diff --git a/.cz.toml b/.cz.toml index aa6714ca..93a398ec 100644 --- a/.cz.toml +++ b/.cz.toml @@ -2,7 +2,7 @@ name = "cz_conventional_commits" version = "2.2.0" version_files = [ - "setup.py", + "pyproject.toml", "docs/source/conf.py", "hypernetx/__init__.py" ] diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b8826ea6..d334589a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,5 +1,4 @@ -name: Continuous Integration - +name: Run tests, linters, formatters on: push: @@ -21,18 +20,14 @@ env: LC_ALL: en_US.utf-8 jobs: - run-tests: - strategy: matrix: - os: [ubuntu-22.04, macos-12, windows-2022] + os: [ubuntu-latest, macos-latest] python: ['3.8', '3.9', '3.10', '3.11'] - runs-on: ${{ matrix.os }} steps: - - run: | echo "This workflow was triggered by: $TRIGGER_PERSON" env: @@ -41,28 +36,35 @@ jobs: - 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 + #---------------------------------------------- + # check-out repo and set-up python + #---------------------------------------------- + - name: Check out repository + uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python }} - uses: actions/setup-python@v4 + id: setup-python + uses: actions/setup-python@v5 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 - - name: Install documentation dependencies - run: | - pip install sphinx sphinx_rtd_theme - pip install .'[documentation]' - - name: Check documentation build + #---------------------------------------------- + # ----- install & configure poetry ----- + #---------------------------------------------- + - name: Install Poetry + uses: snok/install-poetry@v1 + with: + virtualenvs-create: true + virtualenvs-in-project: true + installer-parallel: true + #---------------------------------------------- + # install other testing dependencies + #---------------------------------------------- + - name: Install tox, pytest-github, tox-gh-actions + run: pip install 'tox>=4.4.11' 'pytest-github-actions-annotate-failures>=0.1.7' 'tox-gh-actions' + #---------------------------------------------- + # Run tests, linters defined in Tox + #---------------------------------------------- + - name: Run tests, linters run: | - sphinx-build docs/source _build + tox diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml index 46baff65..aeee0efb 100644 --- a/.github/workflows/documentation.yml +++ b/.github/workflows/documentation.yml @@ -1,19 +1,60 @@ name: Docs + on: [push, workflow_dispatch] + permissions: contents: write + jobs: - docs: + test: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v3 + #---------------------------------------------- + # 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 - run: | - pip install .'[documentation]' + 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: | - sphinx-build docs/source _build + poetry run sphinx-build docs/source _build - name: Deploy if: github.head_ref == 'master' uses: peaceiris/actions-gh-pages@v3 diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml index e765ddc0..6c5990cd 100644 --- a/.github/workflows/publish-to-pypi.yml +++ b/.github/workflows/publish-to-pypi.yml @@ -17,7 +17,6 @@ permissions: jobs: deploy: - runs-on: ubuntu-latest steps: @@ -25,39 +24,18 @@ jobs: - 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 }}" + - uses: actions/checkout@v4 - - uses: actions/checkout@v3 - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: "3.11" - - - name: Install pypa/build - run: >- - python3 -m - pip install - build - --user - - - name: Build a binary wheel and a source tarball - run: >- - python3 -m - build - --sdist - --wheel - --outdir dist/ - . - - - name: Publish distribution đŸ“Ļ to Test PyPI - uses: pypa/gh-action-pypi-publish@release/v1 + - name: Build and publish distribution đŸ“Ļ to Test PyPI + uses: JRubics/poetry-publish@v2.0 with: - password: ${{ secrets.TEST_PYPI_API_TOKEN }} - repository-url: https://test.pypi.org/legacy/ + python_version: "3.11.8" + pypi_token: ${{ secrets.TEST_PYPI_API_TOKEN }} + repository_name: "testpypi" + repository_url: "https://test.pypi.org/legacy/" - - name: Publish distribution đŸ“Ļ to PyPI - if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@release/v1 + - name: Build and publish distribution đŸ“Ļ to PyPI + uses: JRubics/poetry-publish@v2.0 with: - password: ${{ secrets.PYPI_API_TOKEN }} - verbose: true - print-hash: true + python_version: "3.11.18" + pypi_token: ${{ secrets.PYPI_API_TOKEN }} diff --git a/.gitignore b/.gitignore index 86e79c5f..891e468e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,3 @@ -.github/ .DS_Store gitmerge.sh dist @@ -41,3 +40,4 @@ coverage.xml cov.syspath.txt *.whl *dogsAndcats* +pytest_notebooks.xml diff --git a/Makefile b/Makefile index 2596b0c6..a6c38c9b 100644 --- a/Makefile +++ b/Makefile @@ -1,135 +1,119 @@ SHELL = /bin/bash - VENV = venv-hnx PYTHON3 = python3 +############# Manage Environments ############# -## Lint +## Environment using Pip +.PHONY: venv +venv: clean-venv + @$(PYTHON3) -m venv $(VENV); -.PHONY: lint -lint: pylint flake8 mypy +.PHONY: clean-venv +clean-venv: + rm -rf $(VENV) -.PHONY: pylint -pylint: - @$(PYTHON3) -m pylint --recursive=y --persistent=n --verbose hypernetx --exit-zero +.PHONY: install +install: + @$(PYTHON3) -m pip install --upgrade pip + @$(PYTHON3) -m pip install -e . + @$(PYTHON3) -m pip install -r requirements.txt -.PHONY: mypy -mypy: - @$(PYTHON3) -m mypy hypernetx || true +## Environment using Poetry -.PHONY: flake8 -flake8: - @$(PYTHON3) -m flake8 hypernetx --exit-zero +.PHONY: develop +develop: clean-poetry-env + poetry shell + poetry install --with test -.PHONY: format -format: - @$(PYTHON3) -m black hypernetx +.PHONY: requirements.txt +requirements.txt: + poetry export --format requirements.txt --output requirements.txt --without-hashes --with test,widget,tutorials,docs -## Tests - -.PHONY: pre-commit -pre-commit: - pre-commit install - pre-commit run --all-files +############# Running Tests, linters ############# +## Tests .PHONY: test test: coverage run --source=hypernetx -m pytest coverage report -m -.PHONY: test-ci -test-ci: - @$(PYTHON3) -m tox - -.PHONY: test-ci-stash -test-ci-stash: lint-deps lint pre-commit test-deps test-ci +## Tests using Tox +## Includes linting, running tests on jupyter notebooks +.PHONY: test-tox +test-tox: + @$(PYTHON3) -m tox --parallel +### Tests using Poetry + Tox +### Used by Bamboo CI Pipeline, Github Workflows CI Pipeline -.PHONY: test-ci-github -test-ci-github: lint-deps lint pre-commit ci-github-deps test-deps test-ci +.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 -## Continuous Deployment -## Assumes that scripts are run on a container or test server VM -### Publish to PyPi +.PHONY: install-poetry-stash +install-poetry-stash: + pip install poetry==1.8.2 tox -.PHONY: publish-deps -publish-deps: - @$(PYTHON3) -m pip install -e .[packaging] --use-pep517 +.PHONY: run-poetry-tox +run-poetry-tox: + tox --parallel -.PHONY: build-dist -build-dist: publish-deps clean - @$(PYTHON3) -m build --wheel --sdist - @$(PYTHON3) -m twine check dist/* +.PHONY: run-build-docs +run-build-docs: + tox -e build-docs -## 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" - $(PYTHON3) -m twine upload dist/* +.PHONY: clean-poetry-env +clean-poetry-env: + poetry env remove --all +## Lint +.PHONY: lint +lint: pylint flake8 -### Update version - -.PHONY: version-deps -version-deps: - @$(PYTHON3) -m pip install .[releases] --use-pep517 - +.PHONY: pylint +pylint: + @$(PYTHON3) -m pylint --recursive=y --persistent=n --verbose hypernetx -### Documentation +# Todo: fix flake8 errors and remove --exit-zero +.PHONY: flake8 +flake8: + @$(PYTHON3) -m flake8 hypernetx --exit-zero -.PHONY: docs-deps -docs-deps: - @$(PYTHON3) -m pip install .