n", env_name, "python", "--version"])
+    except Exception as e:
         working_dir.mkdir(parents=True, exist_ok=True)
         path = working_dir / "env.yaml"
         try:
@@ -405,7 +414,8 @@ def _test_in_env(
                 ]
                 + (["--quiet"] if settings.CI else [])
             )
-            run_command([CONDA_CMD, "activate", env_name])
+            # double check that environment was created successfully
+            run_command([CONDA_CMD, "run", "-n", env_name, "python", "--version"])
         except Exception as e:
             summary = descr.validation_summary
             summary.add_detail(

tests/test_bioimageio_collection.py

@@ -101,8 +101,8 @@ def depends_on(dep: str) -> bool:
 
         for skip_if_depends_on in (
             "biapy",
-            "git+https://github.com/CAREamics/careamics.git",
-            "careamics",
+            "git+https://github.com/CAREamics/careamics.git",  # TODO: include tests depending on careamics
+            "careamics",  # TODO: include tests depending on careamics
             "inferno",
             "plantseg",
         ):