Switch from setup.py to pyproject.toml (#573)

* add toml * Add .rst readme * fix format * undo readme changes * remove setup.py from manifest * try to fix rtd build * try again * Update .readthedocs.yaml * Update .readthedocs.yaml * fix * fix optional dependency * fix refs to `DiIDView` * add metadata * change find where * Update pyproject.toml * updated requirements * updated README and pyproject.toml * clean up install * Update coverage.yml * try fixing install * Update coverage.yml * attempt to fix tests * try something else * response to review * update publishing commands * clean up some dependencies * removed unnecessary attribution * reduce number of requests to zenodo * format * update tests * fix tests * try to be consistent
xgi-org · Aug 28, 2024 · 9492352 · 9492352
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diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -11,16 +11,15 @@ jobs:
     runs-on: ubuntu-latest
     name: Test coverage
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
       - name: Install packages
         run: |
-          python -m pip install --upgrade pip wheel setuptools
-          pip install -r requirements/default.txt -r requirements/test.txt
-          pip install .
-          python -m pip list
+          pip install --upgrade pip
+          pip install .[test]
+          pip list
       - name: Run tests and collect coverage
         run: |
           cd tests/

diff --git a/.github/workflows/publish_xgi.yml b/.github/workflows/publish_xgi.yml
@@ -21,18 +21,24 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.11'
+        python-version: '3.12'
+
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        python -m pip install setuptools
+        pip install --upgrade pip
+        pip install -U build twine
+    
     - name: Build package
       run: |
-        python setup.py sdist
+        python -m build
+    
+    - name: Verify the distribution
+      run: twine check --strict dist/*
+
     - name: Publish package
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -114,19 +114,18 @@ jobs:
         os: [ubuntu, macos, windows]
         python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install packages
       run: |
-        python -m pip install --upgrade pip wheel setuptools
-        python -m pip install -r requirements/default.txt -r requirements/test.txt -r requirements/documentation.txt
-        python -m pip install .
-        python -m pip list
+        pip install --upgrade pip
+        pip install .[test,docs]
+        pip list
 
     - name: Test XGI
       run: |

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -21,9 +21,7 @@ python:
     - method: pip
       path: .
       extra_requirements:
-        - documentation
-    - method: setuptools
-      path: .
+        - docs
 
 formats:
   - pdf

diff --git a/HOW_TO_CONTRIBUTE.md b/HOW_TO_CONTRIBUTE.md
@@ -28,10 +28,6 @@ Please note we have a [code of conduct](/CODE_OF_CONDUCT.md), please follow it i
 3. Increase the version number in [\_\_init\_\_.py](xgi/__init__.py.py) and [conf.py](docs/source/conf.py) to the new version agreed upon by the core developers. The versioning scheme we use is [SemVer](http://semver.org/).
 4. Commit these changes.
 5. Create a new release on GitHub by selecting "Releases", then clicking "Draft a new release". Click "Choose a tag" and type "v" followed by the version number and then click "Create new tag". The release title will be this same string. Paste the contents of the CHANGELOG into the "Describe this release" field. Click "Publish release".
-6. Run `python setup.py sdist` from the main folder. This will create a zipped file to upload to PyPI and save it to the "dist" folder.
+6. Run `python -m build` from the main folder. This will create a zipped file to upload to PyPI and save it to the "dist" folder.
 6. Using `twine` (a dependency in the [release](requirements/release.txt) requirements file), run `twine upload dist/xgi-[version number].tar.gz`. Enter your username and password.
-4. The new version is now on PyPI.
-
-## Attribution
-
-This Contributing Statement is adapted from [this template by @PurpleBooth](https://gist.github.com/PurpleBooth/b24679402957c63ec426).
+4. The new version is now on PyPI.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,12 +1,8 @@
 include MANIFEST.in
-include setup.py
-include HOW_TO_CONTRIBUTE.md
-include long_description.rst
+include pyproject.toml
 include README.md
 include LICENSE.md
 include CITATION.cff
-include CODE_OF_CONDUCT.md
-include pytest.ini
 
 recursive-include logo *.pdf *.png *.svg
 recursive-include requirements *.txt *.md

