Fix failing build for documentation (#29)

* Add yaml.SafeLoader to conf.py

* Update python versions in CI

* Update tests

* Update readthedocs yml

* Fix req path in yml

* Remove requirements from readthedoc build

* Update badges, doc notebook

* Formatting update to notebook

.github/workflows/python-app.yml

@@ -5,37 +5,37 @@ name: Python application
 
 on:
   push:
-    branches: [ master ]
+    branches: [master]
   pull_request:
-    branches: [ master ]
+    branches: [master]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
+        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==19.3.1
-        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 sktda
-    - name: Upload coverage results
-      run: |
-        bash <(curl -s https://codecov.io/bash)
+      - 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 sktda
+      - name: Upload coverage results
+        run: |
+          bash <(curl -s https://codecov.io/bash)

.readthedocs.yml

@@ -1,9 +1,13 @@
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
 python:
-   version: 3.7
-   install:
-      - method: pip
-        path: .
-        extra_requirements:
-            - docs
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

docs/conf.py

@@ -1,36 +1,39 @@
 # -*- coding: utf-8 -*-
 import os
 import sys
-sys.path.insert(0, os.path.abspath('.'))
-sys.path.append(os.path.abspath('extensions'))
+import yaml
+
+sys.path.insert(0, os.path.abspath("."))
+sys.path.append(os.path.abspath("extensions"))
 from sktda import __version__
 from sktda_docs_config import *
 
-project = 'scikit-tda'
-copyright = '2019, Nathaniel Saul'
-author = 'Nathaniel Saul'
+project = "scikit-tda"
+copyright = "2019, Nathaniel Saul"
+author = "Nathaniel Saul"
 version = __version__
 release = __version__
 
-html_theme_options.update({
-  # Google Analytics info
-  'ga_ua': 'UA-124965309-1',
-  'ga_domain': '',
-  'gh_url': 'scikit-tda'
-})
+html_theme_options.update(
+    {
+        # Google Analytics info
+        "ga_ua": "UA-124965309-1",
+        "ga_domain": "",
+        "gh_url": "scikit-tda",
+    }
+)
 
 html_short_title = project
-htmlhelp_basename = 'scikit-tdadoc'
+htmlhelp_basename = "scikit-tdadoc"
 
 html_context = {}
 
 # Setup library data
-import yaml
-with open('data/libraries.yaml', 'r') as f:
-    libraries = yaml.load(f)
+with open("data/libraries.yaml", "r") as f:
+    libraries = yaml.load(f, Loader=yaml.SafeLoader)
 
 
 # import pdb; pdb.set_trace()
-html_context['libraries'] = libraries
+html_context["libraries"] = libraries
 
-extensions.append('rstjinja')
+extensions.append("rstjinja")

docs/index.rst

@@ -83,8 +83,8 @@ This package is licensed with the MIT license.
   :target: https://zenodo.org/badge/latestdoi/129452930
 .. |Pypi| image:: https://badge.fury.io/py/scikit-tda.svg
   :target: https://badge.fury.io/py/scikit-tda
-.. |Downloads| image:: https://pypip.in/download/scikit-tda/badge.svg
-  :target: https://pypi.python.org/scikit-tda/sktda/
+.. |Downloads| image:: https://img.shields.io/pypi/dm/scikit-tda
+  :target: https://pypi.org/project/scikit-tda/
 
 .. _github: https://github.com/scikit-tda
 .. _twitter: https://twitter.com/scikit_tda

docs/libraries.rst

@@ -11,7 +11,10 @@ To install the entire suite
 
   >>> pip install scikit-tda
 
-Below, you'll find information on each individual package, along with resources to explore more. Each package is well tested, well documented, easy to install, and open for contributions. If you find any bugs in the code or documentation, please let us know on `github <https://github.com/scikit-tda>`_
+Below, you'll find information on each individual package, along with resources
+to explore more. Each package is well tested, well documented, easy to install,
+and open for contributions. If you find any bugs in the code or documentation,
+please let us know on `github <https://github.com/scikit-tda>`_.
 
 
 {% for library in libraries %}
@@ -32,10 +35,8 @@ Below, you'll find information on each individual package, along with resources
 
 .. image:: https://badge.fury.io/py/{{ library["pypi" ]}}.svg
   :target: https://badge.fury.io/py/{{ library["pypi" ]}}
-.. image:: https://pypip.in/download/{{ library["pypi"] }}/badge.svg
+.. image:: https://img.shields.io/pypi/dm/{{ library["pypi"] }}
   :target: https://pypi.python.org/pypi/{{ library["pypi"] }}/
-.. image:: https://travis-ci.org/scikit-tda/{{ library["repo"] }}.svg?branch=master
-  :target: https://travis-ci.org/scikit-tda/{{ library["repo"] }}
 .. image:: https://codecov.io/gh/scikit-tda/{{ library["repo"] }}/branch/master/graph/badge.svg
   :target: https://codecov.io/gh/scikit-tda/{{ library["repo"] }}
 .. image:: https://img.shields.io/badge/License-MIT-yellow.svg
@@ -54,7 +55,10 @@ Below, you'll find information on each individual package, along with resources
 
     >>> pip install {{ library["pypi"] }}
         
-  Check out complete documentation for {{ library["title"] }} at `{{ library["url"] }} <https://{{ library["url"] }}>`_ and the source code at `github.com/scikit-tda/{{ library["repo"] }} <https://github.com/scikit-tda/{{ library["repo"] }}>`_
+  Check out complete documentation for {{ library["title"] }} at `{{
+  library["url"] }} <https://{{ library["url"] }}>`_ and the source code at
+  `github.com/scikit-tda/{{ library["repo"] }}
+  <https://github.com/scikit-tda/{{ library["repo"] }}>`_.
 
 
 {% endfor %}

sktda/__init__.py

@@ -1,6 +1,6 @@
-from ripser import *
-from persim import *
+import ripser
+import persim
 
 import tadasets
 
-from ._version import __version__
+from ._version import __version__

test/test_sktda.py

@@ -7,16 +7,22 @@
 
 import sktda
 
+
 def test_ripser():
     assert "ripser" in dir(sktda)
-    assert callable(sktda.ripser)
+    assert callable(sktda.ripser.ripser)
+
 
 def test_persim():
-    assert "PersImage" in dir(sktda)
-    assert "heat" in dir(sktda)
-    assert "sliced_wasserstein" in dir(sktda)
-    assert "plot_diagrams" in dir(sktda)
+    assert "persim" in dir(sktda)
+    assert "PersImage" in dir(sktda.persim)
+    assert "heat" in dir(sktda.persim)
+    assert "sliced_wasserstein" in dir(sktda.persim)
+    assert "plot_diagrams" in dir(sktda.persim)
+    assert "landscapes" in dir(sktda.persim)
+
 
 def test_tadasets():
+    assert "tadasets" in dir(sktda)
     assert "dsphere" in dir(sktda.tadasets)
     assert "swiss_roll" in dir(sktda.tadasets)