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| author | CoprDistGit <infra@openeuler.org> | 2023-05-10 07:42:06 +0000 |
|---|---|---|
| committer | CoprDistGit <infra@openeuler.org> | 2023-05-10 07:42:06 +0000 |
| commit | b682c41ad36853a6c37767f5c3b16412928672a5 (patch) | |
| tree | 6261bdb1f66fa786790183eb6470e00d7e383ba5 | |
| parent | dcc62fe97f8f667360f4810da344b8dbcd9e928b (diff) | |
automatic import of python-clustergrammer2
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | python-clustergrammer2.spec | 495 | ||||
| -rw-r--r-- | sources | 1 |
3 files changed, 497 insertions, 0 deletions
@@ -0,0 +1 @@ +/clustergrammer2-0.18.0.tar.gz diff --git a/python-clustergrammer2.spec b/python-clustergrammer2.spec new file mode 100644 index 0000000..ecf140f --- /dev/null +++ b/python-clustergrammer2.spec @@ -0,0 +1,495 @@ +%global _empty_manifest_terminate_build 0 +Name: python-clustergrammer2 +Version: 0.18.0 +Release: 1 +Summary: A Custom Jupyter Widget Library +License: BSD +URL: https://github.com/ismms-himc/clustergrammer2 +Source0: https://mirrors.nju.edu.cn/pypi/web/packages/ca/9c/fa7809af5bb14723e09890ef605433dbfef526e8f414931604728b1f5099/clustergrammer2-0.18.0.tar.gz +BuildArch: noarch + +Requires: python3-ipywidgets +Requires: python3-jupyter-sphinx +Requires: python3-nbsphinx +Requires: python3-nbsphinx-link +Requires: python3-pytest-check-links +Requires: python3-pypandoc +Requires: python3-recommonmark +Requires: python3-sphinx +Requires: python3-sphinx-rtd-theme +Requires: python3-pytest +Requires: python3-pytest-cov +Requires: python3-nbval + +%description + +<img src='img/clustergrammer2_logo.png' alt="Clustergramer2" width="350px" > + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?urlpath=lab) + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?filepath=notebooks%2F2.0_CCLE_Gene_Expression.ipynb) + +Clustergrammer2 is an interactive heatmap Jupyter widget built using the [widget-ts-cookiecutter](https://github.com/jupyter-widgets/widget-ts-cookiecutter) library and the WebGL library [regl](https://github.com/regl-project/regl). Clustergrammer2 is built to help researchers interactively explore single cell data (e.g. scRNA-seq). Please see [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html) for examples. + +# Clustergrammer2 Examples + +### Basic Example of Running Clustergrammer2 on MyBinder + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F1.0_Running_Clustergrammer2.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/1.0_Running_Clustergrammer2.ipynb) + +[](http://www.youtube.com/watch?v=UgO5LLvcfB0) + +The above notebook shows how Clustergrammer2 can be used to load a small dataset and visualize a large random DataFrame. By running the notebook on MyBinder using [Jupyter Lab](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?urlpath=lab) it can also be used to visualize a user uploaded dataset. Please see the video tutorial above for more information. + +For additional examples and tutorials please see: + +* [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html) +* [Clustergrammer2-Notebooks](https://github.com/ismms-himc/clustergrammer2-notebooks) GitHub repository + + +### 2,700 PBMC scRNA-seq +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_2700_PBMC_scRNA-seq.ipynb?flush_cache=true) + +[](http://www.youtube.com/watch?v=BEPspcC7vIY) + +Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene expression across thousands of single cells. This method produces thousands of measurements (single cells) across thousands of dimensions (genes). This notebook uses Clustergrammer2 to interactively explore an example dataset measuring the gene expression of 2,700 PBMCs obtained from [10X Genomics](https://www.10xgenomics.com/resources/datasets/). Bulk gene expression signatures of cell types from [CIBERSORT](https://cibersort.stanford.edu/) were used to obtain a tentative cell type for each cell. Please see the video tutorial above for more information. + +# Clustergrammer2 Roadmap +Please see the project [Roadmap](https://github.com/ismms-himc/clustergrammer2/blob/master/ROADMAP.md) for information on where the project is heading. + +# Installation + +A typical installation requires the following commands to be run: + +```bash +pip install clustergrammer2 +jupyter nbextension install --py --sys-prefix clustergrammer2 +jupyter nbextension enable --py --sys-prefix clustergrammer2 +``` + +Optionally: --sys-prefix|--user|--system + +Or, if you use jupyterlab: + +```bash +pip install clustergrammer2 +jupyter labextension install @jupyter-widgets/jupyterlab-manager +``` + +### Embedding the