Pull request #142: Release/v2.2.0

Merge in HYP/hypernetx from release/v2.2.0 to develop

* commit '02b19d03a731ff1b81871cc96ea650766aa207ce':
  bump: version 2.1.4 → 2.2.0
  Update docs on installation, widget; update Readme and Makefile
  Update optional dependencies; cleanup Makefile

.cz.toml

@@ -1,6 +1,6 @@
 [tool.commitizen]
 name = "cz_conventional_commits"
-version = "2.1.4"
+version = "2.2.0"
 version_files = [
     "setup.py",
     "docs/source/conf.py",

Makefile

@@ -25,79 +25,88 @@ flake8:
 format:
 	@$(PYTHON3) -m black hypernetx
 
+
 ## Tests
 
+.PHONY: pre-commit
 pre-commit:
 	pre-commit install
 	pre-commit run --all-files
 
-
+.PHONY: test
 test:
 	coverage run --source=hypernetx -m pytest
 	coverage report -m
 
+.PHONY: test-ci
 test-ci:
 	@$(PYTHON3) -m tox
 
+.PHONY: test-ci-stash
 test-ci-stash: lint-deps lint pre-commit test-deps test-ci
 
+
+.PHONY: test-ci-github
 test-ci-github: lint-deps lint pre-commit ci-github-deps test-deps test-ci
 
-.PHONY: pre-commit test test-ci, test-ci-stash, test-ci-github
 
 ## Continuous Deployment
 ## Assumes that scripts are run on a container or test server VM
-
 ### Publish to PyPi
+
+.PHONY: publish-deps
 publish-deps:
-	@$(PYTHON3) -m pip install -e .'[packaging]' --use-pep517
+	@$(PYTHON3) -m pip install -e .[packaging] --use-pep517
 
+.PHONY: build-dist
 build-dist: publish-deps clean
 	@$(PYTHON3) -m build --wheel --sdist
 	@$(PYTHON3) -m twine check dist/*
 
 ## Assumes the following environment variables are set: TWINE_USERNAME, TWINE_PASSWORD, TWINE_REPOSITORY_URL,
 ## See https://twine.readthedocs.io/en/stable/#environment-variables
+.PHONY: publish-to-pypi
 publish-to-pypi: publish-deps build-dist
 	@echo "Publishing to PyPi"
 	$(PYTHON3) -m twine upload dist/*
 
-.PHONY: build-dist publish-to-pypi publish-deps
 
 ### Update version
 
+.PHONY: version-deps
 version-deps:
-	@$(PYTHON3) -m pip install .'[releases]' --use-pep517
+	@$(PYTHON3) -m pip install .[releases] --use-pep517
 
-.PHONY: version-deps
 
 ### Documentation
 
+.PHONY: docs-deps
 docs-deps:
-	@$(PYTHON3) -m pip install .'[documentation]' --use-pep517
+	@$(PYTHON3) -m pip install .[documentation] --use-pep517
 
-.PHONY: docs-deps
 
 ## Tutorials
 
 .PHONY: tutorial-deps
 tutorial-deps:
-	@$(PYTHON3) -m pip install .'[tutorials]' .'[widget]' --use-pep517
+	@$(PYTHON3) -m pip install .[tutorials] .[widget] --use-pep517
 
 .PHONY: tutorials
 tutorials:
 	jupyter notebook tutorials
 
 
-
 ## Environment
 
+.PHONY: clean-venv
 clean-venv:
 	rm -rf $(VENV)
 
+.PHONY: clean
 clean:
 	rm -rf .out .pytest_cache .tox *.egg-info dist build
 
+.PHONY: venv
 venv: clean-venv
 	@$(PYTHON3) -m venv $(VENV);
 
@@ -107,16 +116,16 @@ ci-github-deps:
 
 .PHONY: lint-deps
 lint-deps:
-	@$(PYTHON3) -m pip install .'[lint]' --use-pep517
+	@$(PYTHON3) -m pip install .[lint] --use-pep517
 
