Metadata-Version: 2.1
Name: bioformats_jar
Version: 2020.5.27
Summary: bioformats_package.jar installer for scyjava
Home-page: https://github.com/tlambert03/bioformats_jar
Author: Talley Lambert
Author-email: talley.lambert@gmail.com
License: GPL-2.0
Project-URL: Source Code, https://github.com/tlambert03/bioformats_jar
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: testing
License-File: LICENSE

# bioformats_jar

[![License](https://img.shields.io/pypi/l/bioformats_jar.svg?color=green)](https://github.com/tlambert03/bioformats_jar/raw/master/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/bioformats_jar.svg?color=green)](https://pypi.org/project/bioformats_jar)
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## deprecated

This package is deprecated.  You should use [scyjava](https://github.com/scijava/scyjava) to download and import jars.  The functionality in this
package can be accomplished using scyjava as follows:

```python
import jpype
import scyjava

scyjava.config.endpoints.append('ome:formats-gpl:6.7.0')
scyjava.start_jvm()
loci = jpype.JPackage("loci")
loci.common.DebugTools.setRootLevel("ERROR")
```

This package remains only for packages that already depend on it.

## usage

```python
from bioformats_jar import get_loci, set_loci_log_level

# start the JVM and get the loci module
loci = get_loci()

# optionally:
set_loci_log_level("DEBUG")  # by default "ERROR"
```

The following environment variables can also be used:

- `BIOFORMATS_VERSION` - version of bioformats to use.  by default "LATEST"
- `BIOFORMATS_LOG_LEVEL` - logging level for loci tools. by default "ERROR"
- `BIOFORMATS_LICENSE` - license version of bioformats to use.  must be either
  `"gpl"` or `"bsd"`.  By default `"gpl"`

*see also:*

- [Bioformats Docs](https://docs.openmicroscopy.org/bio-formats/latest)
- [Javadocs](https://downloads.openmicroscopy.org/bio-formats/latest/api/) with the loci API

## install

```sh
pip install bioformats-jar
```

```sh
conda install -c conda-forge bioformats-jar
```
