From c574aa191b3ef11b4d83a3f34abd97239feeca62 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Fri, 9 Jun 2023 02:35:36 +0000 Subject: automatic import of python-biobb-analysis --- .gitignore | 1 + python-biobb-analysis.spec | 388 +++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 390 insertions(+) create mode 100644 python-biobb-analysis.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..0a3dbe0 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/biobb_analysis-4.0.1.tar.gz diff --git a/python-biobb-analysis.spec b/python-biobb-analysis.spec new file mode 100644 index 0000000..1538b2a --- /dev/null +++ b/python-biobb-analysis.spec @@ -0,0 +1,388 @@ +%global _empty_manifest_terminate_build 0 +Name: python-biobb-analysis +Version: 4.0.1 +Release: 1 +Summary: Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. +License: Apache Software License +URL: https://github.com/bioexcel/biobb_analysis +Source0: https://mirrors.aliyun.com/pypi/web/packages/70/ae/96a066c776608f54ec7b4c74796415be392e195d9dc6718278439c7c5375/biobb_analysis-4.0.1.tar.gz +BuildArch: noarch + +Requires: python3-biobb-common + +%description +[![](https://img.shields.io/github/v/tag/bioexcel/biobb_analysis?label=Version)](https://GitHub.com/bioexcel/biobb_analysis/tags/) +[![](https://img.shields.io/pypi/v/biobb-analysis.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-analysis/) +[![](https://img.shields.io/conda/vn/bioconda/biobb_analysis?label=Conda)](https://anaconda.org/bioconda/biobb_analysis) +[![](https://img.shields.io/conda/dn/bioconda/biobb_analysis?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_analysis) +[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_analysis?tab=tags) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_1) + +[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_analysis) +[![](https://img.shields.io/pypi/pyversions/biobb-analysis.svg?label=Python%20Versions)](https://pypi.org/project/biobb-analysis/) +[![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) +[![](https://img.shields.io/badge/Open%20Source%3f-Yes!-blue)](https://github.com/bioexcel/biobb_analysis) + +[![](https://readthedocs.org/projects/biobb-analysis/badge/?version=latest&label=Docs)](https://biobb-analysis.readthedocs.io/en/latest/?badge=latest) +[![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/) +[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM) +[![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4) +[![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas) + +[![](https://docs.bioexcel.eu/biobb_analysis/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_analysis/junit/report.html) +[![](https://docs.bioexcel.eu/biobb_analysis/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_analysis/coverage/) +[![](https://docs.bioexcel.eu/biobb_analysis/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_analysis/flake8/) +[![](https://img.shields.io/github/last-commit/bioexcel/biobb_analysis?label=Last%20Commit)](https://github.com/bioexcel/biobb_analysis/commits/master) +[![](https://img.shields.io/github/issues/bioexcel/biobb_analysis.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_analysis/issues/) + + +# biobb_analysis + +### Introduction +Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. +Biobb (BioExcel building blocks) packages are Python building blocks that +create new layer of compatibility and interoperability over popular +bioinformatics tools. +The latest documentation of this package can be found in our readthedocs site: +[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/). + +### Version +v4.0.1 2023.1 + +### Installation +Using PIP: + +> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY. + +* Installation: + + + pip install "biobb_analysis>=4.0.1" + + +* Usage: [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) + +Using ANACONDA: + +* Installation: + + + conda install -c bioconda "biobb_analysis>=4.0.1" + + +* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html) + +Using DOCKER: + +* Installation: + + + docker pull quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_1 + + +* Usage: + + + docker run quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_1 + + +Using SINGULARITY: + +**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system. + +* Installation: + + + singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_1 + + +* Usage: + + + singularity exec biobb_analysis.sif + + +The command list and specification can be found at the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html). + +### Copyright & Licensing +This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). + +* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/) +* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) + +Licensed under the +[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. + +![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel") + + + + +%package -n python3-biobb-analysis +Summary: Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. +Provides: python-biobb-analysis +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-biobb-analysis +[![](https://img.shields.io/github/v/tag/bioexcel/biobb_analysis?label=Version)](https://GitHub.com/bioexcel/biobb_analysis/tags/) +[![](https://img.shields.io/pypi/v/biobb-analysis.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-analysis/) +[![](https://img.shields.io/conda/vn/bioconda/biobb_analysis?label=Conda)](https://anaconda.org/bioconda/biobb_analysis) +[![](https://img.shields.io/conda/dn/bioconda/biobb_analysis?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_analysis) +[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_analysis?tab=tags) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_1) + +[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_analysis) +[![](https://img.shields.io/pypi/pyversions/biobb-analysis.svg?label=Python%20Versions)](https://pypi.org/project/biobb-analysis/) +[![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) +[![](https://img.shields.io/badge/Open%20Source%3f-Yes!-blue)](https://github.com/bioexcel/biobb_analysis) + +[![](https://readthedocs.org/projects/biobb-analysis/badge/?version=latest&label=Docs)](https://biobb-analysis.readthedocs.io/en/latest/?badge=latest) +[![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/) +[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM) +[![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4) +[![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas) + +[![](https://docs.bioexcel.eu/biobb_analysis/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_analysis/junit/report.html) +[![](https://docs.bioexcel.eu/biobb_analysis/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_analysis/coverage/) +[![](https://docs.bioexcel.eu/biobb_analysis/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_analysis/flake8/) +[![](https://img.shields.io/github/last-commit/bioexcel/biobb_analysis?label=Last%20Commit)](https://github.com/bioexcel/biobb_analysis/commits/master) +[![](https://img.shields.io/github/issues/bioexcel/biobb_analysis.