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author | CoprDistGit <infra@openeuler.org> | 2023-05-15 09:15:06 +0000 |
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committer | CoprDistGit <infra@openeuler.org> | 2023-05-15 09:15:06 +0000 |
commit | 00bcffd5157f19aad935c221b8ec27c8f472c455 (patch) | |
tree | 5031219ffe4bc6b34b295250264438a961f0cae6 | |
parent | 33da69ae16d8bd0c014f133de3d732320aba9532 (diff) |
automatic import of python-bfio
-rw-r--r-- | .gitignore | 1 | ||||
-rw-r--r-- | python-bfio.spec | 378 | ||||
-rw-r--r-- | sources | 1 |
3 files changed, 380 insertions, 0 deletions
@@ -0,0 +1 @@ +/bfio-2.3.0.tar.gz diff --git a/python-bfio.spec b/python-bfio.spec new file mode 100644 index 0000000..422fd7a --- /dev/null +++ b/python-bfio.spec @@ -0,0 +1,378 @@ +%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) + +[](https://bfio.readthedocs.io/en/latest/?badge=latest) +[](https://pypi.org/project/filepattern/) + + + +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) + +[](https://bfio.readthedocs.io/en/latest/?badge=latest) +[](https://pypi.org/project/filepattern/) + + + +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) + +[](https://bfio.readthedocs.io/en/latest/?badge=latest) +[](https://pypi.org/project/filepattern/) + + + +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 +* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 2.3.0-1 +- Package Spec generated @@ -0,0 +1 @@ +bab5996bfaadab78368cb440bc80d042 bfio-2.3.0.tar.gz |