Merge pull request #302 from hatemhelal/checks

Adding pre-commit checks and github action runners

.github/workflow/lint.yml

@@ -7,7 +7,7 @@ on: []
   #   branches: []
   # pull_request:
   #   branches: []
- 
+
 
 jobs:
   build-linux:
@@ -43,4 +43,4 @@ jobs:
 #        run: mypy --config-file=.mypy.ini .
 
       - name: Test with pytest
-        run: python -m pytest tests
+        run: python -m pytest tests

.github/workflow/pre-commit.yaml

@@ -0,0 +1,14 @@
+name: Pre-Commit Checks
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/[email protected]

.github/workflow/unittest.yaml

@@ -0,0 +1,29 @@
+name: unit tests
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pytest-container:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+
+      - name: Install requirements
+        run: |
+          pip install -U pip
+          pip install .[dev]
+
+      - name: Log installed environment
+        run: |
+          python3 -m pip freeze
+
+      - name: Run unit tests
+        run: |
+          pytest tests

.pre-commit-config.yaml

@@ -0,0 +1,50 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.12.1
+    hooks:
+      - id: black
+        name: Black Formating
+
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        name: Sort imports
+
+  # Failing - to be investigated separately
+  # - repo: local
+  #   hooks:
+  #     - id: pylint
+  #       name: Pylint Checks
+  #       entry: pylint
+  #       language: system
+  #       types: [python]
+  #       args:
+  #         [
+  #           "--rcfile=pyproject.toml", 
+  #           "mace", 
+  #           "tests", 
+  #           "scripts"
+  #         ]  
+
+  # - repo: local
+  #   hooks:
+  #     - id: mypy
+  #       name: mypy type checks
+  #       entry: mypy
+  #       language: system
+  #       types: [python]
+  #       args:
+  #         [
+  #           --config-file=.mypy.ini,
+  #           mace,
+  #           tests,
+  #           scripts
+  #         ]
+

README.md

@@ -164,7 +164,7 @@ mace_eval_configs \
 
 ## Tutorial
 
-You can run our [Colab tutorial](https://colab.research.google.com/drive/1D6EtMUjQPey_GkuxUAbPgld6_9ibIa-V?authuser=1#scrollTo=Z10787RE1N8T) to quickly get started with MACE. 
+You can run our [Colab tutorial](https://colab.research.google.com/drive/1D6EtMUjQPey_GkuxUAbPgld6_9ibIa-V?authuser=1#scrollTo=Z10787RE1N8T) to quickly get started with MACE.
 
 We also have a more detailed user and developer tutorial at https://github.com/ilyes319/mace-tutorials
 
@@ -203,7 +203,7 @@ print(atoms.get_potential_energy())
 
 ### MACE-OFF: Transferable Organic Force Fields
 
-There is a series (small, medium, large) transferable organic force fields. These can be used for the simulation of organic molecules, crystals and molecular liquids, or as a starting point for fine-tuning on a new dataset. The models are released under the [ASL license](https://github.com/gabor1/ASL). 
+There is a series (small, medium, large) transferable organic force fields. These can be used for the simulation of organic molecules, crystals and molecular liquids, or as a starting point for fine-tuning on a new dataset. The models are released under the [ASL license](https://github.com/gabor1/ASL).
 The models are releaed on GitHub at https://github.com/ACEsuit/mace-off.
 If you use them please cite [our paper](https://arxiv.org/abs/2312.15211) which also contains detailed benchmarks and example applications.
 
@@ -220,13 +220,15 @@ print(atoms.get_potential_energy())
 
 ## Development
 
-We use `black`, `isort`, `pylint`, and `mypy`.
-Run the following to format and check your code:
-
-```sh
-bash ./scripts/run_checks.sh
+This project uses [pre-commit](https://pre-commit.com/) to execute code formatting and linting on commit.
+We also use `black`, `isort`, `pylint`, and `mypy`.
+We recommend setting up your development environment by installing the `dev` packages
+into your python environment:
+```bash
+pip install -e ".[dev]"
+pre-commit install
 ```
-
+The second line will initialise `pre-commit` to automaticaly run code checks on commit.
 We have CI set up to check this, but we _highly_ recommend that you run those commands
 before you commit (and push) to avoid accidentally committing bad code.
 

pyproject.toml

@@ -36,4 +36,4 @@ disable = [
 ignore-paths = [
     "^mace/tools/torch_geometric/.*$",
     "^mace/tools/scatter.py$",
-]
+]

setup.cfg

@@ -36,3 +36,10 @@ console_scripts =
 
 [options.extras_require]
 wandb = wandb
+dev =
+    black
+    isort
+    mypy
+    pre-commit
+    pytest
+    pylint

tests/test_calculator.py

@@ -6,10 +6,10 @@
 import ase.io
 import numpy as np
 import pytest
+from ase import build
 from ase.atoms import Atoms
 from ase.calculators.test import gradient_test
 from ase.constraints import ExpCellFilter
-from ase import build
 
 from mace.calculators import mace_mp, mace_off
 from mace.calculators.foundations_models import local_model_path