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authorCoprDistGit <infra@openeuler.org>2023-05-15 09:15:06 +0000
committerCoprDistGit <infra@openeuler.org>2023-05-15 09:15:06 +0000
commit00bcffd5157f19aad935c221b8ec27c8f472c455 (patch)
tree5031219ffe4bc6b34b295250264438a961f0cae6
parent33da69ae16d8bd0c014f133de3d732320aba9532 (diff)
automatic import of python-bfio
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-rw-r--r--python-bfio.spec378
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+/bfio-2.3.0.tar.gz
diff --git a/python-bfio.spec b/python-bfio.spec
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+%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
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 2.3.0-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..6a0f726
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+bab5996bfaadab78368cb440bc80d042 bfio-2.3.0.tar.gz