Ruff + configuration -> pyproject.toml; newer Ruff version in dev env…

…; final Ruff checks and fixes in scripts; added Ruff CI job

.github/workflows/test.yml

@@ -3,6 +3,20 @@ name: Testing Springcraft
 on: [push, pull_request]
 
 jobs:
+  lint:
+    name: Check code style
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - name: Install ruff
+      run: pip install ruff==0.5.2
+    - name: Check code formatting
+      run: ruff format --diff
+    - name: Lint code base
+      run: ruff check
   test:
     name: Testing
 
@@ -19,7 +33,7 @@ jobs:
           auto-update-conda: true
           python-version: '3.10'
       - name: Installing dependencies
-        run: conda install -c conda-forge poetry prody pytest r-bio3d rpy2
+        run: conda install -c conda-forge poetry pytest
       - name: Building distribution
         run: poetry build -f wheel
       - name: Installing distribution

doc/conf.py

@@ -4,22 +4,22 @@
 
 __author__ = "Patrick Kunzmann"
 
-from os.path import realpath, dirname, join
-import types
 import sys
+import types
+from os.path import dirname, join, realpath
+
+import scraper
+import springcraft
 
 # Include 'src/' in PYTHONPATH
 # in order to import the 'Ammolite' package
 doc_path = dirname(realpath(__file__))
 package_path = join(dirname(doc_path), "src")
 sys.path.insert(0, package_path)
-import springcraft
 
 # Include springcraft/doc in PYTHONPATH
 # in order to import modules for example generation etc.
 sys.path.insert(0, doc_path)
-import scraper
-
 
 #### General ####
 

doc/examples/scripts/basic_nma.py

@@ -9,15 +9,14 @@
 # Code source: Jan Krumbach
 # License: BSD 3 clause
 
-import numpy as np
-import matplotlib.pyplot as plt
 import biotite
+import biotite.database.rcsb as rcsb
 import biotite.structure as struc
 import biotite.structure.io.mmtf as mmtf
-import biotite.database.rcsb as rcsb
+import matplotlib.pyplot as plt
+import numpy as np
 import springcraft
 
-
 # Fetch G:T/U Mismatch-specific DNA glycosylase from E. coli
 PDB_ID = "1MUG"
 mmtf_file = mmtf.MMTFFile.read(rcsb.fetch(PDB_ID, "mmtf"))

doc/examples/scripts/normal_mode.py

@@ -9,14 +9,13 @@
 # Code source: Patrick Kunzmann
 # License: BSD 3 clause
 
-import numpy as np
+import ammolite
+import biotite.database.rcsb as rcsb
 import biotite.structure as struc
 import biotite.structure.io.mmtf as mmtf
-import biotite.database.rcsb as rcsb
-import ammolite
+import numpy as np
 import springcraft
 
-
 PNG_SIZE = (800, 800)
 
 

doc/scraper.py

@@ -1,8 +1,9 @@
-from glob import glob
+import datetime
 import shutil
 import tempfile
-import datetime
+import time
 from os.path import getsize
+
 from sphinx_gallery.scrapers import figure_rst
 
 NO_ASSIGN = "___"

environment.yml

@@ -17,4 +17,4 @@ dependencies:
   - sphinx-gallery =0.9.0
   - numpydoc >=0.8
   - ammolite >=0.8
-  - ruff =0.5.2
+  - ruff >=0.6.7

pyproject.toml

@@ -46,10 +46,29 @@ sphinx-gallery = "0.9.0"
 numpydoc = ">= 0.8"
 ammolite = ">=0.8"
 
-
 [build-system]
 requires = ["poetry_core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
 
+[tool.ruff.lint]
+# pyflakes, pycodestyle isort and variable naming
+select = ["F", "E", "W", "I", "TID", "N"]
+ignore = [
+    # In docstrings long lines are often intentional
+    # Most other ocassions are caught by the ruff formatter
+    "E501",
+    # camel cases for forcefields
+    "N802", 
+    # eANM/sdENM as static methods of TabulatedForceField 
+    # should not accept "self" as argument by design
+    "N805",
+    # Due to constants used in functions
+    "N806",
+]
+
+[tool.ruff.lint.per-file-ignores]
+# Due to `from .module import *` imports in `__init__.py` modules
+"__init__.py" = ["F403", "TID252"]
+
 [tool.pytest.ini_options]
 addopts =  "--ignore=tests/data"

src/springcraft/anm.py

@@ -7,10 +7,11 @@
 __author__ = "Patrick Kunzmann"
 __all__ = ["ANM"]
 
