Metadata-Version: 2.1
Name: bioimageio.core
Version: 0.4.4
Summary: Python functionality for the bioimage model zoo
Home-page: https://github.com/bioimage-io/core-bioimage-io-python
Author: Bioimage Team
License: UNKNOWN
Project-URL: Bug Reports, https://github.com/bioimage-io/core-bioimage-io-python/issues
Project-URL: Source, https://github.com/bioimage-io/core-bioimage-io-python
Description: # core-bioimage-io-python
        
        Python specific core utilities for running models in the [BioImage Model Zoo](https://bioimage.io)
        
        ## Installation
        
        ### Via Conda
        
        The `bioimageio.core` package supports various back-ends for running BioimageIO networks:
        
        * Pytorch/Torchscript:
          ```bash
          # cpu installation (if you don't have an nvidia graphics card)
          conda install -c pytorch -c conda-forge bioimageio.core pytorch torchvision cpuonly
        
          # gpu installation
          conda install -c pytorch -c conda-forge bioimageio.core pytorch torchvision cudatoolkit
          ```
        
        * Tensorflow
          ```bash
          # currently only cpu version supported
          conda install -c conda-forge bioimageio.core tensorflow
          ```
        
        * ONNXRuntime
          ```bash
          # currently only cpu version supported
          conda install -c conda-forge bioimageio.core onnxruntime
          ```
          
        ### Via pip
        
        The package is also available via pip:
        ```
        pip install bioimageio.core
        ```
        
        ### Set up Development Environment
        
        To set up a development conda environment run the following commands:
        ```
        conda env create -f dev/environment-base.yaml
        conda activate bio-core-dev
        pip install -e . --no-deps
        ```
        
        There are different environment files that only install tensorflow or pytorch as dependencies available.
        
        ## Command Line
        
        `bioimageio.core` installs a command line interface for testing models and other functionality. You can list all the available commands via:
        ```
        bioimageio
        ```
        
        Check that a model adheres to the model spec:
        ```
        bioimageio validate <MODEL>
        ```
        
        Test a model (including prediction for the test input):
        ```
        bioimageio test-model -m <MODEL>
        ```
        
        Run prediction for an image stored on disc:
        ```
        bioimageio predict-image -m <MODEL> -i <INPUT> -o <OUTPUT>
        ```
        
        ## From python
        
        `bioimageio.core` can be used as a python library. See the notebook [example/bioimageio-core-usage.ipynb](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/bioimageio-core-usage.ipynb) for usage examples.
        
        ## Model Specification
        
        The model specification and its validation tools can be found at https://github.com/bioimage-io/spec-bioimage-io.
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
Provides-Extra: test
Provides-Extra: dev
Provides-Extra: pytorch
Provides-Extra: tensorflow
Provides-Extra: onnx
