From b0526e7d3f593d35d8a5a647128b76a2328616a9 Mon Sep 17 00:00:00 2001 From: CoprDistGit Date: Mon, 15 May 2023 09:04:37 +0000 Subject: automatic import of python-scvelo --- .gitignore | 1 + python-scvelo.spec | 239 +++++++++++++++++++++++++++++++++++++++++++++++++++++ sources | 1 + 3 files changed, 241 insertions(+) create mode 100644 python-scvelo.spec create mode 100644 sources diff --git a/.gitignore b/.gitignore index e69de29..d7d0d18 100644 --- a/.gitignore +++ b/.gitignore @@ -0,0 +1 @@ +/scvelo-0.2.5.tar.gz diff --git a/python-scvelo.spec b/python-scvelo.spec new file mode 100644 index 0000000..637f195 --- /dev/null +++ b/python-scvelo.spec @@ -0,0 +1,239 @@ +%global _empty_manifest_terminate_build 0 +Name: python-scvelo +Version: 0.2.5 +Release: 1 +Summary: RNA velocity generalized through dynamical modeling +License: BSD +URL: https://github.com/theislab/scvelo +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/d7/ca/6669ad5c6765493ea9db0fb54b766d043b09db5a146f178c106b7162d1ef/scvelo-0.2.5.tar.gz +BuildArch: noarch + +Requires: python3-typing-extensions +Requires: python3-anndata +Requires: python3-scanpy +Requires: python3-loompy +Requires: python3-umap-learn +Requires: python3-numba +Requires: python3-numpy +Requires: python3-scipy +Requires: python3-pandas +Requires: python3-scikit-learn +Requires: python3-matplotlib +Requires: python3-black +Requires: python3-hnswlib +Requires: python3-hypothesis +Requires: python3-flake8 +Requires: python3-isort +Requires: python3-louvain +Requires: python3-magic-impute +Requires: python3-pre-commit +Requires: python3-pybind11 +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-igraph +Requires: python3-scanpy +Requires: python3-setuptools +Requires: python3-setuptools-scm +Requires: python3-typing-extensions +Requires: python3-importlib-metadata +Requires: python3-sphinx-rtd-theme +Requires: python3-sphinx-autodoc-typehints +Requires: python3-Jinja2 +Requires: python3-ipykernel +Requires: python3-sphinx +Requires: python3-nbsphinx +Requires: python3-pybind11 +Requires: python3-hnswlib +Requires: python3-igraph +Requires: python3-louvain + +%description +**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on +`Bergen et al. (Nature Biotech, 2020) `_. +RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. +scVelo generalizes the concept of RNA velocity +(`La Manno et al., Nature, 2018 `_) +by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full +transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations. +scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models. +scVelo's key applications +^^^^^^^^^^^^^^^^^^^^^^^^^ +- estimate RNA velocity to study cellular dynamics. +- identify putative driver genes and regimes of regulatory changes. +- infer a latent time to reconstruct the temporal sequence of transcriptomic events. +- estimate reaction rates of transcription, splicing and degradation. +- use statistical tests, e.g., to detect different kinetics regimes. +scVelo has, for instance, recently been used to study immune response in COVID-19 +patients and dynamic processes in human lung regeneration. Find out more in this list of +`application examples `_. +Latest news +^^^^^^^^^^^ +- Aug/2021: `Perspectives paper out in MSB `_ +- Feb/2021: scVelo goes multi-core +- Dec/2020: Cover of `Nature Biotechnology `_ +- Nov/2020: Talk at `Single Cell Biology `_ +- Oct/2020: `Helmholtz Best Paper Award `_ +- Oct/2020: Map cell fates with `CellRank `_ +- Sep/2020: Talk at `Single Cell Omics `_ +- Aug/2020: `scVelo out in Nature Biotech `_ +References +^^^^^^^^^^ +La Manno *et al.* (2018), RNA velocity of single cells, `Nature `_. +Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling, +`Nature Biotech `_. +Bergen *et al.* (2021), RNA velocity - current challenges and future perspectives, +`Molecular Systems Biology `_. +Support +^^^^^^^ +Found a bug or would like to see a feature implemented? Feel free to submit an +`issue `_. +Have a question or would like to start a new discussion? Head over to +`GitHub discussions `_. +In either case, you can also always send us an `email `_. +Your help to improve scVelo is highly appreciated. +For further information visit `scvelo.org `_. + +%package -n python3-scvelo +Summary: RNA velocity generalized through dynamical modeling +Provides: python-scvelo +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-scvelo +**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on +`Bergen et al. (Nature Biotech, 2020) `_. +RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. +scVelo