widget into static HTML Notebooks + +```bash +jupyter nbconvert --to html notebook.ipynb +``` + +# Development + +During development run `npm run watch` for real time updates. When releasing a new version, first confirm that latest version of the front and back ends are working locally (check console logs, etc). + +#### Updating versions +Update the versions in the following files + +##### JavaScript + +* package.json +* widget.ts + +#### Python + +* _version.py +* example.py +* requirements.txt +* _frontend.py + + +#### Webpack + +Run the following commands to build the JavaScript bundle: + +```bash +npm run build +npm run build:nbextension +npm run build:labextension +``` + +Publish to npm using +```bash +npm publish +``` + +These instructions are based on the release instructions from the [jupyter-widgets/widget-ts-cookiecutterREADME](https://github.com/jupyter-widgets/widget-ts-cookiecutter). + +### Bundling the Python Package + +Next, bundle the python package using (optinally delete the old versions under `dist`) + +```bash +python setup.py sdist bdist_wheel +``` + +Then, upload the PYPI: + +```bash +twine upload dist/* +``` + +## Checklist after release + +After releasing a new version several things need to be checked to ensure proper widget functioning. + +### Check Package Managers + +- https://www.npmjs.com/package/clustergrammer2 (can be slow to update) +- https://pypi.org/project/clustergrammer2/ + +### Check HTML Embedding +- Run `jupyter nbconvert --to html introduction_nb.ipynb` (from the examples directory) to generate a static HTML and check that the latest widget is working (uses unpkg.com, like https://unpkg.com/clustergrammer2@0.5.18/dist/index.js) +- Check NBViewer using link to notebook on GitHub (e.g. https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2/blob/master/examples/introduction_nb.ipynb?flush_cache=true). Make sure to use the querystring `flush_cache=True` in the URL to ensure that NBVIewer re-runs nbconvert. + +### Check Cloud Services +- Check MyBinder + +### Note for Sublime Development +Use this in the where section to restrict search +``` +clustergrammer2/*.py,-*/build/* +``` + +# Contact +For issues and concerns please use the [issue tracker](https://github.com/ismms-himc/clustergrammer2/issues) or [gitter](https://gitter.im/clustergrammer2) discussion room. + + + + +%package -n python3-clustergrammer2 +Summary: A Custom Jupyter Widget Library +Provides: python-clustergrammer2 +BuildRequires: python3-devel +BuildRequires: python3-setuptools +BuildRequires: python3-pip +%description -n python3-clustergrammer2 + +<img src='img/clustergrammer2_logo.png' alt="Clustergramer2" width="350px" > + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?urlpath=lab) + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?filepath=notebooks%2F2.0_CCLE_Gene_Expression.ipynb) + +Clustergrammer2 is an interactive heatmap Jupyter widget built using the [widget-ts-cookiecutter](https://github.com/jupyter-widgets/widget-ts-cookiecutter) library and the WebGL library [regl](https://github.com/regl-project/regl). Clustergrammer2 is built to help researchers interactively explore single cell data (e.g. scRNA-seq). Please see [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html) for examples. + +# Clustergrammer2 Examples + +### Basic Example of Running Clustergrammer2 on MyBinder + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F1.0_Running_Clustergrammer2.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/1.0_Running_Clustergrammer2.ipynb) + +[](http://www.youtube.com/watch?v=UgO5LLvcfB0) + +The above notebook shows how Clustergrammer2 can be used to load a small dataset and visualize a large random DataFrame. By running the notebook on MyBinder using [Jupyter Lab](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?urlpath=lab) it can also be used to visualize a user uploaded dataset. Please see the video tutorial above for more information. + +For additional examples and tutorials please see: + +* [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html) +* [Clustergrammer2-Notebooks](https://github.com/ismms-himc/clustergrammer2-notebooks) GitHub repository + + +### 2,700 PBMC scRNA-seq +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_2700_PBMC_scRNA-seq.ipynb?flush_cache=true) + +[](http://www.youtube.com/watch?v=BEPspcC7vIY) + +Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene expression across thousands of single cells. This method produces thousands of measurements (single cells) across thousands of dimensions (genes). This notebook uses Clustergrammer2 to interactively explore an