Pull request #189: Release/2.3.2

Merge in HYP/hypernetx from release/2.3.2 to master

* commit '21b0f6bf044df4138b42fc995653a47e77847f6a':
  bump: version 2.3.1 → 2.3.2
  Fix typos in documentation
  Fix readthdocs script; update publish to pypi workflow
  Modify documentation CI workflow
  Modify constraint python version
  Remove CI scripts from Makefile, Readme
  Remove celluloid, igraph from requirements.txt
  Make decorator dependency loosely constrained
  Remove poetry.lock
  Update github workflow

.cz.toml

@@ -1,6 +1,6 @@
 [tool.commitizen]
 name = "cz_conventional_commits"
-version = "2.3.1"
+version = "2.3.2"
 version_files = [
     "pyproject.toml",
     "docs/source/conf.py",

.github/workflows/publish-to-pypi.yml

@@ -1,12 +1,14 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+# This workflow uses the Github Action, poetry-publish.
+# It will build the HNX package into a wheel and sdist and then publish those artifacts to TestPyPi and PyPi using poetry.
+# Documentation for this action is at: https://github.com/marketplace/actions/publish-python-poetry-package
+# For building and publishing to PyPi in Github Workflows, see https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
 
 # This workflow uses actions that are not certified by GitHub.
 # They are provided by a third-party and are governed by
 # separate terms of service, privacy policy, and support
 # documentation.
 
-name: Upload Python Package
+name: Publish HNX
 
 on:
   release:
@@ -22,23 +24,27 @@ permissions:
   contents: read
 
 jobs:
-  deploy:
+  publish-to-pypi:
     runs-on: ubuntu-latest
-
     steps:
+    - run: |
+        echo "This workflow was triggered by: $TRIGGER_PERSON"
+      env:
+        TRIGGER_PERSON: ${{ inputs.triggeredBy }}
     - 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 }}"
+    - run: echo "Building wheel from branch ${{ github.ref_name }}"
+
     - uses: actions/checkout@v4
 
-    # - name: Build and publish distribution 📦 to Test PyPI
-    #   uses: JRubics/[email protected]
-    #   with:
-    #     python_version: "3.11"
-    #     pypi_token: ${{ secrets.TEST_PYPI_API_TOKEN }}
-    #     repository_name: "testpypi"
-    #     repository_url: "https://test.pypi.org/legacy/"
+    - name: Build and publish distribution 📦 to Test PyPI
+      uses: JRubics/[email protected]
+      with:
+        python_version: "3.11"
+        pypi_token: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        repository_name: "testpypi"
+        repository_url: "https://test.pypi.org/legacy/"
 
     - name: Build and publish distribution 📦 to PyPI
       uses: JRubics/[email protected]

.gitignore

@@ -41,3 +41,4 @@ cov.syspath.txt
 *.whl
 *dogsAndcats*
 pytest_notebooks.xml
+poetry.lock

.readthedocs.yaml

@@ -1,6 +1,8 @@
 # .readthedocs.yaml
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+# Uses poetry to install dependencies
+# See https://docs.readthedocs.io/en/latest/build-customization.html#install-dependencies-with-poetry
 
 # Required
 version: 2
@@ -9,12 +11,24 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.10"
     # You can also specify other tool versions:
     # nodejs: "19"
     # rust: "1.64"
     # golang: "1.19"
 
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      # VIRTUAL_ENV needs to be set manually for now.
+      # See https://github.com/readthedocs/readthedocs.org/pull/11152/
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with docs
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/source/conf.py
@@ -24,11 +38,3 @@ formats:
    - pdf
    - htmlzip
    - epub
-
-# Optionally declare the Python requirements required to build your docs
-python:
-   install:
-   - method: pip
-     path: .
-     extra_requirements:
-       - documentation

LONG_DESCRIPTION.rst

@@ -37,14 +37,12 @@ can be imported using their incidence dictionaries and/or property datafames.**
 What's New
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 #. We've added new functionality to Hypergraphs; you can add and remove nodes, edges, and incidences on Hypergraph.
-#. Arithmetic operations have also been added to Hypergraph: sum, difference, union, intersection
-#. We've also added a new tutorial on basic hypergraph arithmetic operations
-#. Under the hood, the EntitySet has been replaced by HypergraphView, new factory methods have been created to support
-the Hypergraph constructor, and internal classes such as IncidenceStore and PropertyStore help maintain the structure
-and attributes of a Hypergraph
+#. Arithmetic operations have also been added to Hypergraph: sum, difference, union, intersection.
+#. We've also added a new tutorial on basic hypergraph arithmetic operations.
+#. Under the hood, the EntitySet has been replaced by HypergraphView, new factory methods have been created to support the Hypergraph constructor, and internal classes such as IncidenceStore and PropertyStore help maintain the structure and attributes of a Hypergraph.
 
