Pull request #141: Release/v2.2.0

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

* commit '02b19d03a731ff1b81871cc96ea650766aa207ce': (76 commits)
  bump: version 2.1.4 → 2.2.0
  Update docs on installation, widget; update Readme and Makefile
  Update optional dependencies; cleanup Makefile
  Fix tests
  Update installation instructions for widget
  Add images
  Move incidence visualization to tutorial 2
  Fix function call to updated draw function
  Run linter
  Use HNX for ingesting incidence matrix. Also uses HNX to store/access cell weights.
  Modification of draw function to support drawing the star hypergraph
  HYP-365 Silence warnings in tutorials
  Run linter
  removed readded test module
  updated empty hypergraph to have dataframes for properties
  HYP-360 Improve code quality tooling; update Makefile
  Remove unnecessary dependencies for documentation
  Update nb2plots
  Fix github workflow for documentation
  Update tests for soon to be deprecated translate methods
  ...

.coveragerc

@@ -1,5 +1,9 @@
 [run]
-omit = */tests/*
+omit =
+    */tests/*
+    */utils/toys/*
+    */utils/log.py
+
 [report]
 exclude_lines =
     _log

.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",

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+max-line-length=120
+extend-ignore = E203
+exclude =
+    .git,
+    __pycache__,
+    docs/source/conf.py,
+    old,
+    build,
+    dist
+max-complexity = 10

.github/workflows/ci.yml

@@ -59,3 +59,10 @@ jobs:
     - 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
+      run: |
+        sphinx-build docs/source _build

.github/workflows/documentation.yml

@@ -1,5 +1,5 @@
 name: Docs
-on: [push, pull_request, workflow_dispatch]
+on: [push, workflow_dispatch]
 permissions:
     contents: write
 jobs:
@@ -10,12 +10,12 @@ jobs:
       - uses: actions/setup-python@v3
       - name: Install dependencies
         run: |
-          pip install sphinx sphinx_rtd_theme
           pip install .'[documentation]'
       - name: Sphinx build
         run: |
           sphinx-build docs/source _build
       - name: Deploy
+        if: github.head_ref == 'master'
         uses: peaceiris/actions-gh-pages@v3
         with:
           publish_branch: gh-pages

.gitignore

@@ -27,7 +27,7 @@ dist/
 *.egg-info*
 .tox/
 venv*
-.coverage
+.coverage*
 .idea
 *env*
 .venv*

.pre-commit-config.yaml

@@ -13,31 +13,3 @@ repos:
   - id: trailing-whitespace
     exclude: ^(docs/|hypernetx.egg-info/|setup.cfg)
   - id: check-merge-conflict
-
--   repo: https://github.com/psf/black
-    rev: 22.6.0
-    hooks:
-    -   id: black
-        exclude: ^(docs/|hypernetx.egg-info/)
-
-# TODO: Uncomment once typing issues have been resolved and mypy has been
-# correctly configured
-#-   repo: https://github.com/pre-commit/mirrors-mypy
-#    rev: v0.910-1
-#    hooks:
-#      - id: mypy
-#        exclude: (?x)(docs/|tests/)
-#        args: [--no-strict-optional, --ignore-missing-imports]
-
-- repo: local
-  hooks:
-    - id: pylint
-      name: pylint
-      entry: pylint
-      language: system
-      types: [python]
-      args:
-        [
-          "--rcfile=.pylintrc",
-          "--exit-zero" # Always return a 0 (non-error) status code, even if lint errors are found. This is primarily useful in continuous integration scripts.
-        ]

MANIFEST.in

@@ -0,0 +1 @@
+include hypernetx/utils/toys/HarryPotter_Characters.csv

Makefile

@@ -1,76 +1,131 @@
 SHELL = /bin/bash
 
 VENV = venv-hnx
-PYTHON_VENV = $(VENV)/bin/python3
 PYTHON3 = python3
 
 
-## Test
+## Lint
 
-test: test-deps
-	@$(PYTHON3) -m tox
+.PHONY: lint
+lint: pylint flake8 mypy
 
-test-ci: test-deps
-	@$(PYTHON3) -m pip install 'pytest-github-actions-annotate-failures>=0.1.7'
+.PHONY: pylint
+pylint:
+	@$(PYTHON3) -m pylint --recursive=y --persistent=n --verbose hypernetx
+
+.PHONY: mypy
+mypy:
+	@$(PYTHON3) -m mypy hypernetx || true
+
+.PHONY: flake8
+flake8:
+	@$(PYTHON3) -m flake8 hypernetx --exit-zero
+
+.PHONY: format
+format:
+	@$(PYTHON3) -m black hypernetx
+
+
+## Tests
+
+.PHONY: pre-commit
+pre-commit:
 	pre-commit install
 	pre-commit run --all-files
-	@$(PYTHON3) -m tox -e py38 -r
-	@$(PYTHON3) -m tox -e py38-notebooks -r
 
-test-ci-github: test-deps
-	@$(PYTHON3) -m pip install 'pytest-github-actions-annotate-failures>=0.1.7'
+.PHONY: test
+test:
+	coverage run --source=hypernetx -m pytest
+	coverage report -m
+
+.PHONY: test-ci
+test-ci:
 	@$(PYTHON3) -m tox
 
-.PHONY: test, test-ci, test-ci-github
+.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
+
 
 ## Continuous Deployment
 ## Assumes that scripts are run on a container or test server VM
-
 ### Publish to PyPi
+
+.PHONY: publish-deps
 publish-deps:
-	@$(PYTHON3) -m pip install -e .'[packaging]'
+	@$(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:
-	@$(PYTHON3) -m pip install .'[releases]'
+	@$(PYTHON3) -m pip install .[releases] --use-pep517
 
-.PHONY: version-deps
 
-#### Documentation
+### Documentation
 
+.PHONY: docs-deps
 docs-deps:
-	@$(PYTHON3) -m pip install -e .'[documentation]' --use-pep517
+	@$(PYTHON3) -m pip install .[documentation] --use-pep517
+
+
+## Tutorials
+
+.PHONY: tutorial-deps
+tutorial-deps:
+	@$(PYTHON3) -m pip install .[tutorials] .[widget] --use-pep517
+
+.PHONY: tutorials
+tutorials:
+	jupyter notebook tutorials
 
-.PHONY: docs-deps
 
 ## 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);
 
+.PHONY: github-ci-deps
+ci-github-deps:
+	@$(PYTHON3) -m pip install 'pytest-github-actions-annotate-failures>=0.1.7'
+
+.PHONY: lint-deps
+lint-deps:
+	@$(PYTHON3) -m pip install .[lint] --use-pep517
+
+.PHONY: format-deps
+format-deps:
+	@$(PYTHON3) -m pip install .[format] --use-pep517
+
+.PHONY: test-deps
 test-deps:
-	@$(PYTHON3) -m pip install -e .'[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