example dataset measuring the gene expression of 2,700 PBMCs obtained from [10X Genomics](https://www.10xgenomics.com/resources/datasets/). Bulk gene expression signatures of cell types from [CIBERSORT](https://cibersort.stanford.edu/) were used to obtain a tentative cell type for each cell. Please see the video tutorial above for more information. + +# Clustergrammer2 Roadmap +Please see the project [Roadmap](https://github.com/ismms-himc/clustergrammer2/blob/master/ROADMAP.md) for information on where the project is heading. + +# Installation + +A typical installation requires the following commands to be run: + +```bash +pip install clustergrammer2 +jupyter nbextension install --py --sys-prefix clustergrammer2 +jupyter nbextension enable --py --sys-prefix clustergrammer2 +``` + +Optionally: --sys-prefix|--user|--system + +Or, if you use jupyterlab: + +```bash +pip install clustergrammer2 +jupyter labextension install @jupyter-widgets/jupyterlab-manager +``` + +### Embedding the widget into static HTML Notebooks + +```bash +jupyter nbconvert --to html notebook.ipynb +``` + +# Development + +During development run `npm run watch` for real time updates. When releasing a new version, first confirm that latest version of the front and back ends are working locally (check console logs, etc). + +#### Updating versions +Update the versions in the following files + +##### JavaScript + +* package.json +* widget.ts + +#### Python + +* _version.py +* example.py +* requirements.txt +* _frontend.py + + +#### Webpack + +Run the following commands to build the JavaScript bundle: + +```bash +npm run build +npm run build:nbextension +npm run build:labextension +``` + +Publish to npm using +```bash +npm publish +``` + +These instructions are based on the release instructions from the [jupyter-widgets/widget-ts-cookiecutterREADME](https://github.com/jupyter-widgets/widget-ts-cookiecutter). + +### Bundling the Python Package + +Next, bundle the python package using (optinally delete the old versions under `dist`) + +```bash +python setup.py sdist bdist_wheel +``` + +Then, upload the PYPI: + +```bash +twine upload dist/* +``` + +## Checklist after release + +After releasing a new version several things need to be checked to ensure proper widget functioning. + +### Check Package Managers + +- https://www.npmjs.com/package/clustergrammer2 (can be slow to update) +- https://pypi.org/project/clustergrammer2/ + +### Check HTML Embedding +- Run `jupyter nbconvert --to html introduction_nb.ipynb` (from the examples directory) to generate a static HTML and check that the latest widget is working (uses unpkg.com, like https://unpkg.com/clustergrammer2@0.5.18/dist/index.js) +- Check NBViewer using link to notebook on GitHub (e.g. https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2/blob/master/examples/introduction_nb.ipynb?flush_cache=true). Make sure to use the querystring `flush_cache=True` in the URL to ensure that NBVIewer re-runs nbconvert. + +### Check Cloud Services +- Check MyBinder + +### Note for Sublime Development +Use this in the where section to restrict search +``` +clustergrammer2/*.py,-*/build/* +``` + +# Contact +For issues and concerns please use the [issue tracker](https://github.com/ismms-himc/clustergrammer2/issues) or [gitter](https://gitter.im/clustergrammer2) discussion room. + + + + +%package help +Summary: Development documents and examples for clustergrammer2 +Provides: python3-clustergrammer2-doc +%description help + +<img src='img/clustergrammer2_logo.png' alt="Clustergramer2" width="350px" > + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?urlpath=lab) + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?filepath=notebooks%2F2.0_CCLE_Gene_Expression.ipynb) + +Clustergrammer2 is an interactive heatmap Jupyter widget built using the [widget-ts-cookiecutter](https://github.com/jupyter-widgets/widget-ts-cookiecutter) library and the WebGL library [regl](https://github.com/regl-project/regl). Clustergrammer2 is built to help researchers interactively explore single cell data (e.g. scRNA-seq). Please see [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html) for examples. + +# Clustergrammer2 Examples + +### Basic Example of Running Clustergrammer2 on MyBinder + +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F1.0_Running_Clustergrammer2.