-import numpy as np
 import biotite.structure as struc
-from .interaction import compute_hessian
+import numpy as np
+
 from . import nma
+from .interaction import compute_hessian
 
 K_B = 1.380649e-23
 N_A = 6.02214076e23

src/springcraft/forcefield.py

@@ -14,13 +14,13 @@
     "TabulatedForceField",
 ]
 
-import numbers
 import abc
-from os.path import join, dirname, realpath
-import numpy as np
-import biotite.structure as struc
-import biotite.sequence as seq
+import numbers
+from os.path import dirname, join, realpath
 
+import biotite.sequence as seq
+import biotite.structure as struc
+import numpy as np
 
 DATA_DIR = join(dirname(realpath(__file__)), "data")
 
@@ -439,7 +439,7 @@ def __init__(self, atoms, bonded, intra_chain, inter_chain, cutoff_distance):
             raise TypeError(f"Expected 'AtomArray', not {type(atoms).__name__}")
         if not np.all((atoms.atom_name == "CA") & (atoms.element == "C")):
             raise struc.BadStructureError(
-                f"AtomArray does not contain exclusively CA atoms"
+                "AtomArray does not contain exclusively CA atoms"
             )
 
         self._natoms = atoms.array_length()
@@ -756,8 +756,8 @@ def e_anm(atoms, nonbonded_mean=False):
            Protein Science, 7 2578-2586 (1998)
         """
 
-        intra = _load_matrix(f"miyazawa.csv")
-        inter = _load_matrix(f"keskin.csv")
+        intra = _load_matrix("miyazawa.csv")
+        inter = _load_matrix("keskin.csv")
 
         if nonbonded_mean:
             intra = np.average(intra) * np.ones(shape=(20, 20))
@@ -882,7 +882,7 @@ def _convert_to_matrix(value, n_bins):
     3D matrix.
     """
     if np.isnan(value).any():
-        raise IndexError(f"Array contains NaN elements")
+        raise IndexError("Array contains NaN elements")
 
     if isinstance(value, numbers.Number):
         # One value for all distances and types

src/springcraft/gnm.py

@@ -7,10 +7,11 @@
 __author__ = "Patrick Kunzmann, Faisal Islam"
 __all__ = ["GNM"]
 
-import numpy as np
 import biotite.structure as struc
-from .interaction import compute_kirchhoff
+import numpy as np
+
 from . import nma
+from .interaction import compute_kirchhoff
 
 K_B = 1.380649e-23
 N_A = 6.02214076e23

src/springcraft/interaction.py

@@ -7,8 +7,8 @@
 __author__ = "Patrick Kunzmann, Jan Krumbach"
 __all__ = ["compute_kirchhoff", "compute_hessian"]
 
-import numpy as np
 import biotite.structure as struc
+import numpy as np
 
 
 def compute_kirchhoff(coord, force_field, use_cell_list=True):

src/springcraft/nma.py

@@ -16,6 +16,7 @@
 ]
 
 import numpy as np
+
 # -> Import ANM/GNM in functions to prevent circular import error
 
 K_B = 1.380649e-23
@@ -43,8 +44,8 @@ def eigen(enm):
         Eigenvectors of the *Kirchhoff*/*Hessian* matrix.
         ``eig_values[i]`` corresponds to ``eig_vectors[i]``.
     """
-    from .gnm import GNM
     from .anm import ANM
+    from .gnm import GNM
 
     # Assign Kirchhoff/Hessian
     if isinstance(enm, GNM):
@@ -81,8 +82,8 @@ def frequencies(enm):
         The frequency in ascending order of the associated modes'
         Eigenvalues.
     """
-    from .gnm import GNM
     from .anm import ANM
+    from .gnm import GNM
 
     if isinstance(enm, GNM):
         ntriv_modes = 1
@@ -133,8 +134,8 @@ def mean_square_fluctuation(enm, mode_subset=None, tem=None, tem_factors=K_B):
     msqf : ndarray, shape=(n,), dtype=float
         The mean square fluctuations for each atom in the model.
     """
-    from .gnm import GNM
     from .anm import ANM
+    from .gnm import GNM
 
