Pull request #87: Releases/2.0.0.post1

Merge in HYP/hypernetx from releases/2.0.0.post1 to master

* commit 'd31f86baa95780ac2fca6000d2e57b57989d0fa2': (299 commits)
  bump: version 2.0.0 → 2.0.0.post1
  Update Contributing.md
  Pull request #84: Bp2
  Pull request #82: Bp2
  Pull request #81: Cleanup README, setup.cfg; update CI scripts
  Pull request #80: fixed bug in descriptive stats
  Pull request #79: bump: version 1.2.5 → 2.0.0
  updated colab references
  updated versioning
  updated Tutorial ordering and fixed bug in Laplacian...tutorial
  Run linter on codebase
  Update test dependencies, CI scripts, Makefile
  Update README
  Fixed docstring and added hypergraph constructor rst page
  update tutorials and remove conflicts to merge
  updates
  update
  Sync Long description with docs; update readme; fix links
  Fix hyperlinks; point to Github links
  Fix, cleanup demo tutorials; add widget package option in setup.cfg
  ...

.coveragerc

@@ -0,0 +1,5 @@
+[run]
+omit = */tests/*
+[report]
+exclude_lines =
+    _log

.cz.toml

@@ -0,0 +1,21 @@
+[tool.commitizen]
+name = "cz_conventional_commits"
+version = "2.0.0.post1"
+version_files = [
+    "setup.py",
+    "docs/source/conf.py",
+    "hypernetx/__init__.py"
+]
+update_changelog_on_bump = false
+style = [
+    ["qmark", "fg:#ff9d00 bold"],
+    ["question", "bold"],
+    ["answer", "fg:#ff9d00 bold"],
+    ["pointer", "fg:#ff9d00 bold"],
+    ["highlighted", "fg:#ff9d00 bold"],
+    ["selected", "fg:#cc5454"],
+    ["separator", "fg:#cc5454"],
+    ["instruction", ""],
+    ["text", ""],
+    ["disabled", "fg:#858585 italic"]
+]

.github/workflows/ci.yml

@@ -0,0 +1,61 @@
+name: Continuous Integration
+
+
+on:
+  push:
+    branches: [master, develop, release/**]
+  pull_request:
+    types: [opened, synchronize, reopened]
+  workflow_dispatch:
+    inputs:
+      triggeredBy:
+        description: 'Name of team member who is manually triggering this workflow'
+        required: true
+
+defaults:
+  run:
+    shell: bash
+
+env:
+  LANG: en_US.utf-8
+  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']
+
+    runs-on: ${{ matrix.os }}
+
+    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 }}."
+
+    - name: Checkout
+      uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python }}
+      uses: actions/setup-python@v4
+      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/action@v3.0.0
+
+    - name: Run tests
+      run: |
+        make test-ci-github

.gitignore

@@ -1,6 +1,6 @@
-.DS_Store 
-gitmerge.sh 
-dist 
+.DS_Store
+gitmerge.sh
+dist
 hypernetx.egg-info*
 hypernetx.egg-info/PKG-INFO
 hypernetx.egg-info/requires.txt
@@ -26,4 +26,16 @@ vis_develop
 dist/
 *.egg-info*
 .tox/
-venv*
+venv*
+.coverage
+.idea
+*env*
+.venv*
+pylint-results.txt
+*pytest.xml
+*_alt*
+docs/docs
+docs/build
+coverage.xml
+cov.syspath.txt
+*.whl

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.1.0
+  hooks:
+  - id: check-yaml
+  - id: check-json
+  - id: check-toml
+  - id: end-of-file-fixer
+    exclude: ^(docs/|hypernetx.egg-info/)
+  - id: trailing-whitespace
+    exclude: ^(docs/|hypernetx.egg-info/|setup.cfg)
+  - id: check-merge-conflict
+  - id: no-commit-to-branch
+    args: ['--branch', 'master'] # blocks master commits.  To bypass do git commit --allow-empty
+
+-   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.
+        ]