[documentation] --use-pep517 +.PHONY: pre-commit +pre-commit: + pre-commit install + pre-commit run --all-files +############# Packaging and Publishing to PyPi ############# +## Uses Poetry to manage packaging and publishing +## Targets are included as a backup in case the Github Workflows CI can't publish to PyPi and we need to do it manually +## Assumes the following environment variables are set: PYPI_API_TOKEN +.PHONY: publish-to-pypi +publish-to-pypi: build check-long-desc + @echo "Publishing to PyPi" + poetry config pypi-token.pypi PYPI_API_TOKEN + poetry config repositories.pypi https://pypi.org/simple/ + poetry publish --dry-run + #poetry publish -## Tutorials +.PHONY: build +build: clean + poetry build -.PHONY: tutorial-deps -tutorial-deps: - @$(PYTHON3) -m pip install .[tutorials] .[widget] --use-pep517 +.PHONY: check-long-desc +check-long-desc: + poetry run pip install twine + poetry run twine check dist/* +############# Misc ############# .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 $(VENV); - -.PHONY: github-ci-deps -ci-github-deps: - @$(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: - @$(PYTHON3) -m pip install .[testing] --use-pep517 - -.PHONY: all-deps -all-deps: - @$(PYTHON3) -m pip install .[all] --use-pep517 - -.PHONY: install-develop -install-develop: - @$(PYTHON3) -m pip install -e . --use-pep517 + 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 9fd7abc0..1f0728a5 100644 --- a/README.md +++ b/README.md @@ -190,29 +190,71 @@ 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 + +# Create a virtual environment make venv source venv-hnx/bin/activate -pip install . + +# install required dependencies +make install ``` Development =========== Install an editable version ---------------------------- - ``` pip install -e . ``` -Install an editable version with supported applications -------------------------------------------------------- +Install additional dependencies to support testing and jupyter notebooks: +``` +pip install -r requirements.txt +``` -```shell -pip install -e .['all'] +You can also install all these requirements in one Make target: + +``` +make install +``` + +Poetry +====== -# for zsh users -pip install -e .'[all]' +This library uses [Poetry](https://python-poetry.org/docs/) to manage dependencies and packaging. Poetry can also be +used to manage your environment for development. + +Prerequisites +------------- + +* [Install Poetry](https://python-poetry.org/docs/#installation) + + +Configure Poetry +---------------- + +[Configure your Poetry](https://python-poetry.org/docs/configuration/) to create the virtual environment in your project directory: +``` +poetry config virtualenvs.in-project true + +# check the poetry configuration +poetry config --list +``` + +Set up virtual environment +---------------------------- + +Create and activate a virtual environment. +``` +poetry shell +``` + +NOTE: If you plan to use Poetry to manage your virtual environment, you can activate the virtual environment +using poerty: `poetry shell`. Another option is to directly + +Install required dependencies and HyperNetX in editable mode. +``` +poetry install ``` Install support for testing @@ -221,7 +263,7 @@ Install support for testing > ℹī¸ **NOTE:** This project has a pytest configuration file named 'pytest.ini'. By default, pytest will use those configuration settings to run tests. ```shell -make test-deps +poetry install --with test # run tests python -m pytest @@ -237,17 +279,13 @@ open htmlcov/index.html Install support for tutorials ----------------------------- -``` shell -make tutorial-deps +``` +poetry install --with tutorials # open Jupyter notebooks in a browser make tutorials ``` - - - - Code Quality ------------ HyperNetX uses a number of tools to maintain code quality: @@ -257,12 +295,12 @@ HyperNetX uses a number of tools to maintain code quality: Before using these tools, ensure that you install Pylint in your environment: -```shell -make lint-deps +``` +poetry install --with lint ``` - -### Pylint +Pylint +------ [Pylint](https://pylint.pycqa.org/en/latest/index.html) is a static code analyzer for Python-based projects. From the [Pylint docs](https://pylint.pycqa.org/en/latest/index.html#what-is-pylint): @@ -282,37 +320,31 @@ pylint hypernetx --output=pylint-results.txt For more information on configuration, see https://pylint.pycqa.org/en/latest/user_guide/configuration/index.html -### Black - +Black +----- [Black](https://black.readthedocs.io/en/stable/) is a PEP 8 compliant formatter for Python-based project. This tool is highly opinionated about how Python should be formatted and will automagically reformat your code. ```shell -make format-deps black hypernetx ``` Documentation -=============== +------------- -Build and view documentation locally ---------------------------- +Build and view documentation locally: ``` -make docs-deps +poetry install --with docs cd docs make html open docs/build/html/index.html ``` -Editing documentation ----------------------- - 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 ``` @@ -353,7 +385,7 @@ 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, @@ -361,7 +393,7 @@ run the following commands: ```shell # Install commitizen tool to environment -make version-deps +pip install commitizen # Updates version; values for '--increment' can be MAJOR, MINOR, or PATCH # Autocreates a tag and commit for the updated version diff --git a/docs/source/install.rst b/docs/source/install.rst index eb59e085..22948b33 100644 --- a/docs/source/install.rst +++ b/docs/source/install.rst @@ -2,10 +2,6 @@ Installing HyperNetX ******************** - -Installation -############ - The recommended installation method for most users is to create a virtual environment and install HyperNetX from PyPi. @@ -56,13 +52,13 @@ To deactivate your environment, use: >>> .\env-hnx\Scripts\deactivate -Installing Hypernetx -#################### +Installation +############ Regardless of how you install HyperNetX, ensure that your environment is activated and that you are running Python >=3.8. Installing from PyPi -************************* +******************** >>> pip install hypernetx @@ -70,14 +66,10 @@ If you want to use supported applications built upon HyperNetX (e.g. ``hypernetx ``hypernetx.algorithms.contagion``), you can install HyperNetX with those supported applications by using the following command: - >>> pip install hypernetx[all] - -If you are using zsh as your shell, use single quotation marks around the square brackets: - - >>> pip install hypernetx'[all]' + >>> pip install igraph celluloid Installing from Source -************************* +********************** Ensure that you have ``git`` installed. @@ -85,14 +77,14 @@ Ensure that you have ``git`` installed. >>> cd HyperNetX >>> make venv >>> source venv-hnx/bin/activate - >>> pip install . + >>> make install Post-Installation Actions -########################## +######################### Interact with HyperNetX in a REPL -******************************************** +********************************* Ensure that your environment is activated and that you run ``python`` on your terminal to open a REPL: @@ -108,7 +100,7 @@ Ensure that your environment is activated and that you run ``python`` on your te Other Actions if installed from source -******************************************** +************************************** If you have installed HyperNetX from source, you can perform additional actions such as viewing the provided Jupyter notebooks or building the documentation locally. @@ -121,7 +113,6 @@ Viewing jupyter notebooks The following command will automatically open the notebooks in a browser. - >>> make tutorial-deps >>> make tutorials @@ -130,9 +121,7 @@ Building documentation The following commands will build and open a local version of the documentation in a browser: - >>> make docs-deps + >>> pip install sphinx sphinx-autobuild sphinx-rtd-theme