Improved github actions

.github/workflows/sphinx_autodoc.yaml

@@ -1,57 +1,48 @@
-name: Sphinx build docs on push
+name: Build and Deploy Documentation
 on:
--   push
+  push:
+    branches:
+      - main  # or your default branch name
 
 jobs:
-    build:
-        runs-on: ubuntu-latest
-        steps:
-        -   name: Check out main
-            uses: actions/checkout@main
-        -   name: Setup Python
-            uses: actions/setup-python@v2
-            with:
-                python-version: 3.10.13
-        -   name: Install pandoc
-            run: sudo apt-get install -y pandoc
-        -   name: Load cached Poetry installation
-            uses: actions/cache@v2
-            with:
-                path: ~/.local
-                key: poetry-0
-        -   name: Install Poetry
-            uses: snok/install-poetry@v1
-            with:
-                virtualenvs-create: true
-                virtualenvs-in-project: true
-                installer-parallel: true
-        -   name: Poetry disable modern-installation
-            run: poetry config installer.modern-installation false
-        -   name: Load cached venv
-            id: cached-poetry-dependencies
-            uses: actions/cache@v2
-            with:
-                path: .venv
-                key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
-        -   name: Install dependencies
-            if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-            run: poetry install --no-interaction --no-root
-        -   name: Install library
-            run: poetry install --no-interaction
-        -   name: Build documentation
-            run: poetry run make html --directory docs/
-        -   name: Commit files
-            run: |
-                git config --local user.email "action@github.com"
-                git config --local user.name "GitHub Action"
-                touch docs/_build/html/.nojekyll
-                git add -f docs/_build/
-                git commit -m "Update autodoc" -a
-    # using https://github.com/marketplace/actions/push-git-subdirectory-as-branch
-        -   name: Deploy
-            uses: s0/git-publish-subdir-action@develop
-            env:
-                REPO: self
-                BRANCH: gh-pages
-                FOLDER: docs/_build/html
-                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.10.13
+    - name: Install pandoc
+      run: sudo apt-get install -y pandoc
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+    - name: Install dependencies
+      run: |
+        poetry config virtualenvs.create false
+        poetry install --no-interaction
+    - name: Build documentation
+      run: |
+        cd docs
+        poetry run make html
+    -   name: Debug information
+        run: |
+            echo "Current directory:"
+            pwd
+            echo "Directory contents:"
+            ls -R
+            echo "Docs directory contents:"
+            ls -R docs
+
+    -   name: List contents of build directory
+        run: ls -R docs/_build/html
+
+    -   name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+            github_token: ${{ secrets.GITHUB_TOKEN }}
+            publish_dir: ./docs/_build/html
+            force_orphan: true

.github/workflows/test.yaml

@@ -1,57 +1,46 @@
 name: Test
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
 
 jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.9', '3.10']
+        os: [ubuntu-latest, macos-latest]
 
-    test:
-        runs-on: ${{ matrix.os }}
-        defaults:
-            run:
-                shell: bash -e {0}
+    steps:
+    - uses: actions/checkout@v2
 
-        strategy:
-            fail-fast: false
-            matrix:
-                python: [3.8, 3.9, 3.10]
-                os: [ubuntu-latest, macos-latest]
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
 
-        env:
-            OS: ${{ matrix.os }}
-            PYTHON: ${{ matrix.python }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install .[dev,test]
+        pip install pytest pytest-cov codecov
 
-        steps:
-        -   uses: actions/checkout@v2
-        -   name: Set up Python ${{ matrix.python }}
-            uses: actions/setup-python@v4
-            with:
-                python-version: ${{ matrix.python }}
-                cache: pip
-                cache-dependency-path: '**/pyproject.toml'
+    - name: Run tests
+      env:
+        MPLBACKEND: agg
+        PLATFORM: ${{ matrix.os }}
+      run: |
+        pytest -v --cov=./ --cov-report=xml
 
-        -   name: Install test dependencies
-            run: |
-                python -m pip install --upgrade pip wheel
-                pip install codecov
-        -   name: Install dependencies
-            run: |
-                pip install ".[dev,test]"
-        -   name: Install pip dependencies
-            run: |
-                python -m pip install --upgrade pip
-        -   name: Test
-            env:
-                MPLBACKEND: agg
-                PLATFORM: ${{ matrix.os }}
-                DISPLAY: :42
-            run: |
-                pytest -v --cov --color=yes
-        -   name: Upload coverage
-            env:
-                CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
-            run: |
-                codecov --no-color --required --flags unittests
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        file: ./coverage.xml
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: true

.readthedocs.yaml

@@ -10,3 +10,6 @@ python:
   - method: pip
     path: .
   - requirements: docs/src/requirements.txt
+formats:
+  - pdf
+  - epub

README.rst

@@ -26,7 +26,7 @@ All the dependencies are listed in the pyproject.toml file. To install the packa
 
 CURRENT FEATURES:
 
-version 0.9.0
+version 0.9.1
 --------------
 
 - Network creation and manipulation: The package allows for the creation of a network of nodes and edges, with various methods for enrichment analysis. This includes adding and removing nodes and edges, loading a network from a SIF (Simple Interaction Format) file, and adding paths to the edge list of the network.

docs/src/api.rst

@@ -1,12 +1,26 @@
-API
-===
+API Reference
+=============
 
-Import Neko as::
+This page contains the API reference for the Neko package.
+
+Network Class
+-------------
+
+The main class in Neko is the ``Network`` class. You can import it as follows:
+
+.. code-block:: python
 
     from neko.core.network import Network
 
-Network
--------
+Below is a summary of the methods available in the ``Network`` class:
+
+.. autoclass:: neko.core.network.Network
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Method Details
+--------------
 
 .. autosummary::
    :toctree: _autosummary
@@ -26,3 +40,8 @@ Network
    neko.core.network.Network.convert_edgelist_into_genesymbol
    neko.core.network.Network.filter_unsigned_paths
    neko.core.network.Network.is_connected
+
+Other Modules
+-------------
+
+.. Add other modules and classes here as your project grows

docs/src/conf.py

@@ -124,7 +124,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['../src/_static']
 
 html_show_sphinx = False
 html_logo = 'neko_logo.png'

docs/src/contents.rst

@@ -1,17 +1,23 @@
+========
 Contents
 ========
 
 .. toctree::
-   :maxdepth: 3
-
-   index
-   api
+   :maxdepth: 2
+   :caption: User Guide
 
-Notebooks
-=========
+   installation
+   quickstart
+   tutorials
 
 .. toctree::
    :maxdepth: 2
+   :caption: API Reference
+
+   api
+
+.. toctree::
+   :maxdepth: 1
    :caption: Notebooks
 
    notebooks/1_network_building
@@ -20,3 +26,10 @@ Notebooks
    notebooks/4_Connect_upstream
    notebooks/5_ontology
    notebooks/6_tissue_mapping
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Development
+
+   contributing
+   changelog

docs/src/index.rst

@@ -26,7 +26,7 @@ All the dependencies are listed in the pyproject.toml file. To install the packa
 
 CURRENT FEATURES:
 
-version 0.9.0
+version 0.9.1
 --------------
 
 - Network creation and manipulation: The package allows for the creation of a network of nodes and edges, with various methods for enrichment analysis. This includes adding and removing nodes and edges, loading a network from a SIF (Simple Interaction Format) file, and adding paths to the edge list of the network.

docs/src/requirements.txt

@@ -1,7 +1,8 @@
 numpydoc
+sphinx
 nbsphinx
 ipython
-scikit-learn
 skranger
 sphinx_rtd_theme
 pandoc
+ipykernel