.pylintrc

@@ -0,0 +1,13 @@
+[MAIN]
+
+# Specify a score threshold under which the program will exit with error.
+fail-under=5.86
+
+[REPORTS]
+# Tells whether to display a full report or only the messages.
+reports=yes
+
+# Set the output format. Available formats are text, parseable, colorized, json
+# and msvs (visual studio). You can also give a reporter class, e.g.
+# mypackage.mymodule.MyReporterClass.
+output-format=colorized

.readthedocs.yaml

@@ -0,0 +1,31 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+   - htmlzip
+   - epub
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

CODE_OF_CONDUCT.md

@@ -0,0 +1,134 @@
+# Contributor Covenant Code of Conduct
+
+Our shared values as software developers guide us in our day-to-day interactions and decision-making. Our open source projects are no exception. Trust, respect, collaboration and transparency are core values we believe should live and breathe within our projects. Our community welcomes participants from around the world with different experiences, unique perspectives, and great ideas to share.
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+hypernetx@pnnl.gov.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/),
+version 2.1, available at
+https://www.contributor-covenant.org/version/2/1/code_of_conduct.html.

CONTRIBUTING.md

@@ -0,0 +1,39 @@
+# Contributor orientation
+
+If you have ideas for improving this project, we would love to hear from you!
+
+## Orientation
+
+The world of open source is wide; it can be a lot to take in!  If this is your first time working with an open source project, then welcome!    If you're an experienced contributor, then welcome back!  Either way, this online resource might help you [get oriented, or bursh up](https://opensource.guide/how-to-contribute/) on the process.
+
+## Report an issue, bug, or feature request
+
+Here are the [steps to creating an issue on github](https://docs.github.com/en/issues/tracking-your-work-with-issues/quickstart).  When reporting a bug,
+
+- search for related issues on Github. You might be able to get answer without the hassle of creating an issue
+- describe the current behavior and explain which behavior you expected to see instead and why. At this point you can also tell which alternatives do not work for you.
+  - (if applicable) provide error messages
+  - (if applicable) provide a step by step description of the problem; if possible include code that others can use to reproduce it
+  - You may want to **include screenshots and animated GIFs** which help you demonstrate the steps or point out the part which the suggestion is related to. You can use [this tool](https://www.cockos.com/licecap/) to record GIFs on macOS and Windows, and [this tool](https://github.com/colinkeenan/silentcast) or [this tool](https://github.com/GNOME/byzanz) on Linux.
+  - provide clear, specific title
+  - include details on your setup (operating system, python version, etc.)
+- use the most recent version of this library and the source language (e.g. Rust); that fixes a lot of problems
+- here are [more details on getting the most out of issue reporting!](https://marker.io/blog/how-to-write-bug-report)
+
+## Contribute new code
+
+Here is a [step-by-step guide to writing new code, and submiting it to the project](https://docs.github.com/en/get-started/quickstart/contributing-to-projects)
+
+The more you know about a software library, the easier it is to get started writing code.  The best way to learn about this project is its the documentation!  See `README.md` to get started.
+
+
+## Where can I go for help?
+
+If you're stuck or don't know where to begin, then you're in good company -- we've all been there!  We're here to help, and we'd love to hear from you:
+
+- open a issue report on Github
+- email us at <hypernetx@pnnl.gov>
+
+# Code of conduct
+
+Our shared values as software developers guide us in our day-to-day interactions and decision-making. Our open source projects are no exception. Trust, respect, collaboration and transparency are core values we believe should live and breathe within our projects. Our community welcomes participants from around the world with different experiences, unique perspectives, and great ideas to share.  Our  [code of conduct](CODE_OF_CONDUCT) describes these values, and our standards for contributing.

DISCLAIMER.txt

@@ -19,4 +19,4 @@ reflect those of the United States Government or any agency thereof.
 				BATTELLE
 				for the
 		   UNITED STATES DEPARTMENT OF ENERGY
-		    under Contract DE-AC05-76RL01830
+		    under Contract DE-AC05-76RL01830