Update docs (#14)

* Fix broken links, badges in docs, README

* Bump version so that PyPI and docs version coincide

* Remove deprecated deploy instructions

* Add dependabot

* Rename and update test workflow

* Rename and update publishing workflow

* Update readthedocs.yml

* Fix docstrings with missing, incorrect parameters

* Update examples notebook

* Add eyeglasses example to docs

* Include eyeglasses API in docs

.github/dependabot.yml

@@ -0,0 +1,9 @@
+# Set update schedule for GitHub Actions
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"

.github/workflows/build_and_deploy.yml

@@ -0,0 +1,52 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Build and Upload Python Package
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+  release:
+    types:
+      - published
+
+jobs:
+  build_wheel_and_sdist:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Build SDist and wheel
+        run: pipx run build
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: Packages
+          path: dist/*
+
+      - name: Check metadata
+        run: pipx run twine check dist/*
+
+  upload_pypi:
+    name: Upload release to PyPI
+    needs: [build_wheel_and_sdist]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/tadasets
+    permissions:
+      id-token: write
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: Packages
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/python-test.yml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python application
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest-cov
+          pip install -e ".[testing]"
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+          pytest --cov tadasets
+      - name: Upload coverage results
+        run: |
+          bash <(curl -s https://codecov.io/bash)

.readthedocs.yml

@@ -1,9 +1,14 @@
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
 python:
-   version: 3.7
-   install:
-      - method: pip
-        path: .
-        extra_requirements:
-            - docs
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

README.md

@@ -1,12 +1,11 @@
 [![PyPI version](https://badge.fury.io/py/tadasets.svg)](https://badge.fury.io/py/tadasets)
-[![Downloads](https://pypip.in/download/tadasets/badge.svg)](https://pypi.python.org/tadasets/)
-[![Build Status](https://travis-ci.org/scikit-tda/tadasets.svg?branch=master)](https://travis-ci.org/scikit-tda/tadasets)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/tadasets)
 [![Codecov](https://codecov.io/gh/scikit-tda/tadasets/branch/master/graph/badge.svg)](https://codecov.io/gh/scikit-tda/tadasets)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
 
-
-This package provides some nice utilities for creating and loading data sets that are useful for Topological Data Analysis. Currently, we provide various synthetic data sets with particular topological features.
-
+This package provides some nice utilities for creating and loading data sets
+that are useful for Topological Data Analysis. Currently, we provide various
+synthetic data sets with particular topological features.
 
 # Setup
 
@@ -28,7 +27,7 @@ The shape constructors are exposed in a functional interface, each returning a n
 
 Each shape can be embedded in arbitrary ambient dimension by supplying the `ambient` argument. Additionally, noise can be added to the shape through the `noise` argument.
 
-```
+```python
 import tadasets
 
 torus = tadasets.torus(n=2000, c=2, a=1, ambient=200, noise=0.2)
@@ -38,13 +37,10 @@ infty_sign = tadasets.infty_sign(n=3000, noise=0.1)
 eyeglasses = tadasets.eyeglasses(n=1000, r1=1, r2=2, neck_size=.5, noise=0.1, ambient=10)
 ```
 
-Contributions
-------------------
+## Contributions
 
 We welcome contributions of all shapes and sizes. There are lots of opportunities for potential projects, so please get in touch if you would like to help out. Everything from an implementation of your favorite distance, notebooks, examples, and documentation are all equally valuable so please don’t feel you can’t contribute.
 
-If you have ideas for new shapes or features, please do suggest them in an issue and submit a pull request! 
+If you have ideas for new shapes or features, please do suggest them in an issue and submit a pull request!
 
 To contribute please fork the project make your changes and submit a pull request. We will do our best to work through any issues with you and get your code merged into the main branch.
-
-

docs/index.rst

@@ -1,10 +1,4 @@
-.. tadasets documentation master file, created by
-   sphinx-quickstart on Sun Jul 22 20:37:23 2018.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-
-|PyPI version| |Downloads| |License: MIT| |Travis-CI| |Codecov| 
+|PyPI version| |Downloads| |Codecov| |License: MIT|
 
 This package provides some nice utilities for creating and loading data sets that are useful for Topological Data Analysis. Currently, we provide various synthetic data sets with particular topological features.
 
@@ -26,8 +20,10 @@ The shape constructors are exposed in a functional interface, each returning a n
 
 - torus
 - d-sphere
+- sphere
 - swiss roll
 - infinity sign
+- eyeglasses
 
 Each shape can be embedded in arbitrary ambient dimension by supplying the :code:`ambient` argument. Additionally, noise can be added to the shape through the :code:`noise` argument.
 
@@ -38,7 +34,9 @@ Each shape can be embedded in arbitrary ambient dimension by supplying the :code
     torus = tadasets.torus(n=2000, c=2, a=1, ambient=200, noise=0.2)
     swiss_roll = tadasets.swiss_roll(n=2000, r=4, ambient=10, noise=1.2)
     dsphere = tadasets.dsphere(n=1000, d=12, r=3.14, ambient=14, noise=0.14)
+    sphere = tadasets.sphere(n=500,seed=42)
     infty_sign = tadasets.infty_sign(n=3000, noise=0.1)
+    eyeglasses = tadasets.eyeglasses(n=670,r1=10.0,r2=5.0)
 
 Contributions
 ------------------
@@ -59,12 +57,10 @@ To contribute please fork the project make your changes and submit a pull reques
     reference/index
     notebooks/Examples
 
-.. |Downloads| image:: https://pypip.in/download/tadasets/badge.svg
+.. |Downloads| image:: https://img.shields.io/pypi/dm/tadasets
    :target: https://pypi.python.org/tadasets/
 .. |PyPI version| image:: https://badge.fury.io/py/tadasets.svg
    :target: https://badge.fury.io/py/tadasets
-.. |Travis-CI| image:: https://travis-ci.org/scikit-tda/tadasets.svg?branch=master
-    :target: https://travis-ci.org/scikit-tda/tadasets
 .. |Codecov| image:: https://codecov.io/gh/scikit-tda/tadasets/branch/master/graph/badge.svg
     :target: https://codecov.io/gh/scikit-tda/tadasets
 .. |License: MIT| image:: https://img.shields.io/badge/License-MIT-yellow.svg

docs/reference/index.rst

@@ -10,3 +10,4 @@ API Reference
     tadasets.sphere
     tadasets.swiss_roll
     tadasets.infty_sign
+    tadasets.eyeglasses

tadasets/_version.py

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.2.0"