276 validate reference documentation and tutorials (#302)

* add notebook description

* minor fixes

* update basic tutorials

* update notebooks

* minor fixes

* update notebooks

* remove unnecessary datasets

* final tutorial notebook

* remove progressbars and add pytest nbmake tags

* minor fixes visualisation

* add tutorial testing

* fix no GPU problem

* update reference for utils

* auto docstring API improvements

* update degree statistics

* improve docs clustering

* fix

* minor fixes

* docstrings for node similarities

* update DBGNN docstrings

* fixes docstrings netzschleuder

* fix pandas warnings

* fixes core

* improve core docstrings

* fix type annotation dbgnn

* add external packages to autoref for docstrings

* add external references

* fix multi-order model docstrings

* improve algorithm docs

* add karate plot

* fix numpy problems with indexmap

* add docstring testing

* fix linting and static type checking

* fix circular import

* speed up notebook tests

Author: M-Lampert

.github/workflows/docstring_testing.yml

@@ -0,0 +1,36 @@
+name: Docstring Testing
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+
+  pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      # Only run workflow if certain files have been changed.
+      - name: Get changed files
+        id: changed-files
+        uses: tj-actions/changed-files@v42
+        with:
+          files: |
+            .github/workflows/notebook_testing.yml
+            src/**
+            tests/**
+            pyproject.toml
+
+      - name: Setup packages
+        if: steps.changed-files.outputs.any_changed == 'true'
+        uses: ./.github/actions/setup
+
+      - name: Run tests
+        if: steps.changed-files.outputs.any_changed == 'true'
+        run: | # ignore centrality.py because __getattr__ gets overwritten which causes issues with pytest
+          pytest --doctest-modules src/pathpyG/ --ignore="src/pathpyG/algorithms/centrality.py" --no-cov

.github/workflows/linting.yml

@@ -26,7 +26,6 @@ jobs:
         run: pip install ruff
 
       - name: Run linting
-        continue-on-error: true
         run: ruff check .
 
   mypy:
@@ -42,6 +41,5 @@ jobs:
           full_install: false
 
       - name: Check type hints
-        continue-on-error: true
         run: |
           mypy src/pathpyG

.github/workflows/notebook_testing.yml

@@ -0,0 +1,36 @@
+name: Tutorial Notebook Testing
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+
+  pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v5
+
+      # Only run workflow if certain files have been changed.
+      - name: Get changed files
+        id: changed-files
+        uses: tj-actions/changed-files@v42
+        with:
+          files: |
+            .github/workflows/notebook_testing.yml
+            src/**
+            tests/**
+            pyproject.toml
+
+      - name: Setup packages
+        if: steps.changed-files.outputs.any_changed == 'true'
+        uses: ./.github/actions/setup
+
+      - name: Run tests
+        if: steps.changed-files.outputs.any_changed == 'true'
+        run: |
+          pytest --nbmake docs/tutorial/*ipynb --no-cov