diff --git a/README.md b/README.md
@@ -58,8 +58,9 @@ pip install -e .["all"]
 ```
 * If that command does not work, you may try the following instead
 ````zsh
-pip install -e .\[all\]
+pip install -e ."[all]"
 ````
+For more installation options, see the [guide](https://github.com/xgi-org/xgi/blob/main/requirements/README.md).
 
 
 ## Getting Started
@@ -131,4 +132,4 @@ This library may not meet your needs and if this is this case, consider checking
 
 
 **R**
-* [hyperG](https://cran.r-project.org/package=HyperG): An R package for storing and analyzing hypergraphs
+* [hyperG](https://cran.r-project.org/package=HyperG): An R package for storing and analyzing hypergraphs
diff --git a/docs/source/api/core/xgi.core.views.DiEdgeView.rst b/docs/source/api/core/xgi.core.views.DiEdgeView.rst
@@ -24,5 +24,5 @@ xgi.core.views.DiEdgeView
       ~DiEdgeView.dimembers
       ~DiEdgeView.head
       ~DiEdgeView.tail
-      ~DiIDView.filterby
-      ~DiIDView.filterby_attr
+      ~IDView.filterby
+      ~IDView.filterby_attr
diff --git a/docs/source/api/core/xgi.core.views.DiNodeView.rst b/docs/source/api/core/xgi.core.views.DiNodeView.rst
@@ -22,6 +22,6 @@ xgi.core.views.DiNodeView
 
       ~DiNodeView.memberships
       ~DiNodeView.dimemberships
-      ~DiIDView.filterby
-      ~DiIDView.filterby_attr
+      ~IDView.filterby
+      ~IDView.filterby_attr
       ~DiNodeView.isolates
diff --git a/long_description.rst b/long_description.rst
diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,105 @@
+[build-system]
+build-backend = "setuptools.build_meta"
+requires = ["setuptools>=61.2", "wheel"]
+
+[project]
+name = "xgi"
+dynamic = ["version"]
+description = "XGI is a Python package for higher-order networks."
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE.md"}
+authors = [
+    {name = "XGI Developers", email = "[email protected]"}
+]
+maintainers = [
+    {name = "XGI Developers", email = "[email protected]"}
+]
+keywords = [
+    "networks",
+    "higher-order",
+    "higher-order network",
+    "hypergraph",
+    "simplicial complex",
+    "network science",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3 :: Only",
+    "Topic :: Software Development :: Libraries :: Python Modules",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    "numpy>=1.20",
+    "scipy>=1.8",
+    "pandas>=1.3",
+    "networkx>=2.7",
+    "requests>=2.0",
+    "matplotlib>=3.4",
+    "seaborn>=0.10",
+]
+
+[project.urls]
+Documentation = "https://xgi.readthedocs.io/en/stable/"
+"Bug Reports" = "https://github.com/xgi-org/xgi/issues"
+Source = "https://github.com/xgi-org/xgi"
+PyPI = "https://pypi.org/project/xgi/"
+"GitHub Discussions" = "https://github.com/xgi-org/xgi/discussions"
+
+[project.optional-dependencies]
+benchmark = [
+    "hypernetx>=1.0",
+    "asv>=0.5",
+]
+developer = [
+    "black[jupyter]>=24.3",
+    "isort==5.10.1",
+    "pylint>=3.0",
+    "nbqa",
+]
+docs = [
+    "sphinx~=6.0",
+    "sphinx_copybutton",
+    "sphinx-rtd-theme>=1.2",
+    "numpydoc>=1.1",
+    "pillow>=8.2",
+    "matplotlib>=3.3",
+    "sphinx-design",
+    "ipykernel",
+    "nbsphinx",
+    "nbsphinx-link",
+]
+release = [
+    "twine>=3.4",
+    "build>=1.2.1",
+    "wheel>=0.36",
+    "github-changelog",
+]
+test = [
+    "pytest>=7.2",
+    "pytest-cov>=4.0",
+]
+tutorial = [
+    "jupyter>=1.0",
+    "ipython<=8.12.0",
+]
+all = ["xgi[benchmark,developer,docs,release,test,tutorial]"]
+
+[tool.setuptools.packages.find]
+where = ["."]
+
+[tool.setuptools.dynamic.version]
+attr = "xgi.__version__"
diff --git a/requirements/README.md b/requirements/README.md
@@ -1,24 +1,39 @@
-# pip requirements files
+# Installation instructions
 
-## Index
+## pip installing with options
 
+You may wish to selectively install dependencies required for testing, developing, or building certain parts of the project.
+These options are the following:
+
+- `benchmark`: Requirements needed to run the benchmarking notebooks
+- `tutorial`: Requirements needed to run the Jupyter Notebooks with the examples
+- `test`: Requirements needed to run the test suite
+- `docs`: Requirements needed to build the documentation (see the [docs](https://github.com/xgi-org/xgi/tree/main/docs))
+- `developer`: Requirements needed to format the codebase
+- `release`: Requirements needed to release new versions of XGI
+
+```sh
+pip install xgi[option]
+pip install xgi[option1,option2]
+```
+
+## pip installing dependencies (without installing XGI)
+
+You may wish to install the dependencies without actually installing XGI itself. The following are the requirements files to do that:
+
+- `benchmark.txt`: Requirements to run the benchmarking notebooks
 - `default.txt`: Default requirements
 - `tutorial.txt`: Requirements for running the Jupyter Notebooks with the examples
 - `test.txt`: Requirements for running test suite
-- `documentation.txt`: Requirements for building the documentation (see `../docs/`)
+- `docs.txt`: Requirements for building the documentation (see `../docs/`)
 - `developer.txt`: Requirements for developers
 - `release.txt`: Requirements for making releases
 
-## Examples
-
-### Installing requirements
-
+To install these dependencies, simply run
 ```bash
-$ pip install -U -r requirements/default.txt
+$ pip install -U -r requirements/{filename}
 ```
-
-### Running the tests
-
+where the filename is one of the ones listed above. For example, to install the requirements necessary to run the test suite, run
 ```bash
 $ pip install -U -r requirements/default.txt
 $ pip install -U -r requirements/test.txt

diff --git a/requirements/benchmark.txt b/requirements/benchmark.txt
@@ -0,0 +1,4 @@
+# Generated via tools/generate_requirements.py and pre-commit hook.
+# Do not edit this file; modify pyproject.toml instead.
+hypernetx>=1.0
+asv>=0.5
diff --git a/requirements/benchmarks.txt b/requirements/benchmarks.txt