Simplify pre-commit setup

.flake8

@@ -0,0 +1,3 @@
+[flake8]
+max-line-length = 88
+ignore = E203, F811, I002, W503

.github/workflows/pre-commit.yml

@@ -1,33 +1,25 @@
-name: Run pre-commit job
+name: lint
 
 on:
- push:
+  # trigger on pushes to any branch, but not main
+  push:
+    branches-ignore:
+      - main
+  # and also on PRs to main
+  pull_request:
     branches:
-    - main
- pull_request:
-    branches:
-    - main
+      - main
 
 jobs:
- pre-commit-job:
+  pre-commit-job:
     runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: 3.9
-    - name: Install pre-commit hooks
-      run: |
-        pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 \
-          --index-url https://download.pytorch.org/whl/cpu
-        pip install -r requirements.txt
-        pip install pyg-lib==0.2.0 torch-scatter==2.1.1 torch-sparse==0.6.17 \
-          torch-cluster==1.6.1 torch-geometric==2.3.1 \
-          -f https://pytorch-geometric.com/whl/torch-2.0.1+cpu.html
-    - name: Run pre-commit hooks
-      run: |
-        pre-commit run --all-files
+        python-version: ${{ matrix.python-version }}
+    - uses: pre-commit/action@v2.0.3

.pre-commit-config.yaml

@@ -1,51 +1,37 @@
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
     hooks:
-    -   id: check-ast
-    -   id: check-case-conflict
-    -   id: check-docstring-first
-    -   id: check-symlinks
-    -   id: check-toml
-    -   id: check-yaml
-    -   id: debug-statements
-    -   id: end-of-file-fixer
-    -   id: trailing-whitespace
--   repo: local
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
     hooks:
-    -   id: codespell
-        name: codespell
+      - id: codespell
         description: Check for spelling errors
-        language: system
-        entry: codespell
--   repo: local
+
+  - repo: https://github.com/psf/black
+    rev: 22.3.0
     hooks:
-    -   id: black
-        name: black
+      - id: black
         description: Format Python code
-        language: system
-        entry: black
-        types_or: [python, pyi]
--   repo: local
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
     hooks:
-    -   id: isort
-        name: isort
+      - id: isort
         description: Group and sort Python imports
-        language: system
-        entry: isort
-        types_or: [python, pyi, cython]
--   repo: local
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.0.0
     hooks:
-    -   id: flake8
-        name: flake8
+      - id: flake8
         description: Check Python code for correctness, consistency and adherence to best practices
-        language: system
-        entry: flake8 --max-line-length=80 --ignore=E203,F811,I002,W503
-        types: [python]
--   repo: local
-    hooks:
-    -   id: pylint
-        name: pylint
-        entry: pylint -rn -sn
-        language: system
-        types: [python]

CHANGELOG.md

@@ -55,6 +55,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   [\#13](https://github.com/joeloskarsson/neural-lam/pull/13)
   @joeloskarsson
 
+### Maintenance
+
+- simplify pre-commit setup by 1) reducing linting to only cover static
+  analysis excluding imports from external dependencies (this will be handled
+  in build/test cicd action introduced later), 2) pinning versions of linting
+  tools in pre-commit config (and remove from `requirements.txt`) and 3) using
+  github action to run pre-commit.
+  [\#29](https://github.com/mllam/neural-lam/pull/29)
+  @leifdenby
+
+
 ## [v0.1.0](https://github.com/joeloskarsson/neural-lam/releases/tag/v0.1.0)
 
 First tagged release of `neural-lam`, matching Oskarsson et al 2023 publication

neural_lam/models/base_hi_graph_model.py

@@ -36,7 +36,7 @@ def __init__(self, args):
             if level_index < (self.num_levels - 1):
                 up_edges = self.mesh_up_features[level_index].shape[0]
                 down_edges = self.mesh_down_features[level_index].shape[0]
-                print(f"  {level_index}<->{level_index+1}")
+                print(f"  {level_index}<->{level_index + 1}")
                 print(f" - {up_edges} up edges, {down_edges} down edges")
         # Embedders
         # Assume all levels have same static feature dimensionality
@@ -179,9 +179,9 @@ def process_step(self, mesh_rep):
             )
 
             # Update node and edge vectors in lists
-            mesh_rep_levels[level_l] = (
-                new_node_rep  # (B, num_mesh_nodes[l], d_h)
-            )
+            mesh_rep_levels[
+                level_l
+            ] = new_node_rep  # (B, num_mesh_nodes[l], d_h)
             mesh_up_rep[level_l - 1] = new_edge_rep  # (B, M_up[l-1], d_h)
 
         # - PROCESSOR -
@@ -207,9 +207,9 @@ def process_step(self, mesh_rep):
             new_node_rep = gnn(send_node_rep, rec_node_rep, edge_rep)
 
             # Update node and edge vectors in lists
-            mesh_rep_levels[level_l] = (
-                new_node_rep  # (B, num_mesh_nodes[l], d_h)
-            )
+            mesh_rep_levels[
+                level_l
+            ] = new_node_rep  # (B, num_mesh_nodes[l], d_h)
 
         # Return only bottom level representation
         return mesh_rep_levels[0]  # (B, num_mesh_nodes[0], d_h)

plot_graph.py

@@ -48,11 +48,7 @@ def main():
 
     # Load graph data
     hierarchical, graph_ldict = utils.load_graph(args.graph)
-    (
-        g2m_edge_index,
-        m2g_edge_index,
-        m2m_edge_index,
-    ) = (
+    (g2m_edge_index, m2g_edge_index, m2m_edge_index,) = (
         graph_ldict["g2m_edge_index"],
         graph_ldict["m2g_edge_index"],
         graph_ldict["m2m_edge_index"],

requirements.txt

@@ -10,10 +10,6 @@ Cartopy>=0.22.0
 pyproj>=3.4.1
 tueplots>=0.0.8
 plotly>=5.15.0
+
 # for dev
-codespell>=2.0.0
-black>=21.9b0
-isort>=5.9.3
-flake8>=4.0.1
-pylint>=3.0.3
 pre-commit>=2.15.0