sphinx-copybutton >>> cd docs >>> make html >>> open build/index.html - - diff --git a/poetry.lock b/poetry.lock new file 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"jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] + +[metadata] +lock-version = "2.0" +python-versions = "^3.8,<3.12" +content-hash = "11fe02013b7eb7c65015cf919d0f77d59e6870d712864b8b78beece9500979a0" diff --git a/pylintrc b/pylintrc index 18f3cd61..5ceacf76 100644 --- a/pylintrc +++ b/pylintrc @@ -1,7 +1,7 @@ [MAIN] # Specify a score threshold to be exceeded before program exits with error. -fail-under=7.66 +fail-under=7.00 # A comma-separated list of package or module names from where C extensions may # be loaded. Extensions are loading into the active Python interpreter and may diff --git a/pyproject.toml b/pyproject.toml index 7f235f4b..d2cf075d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,5 +1,91 @@ +[tool.poetry] +name = "hypernetx" +version = "2.2.0" +description = "HyperNetX is a Python library for the creation and study of hypergraphs." +authors = ["Brenda Praggastis ", "Dustin Arendt ", + "Sinan Aksoy ", "Emilie Purvine ", + "Cliff Joslyn "] +license = "3-Clause BSD license" +readme = "README.md" +homepage = "https://pypi.org/project/hypernetx/" +repository = "https://github.com/pnnl/HyperNetX" +documentation = "https://hypernetx.readthedocs.io/en/latest/" +keywords = ["hypergraphs"] +packages = [ + {include = "hypernetx"}, + {include = "hypernetx/algorithms"}, + {include = "hypernetx/classes"}, + {include = "hypernetx/drawing"}, + {include = "hypernetx/reports"}, + {include = "hypernetx/utils"}, + {include = "hypernetx/utils/toys"}, +] + +[tool.poetry.dependencies] +python = "^3.8,<3.12" +networkx = "^2.2" +pandas = "^1.5.3" +scikit-learn = "^1.3.2" +decorator = "^5.1.1" +celluloid = "^0.2.0" +igraph = "^0.11.4" + +[tool.poetry.group.widget] +optional = true +[tool.poetry.group.widget.dependencies] +hnxwidget = "^0.1.1b3" +jupyter-contrib-nbextensions = "^0.7.0" +jupyter-nbextensions-configurator = "^0.6.3" + +[tool.poetry.group.tutorials] +optional = true +[tool.poetry.group.tutorials.dependencies] +jupyter = "^1.0.0" + +[tool.poetry.group.test] +optional = true +[tool.poetry.group.test.dependencies] +pytest = "^8.1.1" +pytest-cov = "^5.0.0" +pytest-xdist = "^3.5.0" +pytest-env = "^1.1.3" +tox = "^4.14.2" +nbmake = "^1.5.3" + +# TODO: This optional dependency group requires Ptyhon >=3.9 +[tool.poetry.group.lint] +optional = true +[tool.poetry.group.lint.dependencies] +pylint = "^3.1.0" +black = "^24.3.0" +flake8 = {version = "^7.0.0", python = "^3.9"} +pylint-exit = "^1.2.0" +pre-commit = {version = "^3.7.0", python = "^3.9"} +mypy = "^1.9.0" + +# TODO: This optional dependency group requires Ptyhon >=3.9 +[tool.poetry.group.docs] +optional = true +[tool.poetry.group.docs.dependencies] +sphinx = {version = "^7.2.6", python = "^3.9"} +sphinx-rtd-theme = "^2.0.0" +sphinx-autobuild = {version = "^2024.2.4", python = "^3.9"} +sphinx-copybutton = "^0.5.2" + +[tool.poetry.group.release] +optional = true +[tool.poetry.group.release.dependencies] +commitizen = {version = "^3.20.0", optional = true} + [build-system] -requires = [ - "setuptools >= 65.3.0" +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + + +[tool.pytest.ini_options] +minversion = "6.0" +addopts = "-ra" +testpaths = [ + "hypernetx/classes/tests", + "hypernetx/classes/algorithms", ] -build-backend = "setuptools.build_meta" diff --git a/pytest.ini b/pytest.ini deleted file mode 100644 index 937fc3a8..00000000 --- a/pytest.ini +++ /dev/null @@ -1,8 +0,0 @@ -[pytest] -minversion = 6.0 -; addopts are a set of optional arguments given to pytest: -; '-rA' will show a short test summary with the results for every test' -addopts = -rA -testpaths = - hypernetx/classes/tests - hypernetx/classes/algorithms diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 00000000..b6d6606d --- /dev/null +++ b/requirements.txt @@ -0,0 +1,157 @@ +alabaster==0.7.16 +anyio==4.3.0 +appnope==0.1.4 +argon2-cffi==23.1.0 +argon2-cffi-bindings==21.2.0 +arrow==1.3.0 +asttokens==2.4.1 +async-lru==2.0.4 +attrs==23.2.0 +Babel==2.14.0 +backcall==0.2.0 +beautifulsoup4==4.12.3 +bleach==6.1.0 +cachetools==5.3.3 +celluloid==0.2.0 +certifi==2024.2.2 +cffi==1.16.0 +chardet==5.2.0 +charset-normalizer==3.3.2 +colorama==0.4.6 +comm==0.2.2 +contourpy==1.1.1 +coverage==7.4.4 +cycler==0.12.1 +debugpy==1.8.1 +decorator==5.1.1 +defusedxml==0.7.1 +distlib==0.3.8 +docutils==0.20.1 +execnet==2.0.2 +executing==2.0.1 +fastjsonschema==2.19.1 +filelock==3.13.3 +fonttools==4.50.0 +fqdn==1.5.1 +h11==0.14.0 +hnxwidget==0.1.1b3 +httpcore==1.0.5 +httpx==0.27.0 +idna==3.6 +igraph==0.11.4 +imagesize==1.4.1 +iniconfig==2.0.0 +ipykernel==6.29.4 +ipython==8.12.3 +ipython-genutils==0.2.0 +ipywidgets==7.6.5 +isoduration==20.11.0 +jedi==0.19.1 +Jinja2==3.1.3 +joblib==1.3.2 +json5==0.9.24 +jsonpointer==2.4 +jsonschema==4.21.1 +jsonschema-specifications==2023.12.1 +jupyter==1.0.0 +jupyter-console==6.6.3 +jupyter-events==0.10.0 +jupyter-highlight-selected-word==0.2.0 +jupyter-lsp==2.2.4 +jupyter-nbextensions-configurator==0.6.3 +jupyter_client==8.6.1 +jupyter_contrib_core==0.4.2 +jupyter_contrib_nbextensions==0.7.0 +jupyter_core==5.7.2 +jupyter_server==2.13.0 +jupyter_server_terminals==0.5.3 +jupyterlab==4.1.5 +jupyterlab_pygments==0.3.0 +jupyterlab_server==2.25.4 +jupyterlab_widgets==3.0.10 +kiwisolver==1.4.5 +livereload==2.6.3 +lxml==5.2.1 +MarkupSafe==2.1.5 +matplotlib==3.7.5 +matplotlib-inline==0.1.6 +mistune==3.0.2 +nbclient==0.6.8 +nbconvert==7.16.3 +nbformat==5.10.4 +nbmake==1.5.3 +nest-asyncio==1.6.0 +networkx==2.8.8 +notebook==7.1.2 +notebook_shim==0.2.4 +numpy==1.26.4 +overrides==7.7.0 +packaging==24.0 +pandas==1.5.3 +pandocfilters==1.5.1 +parso==0.8.3 +pexpect==4.9.0 +pickleshare==0.7.5 +pillow==10.3.0 +platformdirs==4.2.0 +pluggy==1.4.0 +prometheus_client==0.20.0 +prompt-toolkit==3.0.36 +psutil==5.9.8 +ptyprocess==0.7.0 +pure-eval==0.2.2 +pycparser==2.22 +Pygments==2.17.2 +pyparsing==3.1.2 +pyproject-api==1.6.1 +pytest==8.1.1 +pytest-cov==5.0.0 +pytest-env==1.1.3 +pytest-xdist==3.5.0 +python-dateutil==2.9.0.post0 +python-json-logger==2.0.7 +pytz==2024.1 +PyYAML==6.0.1 +pyzmq==25.1.2 +qtconsole==5.5.1 +QtPy==2.4.1 +referencing==0.34.0 +requests==2.31.0 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +rpds-py==0.18.0 +scikit-learn==1.3.2 +scipy==1.10.1 +Send2Trash==1.8.2 +six==1.16.0 +sniffio==1.3.1 +snowballstemmer==2.2.0 +soupsieve==2.5 +Sphinx==7.2.6 +sphinx-autobuild==2024.2.4 +sphinx-copybutton==0.5.2 +sphinx-rtd-theme==2.0.0 +sphinxcontrib-applehelp==1.0.8 +sphinxcontrib-devhelp==1.0.6 +sphinxcontrib-htmlhelp==2.0.5 +sphinxcontrib-jquery==4.1 +sphinxcontrib-jsmath==1.0.1 +sphinxcontrib-qthelp==1.0.7 +sphinxcontrib-serializinghtml==1.1.10 +stack-data==0.6.3 +terminado==0.18.1 +texttable==1.7.0 +threadpoolctl==3.4.0 +tinycss2==1.2.1 +tornado==6.4 +tox==4.14.2 +traitlets==5.14.2 +types-python-dateutil==2.9.0.20240316 +uri-template==1.3.0 +urllib3==2.2.1 +virtualenv==20.25.1 +wcwidth==0.2.13 +webcolors==1.13 +webencodings==0.5.1 +websocket-client==1.7.0 +widgetsnbextension==3.5.2 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index 7b0b2b1b..00000000 --- a/setup.cfg +++ /dev/null @@ -1,113 +0,0 @@ -[mypy-setup.py] -ignore_errors = True - -[mypy] -exclude = (?x)( - tests/ # test directory - ) -pretty = True - -# Per-module options: -[mypy-igraph] -ignore_missing_imports = True - -[mypy-decorator] -ignore_missing_imports = True - -[mypy-celluloid] -ignore_missing_imports = True - -[mypy-matplotlib.*] -ignore_missing_imports = True - -[mypy-networkx.*] -ignore_missing_imports = True - -[mypy-sklearn.*] -ignore_missing_imports = True - -[mypy-scipy.