diff --git a/.cz.toml b/.cz.toml index 0a0a565c..d8d50859 100644 --- a/.cz.toml +++ b/.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", diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml deleted file mode 100644 index aeee0efb..00000000 --- a/.github/workflows/documentation.yml +++ /dev/null @@ -1,65 +0,0 @@ -name: Docs - -on: [push, workflow_dispatch] - -permissions: - contents: write - -jobs: - test: - runs-on: ubuntu-latest - steps: - #---------------------------------------------- - # 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 - 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: | - poetry run sphinx-build docs/source _build - - name: Deploy - if: github.head_ref == 'master' - uses: peaceiris/actions-gh-pages@v3 - with: - publish_branch: gh-pages - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: _build/ - force_orphan: true diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index b31cbfb8..c7786783 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.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/poetry-publish@v2.0 - # 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/poetry-publish@v2.0 + with: + python_version: "3.11" + pypi_token: ${{ secrets.TEST_PYPI_API_TOKEN }} + repository_name: "testpypi" + repository_url: "https://test.pypi.org/legacy/" - name: Build and publish distribution 📦 to PyPI uses: JRubics/poetry-publish@v2.0 diff --git a/.gitignore b/.gitignore index 891e468e..4a19478d 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,4 @@ cov.syspath.txt *.whl *dogsAndcats* pytest_notebooks.xml +poetry.lock diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 51c9eeb7..8c9819ce 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -1,6 +1,8 @@ # .readthedocs.yaml # Read the Docs configuration file # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details +# Uses poetry to install dependencies +# See https://docs.readthedocs.io/en/latest/build-customization.html#install-dependencies-with-poetry # Required version: 2 @@ -9,12 +11,24 @@ version: 2 build: os: ubuntu-22.04 tools: - python: "3.11" + python: "3.10" # You can also specify other tool versions: # nodejs: "19" # rust: "1.64" # golang: "1.19" + jobs: + post_create_environment: + # Install poetry + # https://python-poetry.org/docs/#installing-manually + - pip install poetry + post_install: + # Install dependencies with 'docs' dependency group + # https://python-poetry.org/docs/managing-dependencies/#dependency-groups + # VIRTUAL_ENV needs to be set manually for now. + # See https://github.com/readthedocs/readthedocs.org/pull/11152/ + - VIRTUAL_ENV=$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 diff --git a/LONG_DESCRIPTION.rst b/LONG_DESCRIPTION.rst index 4609d9be..ee816721 100644 --- a/LONG_DESCRIPTION.rst +++ b/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. diff --git a/Makefile b/Makefile index 9d9dd79a..b40349d4 100644 --- a/Makefile +++ b/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 diff --git a/README.md b/README.md index 55e60eaf..ab3c519e 100644 --- a/README.md +++ b/README.md @@ -72,37 +72,37 @@ Google Colab Open In Colab Basic 1 - HNX Basics -
+
Open In Colab Basic 2 - Visualization Methods -
+
Open In Colab Basic 3 - LesMis Case Study -
+
Open In Colab Basic 4 - LesMis Visualizations-Book Tour -
+
Open In Colab Basic 5 - HNX attributed hypergraph -
+
Open In Colab Basic 6 - Hypergraph Arithmetic.ipynb -
+
Jupyter Notebooks @@ -115,7 +115,7 @@ Installation The recommended installation method for most users is to create a virtual environment and install HyperNetX from PyPi. -HyperNetX may be cloned or forked from [Github](https://github.com/pnnl/HyperNetX). +HyperNetX may be cloned or forked from [GitHub](https://github.com/pnnl/HyperNetX). Prerequisites ------------- @@ -168,7 +168,7 @@ To deactivate your environment, use: Installing HyperNetX ==================== -Regardless of how you install HyperNetX, ensure that your environment is activated and that you are running Python >=3.8. +Regardless of how you install HyperNetX, ensure that your environment is activated and that you are running Python >=3.10. Installing from PyPi @@ -261,6 +261,9 @@ Install support for testing ```shell poetry install --with test +# activate your virtual environment created by poetry +poetry shell + # run tests python -m pytest @@ -275,9 +278,12 @@ open htmlcov/index.html Install support for tutorials ----------------------------- -``` +```shell poetry install --with tutorials +# activate your virtual environment created by poetry +poetry shell + # open Jupyter notebooks in a browser make tutorials ``` @@ -291,8 +297,10 @@ HyperNetX uses a number of tools to maintain code quality: Before using these tools, ensure that you install Pylint in your environment: -``` +```shell poetry install --with lint +# activate your virtual environment created by poetry +poetry shell ``` Pylint @@ -325,13 +333,30 @@ Black black hypernetx ``` +Pre-commit +--------- + +Use the [pre-commit framework](https://pre-commit.com/) to automatically point out issues and resolve those issues before code review. +It is highly recommended to install pre-commit in your development environment so that issues with your code can be found before you submit a +pull request. More importantly, using pre-commit will automatically format your code changes so that they pass the CI build. For example, pre-commit will +automatically run the formatter Black on your code changes. + +```shell +pre-commit install + +# Once installed, pre-commit will be triggered every time you make a commit in your environment +``` + Documentation ------------- Build and view documentation locally: -``` +```shell poetry install --with docs +# activate your virtual environment created by poetry +poetry shell + cd docs make html open docs/build/html/index.html @@ -340,7 +365,7 @@ open docs/build/html/index.html 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. -``` +```shell cd docs make livehtml ``` @@ -360,49 +385,12 @@ Click on `http://127.0.0.1:8000/install.html` to open the docs on your browser. you change a document file, it will automatically render on your browser, allowing you to verify your document changes. -Continuous Integration -====================== - -This project runs Continuous Integration (CI) using GitHub Actions. Normally, CI runs -on pull requests, pushes to certain branches, and other events. - -Maintainers of the GitHub repository can manually trigger CI using [GitHub CLI](https://cli.github.com/). See instructions below on how to manually trigger CI on GitHub Actions: - -```commandline -# login to Github -gh auth login --with-token < ~/.ssh/tokens/ - -# Trigger CI -gh workflow run ci.yml --repo pnnl/HyperNetX --ref --field triggeredBy="" - -# Get the status of the workflow -gh run list --workflow=ci.yml --repo pnnl/HyperNetX -``` - - -Versioning -========== - -This project uses [`commitizen`](https://github.com/commitizen-tools/commitizen) to manage versioning. -The files where "version" will be updated are listed in the '.cz.toml' file. To create a new version and the associated tag, -run the following commands: - -```shell -# Install commitizen tool to environment -pip install commitizen - -# Updates version; values for '--increment' can be MAJOR, MINOR, or PATCH -# Autocreates a tag and commit for the updated version -cz bump --increment MAJOR --dry-run -cz bump --increment MAJOR -``` - Notice ====== This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof. -
+ 
    PACIFIC NORTHWEST NATIONAL LABORATORY
    operated by
diff --git a/docs/source/conf.py b/docs/source/conf.py
index ad0e264d..0abb590e 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -19,7 +19,7 @@
 import os
 
