Changelog

0.9.6¤

  • bump bioimageio.spec library version to 0.5.7.4
  • increase default reprducibility tolerance
  • unify quantile (vs percentile) variable names
  • add quantile computation method parameter
  • accept SampleQuantile or DatasetQuantile as min/max arguments to proc_ops.Clip
  • save actual output during model testing only if an explicit working directory was specified to produce less clutter

0.9.5¤

  • bump bioimageio.spec library version to 0.5.6.0
  • improved ONNX export from pytorch state dict or torchscript using torch dynamo
  • default opset_version for pytorch_to_onnx/torchscript_for_onnx conversions bumped to 18.

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 It works by simply trying option --summary (new option name) and --summary-path (outdated option name)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¤

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
  • (in model inference testing) stop assuming model inputs are tileable

0.6.2¤

0.6.1¤

0.6.0¤

  • add compatibility with new bioimageio.spec 0.5 (0.5.2post1)
  • improve interfaces

0.5.10¤