 What's Changed
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 #. Documentation has received a major update; the Glossary and docstrings of Hypergraph have been updated.
-#. HNX now requires Python ^3.10,<=3.12
+#. HNX now requires Python >=3.10,<4.0.0
 #. We've upgraded all the underlying core libraries to the latest versions.

Makefile

@@ -4,7 +4,7 @@ PYTHON3 = python3
 
 ############# Manage Environments #############
 
-## Environment using Pip
+## Create environment using Pip
 .PHONY: venv
 venv: clean-venv
 	@$(PYTHON3) -m venv $(VENV);
@@ -19,19 +19,28 @@ install:
 	@$(PYTHON3) -m pip install -e .
 	@$(PYTHON3) -m pip install -r requirements.txt
 
-## Environment using Poetry
+## Create environment using Poetry
 
-.PHONY: develop
-develop: clean-poetry-env
-	poetry shell
+.PHONY: install-with-poetry
+install-with-poetry:
+	poetry env remove --all
 	poetry install --with test
 
-
+## Create new requirements.txt from current poetry environment
 .PHONY: requirements.txt
 requirements.txt:
 	poetry export --format requirements.txt --output requirements.txt --without-hashes --with test,widget,tutorials,docs
 
-############# Running Tests, linters #############
+############# Tutorials #############
+.PHONY: tutorials
+tutorials:
+	jupyter notebook tutorials
+
+.PHONY: clean
+clean:
+	rm -rf .out .pytest_cache .tox *.egg-info dist build _build pytest.xml pytest_notebooks.xml .coverage
+
+############# Running Tests, linters, formatters #############
 
 ## Tests
 .PHONY: test
@@ -45,37 +54,12 @@ test-core:
 	coverage report -m
 
 
-## Tests using Tox
+## Run test on Tox framework
 ## Includes linting, running tests on jupyter notebooks
 .PHONY: test-tox
 test-tox:
 	@$(PYTHON3) -m tox --parallel
 
-### Tests using Poetry + Tox
-### Used by Bamboo CI Pipeline, Github Workflows CI Pipeline
-
-.PHONY: test-ci-stash
-test-ci-stash: install-poetry-stash run-poetry-tox clean-poetry-env
-
-.PHONY: build-docs-stash
-build-docs-stash: install-poetry-stash run-build-docs clean-poetry-env
-
-.PHONY: install-poetry-stash
-install-poetry-stash:
-	pip install poetry==1.8.2 tox
-
-.PHONY: run-poetry-tox
-run-poetry-tox:
-	tox --parallel
-
-.PHONY: run-build-docs
-run-build-docs:
-	tox -e build-docs
-
-.PHONY: clean-poetry-env
-clean-poetry-env:
-	poetry env remove --all
-
 ## Lint
 .PHONY: lint
 lint: pylint flake8
@@ -89,37 +73,8 @@ pylint:
 flake8:
 	@$(PYTHON3) -m flake8 hypernetx --exit-zero
 
+## precommit hooks that include formatter (Black)
 .PHONY: pre-commit
 pre-commit:
 	pre-commit install
 	pre-commit run --all-files
-
-############# Packaging and Publishing to PyPi #############
-## Uses Poetry to manage packaging and publishing
-## Targets are included as a backup in case the Github Workflows CI can't publish to PyPi and we need to do it manually
-## Assumes the following environment variables are set: PYPI_API_TOKEN
-.PHONY: publish-to-pypi
-publish-to-pypi: build check-long-desc
-	@echo "Publishing to PyPi"
-	poetry config pypi-token.pypi PYPI_API_TOKEN
-	poetry config repositories.pypi https://pypi.org/simple/
-	poetry publish --dry-run
-	#poetry publish
-
-.PHONY: build
-build: clean
-	poetry build
-
-.PHONY: check-long-desc
-check-long-desc:
-	poetry run pip install twine
-	poetry run twine check dist/*
-
-############# Misc #############
-.PHONY: tutorials
-tutorials:
-	jupyter notebook tutorials
-
-.PHONY: clean
-clean:
-	rm -rf .out .pytest_cache .tox *.egg-info dist build _build pytest.xml pytest_notebooks.xml .coverage