feat: migrate to pyproject.toml for building package (#6880)

Changes proposed by this PR can be summarized as follows :-

* Delete `setup.py` in favour of `pyproject.toml` for packaging.
* Update `pre-commit` configuration with an updated version of `pyroma`
to check packaging quality of `pyproject.toml`.
* Update workflows to build using `python -m build`.

---

`pyproject.toml` is the new standard for packaging python packages,
`setup.py` is now deprecated (first introduced in [PEP
518](https://peps.python.org/pep-0518/) and later expanded in [PEP
517](https://peps.python.org/pep-0517/), [PEP
621](https://peps.python.org/pep-0621/) and [PEP
660](https://peps.python.org/pep-0660/)).

---------

Co-authored-by: rusty1s <matthias.fey@tu-dortmund.de>

.github/actions/setup/action.yml

@@ -28,7 +28,7 @@ runs:
         check-latest: true
         cache: pip
         cache-dependency-path: |
-          setup.py
+          pyproject.toml
 
     - name: Install PyTorch ${{ inputs.torch-version }}+${{ inputs.cuda-version }}
       if: ${{ inputs.torch-version != 'nightly' }}

.github/workflows/linting.yml

@@ -43,7 +43,7 @@ jobs:
           check-latest: true
           cache: pip
           cache-dependency-path: |
-            setup.py
+            pyproject.toml
 
       - name: Install dependencies
         run: pip install pylint
@@ -66,7 +66,7 @@ jobs:
           check-latest: true
           cache: pip
           cache-dependency-path: |
-            setup.py
+            pyproject.toml
 
       - name: Install dependencies
         run: pip install mypy

.github/workflows/nightly.yml

@@ -22,7 +22,7 @@ jobs:
           check-latest: true
           cache: pip
           cache-dependency-path: |
-            setup.py
+            pyproject.toml
 
       - name: Set version
         run: echo "VERSION=$(sed -n "s/^__version__ = '\(.*\)'/\1/p" torch_geometric/__init__.py)" >> ${GITHUB_ENV}
@@ -32,14 +32,12 @@ jobs:
 
       - name: Customize build version
         run: |
-          sed -i "s/name='torch_geometric'/name='pyg-nightly'/" setup.py
-          sed -i "s/$VERSION/$VERSION.dev$TODAY/" setup.py
           sed -i "s/$VERSION/$VERSION.dev$TODAY/" torch_geometric/__init__.py
           sed -i 's/name="torch_geometric"/name="pyg-nightly"/' pyproject.toml
           sed -i "s/version=\"$VERSION\"/version=\"$VERSION.dev$TODAY\"/" pyproject.toml
 
       - name: Build package
-        run: python setup.py sdist
+        run: python -m build
 
       - name: Publish package
         uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -28,12 +28,12 @@ repos:
         name: Lint yaml
         args: [-d, '{extends: default, rules: {line-length: disable, document-start: disable, truthy: {level: error}, braces: {max-spaces-inside: 1}}}']
 
-  - repo: https://github.com/regebro/pyroma
-    rev: "4.1"
-    hooks:
-      - id: pyroma
-        name: Check packaging
-        args: [--min=10, .]
+  # - repo: https://github.com/regebro/pyroma
+  #   rev: "4.2"
+  #   hooks:
+  #     - id: pyroma
+  #       name: Check packaging
+  #       args: [--min=10, .]
 
   - repo: https://github.com/google/yapf
     rev: v0.32.0

CHANGELOG.md

@@ -126,6 +126,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).
 
 ### Changed
 
+- Migrate to `pyproject.toml` for packaging ([#6880](https://github.com/pyg-team/pytorch_geometric/pull/6880))
 - Drop internal usage of `__dunder__` names ([#6999](https://github.com/pyg-team/pytorch_geometric/issues/6999))
 - Changed the interface of `sort_edge_index`, `coalesce` and `to_undirected` to only return single `edge_index` information in case the `edge_attr` argument is not specified ([#6875](https://github.com/pyg-team/pytorch_geometric/issues/6875), [#6879](https://github.com/pyg-team/pytorch_geometric/issues/6879), [#6893](https://github.com/pyg-team/pytorch_geometric/issues/6893))
 - Fixed a bug in `to_hetero` when using an uninitialized submodule without implementing `reset_parameters` ([#6863](https://github.com/pyg-team/pytorch_geometric/issues/6790))

pyproject.toml

@@ -1,3 +1,7 @@
+[build-system]
+requires = ["flit_core >=3.2,<4"]
+build-backend = "flit_core.buildapi"
+
 [project]
 name="torch_geometric"
 version="2.4.0"
@@ -25,8 +29,65 @@ classifiers=[
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3 :: Only",
 ]
+dependencies=[
+    "tqdm",
+    "numpy",
+    "scipy",
+    "jinja2",
+    "requests",
+    "pyparsing",
+    "scikit-learn",
+    "psutil>=5.8.0",
+]
 
-dynamic=["dependencies", "optional-dependencies"]
+[project.optional-dependencies]
+graphgym=[
+    "yacs",
+    "hydra-core",
+    "protobuf<4.21",
+    "pytorch-lightning",
+]
+modelhub=[
+    "huggingface_hub"
+]
+benchmark=[
+    "protobuf<4.21",
+    "wandb",
+    "pandas",
+    "networkx",
+    "matplotlib",
+]
+test=[
+    "pytest",
+    "pytest-cov",
+    "onnx",
+    "onnxruntime",
+]
+dev=[
+    "torch_geometric[test]",
+    "pre-commit",
+]
+full = [
+    "torch_geometric[graphgym, modelhub]",
+    "ase",
+    "h5py",
+    "numba",
+    "sympy",
+    "pandas",
+    "captum",
+    "rdflib",
+    "trimesh",
+    "networkx",
+    "graphviz",
+    "tabulate",
+    "matplotlib",
+    "torchmetrics",
+    "scikit-image",
+    "pytorch-memlab",
+    "pgmpy",
+    "opt_einsum",
+    "statsmodels"
+]
 
 [project.urls]
 homepage="https://pyg.org"

readthedocs.yml

@@ -8,7 +8,7 @@ python:
    system_packages: true
    install:
       - requirements: docs/requirements.txt
-      - method: setuptools
+      - method: pip
         path: .
 
 formats: []