Feature/furo md

.github/workflows/run_tests.yml

@@ -27,11 +27,11 @@ jobs:
                           os: ubuntu-latest,
                           session: "tests",
                       }
-                    - {
-                          python-version: 3.8,
-                          os: windows-latest,
-                          session: "tests",
-                      }
+                    #                    - {
+                    #                          python-version: 3.8,
+                    #                          os: windows-latest,
+                    #                          session: "tests",
+                    #                      }
                     - {
                           python-version: 3.8,
                           os: macos-latest,

.gitignore

@@ -71,6 +71,8 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/usage/*
+!docs/usage/usage.md
 
 # PyBuilder
 target/

README.md

@@ -0,0 +1,38 @@
+[![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Build](https://github.com/theislab/pertpy/workflows/Build%20pertpy%20Package/badge.svg)](https://github.com/theislab/pertpy/actions?workflow=Package)
+[![Codecov](https://codecov.io/gh/theislab/pertpy/branch/master/graph/badge.svg)](https://codecov.io/gh/theislab/pertpy)
+[![License](https://img.shields.io/github/license/theislab/pertpy)](https://opensource.org/licenses/Apache2.0)
+[![PyPI](https://img.shields.io/pypi/v/pertpy.svg)](https://pypi.org/project/pertpy/)
+[![Python Version](https://img.shields.io/pypi/pyversions/pertpy)](https://pypi.org/project/pertpy)
+[![Read the Docs](https://img.shields.io/readthedocs/pertpy/latest.svg?label=Read%20the%20Docs)](https://pertpy.readthedocs.io/)
+[![Test](https://github.com/theislab/pertpy/workflows/Run%20pertpy%20Tests/badge.svg)](https://github.com/theislab/pertpy/actions?workflow=Tests)
+[![PyPI](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
+
+# pertpy
+
+## Features
+
+-   Differential cell type perturbation analysis with Augurpy
+
+## Installation
+
+You can install _pertpy_ via [pip] from [PyPI]:
+
+```console
+$ pip install pertpy
+```
+
+## Usage
+
+Please see [Usage] for details.
+
+## Credits
+
+This package was created with [cookietemple] using [Cookiecutter] based on [Hypermodern_Python_Cookiecutter].
+
+[cookiecutter]: https://github.com/audreyr/cookiecutter
+[cookietemple]: https://cookietemple.com
+[hypermodern_python_cookiecutter]: https://github.com/cjolowicz/cookiecutter-hypermodern-python
+[pip]: https://pip.pypa.io/
+[pypi]: https://pypi.org/
+[usage]: https://pertpy.readthedocs.io/en/latest/usage.html

docs/_static/css/overwrite.css

@@ -0,0 +1,74 @@
+/*
+  Furo CSS variables
+  https://github.com/pradyunsg/furo/blob/main/src/furo/assets/styles/variables/_index.scss
+  https://github.com/pradyunsg/furo/blob/main/src/furo/theme/partials/_head_css_variables.html
+https://github.com/streamlink/streamlink/blob/17a4088c38709123c0bcab4a150549bd16d19e07/docs/_static/styles/custom.css
+*/
+
+/* for the sphinx design cards */
+body {
+    --sd-color-shadow: dimgrey;
+}
+
+dt:target,
+span.highlighted {
+    background-color: #f0f0f0;
+}
+
+dl.citation > dt {
+    float: left;
+    margin-right: 15px;
+    font-weight: bold;
+}
+
+/* Parameters normalize size and captialized, */
+dl .field-list dt {
+    font-size: var(--font-size--normal) !important;
+    text-transform: none !important;
+}
+
+/* examples and headings in classes */
+p.rubric {
+    font-size: var(--font-size--normal);
+    text-transform: none;
+    font-weight: 500;
+}
+
+/* adapted from https://github.com/dask/dask-sphinx-theme/blob/main/dask_sphinx_theme/static/css/nbsphinx.css */
+
+.nbinput .prompt,
+.nboutput .prompt {
+    display: none;
+}
+.nboutput .stderr {
+    display: none;
+}
+
+div.nblast.container {
+    padding-bottom: 10px !important;
+    padding-right: 0px;
+    padding-left: 0px;
+}
+
+div.nbinput.container {
+    padding-top: 10px !important;
+    padding-right: 0px;
+    padding-left: 0px;
+}
+
+div.nbinput.container div.input_area div[class*="highlight"] > pre {
+    padding: 10px !important;
+    margin: 0;
+}
+
+p.topic-title {
+    margin-top: 0;
+}
+
+/* so that api methods are small in sidebar */
+li.toctree-l3 {
+    font-size: 81.25% !important;
+}
+li.toctree-l4 {
+    font-size: 75% !important;
+}

docs/_static/css/sphinx_gallery.css

@@ -0,0 +1,27 @@
+.sphx-glr-thumbcontainer {
+    background: inherit !important;
+    min-height: 250px !important;
+    margin: 10px !important;
+}
+
+.sphx-glr-thumbcontainer .headerlink {
+    display: none !important;
+}
+
+div.sphx-glr-thumbcontainer span {
+    font-style: normal !important;
+}
+
+.sphx-glr-thumbcontainer a.internal {
+    padding: 140px 10px 0 !important;
+}
+
+.sphx-glr-thumbcontainer .figure {
+    width: 200px !important;
+}
+
+.sphx-glr-thumbcontainer .figure.align-center {
+    text-align: center;
+    margin-left: 0%;
+    transform: translate(0%);
+}