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/1.0_Running_Clustergrammer2.ipynb) + +[](http://www.youtube.com/watch?v=UgO5LLvcfB0) + +The above notebook shows how Clustergrammer2 can be used to load a small dataset and visualize a large random DataFrame. By running the notebook on MyBinder using [Jupyter Lab](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?urlpath=lab) it can also be used to visualize a user uploaded dataset. Please see the video tutorial above for more information. + +For additional examples and tutorials please see: + +* [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html) +* [Clustergrammer2-Notebooks](https://github.com/ismms-himc/clustergrammer2-notebooks) GitHub repository + + +### 2,700 PBMC scRNA-seq +[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_2700_PBMC_scRNA-seq.ipynb?flush_cache=true) + +[](http://www.youtube.com/watch?v=BEPspcC7vIY) + +Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene expression across thousands of single cells. This method produces thousands of measurements (single cells) across thousands of dimensions (genes). This notebook uses Clustergrammer2 to interactively explore an example dataset measuring the gene expression of 2,700 PBMCs obtained from [10X Genomics](https://www.10xgenomics.com/resources/datasets/). Bulk gene expression signatures of cell types from [CIBERSORT](https://cibersort.stanford.edu/) were used to obtain a tentative cell type for each cell. Please see the video tutorial above for more information. + +# Clustergrammer2 Roadmap +Please see the project [Roadmap](https://github.com/ismms-himc/clustergrammer2/blob/master/ROADMAP.md) for information on where the project is heading. + +# Installation + +A typical installation requires the following commands to be run: + +```bash +pip install clustergrammer2 +jupyter nbextension install --py --sys-prefix clustergrammer2 +jupyter nbextension enable --py --sys-prefix clustergrammer2 +``` + +Optionally: --sys-prefix|--user|--system + +Or, if you use jupyterlab: + +```bash +pip install clustergrammer2 +jupyter labextension install @jupyter-widgets/jupyterlab-manager +``` + +### Embedding the widget into static HTML Notebooks + +```bash +jupyter nbconvert --to html notebook.ipynb +``` + +# Development + +During development run `npm run watch` for real time updates. When releasing a new version, first confirm that latest version of the front and back ends are working locally (check console logs, etc). + +#### Updating versions +Update the versions in the following files + +##### JavaScript + +* package.json +* widget.ts + +#### Python + +* _version.py +* example.py +* requirements.txt +* _frontend.py + + +#### Webpack + +Run the following commands to build the JavaScript bundle: + +```bash +npm run build +npm run build:nbextension +npm run build:labextension +``` + +Publish to npm using +```bash +npm publish +``` + +These instructions are based on the release instructions from the [jupyter-widgets/widget-ts-cookiecutterREADME](https://github.com/jupyter-widgets/widget-ts-cookiecutter). + +### Bundling the Python Package + +Next, bundle the python package using (optinally delete the old versions under `dist`) + +```bash +python setup.py sdist bdist_wheel +``` + +Then, upload the PYPI: + +```bash +twine upload dist/* +``` + +## Checklist after release + +After releasing a new version several things need to be checked to ensure proper widget functioning. + +### Check Package Managers + +- https://www.npmjs.com/package/clustergrammer2 (can be slow to update) +- https://pypi.org/project/clustergrammer2/ + +### Check HTML Embedding +- Run `jupyter nbconvert --to html introduction_nb.ipynb` (from the examples directory) to generate a static HTML and check that the latest widget is working (uses unpkg.com, like https://unpkg.com/clustergrammer2@0.5.18/dist/index.js) +- Check NBViewer using link to notebook on GitHub (e.g. https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2/blob/master/examples/introduction_nb.ipynb?flush_cache=true). Make sure to use the querystring `flush_cache=True` in the URL to ensure that NBVIewer re-runs nbconvert. + +### Check Cloud Services +- Check MyBinder + +### Note for Sublime Development +Use this in the where section to restrict search +``` +clustergrammer2/*.py,-*/build/* +``` + +# Contact +For issues and concerns please use the [issue tracker](https://github.com/ismms-himc/clustergrammer2/issues) or [gitter](https://gitter.im/clustergrammer2) discussion room. + + + + +%prep +%autosetup -n clustergrammer2-0.18.0 + +%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-clustergrammer2 -f filelist.lst +%dir %{python3_sitelib}/* + +%files help -f doclist.lst +%{_docdir}/* + +%changelog +* Wed May 10 2023 Python_Bot <Python_Bot@openeuler.org> - 0.18.0-1 +- Package Spec generated @@ -0,0 +1 @@ +e963e0f1f0e58fbdc5e968f3dd7e80e2 clustergrammer2-0.18.0.tar.gz |