 .PHONY: format-deps
 format-deps:
-	@$(PYTHON3) -m pip install .'[format]' --use-pep517
+	@$(PYTHON3) -m pip install .[format] --use-pep517
 
+.PHONY: test-deps
 test-deps:
-	@$(PYTHON3) -m pip install .'[testing]' --use-pep517
+	@$(PYTHON3) -m pip install .[testing] --use-pep517
 
+.PHONY: all-deps
 all-deps:
-	@$(PYTHON3) -m pip install -e .'[all]' --use-pep517
-
-.PHONY: clean clean-venv venv all-deps test-deps
+	@$(PYTHON3) -m pip install .[all] --use-pep517

README.md

@@ -150,8 +150,8 @@ conda activate venv-hnx
 
 
 ```shell
-virtualenv env-hnx
-source env-hnx/bin/activate
+virtualenv venv-hnx
+source venv-hnx/bin/activate
 ```
 
 
@@ -190,19 +190,11 @@ Ensure that you have [git](https://git-scm.com/book/en/v2/Getting-Started-Instal
 ```shell
 git clone https://github.com/pnnl/HyperNetX.git
 cd HyperNetX
+make venv
+source venv-hnx/bin/activate
 pip install .
 ```
 
-Post-Installation Actions
-=========================
-
-Running Tests
--------------
-
-```shell
-python -m pytest
-```
-
 Development
 ===========
 
@@ -213,10 +205,13 @@ Install an editable version
 pip install -e .
 ```
 
-Install an editable version with access to jupyter notebooks
-------------------------------------------------------------
+Install an editable version with supported applications
+-------------------------------------------------------
 
 ```shell
+pip install -e .['all']
+
+# for zsh users
 pip install -e .'[all]'
 ```
 
@@ -226,7 +221,7 @@ Install support for testing
 > ℹ️ **NOTE:** This project has a pytest configuration file named 'pytest.ini'. By default, pytest will use those configuration settings to run tests.
 
 ```shell
-pip install .'[testing]'
+make test-deps
 
 # run tests
 python -m pytest
@@ -243,20 +238,14 @@ Install support for tutorials
 -----------------------------
 
 ``` shell
-pip install .'[tutorials]'
+make tutorial-deps
+
+# open Jupyter notebooks in a browser
+make tutorials
 ```
 
-Install support for documentation
----------------------------------
 
-```shell
-pip install .'[documentation]'
-cd docs
 
-## This will generate the documentation in /docs/build/
-## Open them in your browser with docs/build/html/index.html
-make html
-```
 
 
 Code Quality
@@ -269,7 +258,7 @@ HyperNetX uses a number of tools to maintain code quality:
 Before using these tools, ensure that you install Pylint in your environment:
 
 ```shell
-pip install .'[lint]'
+make lint-deps
 ```
 
 
@@ -299,6 +288,7 @@ For more information on configuration, see https://pylint.pycqa.org/en/latest/us
 
 
 ```shell
+make format-deps
 black hypernetx
 ```
 
@@ -309,19 +299,20 @@ Build and view documentation locally
 ---------------------------
 
 ```
+make docs-deps
 cd docs
 make html
 open docs/build/html/index.html
 ```
 
 Editing documentation
 ----------------------
-NOTE: make sure you install the required dependencies using: `make docs-deps`
 
 When editing documentation, you can auto-rebuild the documentation locally so that you can view your document changes
 live on the browser without having to rebuild every time you have a change.
 
 ```
+make docs-deps
 cd docs
 make livehtml
 ```

docs/source/classes/classes.rst

@@ -4,14 +4,6 @@ classes package
 Submodules
 ----------
 
-classes.entity module
----------------------
-
-.. automodule:: classes.entity
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 classes.entityset module
 ------------------------
 

docs/source/conf.py

@@ -19,7 +19,7 @@
 import os
 
 
-__version__ = "2.1.4"
+__version__ = "2.2.0"
 
 
 # If extensions (or modules to document with autodoc) are in another directory,