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diff --git a/python-webknossos.spec b/python-webknossos.spec new file mode 100644 index 0000000..37494d6 --- /dev/null +++ b/python-webknossos.spec @@ -0,0 +1,259 @@ +%global _empty_manifest_terminate_build 0 +Name: python-webknossos +Version: 0.12.5 +Release: 1 +Summary: Python API for working with WEBKNOSSOS datasets, annotations, and for WEBKNOSSOS server interaction. +License: AGPL-3.0 +URL: https://docs.webknossos.org/webknossos-py +Source0: https://mirrors.aliyun.com/pypi/web/packages/59/50/a20646236f3a67fb8d30300508a78b64019be0c042856980405cff91476d/webknossos-0.12.5.tar.gz +BuildArch: noarch + +Requires: python3-aiohttp +Requires: python3-attrs +Requires: python3-boltons +Requires: python3-cattrs +Requires: python3-cluster_tools +Requires: python3-fsspec +Requires: python3-httpx +Requires: python3-loxun +Requires: python3-natsort +Requires: python3-networkx +Requires: python3-numcodecs +Requires: python3-numpy +Requires: python3-psutil +Requires: python3-dateutil +Requires: python3-dotenv +Requires: python3-rich +Requires: python3-scikit-image +Requires: python3-scipy +Requires: python3-typing-extensions +Requires: python3-universal-pathlib +Requires: python3-wkw +Requires: python3-zarr +Requires: python3-zipp +Requires: python3-imagecodecs +Requires: python3-JPype1 +Requires: python3-pims +Requires: python3-tifffile +Requires: python3-pylibCZIrw + +%description +# WEBKNOSSOS Python Library +[](https://pypi.python.org/pypi/webknossos) +[](https://pypi.python.org/pypi/webknossos) +[](https://github.com/scalableminds/webknossos-libs/actions?query=workflow%3A%22CI%22) +[](https://docs.webknossos.org/webknossos-py) +[](https://github.com/psf/black) + +Python API for working with [WEBKNOSSOS](https://webknossos.org) datasets, annotations, and for WEBKNOSSOS server interaction. + +For the WEBKNOSSOS server, please refer to https://github.com/scalableminds/webknossos. + +## Features + +- easy-to-use dataset API for reading/writing/editing raw 2D/3D image data and volume annotations/segmentation in WEBKNOSSOS wrap (*.wkw) format + - add/remove layers + - update metadata (`datasource-properties.json`) + - up/downsample layers + - compress layers + - add/remove magnifications + - execute any of the `wkCuber` operations from your code +- manipulation of WEBKNOSSOS skeleton annotations (*.nml) as Python objects + - access to nodes, comments, trees, bounding boxes, metadata, etc. + - create new skeleton annotation from Graph structures or Python objects +- interaction, connection & scripting with your WEBKNOSSOS instance over the REST API + - up- & downloading annotations and datasets + +Please refer to [the documentation for further instructions](https://docs.webknossos.org/webknossos-py). + +## Installation +The `webknossos` package requires at least Python 3.8. + +You can install it from [pypi](https://pypi.org/project/webknossos/), e.g. via pip: + +```bash +pip install webknossos +``` + +## Examples +See the [examples folder](examples) or the [the documentation](https://docs.webknossos.org/webknossos-py). + +## Contributions & Development +Please see the [respective documentation page](https://docs.webknossos.org/webknossos-py/development.html). + +## License +[AGPLv3](https://www.gnu.org/licenses/agpl-3.0.html) +Copyright [scalable minds](https://scalableminds.com) + +## Test Data Credits +Excerpts for testing purposes have been sampled from: + +* Dow Jacobo Hossain Siletti Hudspeth (2018). **Connectomics of the zebrafish's lateral-line neuromast reveals wiring and miswiring in a simple microcircuit.** eLife. [DOI:10.7554/eLife.33988](https://elifesciences.org/articles/33988) +* Zheng Lauritzen Perlman Robinson Nichols Milkie Torrens Price Fisher Sharifi Calle-Schuler Kmecova Ali Karsh Trautman Bogovic Hanslovsky Jefferis Kazhdan Khairy Saalfeld Fetter Bock (2018). **A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.** Cell. [DOI:10.1016/j.cell.2018.06.019](https://www.cell.com/cell/fulltext/S0092-8674(18)30787-6). License: [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/) +* Bosch Ackels Pacureanu et al (2022). **Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy.** Nature Communications. [DOI:10.1038/s41467-022-30199-6](https://www.nature.com/articles/s41467-022-30199-6) + + +%package -n python3-webknossos +Summary: Python API for working with WEBKNOSSOS datasets, annotations, and for WEBKNOSSOS server interaction. +Provides: python-webknossos +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-webknossos +# WEBKNOSSOS Python Library +[](https://pypi.python.org/pypi/webknossos) +[](https://pypi.python.org/pypi/webknossos) +[](https://github.com/scalableminds/webknossos-libs/actions?query=workflow%3A%22CI%22) +[](https://docs.webknossos.org/webknossos-py) +[](https://github.com/psf/black) + +Python API for working with [WEBKNOSSOS](https://webknossos.org) datasets, annotations, and for WEBKNOSSOS server interaction. + +For the WEBKNOSSOS server, please refer to https://github.com/scalableminds/webknossos. + +## Features + +- easy-to-use dataset API for reading/writing/editing raw 2D/3D image data and volume annotations/segmentation in WEBKNOSSOS wrap (*.wkw) format + - add/remove layers + - update metadata (`datasource-properties.json`) + - up/downsample layers + - compress layers + - add/remove magnifications + - execute any of the `wkCuber` operations from your code +- manipulation of WEBKNOSSOS skeleton annotations (*.nml) as Python objects + - access to nodes, comments, trees, bounding boxes, metadata, etc. + - create new skeleton annotation from Graph structures or Python objects +- interaction, connection & scripting with your WEBKNOSSOS instance over the REST API + - up- & downloading annotations and datasets + +Please refer to [the documentation for further instructions](https://docs.webknossos.org/webknossos-py). + +## Installation +The `webknossos` package requires at least Python 3.8. + +You can install it from [pypi](https://pypi.org/project/webknossos/), e.g. via pip: + +```bash +pip install webknossos +``` + +## Examples +See the [examples folder](examples) or the [the documentation](https://docs.webknossos.org/webknossos-py). + +## Contributions & Development +Please see the [respective documentation page](https://docs.webknossos.org/webknossos-py/development.html). + +## License +[AGPLv3](https://www.gnu.org/licenses/agpl-3.0.html) +Copyright [scalable minds](https://scalableminds.com) + +## Test Data Credits +Excerpts for testing purposes have been sampled from: + +* Dow Jacobo Hossain Siletti Hudspeth (2018). **Connectomics of the zebrafish's lateral-line neuromast reveals wiring and miswiring in a simple microcircuit.** eLife. [DOI:10.7554/eLife.33988](https://elifesciences.org/articles/33988) +* Zheng Lauritzen Perlman Robinson Nichols Milkie Torrens Price Fisher Sharifi Calle-Schuler Kmecova Ali Karsh Trautman Bogovic Hanslovsky Jefferis Kazhdan Khairy Saalfeld Fetter Bock (2018). **A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.** Cell. [DOI:10.1016/j.cell.2018.06.019](https://www.cell.com/cell/fulltext/S0092-8674(18)30787-6). License: [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/) +* Bosch Ackels Pacureanu et al (2022). **Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy.** Nature Communications. [DOI:10.1038/s41467-022-30199-6](https://www.nature.com/articles/s41467-022-30199-6) + + +%package help +Summary: Development documents and examples for webknossos +Provides: python3-webknossos-doc +%description help +# WEBKNOSSOS Python Library +[](https://pypi.python.org/pypi/webknossos) +[](https://pypi.python.org/pypi/webknossos) +[](https://github.com/scalableminds/webknossos-libs/actions?query=workflow%3A%22CI%22) +[](https://docs.webknossos.org/webknossos-py) +[](https://github.com/psf/black) + +Python API for working with [WEBKNOSSOS](https://webknossos.org) datasets, annotations, and for WEBKNOSSOS server interaction. + +For the WEBKNOSSOS server, please refer to https://github.com/scalableminds/webknossos. + +## Features + +- easy-to-use dataset API for reading/writing/editing raw 2D/3D image data and volume annotations/segmentation in WEBKNOSSOS wrap (*.wkw) format + - add/remove layers + - update metadata (`datasource-properties.json`) + - up/downsample layers + - compress layers + - add/remove magnifications + - execute any of the `wkCuber` operations from your code +- manipulation of WEBKNOSSOS skeleton annotations (*.nml) as Python objects + - access to nodes, comments, trees, bounding boxes, metadata, etc. + - create new skeleton annotation from Graph structures or Python objects +- interaction, connection & scripting with your WEBKNOSSOS instance over the REST API + - up- & downloading annotations and datasets + +Please refer to [the documentation for further instructions](https://docs.webknossos.org/webknossos-py). + +## Installation +The `webknossos` package requires at least Python 3.8. + +You can install it from [pypi](https://pypi.org/project/webknossos/), e.g. via pip: + +```bash +pip install webknossos +``` + +## Examples +See the [examples folder](examples) or the [the documentation](https://docs.webknossos.org/webknossos-py). + +## Contributions & Development +Please see the [respective documentation page](https://docs.webknossos.org/webknossos-py/development.html). + +## License +[AGPLv3](https://www.gnu.org/licenses/agpl-3.0.html) +Copyright [scalable minds](https://scalableminds.com) + +## Test Data Credits +Excerpts for testing purposes have been sampled from: + +* Dow Jacobo Hossain Siletti Hudspeth (2018). **Connectomics of the zebrafish's lateral-line neuromast reveals wiring and miswiring in a simple microcircuit.** eLife. [DOI:10.7554/eLife.33988](https://elifesciences.org/articles/33988) +* Zheng Lauritzen Perlman Robinson Nichols Milkie Torrens Price Fisher Sharifi Calle-Schuler Kmecova Ali Karsh Trautman Bogovic Hanslovsky Jefferis Kazhdan Khairy Saalfeld Fetter Bock (2018). **A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster.** Cell. [DOI:10.1016/j.cell.2018.06.019](https://www.cell.com/cell/fulltext/S0092-8674(18)30787-6). License: [CC BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/) +* Bosch Ackels Pacureanu et al (2022). **Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy.** Nature Communications. [DOI:10.1038/s41467-022-30199-6](https://www.nature.com/articles/s41467-022-30199-6) + + +%prep +%autosetup -n webknossos-0.12.5 + +%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-webknossos -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri Jun 09 2023 Python_Bot <Python_Bot@openeuler.org> - 0.12.5-1 +- Package Spec generated |