Merge pull request #161 from talagayev/add_ruff

Transition to `Ruff` Formatter

Author: talagayev

.github/workflows/CI-CD.yml

@@ -32,9 +32,20 @@ jobs:
         run: |
           pip install .
 
-      - name: Install linter and formatter
+      - name: Install linting tools
         run: |
-          python -m pip install shyaml flake8 black black-nb flake8-nb
+          python -m pip install shyaml flake8 black black-nb flake8-nb ruff
+
+      - name: Check Ruff formatting
+        id: ruff-format
+        continue-on-error: true
+        run: |
+          ruff format --check .
+
+      - name: Provide Ruff formatting guidance
+        if: steps.ruff-format.outcome == 'failure'
+        run: |
+          echo "::warning::Ruff formatting issues detected. Run 'ruff format .' locally to apply formatting fixes."
 
       - name: Run black formatter
         run: |

CHANGELOG.md

@@ -27,7 +27,8 @@ talagayev
 - Fixes numpy error in due current incompatbility with parmed (2025-10-19, PR #160)
 
 ### Changed
-
+- Transition to `Ruff` linting with `Black` style (2025-10-20, PR #161)
+- 
 ## Version 1.1.1
 
 ### Authors

README.md

@@ -10,7 +10,9 @@ OpenMMDL @ Molecular Design Lab
 | **Availability**   | [![Condaforge][badge_conda_forge]][url_conda_forge] ![Docker][badge_docker]|
 | **Workflows**      | ![CI_CD][badge_ci_cd] ![CodeQL][badge_codeql]|
 | **Documentation**  | [![docs][badge_docs]][url_docs] [![codecov][badge_codecov]][url_codecov]|
-| **Dependencies**   | [![rdkit][badge_rdkit]][url_rdkit] [![mdanalysis][badge_mda]][url_mda] [![Code style: black][badge_black]][url_black]|
+| **Style**          | [![Code style: black][badge_black]][url_black]|
+| **Linting**        | [![ruff][badge_ruff]][url_ruff]|
+| **Dependencies**   | [![rdkit][badge_rdkit]][url_rdkit] [![mdanalysis][badge_mda]][url_mda]|
 | **License**        | [![License: GPL v2][badge_license]][url_license]|
 
