extend pre-commit (pyg-team#4292)

* extend pre-commit

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* update

* remove unused hooks

* added name

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Matthias Fey <[email protected]>

.github/workflows/linting.yml

@@ -8,85 +8,8 @@ on:  # yamllint disable-line rule:truthy
 
 jobs:
 
-  flake8:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install dependencies
-        run: |
-          pip install flake8
-
-      - name: Run linting
-        run: |
-          flake8 .
-
-  pyroma:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install dependencies
-        run: |
-          pip install pyroma
-
-      - name: Check package metadata
-        run: |
-          pyroma --min=10 .
-
-  yamllint:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install dependencies
-        run: |
-          pip install yamllint
-
-      - name: Run linting
-        run: |
-          yamllint .
-
-  isort:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.9
-
-      - name: Install dependencies
-        run: |
-          pip install isort
-
-      - name: Run linting
-        run: |
-          isort --check-only .
-
   pylint:
     runs-on: ubuntu-latest
-
     steps:
       - uses: actions/checkout@v2
 
@@ -96,17 +19,14 @@ jobs:
           python-version: 3.9
 
       - name: Install dependencies
-        run: |
-          pip install pylint
+        run: pip install pylint
 
       - name: Run linting
         continue-on-error: true
-        run: |
-          pylint **/*.py
+        run: pylint **/*.py
 
   mypy:
     runs-on: ubuntu-latest
-
     steps:
       - uses: actions/checkout@v2
 
@@ -116,8 +36,7 @@ jobs:
           python-version: 3.9
 
       - name: Install dependencies
-        run: |
-          pip install mypy
+        run: pip install mypy
 
       - name: Check type hints
         continue-on-error: true

.pre-commit-config.yaml

@@ -2,6 +2,25 @@ ci:
   autoupdate_schedule: quarterly
 
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-yaml
+        exclude: |
+          (?x)^(
+              conda/pytorch-geometric/meta.yaml|
+              conda/pyg/meta.yaml
+          )$
+
+  - repo: https://github.com/regebro/pyroma
+    rev: "3.2"
+    hooks:
+      - id: pyroma
+        name: Check packaging
+        args: [--min=10, .]
+
   - repo: https://github.com/pre-commit/mirrors-yapf
     rev: v0.31.0
     hooks:
@@ -13,3 +32,9 @@ repos:
     hooks:
       - id: isort
         name: Sort imports
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        name: Check PEP8

benchmark/kernel/README.md

@@ -22,7 +22,7 @@ Run (or modify) the whole test suite via
 $ python main.py
 ```
 
-For more comprehensive time-measurement and memory usage information, you may use 
+For more comprehensive time-measurement and memory usage information, you may use
 
 ```
 $ python main_performance.py

docker/Dockerfile

@@ -66,7 +66,7 @@ ENV NVIDIA_REQUIRE_CUDA "cuda>=10.0 brand=tesla,driver>=384,driver<385 brand=tes
 
 # PyTorch (Geometric) installation
 RUN rm /etc/apt/sources.list.d/cuda.list && \
-    rm /etc/apt/sources.list.d/nvidia-ml.list 
+    rm /etc/apt/sources.list.d/nvidia-ml.list
 
 RUN apt-get update &&  apt-get install -y \
     curl \

docs/source/modules/profile.rst

@@ -12,4 +12,3 @@ torch_geometric.profile
 .. automodule:: torch_geometric.profile
     :members:
     :undoc-members:
-

examples/quiver/README.md

@@ -37,4 +37,4 @@ python multi_gpu_quiver.py
 
 ### Distributed Training
 
-A Quiver-based distributed PyG example is coming soon.
+A Quiver-based distributed PyG example is coming soon.

graphgym/grids/example.txt

@@ -15,4 +15,3 @@ gnn.layers_mp l_mp [2,4,6,8]
 gnn.layers_post_mp l_post [2,3]
 gnn.stage_type stage ['skipsum','skipconcat']
 gnn.agg agg ['add','mean','max']
-

graphgym/sample/dimensions.txt

@@ -1 +1 @@
-act bn drop agg l_mp l_pre l_post stage batch lr optim epoch
+act bn drop agg l_mp l_pre l_post stage batch lr optim epoch

graphgym/sample/dimensionsatt.txt

@@ -1 +1 @@
-l_tw
+l_tw

torch_geometric/nn/sequential.jinja

@@ -27,4 +27,3 @@ class {{cls_name}}(torch.nn.Module):
     def __repr__(self) -> str:
         return 'Sequential(\n{}\n)'.format('\n'.join(
             [f'  ({idx}): ' + str(self[idx]) for idx in range(len(self))]))
-