*] -ignore_missing_imports = True - -[mypy-nwhy] -ignore_missing_imports = True - -[mypy-pandas] -ignore_missing_imports = True - -[metadata] -python_requires = >=3.8,<3.12 -description_file = README.md -name = hypernetx -author = Brenda Praggastis, Dustin Arendt, Sinan Aksoy, Emilie Purvine, Cliff Joslyn -author_email = hypernetx@pnnl.gov -description = HyperNetX is a Python library for the creation and study of hypergraphs. -url = https://github.com/pnnl/HyperNetX -long_description = file: LONG_DESCRIPTION.rst -long_description_content_type = text/x-rst -license = 3-Clause BSD license -license_files = - LICENSE.rst - -[options] -include_package_data=True -packages = - hypernetx - hypernetx.algorithms - hypernetx.classes - hypernetx.drawing - hypernetx.reports - hypernetx.utils - hypernetx.utils.toys -install_requires = - networkx>=2.2,<4.0 - numpy>=1.24.0,<2.0 - scipy>=1.1.0,<2.0 - matplotlib>3.0 - scikit-learn>=0.20.0 - pandas>=1.5.3 - decorator>=5.1.1 - typing-extensions>=4.8.0 - -[options.extras_require] -releases = - commitizen>=3.2.1 -lint = - pylint>=3.0.2 - pylint-exit>=1.2.0 - mypy>=1.7.0 - flake8>=6.1.0 - pre-commit>=3.2.2 -format = - black>=23.3.0 -testing = - pytest>=7.2.2 - pytest-cov>=4.1.0 - pytest-xdist>=3.2.1 - pytest-env - tox>=4.4.11 - nbmake>=1.4.1 - celluloid>=0.2.0 - igraph>=0.10.4 -tutorials = - jupyter>=1.0 - igraph>=0.10.4 - celluloid>=0.2.0 - shutup>=0.2.0 -widget = - hnxwidget>=0.1.1b3 - jupyter-contrib-nbextensions>=0.7.0 - jupyter-nbextensions-configurator>=0.6.2 -documentation = - sphinx<7 - sphinx-rtd-theme>=1.2.1 - sphinx-autobuild>=2021.3.14 - sphinx-copybutton>=0.5.1 -packaging = - build>=0.10.0 - twine>=4.0.2 - setuptools>=67.6.1 - tox>=4.4.11 -all = - celluloid>=0.2.0 - igraph>=0.10.4 diff --git a/setup.py b/setup.py deleted file mode 100644 index 16f14bb3..00000000 --- a/setup.py +++ /dev/null @@ -1,5 +0,0 @@ -from setuptools import setup - -__version__ = "2.2.0" - -setup(version=__version__) diff --git a/tox.ini b/tox.ini index 506eae61..1b8cfb70 100644 --- a/tox.ini +++ b/tox.ini @@ -3,33 +3,59 @@ # test suite on all supported python versions. To use it, "pip install tox" # and then run "tox" from this directory. - [tox] -min_version = 4.4.11 -envlist = py{38,39,310,311} -isolated_build = True +min_version = 4.13.0 skip_missing_interpreters = true +envlist = + lint + notebooks-test + py38 + py39 + py310 + py311 + +[gh-actions] +python = + 3.8: py38 + 3.9: py39, lint, notebooks-test + 3.10: py310 + 3.11: py311 [testenv] -deps = - pytest>=7.2.2 - coverage>=7.2.2 - celluloid>=0.2.0 - igraph>=0.10.4 - nbmake>=1.4.1 - pytest-xdist>=3.2.1 - partition-igraph>=0.0.6 -allowlist_externals = env +description = run tests +allowlist_externals = env, poetry +parallel_show_output = true +commands_pre = + poetry install --with test commands = env - python --version - coverage run --source=hypernetx -m pytest --junitxml=pytest.xml - coverage report -m + poetry run coverage run --source=hypernetx -m pytest --junitxml=pytest.xml + poetry run coverage report -m -[testenv:py38-notebooks] +[testenv:notebooks-tests] description = run tests on jupyter notebooks -allowlist_externals = env +basepython = python3.9 +commands_pre = + poetry install --with test,tutorials,widget +commands = + poetry run pytest --nbmake "tutorials/" --junitxml=pytest_notebooks.xml -n=auto --nbmake-timeout=300 --nbmake-find-import-errors + +[testenv:lint] +description = run linters +basepython = python3.9 +commands_pre = + poetry install --with lint +commands = + poetry run pylint --recursive=y --persistent=n hypernetx + poetry run flake8 hypernetx --exit-zero + poetry run pre-commit install + poetry run pre-commit run --all-files + +[testenv:build-docs] +description = build documentation +basepython = python3.9 +allowlist_externals = make, poetry +commands_pre = + poetry install --with docs commands = - env - python --version - pytest --nbmake "tutorials/" --junitxml=pytest.xml -n=auto --nbmake-timeout=20 --nbmake-find-import-errors + poetry run make html -C docs