From e1f6c580c7c5170e1aa2d9cd6eff6ca3b6be1bfe Mon Sep 17 00:00:00 2001 From: Brendt Wohlberg Date: Mon, 29 Apr 2024 16:12:16 -0600 Subject: [PATCH] Fix badge layout in main README (#516) * Try to change image layout * Undo changes * Add md version * Attempt to remove newlines * Add newline * Add newlines * Remove rst version * Update manifest * Move badge * Layout experiment * Remove space between rows of badges * Update action version --- .github/workflows/pytest_macos.yml | 2 +- .github/workflows/pytest_ubuntu.yml | 2 +- .github/workflows/test_examples.yml | 2 +- MANIFEST.in | 2 +- README.md | 70 ++++++++++++++++++++++ README.rst | 91 ----------------------------- 6 files changed, 74 insertions(+), 95 deletions(-) create mode 100644 README.md delete mode 100644 README.rst diff --git a/.github/workflows/pytest_macos.yml b/.github/workflows/pytest_macos.yml index b43d700b9..25b85b256 100644 --- a/.github/workflows/pytest_macos.yml +++ b/.github/workflows/pytest_macos.yml @@ -29,7 +29,7 @@ jobs: submodules: recursive # Set up conda/mamba environment - name: Set up mambaforge - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: miniforge-variant: Mambaforge miniforge-version: latest diff --git a/.github/workflows/pytest_ubuntu.yml b/.github/workflows/pytest_ubuntu.yml index 37127efbd..617d914f8 100644 --- a/.github/workflows/pytest_ubuntu.yml +++ b/.github/workflows/pytest_ubuntu.yml @@ -29,7 +29,7 @@ jobs: submodules: recursive # Set up conda/mamba environment - name: Set up mambaforge - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: miniforge-variant: Mambaforge miniforge-version: latest diff --git a/.github/workflows/test_examples.yml b/.github/workflows/test_examples.yml index 1f2d18c8f..aba9ebc88 100644 --- a/.github/workflows/test_examples.yml +++ b/.github/workflows/test_examples.yml @@ -27,7 +27,7 @@ jobs: submodules: recursive # Set up conda/mamba environment - name: Set up mambaforge - uses: conda-incubator/setup-miniconda@v2 + uses: conda-incubator/setup-miniconda@v3 with: miniforge-variant: Mambaforge miniforge-version: latest diff --git a/MANIFEST.in b/MANIFEST.in index c2b2ff271..9cbc39a62 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,5 +1,5 @@ include MANIFEST.in -include README.rst +include README.md include CHANGES.rst include LICENSE include setup.py diff --git a/README.md b/README.md new file mode 100644 index 000000000..e1caf27d4 --- /dev/null +++ b/README.md @@ -0,0 +1,70 @@ +[![Python \>= 3.8](https://img.shields.io/badge/python-3.8+-green.svg)](https://www.python.org/) +[![Package License](https://img.shields.io/github/license/lanl/scico.svg)](https://github.com/lanl/scico/blob/main/LICENSE) +[![Code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![Documentation Status](https://readthedocs.org/projects/scico/badge/?version=latest)](http://scico.readthedocs.io/en/latest/?badge=latest) +[![JOSS paper](https://joss.theoj.org/papers/10.21105/joss.04722/status.svg)](https://doi.org/10.21105/joss.04722)\ +[![Lint status](https://github.com/lanl/scico/actions/workflows/lint.yml/badge.svg)](https://github.com/lanl/scico/actions/workflows/lint.yml) +[![Test status](https://github.com/lanl/scico/actions/workflows/pytest_ubuntu.yml/badge.svg)](https://github.com/lanl/scico/actions/workflows/pytest_ubuntu.yml) +[![Test coverage](https://codecov.io/gh/lanl/scico/branch/main/graph/badge.svg?token=wQimmjnzFf)](https://codecov.io/gh/lanl/scico) +[![CodeFactor](https://www.codefactor.io/repository/github/lanl/scico/badge/main)](https://www.codefactor.io/repository/github/lanl/scico/overview/main)\ +[![PyPI package version](https://badge.fury.io/py/scico.svg)](https://badge.fury.io/py/scico) +[![PyPI download statistics](https://static.pepy.tech/personalized-badge/scico?period=month&left_color=grey&right_color=brightgreen)](https://pepy.tech/project/scico) +[![Conda Forge Release](https://img.shields.io/conda/vn/conda-forge/scico.svg)](https://anaconda.org/conda-forge/scico)\ +[![View notebooks at nbviewer](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/lanl/scico-data/tree/main/notebooks/index.ipynb) +[![Run notebooks on binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/lanl/scico-data/binder?labpath=notebooks%2Findex.ipynb) +[![Run notebooks on google colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/lanl/scico-data/blob/colab/notebooks/index.ipynb) + + +# Scientific Computational Imaging Code (SCICO) + +SCICO is a Python package for solving the inverse problems that arise in +scientific imaging applications. Its primary focus is providing methods +for solving ill-posed inverse problems by using an appropriate prior +model of the reconstruction space. SCICO includes a growing suite of +operators, cost functionals, regularizers, and optimization routines +that may be combined to solve a wide range of problems, and is designed +so that it is easy to add new building blocks. SCICO is built on top of +[JAX](https://github.com/google/jax), which provides features such as +automatic gradient calculation and GPU acceleration. + +[Documentation](https://scico.rtfd.io/) is available online. If you use +this software for published work, please cite the corresponding [JOSS +Paper](https://doi.org/10.21105/joss.04722) (see bibtex entry +`balke-2022-scico` in `docs/source/references.bib`). + +# Installation + +See the [online +documentation](https://scico.rtfd.io/en/latest/install.html) for +installation instructions. + +# Usage Examples + +Usage examples are available as Python scripts and Jupyter Notebooks. +Example scripts are located in `examples/scripts`. The corresponding +Jupyter Notebooks are provided in the +[scico-data](https://github.com/lanl/scico-data) submodule and symlinked +to `examples/notebooks`. They are also viewable on +[GitHub](https://github.com/lanl/scico-data/tree/main/notebooks) or +[nbviewer](https://nbviewer.jupyter.org/github/lanl/scico-data/tree/main/notebooks/index.ipynb), +or can be run online by +[binder](https://mybinder.org/v2/gh/lanl/scico-data/binder?labpath=notebooks%2Findex.ipynb). + +# License + +SCICO is distributed as open-source software under a BSD 3-Clause +License (see the `LICENSE` file for details). + +LANL open source approval reference C20091. + +\(c\) 2020-2024. Triad National Security, LLC. All rights reserved. This +program was produced under U.S. Government contract 89233218CNA000001 +for Los Alamos National Laboratory (LANL), which is operated by Triad +National Security, LLC for the U.S. Department of Energy/National +Nuclear Security Administration. All rights in the program are reserved +by Triad National Security, LLC, and the U.S. Department of +Energy/National Nuclear Security Administration. The Government has +granted for itself and others acting on its behalf a nonexclusive, +paid-up, irrevocable worldwide license in this material to reproduce, +prepare derivative works, distribute copies to the public, perform +publicly and display publicly, and to permit others to do so. diff --git a/README.rst b/README.rst deleted file mode 100644 index 53a31df75..000000000 --- a/README.rst +++ /dev/null @@ -1,91 +0,0 @@ -.. image:: https://img.shields.io/badge/python-3.8+-green.svg - :target: https://www.python.org/ - :alt: Python >= 3.8 - -.. image:: https://img.shields.io/github/license/lanl/scico.svg - :target: https://github.com/lanl/scico/blob/main/LICENSE - :alt: Package License - -.. image:: https://img.shields.io/badge/code%20style-black-000000.svg - :target: https://github.com/psf/black - :alt: Code style - -.. image:: https://readthedocs.org/projects/scico/badge/?version=latest - :target: http://scico.readthedocs.io/en/latest/?badge=latest - :alt: Documentation Status - -.. image:: https://github.com/lanl/scico/actions/workflows/lint.yml/badge.svg - :target: https://github.com/lanl/scico/actions/workflows/lint.yml - :alt: Lint status - -.. image:: https://github.com/lanl/scico/actions/workflows/pytest_ubuntu.yml/badge.svg - :target: https://github.com/lanl/scico/actions/workflows/pytest_ubuntu.yml - :alt: Test status - -.. image:: https://codecov.io/gh/lanl/scico/branch/main/graph/badge.svg?token=wQimmjnzFf - :target: https://codecov.io/gh/lanl/scico - :alt: Test coverage - -.. image:: https://www.codefactor.io/repository/github/lanl/scico/badge/main - :target: https://www.codefactor.io/repository/github/lanl/scico/overview/main - :alt: CodeFactor - -.. image:: https://badge.fury.io/py/scico.svg - :target: https://badge.fury.io/py/scico - :alt: PyPI package version - -.. image:: https://static.pepy.tech/personalized-badge/scico?period=month&left_color=grey&right_color=brightgreen - :target: https://pepy.tech/project/scico - :alt: PyPI download statistics - -.. image:: https://img.shields.io/conda/vn/conda-forge/scico.svg - :target: https://anaconda.org/conda-forge/scico - :alt: Conda Forge Release - -.. image:: https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg - :target: https://nbviewer.jupyter.org/github/lanl/scico-data/tree/main/notebooks/index.ipynb - :alt: View notebooks at nbviewer - -.. image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/lanl/scico-data/binder?labpath=notebooks%2Findex.ipynb - :alt: Run notebooks on binder - -.. image:: https://colab.research.google.com/assets/colab-badge.svg - :target: https://colab.research.google.com/github/lanl/scico-data/blob/colab/notebooks/index.ipynb - :alt: Run notebooks on google colab - -.. image:: https://joss.theoj.org/papers/10.21105/joss.04722/status.svg - :target: https://doi.org/10.21105/joss.04722 - :alt: JOSS paper - - - -Scientific Computational Imaging Code (SCICO) -============================================= - -SCICO is a Python package for solving the inverse problems that arise in scientific imaging applications. Its primary focus is providing methods for solving ill-posed inverse problems by using an appropriate prior model of the reconstruction space. SCICO includes a growing suite of operators, cost functionals, regularizers, and optimization routines that may be combined to solve a wide range of problems, and is designed so that it is easy to add new building blocks. SCICO is built on top of `JAX `_, which provides features such as automatic gradient calculation and GPU acceleration. - -`Documentation `_ is available online. If you use this software for published work, please cite the corresponding `JOSS Paper `_ (see bibtex entry ``balke-2022-scico`` in ``docs/source/references.bib``). - - -Installation -============ - -See the `online documentation `_ for installation instructions. - - -Usage Examples -============== - -Usage examples are available as Python scripts and Jupyter Notebooks. Example scripts are located in ``examples/scripts``. The corresponding Jupyter Notebooks are provided in the `scico-data `_ submodule and symlinked to ``examples/notebooks``. They are also viewable on `GitHub `_ or `nbviewer `_, or can be run online by `binder `_. - - -License -======= - -SCICO is distributed as open-source software under a BSD 3-Clause License (see the ``LICENSE`` file for details). - -LANL open source approval reference C20091. - -(c) 2020-2024. Triad National Security, LLC. All rights reserved. -This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government has granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.