 
-__version__ = "2.3.1"
+__version__ = "2.3.2"
 
 
 # If extensions (or modules to document with autodoc) are in another directory,
diff --git a/docs/source/overview/index.rst b/docs/source/overview/index.rst
index 22d1543e..e49811f5 100644
--- a/docs/source/overview/index.rst
+++ b/docs/source/overview/index.rst
@@ -54,7 +54,7 @@ available on `GitHub `_
         Open In Colab
           Basic 6 - Hypergraph Arithmetic.ipynb
       
-   

+   


    Additional Tutorials may be found in the Tutorials Folder.
diff --git a/hypernetx/__init__.py b/hypernetx/__init__.py index 25340bdd..1a686e22 100644 --- a/hypernetx/__init__.py +++ b/hypernetx/__init__.py @@ -11,4 +11,4 @@ from hypernetx.utils import * from hypernetx.utils.toys import * -__version__ = "2.3.1" +__version__ = "2.3.2" diff --git a/poetry.lock b/poetry.lock deleted file mode 100644 index b0fb80b9..00000000 --- a/poetry.lock +++ /dev/null @@ -1,4278 +0,0 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. - -[[package]] -name = "alabaster" -version = "0.7.16" -description = "A light, configurable Sphinx theme" -optional = false -python-versions = ">=3.9" -files = [ - {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"}, - {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"}, -] - -[[package]] -name = "ansi2html" -version = "1.9.1" -description = "Convert text with ANSI color codes to HTML or to LaTeX" -optional = false -python-versions = ">=3.7" -files = [ - 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