Merge pull request #432 from bioimage-io/zipfile

support zipfile.ZipFile, improve docs and improve get_io_sample_block_metas

Author: FynnBe

.github/workflows/build.yaml

@@ -49,14 +49,29 @@ jobs:
         post-cleanup: 'all'
     - name: additional setup
       run: pip install --no-deps -e .
+    - name: Get Date
+      id: get-date
+      run: |
+        echo "date=$(date +'%Y-%b')"
+        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
+      shell: bash
+    - uses: actions/cache@v4
+      with:
+        path: bioimageio_cache
+        key: "test-spec-conda-${{ steps.get-date.outputs.date }}"
     - name: pytest-spec-conda
       run: pytest --disable-pytest-warnings
+      env:
+        BIOIMAGEIO_CACHE_PATH: bioimageio_cache
 
   test-spec-main:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ['3.8', '3.12']
+        include:
+          - python-version: '3.12'
+            is-dev-version: true
     steps:
     - uses: actions/checkout@v4
     - name: Install Conda environment with Micromamba
@@ -83,35 +98,83 @@ jobs:
         pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
     - name: additional setup core
       run: pip install --no-deps -e .
+    - name: Get Date
+      id: get-date
+      run: |
+        echo "date=$(date +'%Y-%b')"
+        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
+      shell: bash
+    - uses: actions/cache@v4
+      with:
+        path: bioimageio_cache
+        key: "test-spec-main-${{ steps.get-date.outputs.date }}"
     - name: pytest-spec-main
       run: pytest --disable-pytest-warnings
-    - if: matrix.python-version == '3.12' && github.event_name == 'pull_request'
+      env:
+        BIOIMAGEIO_CACHE_PATH: bioimageio_cache
+    - if: matrix.is-dev-version && github.event_name == 'pull_request'
       uses: orgoro/[email protected]
       with:
         coverageFile: coverage.xml
         token: ${{ secrets.GITHUB_TOKEN }}
-    - if: matrix.python-version == '3.12' && github.ref == 'refs/heads/main'
+    - if: matrix.is-dev-version && github.ref == 'refs/heads/main'
       run: |
         pip install genbadge[coverage]
         genbadge coverage --input-file coverage.xml --output-file ./dist/coverage/coverage-badge.svg
         coverage html -d dist/coverage
-    - if: matrix.python-version == '3.12' && github.ref == 'refs/heads/main'
+    - if: matrix.is-dev-version && github.ref == 'refs/heads/main'
       uses: actions/upload-artifact@v4
       with:
         name: coverage
         retention-days: 1
         path: dist
 
 
-  test-tf:
+  test-spec-main-tf:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.11']
+        python-version: ['3.9', '3.12']
     steps:
     - uses: actions/checkout@v4
-    - name: Install Conda environment with Micromamba
-      uses: mamba-org/setup-micromamba@v1
+    - uses: mamba-org/setup-micromamba@v1
+      with:
+        cache-downloads: true
+        cache-environment: true
+        environment-file: dev/env-tf.yaml
+        condarc: |
+          channel-priority: flexible
+        create-args: >-
+          python=${{ matrix.python-version }}
+        post-cleanup: 'all'
+    - name: additional setup spec
+      run: |
+        conda remove --yes --force bioimageio.spec || true  # allow failure for cached env
+        pip install --no-deps git+https://github.com/bioimage-io/spec-bioimage-io
+    - name: additional setup core
+      run: pip install --no-deps -e .
+    - name: Get Date
+      id: get-date
+      run: |
+        echo "date=$(date +'%Y-%b')"
+        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
+      shell: bash
+    - uses: actions/cache@v4
+      with:
+        path: bioimageio_cache
+        key: "test-spec-main-tf-${{ steps.get-date.outputs.date }}"
+    - run: pytest --disable-pytest-warnings
+      env:
+        BIOIMAGEIO_CACHE_PATH: bioimageio_cache
+
+  test-spec-conda-tf:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.9', '3.12']
+    steps:
+    - uses: actions/checkout@v4
+    - uses: mamba-org/setup-micromamba@v1
       with:
         cache-downloads: true
         cache-environment: true
@@ -123,8 +186,20 @@ jobs:
         post-cleanup: 'all'
     - name: additional setup
       run: pip install --no-deps -e .
+    - name: Get Date
+      id: get-date
+      run: |
+        echo "date=$(date +'%Y-%b')"
+        echo "date=$(date +'%Y-%b')" >> $GITHUB_OUTPUT
+      shell: bash
+    - uses: actions/cache@v4
+      with:
+        path: bioimageio_cache
+        key: "test-spec-conda-tf-${{ steps.get-date.outputs.date }}"
     - name: pytest-spec-tf
       run: pytest --disable-pytest-warnings
+      env:
+        BIOIMAGEIO_CACHE_PATH: bioimageio_cache
 
