Add ruff-precommit, remove pydocstyle (#138)

* add ruff changes

* remove import *

* change max line length back to 80

.github/workflows/pytest.yml

@@ -2,7 +2,6 @@ name: pytest
 
 on:
   push:
-    # Action will run when any changes to these paths are pushed or pr'ed to master
     branches: [ main ]
     paths:
       - flowermd/**
@@ -26,6 +25,7 @@ on:
 
 jobs:
   pytest:
+    if: github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:

.pre-commit-config.yaml

@@ -1,27 +1,27 @@
 ci:
   autofix_commit_msg: |
     [pre-commit.ci] auto fixes from pre-commit.com hooks
-
     for more information, see https://pre-commit.ci
   autofix_prs: true
   autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
   autoupdate_schedule: weekly
   skip: [ ]
   submodules: false
-
 repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.2 # Ruff version
+    hooks:
+      - id: ruff
+        args: [--fix, --extend-ignore=E203]
+      - id: ruff-format
+        args: [ --line-length=80 ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
         exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*'
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-        args: [ --line-length=80 ]
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
@@ -30,19 +30,3 @@ repos:
         args:
           [ --profile=black, --line-length=80 ]
         exclude: 'flowermd/tests/assets/.* '
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        args:
-          - --max-line-length=80
-          - --extend-ignore=E203
-        exclude: '__init__.py'
-
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: '6.3.0'
-    hooks:
-      - id: pydocstyle
-        exclude: ^(flowermd/tests/|flowermd/internal/|flowermd/utils|setup.py|flowermd/__version__.py|docs/)
-        args: [ --convention=numpy ]

flowermd/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """flowerMD package."""
 
 from .base import (

flowermd/assets/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """Paths to the assets used by flowerMD."""
 
 from .forcefields import FF_DIR

flowermd/base/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """Base classes for flowerMD."""
 
 from .forcefield import BaseHOOMDForcefield, BaseXMLForcefield

flowermd/base/molecule.py

@@ -314,7 +314,7 @@ def _identify_bond_types(self, gmso_molecule):
                 or bond.connection_members[1].name
             )
             bond_connections = [p1_name, p2_name]
-            if not tuple(bond_connections[::-1]) in self.bond_types:
+            if tuple(bond_connections[::-1]) not in self.bond_types:
                 self.bond_types.add(tuple(bond_connections))
 
     def _identify_angle_types(self, gmso_molecule):
@@ -341,7 +341,7 @@ def _identify_angle_types(self, gmso_molecule):
                 or angle.connection_members[2].name
             )
             angle_connections = [p1_name, p2_name, p3_name]
-            if not tuple(angle_connections[::-1]) in self.angle_types:
+            if tuple(angle_connections[::-1]) not in self.angle_types:
                 self.angle_types.add(tuple(angle_connections))
 
     def _identify_dihedral_types(self, gmso_molecule):
@@ -372,7 +372,7 @@ def _identify_dihedral_types(self, gmso_molecule):
                 or dihedral.connection_members[3].name
             )
             dihedral_connections = [p1_name, p2_name, p3_name, p4_name]
-            if not tuple(dihedral_connections[::-1]) in self.dihedral_types:
+            if tuple(dihedral_connections[::-1]) not in self.dihedral_types:
                 self.dihedral_types.add(tuple(dihedral_connections))
 
     def _identify_improper_types(self, gmso_molecule):
@@ -403,7 +403,7 @@ def _identify_improper_types(self, gmso_molecule):
                 or improper.connection_members[3].name
             )
             improper_connections = [p1_name, p2_name, p3_name, p4_name]
-            if not tuple(improper_connections[::-1]) in self.improper_types:
+            if tuple(improper_connections[::-1]) not in self.improper_types:
                 self.improper_types.add(tuple(improper_connections))
 
     def _identify_topology_information(self, gmso_molecule):

flowermd/internal/__init__.py

@@ -1,2 +1,3 @@
+# ruff: noqa: F401
 from .ff_utils import xml_to_gmso_ff
 from .utils import check_return_iterable, validate_ref_value

flowermd/library/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """Library of predefined molecules, recipes and forcefields."""
 
 from .forcefields import (

flowermd/modules/surface_wetting/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """Surface wetting module for FlowerMD."""
 
 from .surface_wetting import (

flowermd/modules/welding/__init__.py

@@ -1,3 +1,4 @@
+# ruff: noqa: F401
 """Welding module for FlowerMD."""
 
 from .utils import add_void_particles

flowermd/tests/__init__.py

@@ -1 +1,2 @@
+# ruff: noqa: F401
 from .base_test import BaseTest

flowermd/tests/base_test.py

@@ -169,7 +169,7 @@ def __init__(self, lengths, num_mols, **kwargs):
                     bond_indices=bond_indices,
                     bond_length=bond_length,
                     bond_orientation=bond_orientation,
-                    **kwargs
+                    **kwargs,
                 )
 
         return _PolyEthylene
@@ -189,7 +189,7 @@ def __init__(self, lengths, num_mols, **kwargs):
                     bond_indices=bond_indices,
                     bond_length=bond_length,
                     bond_orientation=bond_orientation,
-                    **kwargs
+                    **kwargs,
                 )
 
         return _PPS
@@ -209,7 +209,7 @@ def __init__(self, lengths, num_mols, **kwargs):
                     bond_indices=bond_indices,
                     bond_length=bond_length,
                     bond_orientation=bond_orientation,
-                    **kwargs
+                    **kwargs,
                 )
 
         return _PolyDME

flowermd/utils/__init__.py

@@ -1,4 +1,13 @@
-from .actions import *
+# ruff: noqa: F401
+"""Helpful utility functions for use with flowerMD."""
+
+from .actions import (
+    PullParticles,
+    ScaleEpsilon,
+    ScaleSigma,
+    StdOutLogger,
+    UpdateWalls,
+)
 from .base_types import HOOMDThermostats
 from .rigid_body import create_rigid_body
 from .utils import (