Merge branch 'wolberlab:main' into Charm2024_implementation

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

@@ -15,6 +15,20 @@ The rules for this file:
     * YYYY-MM-DD date format (following ISO 8601)
   * accompany each entry with github issue/PR number (Issue #xyz)
 -->
+## Version 1.1.2
+
+### Authors
+talagayev
+
+### Added
+
+### Fixed
+- Fixes import error in `visualization.ipynb` (2025-10-14, PR #159)
+- 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]|
 
 
@@ -177,7 +179,7 @@ Start the analysis with the following Inputs:
 
 
 #### Visualization
-Most of the analysis outputs are JEPG images and do not need any further preparation to be viewed.
+Most of the analysis outputs are JPEG images and do not need any further preparation to be viewed.
 
 For the visualization of your complex with interaction pointclouds you can use NGLView with the jupyter notebook prepared in the **OpenMMDL** repository or visualize the pointclouds in PyMOL.
 
@@ -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,AAABAAEAEBAAAAEAIAAoBAAAFgAAACgAAAAQAAAAIAAAAAEAIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJD+XwCY/fEAkf3uAJf97wGT/a+HfHaoiIWE7n9/f+6Hh4fvgICAjwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACT/yYAlP//AJ///wCg//8JjvOchXly1oaGhv+Ghob/j4+P/39/f3IAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAJH8aQCY/8wAkv2kfY+elJ6al/yVlZX7iIiI8H9/f7h/f38UAAAAAAAAAAAAAAAAAAAAAAAAAAB/f38egYF/noqAebF8gYaagnx3oFpUUtZpaWr/WFhY8zo6OmT///8BAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAgICAn46Ojv+Hh4b/jouJ/4iGhfcAAADnAAAA/wAAAP8AAADIAAAAAwCj/zIAnf2VAJD/PAAAAAAAAAAAAAAAAICAgNGHh4f/gICA/4SEhP+Xl5f/AwMD/wAAAP8AAAD/AAAA/wAAAB8Aov9/ALr//wCS/Z0AAAAAAAAAAAAAAACBgYGOjo6O/4mJif+Pj4//iYmJ/wAAAOAAAAD+AAAA/wAAAP8AAABhAP7+FgCi/38Axf4fAAAAAAAAAAAAAAAAiIiID4GBgYKCgoKogoB+fYSEgZhgYGDZXl5e/m9vb/9ISEjpEBAQxw8AAFQAAAAAAAAANQAAADcAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAjo6Mb5iYmP+cnJz/jY2N95CQkO4pKSn/AAAA7gAAAP0AAAD7AAAAhgAAAAEAAAAAAAAAAACL/gsAkv2uAJX/QQAAAAB9fX3egoKC/4CAgP+NjY3/c3Nz+wAAAP8AAAD/AAAA/wAAAPUAAAAcAAAAAAAAAAAAnP4NAJL9rgCR/0YAAAAAfX19w4ODg/98fHz/i4uL/4qKivwAAAD/AAAA/wAAAP8AAAD1AAAAGwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALGxsVyqqqr/mpqa/6mpqf9KSUn/AAAA5QAAAPkAAAD5AAAAhQAAAAEAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADkUFBSuZ2dn/3V1df8uLi7bAAAATgBGfyQAAAA2AAAAMwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAB0AAADoAAAA/wAAAP8AAAD/AAAAWgC3/2AAnv3eAJ/+dgAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA9AAAA/wAAAP8AAAD/AAAA/wAKDzEAnP3WAKn//wCS/OgAf/8MAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAIQAAANwAAADtAAAA7QAAAMAAABUMAJn9gwCe/e0Aj/2LAP//AQAAAAAAAAAA
 [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",
+    ),
 ]
 
 

environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - sqlite>=3.40
   - pytest>=6.1.2
   - pytest-runner
-  - numpy
+  - numpy~=2.2.6
   - plip
   - requests>=2.28.1
   - rdkit>=2022.03.5