     if not isinstance(enm, (GNM, ANM)):
         raise ValueError("Instance of GNM/ANM class expected.")
@@ -215,8 +216,8 @@ def bfactor(enm, mode_subset=None, tem=None, tem_factors=K_B):
     bfac_values : ndarray, shape=(n,), dtype=float
         B-factors of C-alpha atoms.
     """
-    from .gnm import GNM
     from .anm import ANM
+    from .gnm import GNM
 
     if not isinstance(enm, (GNM, ANM)):
         raise ValueError("Instance of GNM/ANM class expected.")
@@ -287,8 +288,8 @@ def dcc(enm, mode_subset=None, norm=True, tem=None, tem_factors=K_B):
     for 'mode_subset' and 'memory_efficient' are passed to the function.
     """
 
-    from .gnm import GNM
     from .anm import ANM
+    from .gnm import GNM
 
     eig_values, eig_vectors = enm.eigen()
     n_nodes = len(enm._coord)

tests/data/test_data_prep_prody_bio3d.py

@@ -1,18 +1,16 @@
-import abc
 import os
-from os import path
 
+import biotite.database.rcsb as rcsb
 import biotite.structure as struc
 import biotite.structure.io as bstio
 import biotite.structure.io.pdb as pdb
-import biotite.database.rcsb as rcsb
 import numpy as np
 import prody
 import rpy2.robjects as robjects
-from rpy2.robjects.packages import importr
-from rpy2.robjects.vectors import DataFrame as DataFrame_r
 from rpy2.robjects import numpy2ri
 from rpy2.robjects.conversion import localconverter
+from rpy2.robjects.packages import importr
+from rpy2.robjects.vectors import DataFrame as DataFrame_r
 
 FETCH_PDB_IDS = ["1l2y", "7cal"]
 
@@ -184,7 +182,7 @@ def prody_enm_nma(enm_type, structure_path, cutoff_list, output_markers="all"):
 def bio3d_anm_nma(structure_path, bio3d_ff, output_markers="all"):
     # Check bio3d_ff and outputs
     accepted_bio3d_ff = ["calpha", "sdenm", "pfanm"]
-    if not bio3d_ff in accepted_bio3d_ff:
+    if bio3d_ff not in accepted_bio3d_ff:
         raise ValueError(
             "Onle the following bio3d FFs are accepted: \n", f"{accepted_bio3d_ff}"
         )

tests/test_anm.py

@@ -1,12 +1,13 @@
+import glob
 import itertools
-from multiprocessing.spawn import prepare
 from os.path import basename, join
-import glob
-import numpy as np
-import pytest
+
 import biotite.structure as struc
 import biotite.structure.io.pdb as pdb
+import numpy as np
+import pytest
 import springcraft
+
 from .util import data_dir
 
 

tests/test_forcefield.py

@@ -1,12 +1,13 @@
-import itertools
 from os.path import join
-import numpy as np
-import pytest
+
+import biotite.sequence as seq
 import biotite.structure as struc
 import biotite.structure.io.pdb as pdb
-import biotite.sequence as seq
+import numpy as np
+import pytest
 import springcraft
 from springcraft.forcefield import InvariantForceField
+
 from .util import data_dir
 
 
@@ -330,6 +331,7 @@ def test_tabulated_forcefield_predefined(atoms, name):
     meth = getattr(springcraft.TabulatedForceField, name)
     ff = meth(atoms)
 
+    assert ff is not None
 
 def test_parameterfree_forcefield():
     """

tests/test_gnm.py

@@ -1,9 +1,11 @@
 import itertools
-from os.path import join, basename
+from os.path import basename, join
+
+import biotite.structure.io.pdb as pdb
 import numpy as np
 import pytest
-import biotite.structure.io.pdb as pdb
 import springcraft
+
 from .util import data_dir
 
 

tests/test_interaction.py

@@ -1,9 +1,10 @@
 import itertools
 from os.path import join
+
 import numpy as np
 import pytest
-import biotite.structure.io.pdb as pdb
 import springcraft
+
 from .util import data_dir
 
 

tests/test_version.py

@@ -1,5 +1,6 @@
 import re
-from os.path import join, dirname, realpath
+from os.path import dirname, join, realpath
+
 from springcraft import __version__