 
@@ -199,7 +201,7 @@ run visualization_pymol.py
 openmdl_visualization PATH_TO_interacting_waters.pdb, modulePATH_TO_clouds.json
 ```
 ## Copyright
-Copyright (c) 2022, Valerij Talagayev, Yu Chen,  Niklas Piet Doering & Leon Obendorf (Wolber lab)
+Copyright (c) 2022, Valerij Talagayev, Yu Chen, Niklas Piet Doering & Leon Obendorf (Wolber lab)
 
 ### Citation
 If you use OpenMMDL in your research, please cite the following [paper](https://doi.org/10.1021/acs.jcim.4c02158).
@@ -231,6 +233,7 @@ This Project is based on the
 [badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
 [badge_black]: https://img.shields.io/badge/code%20style-black-000000.svg
 [badge_license]: https://img.shields.io/badge/License-MIT-blue.svg
+[badge_ruff]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
 [badge_docker]: https://img.shields.io/badge/Docker-2496ED?logo=docker&logoColor=fff
 
 [url_latest_release]: https://github.com/wolberlab/openmmdl/releases
@@ -242,4 +245,5 @@ This Project is based on the
 [url_rdkit]: https://www.rdkit.org/
 [url_mda]: https://www.mdanalysis.org
 [url_black]: https://github.com/psf/black
+[url_ruff]: https://github.com/astral-sh/ruff
 [url_license]: https://opensource.org/licenses/MIT

devtools/scripts/create_conda_env.py

@@ -6,9 +6,11 @@
 import subprocess as sp
 from tempfile import TemporaryDirectory
 from contextlib import contextmanager
+
 # YAML imports
 try:
     import yaml  # PyYAML
+
     loader = yaml.safe_load
 except ImportError:
     try:
@@ -17,19 +19,22 @@
         try:
             # Load Ruamel YAML from the base conda environment
             from importlib import util as import_util
-            CONDA_BIN = os.path.dirname(os.environ['CONDA_EXE'])
-            ruamel_yaml_path = glob.glob(os.path.join(CONDA_BIN, '..',
-                                                      'lib', 'python*.*', 'site-packages',
-                                                      'ruamel_yaml', '__init__.py'))[0]
+
+            CONDA_BIN = os.path.dirname(os.environ["CONDA_EXE"])
+            ruamel_yaml_path = glob.glob(
+                os.path.join(CONDA_BIN, "..", "lib", "python*.*", "site-packages", "ruamel_yaml", "__init__.py")
+            )[0]
             # Based on importlib example, but only needs to load_module since its the whole package, not just
             # a module
-            spec = import_util.spec_from_file_location('ruamel_yaml', ruamel_yaml_path)
+            spec = import_util.spec_from_file_location("ruamel_yaml", ruamel_yaml_path)
             yaml = spec.loader.load_module()
         except (KeyError, ImportError, IndexError):
-            raise ImportError("No YAML parser could be found in this or the conda environment. "
-                              "Could not find PyYAML or Ruamel YAML in the current environment, "
-                              "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. " 
-                              "Environment not created!")
+            raise ImportError(
+                "No YAML parser could be found in this or the conda environment. "
+                "Could not find PyYAML or Ruamel YAML in the current environment, "
+                "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. "
+                "Environment not created!"
+            )
     loader = yaml.YAML(typ="safe").load  # typ="safe" avoids odd typing on output
 
 
@@ -46,13 +51,10 @@ def temp_cd():
 
 
 # Args
-parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.')
-parser.add_argument('-n', '--name', type=str,
-                    help='The name of the created Python environment')
-parser.add_argument('-p', '--python', type=str,
-                    help='The version of the created Python environment')
-parser.add_argument('conda_file',
-                    help='The file for the created Python environment')
+parser = argparse.ArgumentParser(description="Creates a conda environment from file for a given Python version.")
+parser.add_argument("-n", "--name", type=str, help="The name of the created Python environment")
+parser.add_argument("-p", "--python", type=str, help="The version of the created Python environment")
+parser.add_argument("conda_file", help="The file for the created Python environment")
 
 args = parser.parse_args()
 
@@ -63,16 +65,16 @@ def temp_cd():
 python_replacement_string = "python {}*".format(args.python)
 
 try:
-    for dep_index, dep_value in enumerate(yaml_script['dependencies']):
-        if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value):  # Match explicitly 'python' and its formats
-            yaml_script['dependencies'].pop(dep_index)
+    for dep_index, dep_value in enumerate(yaml_script["dependencies"]):
+        if re.match("python([ ><=*]+[0-9.*]*)?$", dep_value):  # Match explicitly 'python' and its formats
+            yaml_script["dependencies"].pop(dep_index)
             break  # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse
 except (KeyError, TypeError):
     # Case of no dependencies key, or dependencies: None
-    yaml_script['dependencies'] = []
+    yaml_script["dependencies"] = []
 finally:
     # Ensure the python version is added in. Even if the code does not need it, we assume the env does
-    yaml_script['dependencies'].insert(0, python_replacement_string)
+    yaml_script["dependencies"].insert(0, python_replacement_string)
 
 # Figure out conda path
 if "CONDA_EXE" in os.environ:
@@ -90,6 +92,6 @@ def temp_cd():
 # Write to a temp directory which will always be cleaned up
 with temp_cd():
     temp_file_name = "temp_script.yaml"
-    with open(temp_file_name, 'w') as f:
+    with open(temp_file_name, "w") as f:
         f.write(yaml.dump(yaml_script))
     sp.call("{} env create -n {} -f {}".format(conda_path, args.name, temp_file_name), shell=True)

docs/conf.py

@@ -15,21 +15,23 @@
 # Incase the project was not installed
 import os
 import sys
-sys.path.insert(0, os.path.abspath('..'))
 
+sys.path.insert(0, os.path.abspath(".."))
 
 
 # -- Project information -----------------------------------------------------
 
-project = 'openmmdl'
-copyright = ("2022, Valerij Talagayev, Yu Chen, Niklas Piet Doering & Leon Obendorf. Project structure based on the "
-             "Computational Molecular Science Python Cookiecutter version 1.1")
-author = 'Valerij Talagayev & Yu Chen'
+project = "openmmdl"
+copyright = (
+    "2022, Valerij Talagayev, Yu Chen, Niklas Piet Doering & Leon Obendorf. Project structure based on the "
+    "Computational Molecular Science Python Cookiecutter version 1.1"
+)
+author = "Valerij Talagayev & Yu Chen"
 
 # The short X.Y version
-version = ''
+version = ""
 # The full version, including alpha/beta/rc tags
-release = ''
+release = ""
 
 
 # -- General configuration ---------------------------------------------------
@@ -58,16 +60,16 @@
 napoleon_use_ivar = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = '.rst'
+source_suffix = ".rst"
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -79,18 +81,18 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'default'
+pygments_style = "default"
 
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'renku'
+html_theme = "renku"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -101,7 +103,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -117,7 +119,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'openmmdldoc'
+htmlhelp_basename = "openmmdldoc"
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -126,15 +128,12 @@
     # The paper size ('letterpaper' or 'a4paper').
     #
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     #
     # 'preamble': '',
-
     # Latex figure (float) alignment
     #
     # 'figure_align': 'htbp',
@@ -144,19 +143,15 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'openmmdl.tex', 'openmmdl Documentation',
-     'openmmdl', 'manual'),
+    (master_doc, "openmmdl.tex", "openmmdl Documentation", "openmmdl", "manual"),
 ]
 
 
 # -- Options for manual page output ------------------------------------------
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'openmmdl', 'openmmdl Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "openmmdl", "openmmdl Documentation", [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -165,9 +160,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'openmmdl', 'openmmdl Documentation',
-     author, 'openmmdl', 'Preparation and Simulation of protein-ligand complexes',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "openmmdl",
+        "openmmdl Documentation",
+        author,
+        "openmmdl",
+        "Preparation and Simulation of protein-ligand complexes",
+        "Miscellaneous",
+    ),
 ]