   conda-build:
     runs-on: ubuntu-latest
@@ -164,20 +239,11 @@ jobs:
           path: dist
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
           cache: 'pip'
       - run: pip install -e .[dev]
-      - id: get_version
-        run: python -c 'import bioimageio.core;print(f"version={bioimageio.core.__version__}")' >> $GITHUB_OUTPUT
       - name: Generate developer docs
-        run: |
-          pdoc \
-          --docformat google \
-          --logo https://bioimage.io/static/img/bioimage-io-logo.svg \
-          --logo-link https://bioimage.io/ \
-          --favicon https://bioimage.io/static/img/bioimage-io-icon-small.svg \
-          --footer-text 'bioimageio.core ${{steps.get_version.outputs.version}}' \
-          -o ./dist bioimageio.core
+        run: ./scripts/pdoc/run.sh
       - run: cp README.md ./dist/README.md
       - name: copy rendered presentations
         run: |

README.md

@@ -375,6 +375,24 @@ The model specification and its validation tools can be found at <https://github
 
 ## Changelog
 
+### 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)

bioimageio/core/VERSION

@@ -1,3 +1,3 @@
 {
-    "version": "0.6.10"
+    "version": "0.7.0"
 }

bioimageio/core/__init__.py

@@ -2,7 +2,6 @@
 .. include:: ../../README.md
 """
 
-from bioimageio.core.stat_measures import Stat
 from bioimageio.spec import (
     build_description,
     dump_description,
@@ -16,16 +15,38 @@
     validate_format,
 )
 
-from . import digest_spec
+from . import (
+    axis,
+    block_meta,
+    cli,
+    commands,
+    common,
+    digest_spec,
+    io,
+    model_adapters,
+    prediction,
+    proc_ops,
+    proc_setup,
+    sample,
+    stat_calculators,
+    stat_measures,
+    tensor,
+)
 from ._prediction_pipeline import PredictionPipeline, create_prediction_pipeline
-from ._resource_tests import load_description_and_test, test_description, test_model
+from ._resource_tests import (
+    enable_determinism,
+    load_description_and_test,
+    test_description,
+    test_model,
+)
 from ._settings import settings
 from .axis import Axis, AxisId
 from .block_meta import BlockMeta
 from .common import MemberId
 from .prediction import predict, predict_many
 from .sample import Sample
 from .stat_calculators import compute_dataset_measures
+from .stat_measures import Stat
 from .tensor import Tensor
 from .utils import VERSION
 
@@ -34,19 +55,29 @@
 
 # aliases
 test_resource = test_description
+"""alias of `test_description`"""
 load_resource = load_description
+"""alias of `load_description`"""
 load_model = load_model_description
+"""alias of `load_model_description`"""
 
 __all__ = [
     "__version__",
+    "axis",
     "Axis",
     "AxisId",
+    "block_meta",
     "BlockMeta",
     "build_description",
+    "cli",
+    "commands",
+    "common",
     "compute_dataset_measures",
     "create_prediction_pipeline",
     "digest_spec",
     "dump_description",
+    "enable_determinism",
+    "io",
     "load_dataset_description",
     "load_description_and_test",
     "load_description_and_validate_format_only",
@@ -55,15 +86,23 @@
     "load_model",
     "load_resource",
     "MemberId",
+    "model_adapters",
     "predict_many",
     "predict",
+    "prediction",
     "PredictionPipeline",
+    "proc_ops",
+    "proc_setup",
+    "sample",
     "Sample",
     "save_bioimageio_package_as_folder",
     "save_bioimageio_package",
     "save_bioimageio_yaml_only",
     "settings",
+    "stat_calculators",
+    "stat_measures",
     "Stat",
+    "tensor",
     "Tensor",
     "test_description",
     "test_model",

bioimageio/core/_prediction_pipeline.py

@@ -164,20 +164,20 @@ def predict_sample_without_blocking(
                 if out is not None
             },
             stat=sample.stat,
-            id=self.get_output_sample_id(sample.id),
+            id=sample.id,
         )
         if not skip_postprocessing:
             self.apply_postprocessing(output)
 
         return output
 
     def get_output_sample_id(self, input_sample_id: SampleId):
-        if input_sample_id is None:
-            return None
-        else:
-            return f"{input_sample_id}_" + (
-                self.model_description.id or self.model_description.name
-            )
+        warnings.warn(
+            "`PredictionPipeline.get_output_sample_id()` is deprecated and will be"
+            + " removed soon. Output sample id is equal to input sample id, hence this"
+            + " function is not needed."
+        )
+        return input_sample_id
 
     def predict_sample_with_fixed_blocking(
         self,