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_analysis/issues/) + + +# biobb_analysis + +### Introduction +Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. +Biobb (BioExcel building blocks) packages are Python building blocks that +create new layer of compatibility and interoperability over popular +bioinformatics tools. +The latest documentation of this package can be found in our readthedocs site: +[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/). + +### Version +v4.0.1 2023.1 + +### Installation +Using PIP: + +> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY. + +* Installation: + + + pip install "biobb_analysis>=4.0.1" + + +* Usage: [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) + +Using ANACONDA: + +* Installation: + + + conda install -c bioconda "biobb_analysis>=4.0.1" + + +* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html) + +Using DOCKER: + +* Installation: + + + docker pull quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_1 + + +* Usage: + + + docker run quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_1 + + +Using SINGULARITY: + +**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system. + +* Installation: + + + singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_1 + + +* Usage: + + + singularity exec biobb_analysis.sif + + +The command list and specification can be found at the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html). + +### Copyright & Licensing +This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). + +* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/) +* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) + +Licensed under the +[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. + +![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel") + + + + +%package help +Summary: Development documents and examples for biobb-analysis +Provides: python3-biobb-analysis-doc +%description help +[![](https://img.shields.io/github/v/tag/bioexcel/biobb_analysis?label=Version)](https://GitHub.com/bioexcel/biobb_analysis/tags/) +[![](https://img.shields.io/pypi/v/biobb-analysis.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-analysis/) +[![](https://img.shields.io/conda/vn/bioconda/biobb_analysis?label=Conda)](https://anaconda.org/bioconda/biobb_analysis) +[![](https://img.shields.io/conda/dn/bioconda/biobb_analysis?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_analysis) +[![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_analysis?tab=tags) +[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_1) + +[![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_analysis) +[![](https://img.shields.io/pypi/pyversions/biobb-analysis.svg?label=Python%20Versions)](https://pypi.org/project/biobb-analysis/) +[![](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) +[![](https://img.shields.io/badge/Open%20Source%3f-Yes!-blue)](https://github.com/bioexcel/biobb_analysis) + +[![](https://readthedocs.org/projects/biobb-analysis/badge/?version=latest&label=Docs)](https://biobb-analysis.readthedocs.io/en/latest/?badge=latest) +[![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/) +[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM) +[![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4) +[![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas) + +[![](https://docs.bioexcel.eu/biobb_analysis/junit/testsbadge.svg)](https://docs.bioexcel.eu/biobb_analysis/junit/report.html) +[![](https://docs.bioexcel.eu/biobb_analysis/coverage/coveragebadge.svg)](https://docs.bioexcel.eu/biobb_analysis/coverage/) +[![](https://docs.bioexcel.eu/biobb_analysis/flake8/flake8badge.svg)](https://docs.bioexcel.eu/biobb_analysis/flake8/) +[![](https://img.shields.io/github/last-commit/bioexcel/biobb_analysis?label=Last%20Commit)](https://github.com/bioexcel/biobb_analysis/commits/master) +[![](https://img.shields.io/github/issues/bioexcel/biobb_analysis.svg?color=brightgreen&label=Issues)](https://GitHub.com/bioexcel/biobb_analysis/issues/) + + +# biobb_analysis + +### Introduction +Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. +Biobb (BioExcel building blocks) packages are Python building blocks that +create new layer of compatibility and interoperability over popular +bioinformatics tools. +The latest documentation of this package can be found in our readthedocs site: +[latest API documentation](http://biobb_analysis.readthedocs.io/en/latest/). + +### Version +v4.0.1 2023.1 + +### Installation +Using PIP: + +> **Important:** PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY. + +* Installation: + + + pip install "biobb_analysis>=4.0.1" + + +* Usage: [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) + +Using ANACONDA: + +* Installation: + + + conda install -c bioconda "biobb_analysis>=4.0.1" + + +* Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-analysis.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html) + +Using DOCKER: + +* Installation: + + + docker pull quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_1 + + +* Usage: + + + docker run quay.io/biocontainers/biobb_analysis:4.0.1--pyhdfd78af_1 + + +Using SINGULARITY: + +**MacOS users**: it's strongly recommended to avoid Singularity and use **Docker** as containerization system. + +* Installation: + + + singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.0.1--pyhdfd78af_1 + + +* Usage: + + + singularity exec biobb_analysis.sif + + +The command list and specification can be found at the [Command Line documentation](https://biobb-analysis.readthedocs.io/en/latest/command_line.html). + +### Copyright & Licensing +This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)). + +* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/) +* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/) + +Licensed under the +[Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details. + +![](https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png "Bioexcel") + + + + +%prep +%autosetup -n biobb_analysis-4.0.1 + +%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-biobb-analysis -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Fri Jun 09 2023 Python_Bot - 4.0.1-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..35ab3fa --- /dev/null +++ b/sources @@ -0,0 +1 @@ +ffc080a6f8a6c3bd46a750f44999b57a biobb_analysis-4.0.1.tar.gz -- cgit v1.2.3