generalizes the concept of RNA velocity +(`La Manno et al., Nature, 2018 `_) +by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full +transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations. +scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models. +scVelo's key applications +^^^^^^^^^^^^^^^^^^^^^^^^^ +- estimate RNA velocity to study cellular dynamics. +- identify putative driver genes and regimes of regulatory changes. +- infer a latent time to reconstruct the temporal sequence of transcriptomic events. +- estimate reaction rates of transcription, splicing and degradation. +- use statistical tests, e.g., to detect different kinetics regimes. +scVelo has, for instance, recently been used to study immune response in COVID-19 +patients and dynamic processes in human lung regeneration. Find out more in this list of +`application examples `_. +Latest news +^^^^^^^^^^^ +- Aug/2021: `Perspectives paper out in MSB `_ +- Feb/2021: scVelo goes multi-core +- Dec/2020: Cover of `Nature Biotechnology `_ +- Nov/2020: Talk at `Single Cell Biology `_ +- Oct/2020: `Helmholtz Best Paper Award `_ +- Oct/2020: Map cell fates with `CellRank `_ +- Sep/2020: Talk at `Single Cell Omics `_ +- Aug/2020: `scVelo out in Nature Biotech `_ +References +^^^^^^^^^^ +La Manno *et al.* (2018), RNA velocity of single cells, `Nature `_. +Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling, +`Nature Biotech `_. +Bergen *et al.* (2021), RNA velocity - current challenges and future perspectives, +`Molecular Systems Biology `_. +Support +^^^^^^^ +Found a bug or would like to see a feature implemented? Feel free to submit an +`issue `_. +Have a question or would like to start a new discussion? Head over to +`GitHub discussions `_. +In either case, you can also always send us an `email `_. +Your help to improve scVelo is highly appreciated. +For further information visit `scvelo.org `_. + +%package help +Summary: Development documents and examples for scvelo +Provides: python3-scvelo-doc +%description help +**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on +`Bergen et al. (Nature Biotech, 2020) `_. +RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics. +scVelo generalizes the concept of RNA velocity +(`La Manno et al., Nature, 2018 `_) +by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full +transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations. +scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models. +scVelo's key applications +^^^^^^^^^^^^^^^^^^^^^^^^^ +- estimate RNA velocity to study cellular dynamics. +- identify putative driver genes and regimes of regulatory changes. +- infer a latent time to reconstruct the temporal sequence of transcriptomic events. +- estimate reaction rates of transcription, splicing and degradation. +- use statistical tests, e.g., to detect different kinetics regimes. +scVelo has, for instance, recently been used to study immune response in COVID-19 +patients and dynamic processes in human lung regeneration. Find out more in this list of +`application examples `_. +Latest news +^^^^^^^^^^^ +- Aug/2021: `Perspectives paper out in MSB `_ +- Feb/2021: scVelo goes multi-core +- Dec/2020: Cover of `Nature Biotechnology `_ +- Nov/2020: Talk at `Single Cell Biology `_ +- Oct/2020: `Helmholtz Best Paper Award `_ +- Oct/2020: Map cell fates with `CellRank `_ +- Sep/2020: Talk at `Single Cell Omics `_ +- Aug/2020: `scVelo out in Nature Biotech `_ +References +^^^^^^^^^^ +La Manno *et al.* (2018), RNA velocity of single cells, `Nature `_. +Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling, +`Nature Biotech `_. +Bergen *et al.* (2021), RNA velocity - current challenges and future perspectives, +`Molecular Systems Biology `_. +Support +^^^^^^^ +Found a bug or would like to see a feature implemented? Feel free to submit an +`issue `_. +Have a question or would like to start a new discussion? Head over to +`GitHub discussions `_. +In either case, you can also always send us an `email `_. +Your help to improve scVelo is highly appreciated. +For further information visit `scvelo.org `_. + +%prep +%autosetup -n scvelo-0.2.5 + +%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-scvelo -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Mon May 15 2023 Python_Bot - 0.2.5-1 +- Package Spec generated diff --git a/sources b/sources new file mode 100644 index 0000000..cd94e77 --- /dev/null +++ b/sources @@ -0,0 +1 @@ +0d98dbad1515d8aa463e0386cb2d9de0 scvelo-0.2.5.tar.gz -- cgit v1.2.3