Pull request #186: Release2.3.0

Merge in HYP/hypernetx from release2.3.0 to master * commit 'addea711f4a751c0526a77437c98e79d1a8d119f': (267 commits) bump: version 2.2.0 → 2.3.0 Update changelog Update release notes; add changelog Fix propertystore docstrings Fix math syntax error Fixup hyp_view docstrings edited as per Pylint. Fixed typos and edited wording in some docstrings Updated as per suggestions from Pylint updated publications,editted typos and syntax errors, and updated Colab references for when we push to master. editted text updated Tutorials fixing tutorials for colab Linter updating rst files and hypergraph.py for doc string updated tutorials Linter merge merging Update Tutorial 8 - Generative Models.ipynb Update hypergraph_modularity.py ...
pnnl · May 17, 2024 · bb2a2fb · bb2a2fb
2 parents 706d842 + addea71
commit bb2a2fb
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diff --git a/.cz.toml b/.cz.toml
@@ -1,8 +1,8 @@
 [tool.commitizen]
 name = "cz_conventional_commits"
-version = "2.2.0"
+version = "2.3.0"
 version_files = [
-    "setup.py",
+    "pyproject.toml",
     "docs/source/conf.py",
     "hypernetx/__init__.py"
 ]

diff --git a/.github/workflows/cff.yml b/.github/workflows/cff.yml
@@ -0,0 +1,20 @@
+on:
+  push:
+    paths:
+      - CITATION.cff
+  workflow_dispatch:
+
+name: CITATION.cff
+jobs:
+  Validate-CITATION-cff:
+    runs-on: ubuntu-latest
+    name: Validate CITATION.cff
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Validate CITATION.cff
+        uses: dieghernan/cff-validator@v3
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,5 +1,4 @@
-name: Continuous Integration
-
+name: Run tests, linters, formatters
 
 on:
   push:
@@ -21,18 +20,14 @@ env:
   LC_ALL: en_US.utf-8
 
 jobs:
-
   run-tests:
-
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-12, windows-2022]
-        python: ['3.8', '3.9', '3.10', '3.11']
-
+        os: [ubuntu-latest, macos-latest]
+        python: ['3.10', '3.11', '3.12']
     runs-on: ${{ matrix.os }}
 
     steps:
-
     - run: |
         echo "This workflow was triggered by: $TRIGGER_PERSON"
       env:
@@ -41,28 +36,35 @@ jobs:
     - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
     - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
 
-    - name: Checkout
-      uses: actions/checkout@v3
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+    - name: Check out repository
+      uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v4
+      id: setup-python
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
 
-    - name: Install Pylint
-      run: pip install pylint
-
-    # https://github.com/pre-commit/action
-    - name: Run pre-commit hooks
-      uses: pre-commit/[email protected]
-
-    - name: Run tests
-      run: |
-        make test-ci-github
-    - name: Install documentation dependencies
-      run: |
-        pip install sphinx sphinx_rtd_theme
-        pip install .'[documentation]'
-    - name:  Check documentation build
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs-create: true
+        virtualenvs-in-project: true
+        installer-parallel: true
+      #----------------------------------------------
+      # install other testing dependencies
+      #----------------------------------------------
+    - name: Install tox, pytest-github, tox-gh-actions
+      run: pip install 'tox>=4.4.11' 'pytest-github-actions-annotate-failures>=0.1.7' 'tox-gh-actions'
+      #----------------------------------------------
+      #     Run tests, linters defined in Tox
+      #----------------------------------------------
+    - name: Run tests, linters
       run: |
-        sphinx-build docs/source _build
+        tox
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -1,19 +1,60 @@
 name: Docs
+
 on: [push, workflow_dispatch]
+
 permissions:
     contents: write
+
 jobs:
-  docs:
+  test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v3
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up python
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11.8'
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+          installer-parallel: true
+
+      #----------------------------------------------
+      #       load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v4
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
       - name: Install dependencies
-        run: |
-          pip install .'[documentation]'
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install your root project, if required
+      #----------------------------------------------
+      - name: Install project
+        run: poetry install --all-extras --no-interaction --with docs
+      #----------------------------------------------
+      #              publish documentation
+      #----------------------------------------------
       - name: Sphinx build
         run: |
-          sphinx-build docs/source _build
+          poetry run sphinx-build docs/source _build
       - name: Deploy
         if: github.head_ref == 'master'
         uses: peaceiris/actions-gh-pages@v3

diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -17,47 +17,25 @@ permissions:
 
 jobs:
   deploy:
-
     runs-on: ubuntu-latest
 
     steps:
     - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event."
     - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!"
     - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}."
     - run: echo "Building wheel from tag ${{ github.ref_name }}"
+    - uses: actions/checkout@v4
 
-    - uses: actions/checkout@v3
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.11"
-
-    - name: Install pypa/build
-      run: >-
-        python3 -m
-        pip install
-        build
-        --user
-
-    - name: Build a binary wheel and a source tarball
-      run: >-
-        python3 -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
-
-    - name: Publish distribution 📦 to Test PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+    - name: Build and publish distribution 📦 to Test PyPI
+      uses: JRubics/[email protected]
       with:
-        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-        repository-url: https://test.pypi.org/legacy/
+        python_version: "3.11.8"
+        pypi_token: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_name: "testpypi"
+        repository_url: "https://test.pypi.org/legacy/"
 
-    - name: Publish distribution 📦 to PyPI
-      if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@release/v1
+    - name: Build and publish distribution 📦 to PyPI
+      uses: JRubics/[email protected]
       with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
-        verbose: true
-        print-hash: true
+        python_version: "3.11.18"
+        pypi_token: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/.gitignore b/.gitignore
@@ -39,3 +39,5 @@ docs/build
 coverage.xml
 cov.syspath.txt
 *.whl
+*dogsAndcats*
+pytest_notebooks.xml
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,3 +13,7 @@ repos:
   - id: trailing-whitespace
     exclude: ^(docs/|hypernetx.egg-info/|setup.cfg)
   - id: check-merge-conflict
+- repo: https://github.com/psf/black
+  rev: 24.3.0
+  hooks:
+  - id: black