%global _empty_manifest_terminate_build 0 Name: python-bfio Version: 2.3.0 Release: 1 Summary: Simple reading and writing classes for tiled tiffs using Bioformats. License: MIT License URL: https://pypi.org/project/bfio/ Source0: https://mirrors.nju.edu.cn/pypi/web/packages/93/b8/dff392fe616dff6e7094d690593d8288d32cd1455b9282a0b9375e3147ec/bfio-2.3.0.tar.gz BuildArch: noarch Requires: python3-tifffile Requires: python3-imagecodecs Requires: python3-numpy Requires: python3-ome-types Requires: python3-lxml Requires: python3-zarr Requires: python3-bioformats-jar Requires: python3-bioformats-jar Requires: python3-zarr Requires: python3-requests Requires: python3-bioformats-jar Requires: python3-zarr %description # **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.0) [![Documentation Status](https://readthedocs.org/projects/bfio/badge/?version=latest)](https://bfio.readthedocs.io/en/latest/?badge=latest) [![PyPI](https://img.shields.io/pypi/v/bfio)](https://pypi.org/project/filepattern/) ![PyPI - Downloads](https://img.shields.io/pypi/dm/bfio) ![Bower](https://img.shields.io/bower/l/MI) This tool is a simplified but powerful interface to [Bioformats](https://www.openmicroscopy.org/bio-formats/) using jpype for direct access to the library. This tool is designed with scalable image analysis in mind, with a simple interface to treat any image like a memory mapped array. Docker containers with all necessary components are available (see **Docker Containers** section). ## Summary - [Installation](#installation) - [Docker](#docker) - [Documentation](#documentation) - [Contributing](#contributing) - [Versioning](#versioning) - [Authors](#authors) - [License](#license) - [Acknowledgments](#acknowledgments) ## Installation ### Setting up Java **Note:** `bfio` can be used without Java, but only the `python` and `zarr` backends will be useable. Only files in tiled OME Tiff or OME Zarr format can be read/written. In order to use the `Java` backend, it is necessary to first install the JDK. The `bfio` package is generally tested with [JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html), but JDK 11 and later also appear to work. ### Installing bfio The `bfio` package and the core dependencies (numpy, tifffile, imagecodecs) can be installed using pip: `pip install bfio` Additionally, `bfio` with other dependencies can be installed: 1. `pip install bfio[bioformats]` - Adds support for BioFormats/Java. See [License](#license) for additional information. 2. `pip install bfio[zarr]` - Adds support for OME Zarr 3. `pip install bfio[all]` - Installs all dependencies. ## Docker ### labshare/polus-bfio-util:2.3.0 Ubuntu based container with bfio and all dependencies (including Java). ### labshare/polus-bfio-util:2.3.0-imagej Same as above, except comes with ImageJ and PyImageJ. ### labshare/polus-bfio-util:2.3.0-tensorflow Tensorflow container with bfio isntalled. ## Documentation Documentation and examples are available on [Read the Docs](https://bfio.readthedocs.io/en/latest/). ## Versioning We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/PurpleBooth/a-good-readme-template/tags). ## Authors Nick Schaub (nick.schaub@nih.gov, nick.schaub@labshare.org) ## License This project is licensed under the [MIT License](LICENSE) Creative Commons License - see the [LICENSE](LICENSE) file for details. **NOTE** Bioformats is licensed under GPL, and as a consequence so is the `bioformats_jar` package. These packages and libraries are installed when using the `bfio[bioformats]` option. ## Acknowledgments - Parts of this code were written/modified from existing code found in `tifffile`. %package -n python3-bfio Summary: Simple reading and writing classes for tiled tiffs using Bioformats. Provides: python-bfio BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-bfio # **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.0) [![Documentation Status](https://readthedocs.org/projects/bfio/badge/?version=latest)](https://bfio.readthedocs.io/en/latest/?badge=latest) [![PyPI](https://img.shields.io/pypi/v/bfio)](https://pypi.org/project/filepattern/) ![PyPI - Downloads](https://img.shields.io/pypi/dm/bfio) ![Bower](https://img.shields.io/bower/l/MI) This tool is a simplified but powerful interface to [Bioformats](https://www.openmicroscopy.org/bio-formats/) using jpype for direct access to the library. This tool is designed with scalable image analysis in mind, with a simple interface to treat any image like a memory mapped array. Docker containers with all necessary components are available (see **Docker Containers** section). ## Summary - [Installation](#installation) - [Docker](#docker) - [Documentation](#documentation) - [Contributing](#contributing) - [Versioning](#versioning) - [Authors](#authors) - [License](#license) - [Acknowledgments](#acknowledgments) ## Installation ### Setting up Java **Note:** `bfio` can be used without Java, but only the `python` and `zarr` backends will be useable. Only files in tiled OME Tiff or OME Zarr format can be read/written. In order to use the `Java` backend, it is necessary to first install the JDK. The `bfio` package is generally tested with [JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html), but JDK 11 and later also appear to work. ### Installing bfio The `bfio` package and the core dependencies (numpy, tifffile, imagecodecs) can be installed using pip: `pip install bfio` Additionally, `bfio` with other dependencies can be installed: 1. `pip install bfio[bioformats]` - Adds support for BioFormats/Java. See [License](#license) for additional information. 