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

@@ -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

.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

.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

MANIFEST.in

@@ -1,5 +1,5 @@
 include MANIFEST.in
-include README.rst
+include README.md
 include CHANGES.rst
 include LICENSE
 include setup.py

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.