Update docs build

.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/kmapper
+    permissions:
+      id-token: write
+    if: github.event_name == 'release' && github.event.action == 'published'
+    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: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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 kmapper
+      - 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

RELEASE.md

@@ -1,11 +1,16 @@
 # Release log
 
-
 ## Unreleased
 
 ### Added
+
 - ability to live-update the min-intersection threshold for edges on the d3 vis (#231)
 
+### Fixed/Changed
+
+- Update docs and sphinx-gallery to build again.
+- Update CI/CD runners to test modern versions of python; drop python 3.7 compatibility.
+- Change visual tests to use built-in `int` type rather than `np.uint8`.
 
 ## 2.0.1
 
@@ -22,7 +27,6 @@
   during an AND or OR search query again directly reflects the number of items within the node. (#227)
 - The default search mode is now AND -- because that's the expected behavior, because that's how the google works (#227)
 
-
 ## 2.0.0
 
 ### Visualization
@@ -46,7 +50,7 @@ All of the below changes apply to kmapper's D3 html visualization.
 - multiple `color_values` arrays can be passed, and switched between interactively in the display.
 - the node color function can be specified, as a string, to any function available on the numpy base class (e.g.,
   'mean', 'median', 'max', 'min'. (Before, the only available function was `np.mean`.
-    - Multiple node color functions can be specified, and toggled between interactively in the display.
+  - Multiple node color functions can be specified, and toggled between interactively in the display.
 - The toolbar display now uses css flexbox, which avoids overlap-problems on smaller viewports.
 
 ### Kmapper
@@ -55,63 +59,73 @@ All of the below changes apply to kmapper's D3 html visualization.
 - only support python >= 3.6
 
 ## 1.4.1
+
 - New CI/CD pipeline
 
 ## 1.4
+
 - More flexible visualization coloring (PR 190)
 - Better support for sparse matrices (PR 189)
 - Better support for precomputed distance matrices (PR 184)
 
 ## 1.3.x
+
 - A series of releases to support JOSS submission
 
 ## 1.3.0 (October 12, 2019)
+
 - JOSS Release -- final revision
 - Allow sparse matrices in `map` function (PR #163)
 - Use sphinx-gallery for documentation examples (#164)
 - Removed mutable arguments (#165)
 
 ## 1.2.0 (Feb 18, 2019)
+
 - New implementation of the cover API makes it consistent with the literature (your % overlap will probably have to be decreased when updating).
 - New documentation website (kepler-mapper.scikit-tda.org).
 
 ## 1.1.6 (Nov 8, 2018)
+
 - Plotly visualization interface.
 - Networkx adapter
 - Bug fixes
 - Scikit-tda integration
 
 ## 1.1.2
+
 - Bug fix, setup.py did not include static directory so installation visualizations did not work when installed from pypi.
 - Add Jupyter notebook support
 
 ## 1.1
+
 - Massive visualization upgrades
 - Separation of HTML, JS, CSS, and Python code
 - New nerves and covers API
 - Documentation site
 
 ## 1.0.1
+
 - Convert versioning scheme to major.minor.micro
 - Restructure library to be compatible with PyPi installation
 - Minor bug fixes
 - Include preliminary unit test suite
 - Refactor, extract helper classes and helper functions
 
-
 # Release log - Pre-alpha
 
 ## v00009
 
 ## v00008
 
 ## v00007
+
 - Add L2^Norm Lens
 - Add Winsconsin Breast Cancer Data Anomaly Detection Example
 - Fixed bug: k-means with set number of clusters higher than min_cluster_samples
 - Add self.inverse_X for new future feature: transforming on unseen data.
 
 ## v00006
+
 - Removed link_local functionality
 - Halved the number of edges drawn (no two-way edges)
 - Added support for clustering on the inverse image
@@ -121,20 +135,23 @@ All of the below changes apply to kmapper's D3 html visualization.
 - Added 7 projections/lenses from statistics
 
 ## v00005
+
 - Made Python 3 compatible
 - Ability to turn off title, meta and tooltips
 - Ability to set the window height and width of HTML output
 - Added basic support for another color function: average signal
 - De-emphasized link_local functionality, since its current implementation is no good.
 
 ## v00004
+
 - Added dimensionality reduction
 - Added "digits" case study
 - changed fit to fit_transform and return of data
 - added tooltips
 - added support for custom tooltips
 
 ## v00003
+
 - Refactored dimension index to use a list of arbitrary dimensions
 - Improved verbosity
 - Added levels of verbosity
@@ -144,6 +161,7 @@ All of the below changes apply to kmapper's D3 html visualization.
 - Added a gallery in the example directory
 
 ## v00002
+
 - Added a multi-dimensional mode: use all dimensions.
 - Added case study: 3D point cloud data for animals
 - Added case study: Make circles
@@ -154,6 +172,7 @@ All of the below changes apply to kmapper's D3 html visualization.
 - Added release log
 
 ## v00001
+
 - Wrote class
 - Wrote documentation
 - Added license

docs/_static/gallery-override.css

@@ -1,15 +1,18 @@
 .sphx-glr-thumbcontainer {
-    min-height: 280px !important;
-    margin: 20px !important;
+  min-height: 320px !important;
+  margin: 20px !important;
 }
 .sphx-glr-thumbcontainer .figure {
-    width: 280px !important;
+  width: 320px !important;
 }
 .sphx-glr-thumbcontainer img {
-    max-height: 280px !important;
-    width: 280px !important;
-    max-width: 280px;
+  max-height: 250px !important;
+  width: 250px !important;
+  max-width: 320px;
 }
 .sphx-glr-thumbcontainer a.internal {
-    padding: 220px 10px 0 !important;
+  padding: 220px 10px 0 !important;
+}
+.sphx-glr-thumbnails {
+  grid-template-columns: repeat(auto-fill, minmax(320px, 1fr));
 }