2. `pip install bfio[zarr]` - Adds support for OME Zarr 3. `pip install bfio[all]` - Installs all dependencies. ## Docker ### labshare/polus-bfio-util:2.3.0 Ubuntu based container with bfio and all dependencies (including Java). ### labshare/polus-bfio-util:2.3.0-imagej Same as above, except comes with ImageJ and PyImageJ. ### labshare/polus-bfio-util:2.3.0-tensorflow Tensorflow container with bfio isntalled. ## Documentation Documentation and examples are available on [Read the Docs](https://bfio.readthedocs.io/en/latest/). ## Versioning We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/PurpleBooth/a-good-readme-template/tags). ## Authors Nick Schaub (nick.schaub@nih.gov, nick.schaub@labshare.org) ## License This project is licensed under the [MIT License](LICENSE) Creative Commons License - see the [LICENSE](LICENSE) file for details. **NOTE** Bioformats is licensed under GPL, and as a consequence so is the `bioformats_jar` package. These packages and libraries are installed when using the `bfio[bioformats]` option. ## Acknowledgments - Parts of this code were written/modified from existing code found in `tifffile`. %package help Summary: Development documents and examples for bfio Provides: python3-bfio-doc %description help # **B**io**F**ormats **I**nput/**O**utput utility (bfio 2.3.0) [![Documentation Status](https://readthedocs.org/projects/bfio/badge/?version=latest)](https://bfio.readthedocs.io/en/latest/?badge=latest) [![PyPI](https://img.shields.io/pypi/v/bfio)](https://pypi.org/project/filepattern/) ![PyPI - Downloads](https://img.shields.io/pypi/dm/bfio) ![Bower](https://img.shields.io/bower/l/MI) This tool is a simplified but powerful interface to [Bioformats](https://www.openmicroscopy.org/bio-formats/) using jpype for direct access to the library. This tool is designed with scalable image analysis in mind, with a simple interface to treat any image like a memory mapped array. Docker containers with all necessary components are available (see **Docker Containers** section). ## Summary - [Installation](#installation) - [Docker](#docker) - [Documentation](#documentation) - [Contributing](#contributing) - [Versioning](#versioning) - [Authors](#authors) - [License](#license) - [Acknowledgments](#acknowledgments) ## Installation ### Setting up Java **Note:** `bfio` can be used without Java, but only the `python` and `zarr` backends will be useable. Only files in tiled OME Tiff or OME Zarr format can be read/written. In order to use the `Java` backend, it is necessary to first install the JDK. The `bfio` package is generally tested with [JDK 8](https://docs.oracle.com/javase/8/docs/technotes/guides/install/install_overview.html), but JDK 11 and later also appear to work. ### Installing bfio The `bfio` package and the core dependencies (numpy, tifffile, imagecodecs) can be installed using pip: `pip install bfio` Additionally, `bfio` with other dependencies can be installed: 1. `pip install bfio[bioformats]` - Adds support for BioFormats/Java. See [License](#license) for additional information. 2. `pip install bfio[zarr]` - Adds support for OME Zarr 3. `pip install bfio[all]` - Installs all dependencies. ## Docker ### labshare/polus-bfio-util:2.3.0 Ubuntu based container with bfio and all dependencies (including Java). ### labshare/polus-bfio-util:2.3.0-imagej Same as above, except comes with ImageJ and PyImageJ. ### labshare/polus-bfio-util:2.3.0-tensorflow Tensorflow container with bfio isntalled. ## Documentation Documentation and examples are available on [Read the Docs](https://bfio.readthedocs.io/en/latest/). ## Versioning We use [SemVer](http://semver.org/) for versioning. For the versions available, see the [tags on this repository](https://github.com/PurpleBooth/a-good-readme-template/tags). ## Authors Nick Schaub (nick.schaub@nih.gov, nick.schaub@labshare.org) ## License This project is licensed under the [MIT License](LICENSE) Creative Commons License - see the [LICENSE](LICENSE) file for details. **NOTE** Bioformats is licensed under GPL, and as a consequence so is the `bioformats_jar` package. These packages and libraries are installed when using the `bfio[bioformats]` option. ## Acknowledgments - Parts of this code were written/modified from existing code found in `tifffile`. %prep %autosetup -n bfio-2.3.0 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-bfio -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Tue May 30 2023 Python_Bot - 2.3.0-1 - Package Spec generated