Update dev tools

.pre-commit-config.yaml

@@ -5,100 +5,87 @@ ci:
 exclude: ^tests/conftest/|^.vscode/|^posebusters/datasets/pdb
 
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      # - id: no-commit-to-branch # branch protected on github
+      - id: forbid-submodules
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-docstring-first
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-ast
+      - id: debug-statements
+      - id: destroyed-symlinks
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
+      - id: name-tests-test
+        args: [--pytest-test-first]
+      - id: sort-simple-yaml
 
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.5.0
-  hooks:
-    # - id: no-commit-to-branch # branch protected on github
-    - id: forbid-submodules
-    - id: check-added-large-files
-    - id: check-case-conflict
-    - id: check-docstring-first
-    - id: check-merge-conflict
-    - id: check-symlinks
-    - id: check-yaml
-    - id: check-toml
-    - id: check-json
-    - id: check-ast
-    - id: debug-statements
-    - id: destroyed-symlinks
-    - id: detect-private-key
-    - id: end-of-file-fixer
-    - id: mixed-line-ending
-    - id: requirements-txt-fixer
-    - id: trailing-whitespace
-    - id: name-tests-test
-      args: [--pytest-test-first]
-    - id: sort-simple-yaml
-
-- repo: https://github.com/pre-commit/pygrep-hooks
-  rev: v1.10.0
-  hooks:
-    - id: python-check-blanket-noqa
-    - id: python-check-blanket-type-ignore
-    - id: python-no-log-warn
-    - id: python-no-eval
-    - id: python-use-type-annotations
-    - id: rst-backticks
-    - id: rst-directive-colons
-    - id: rst-inline-touching-normal
-    - id: text-unicode-replacement-char
-
-# update syntax
-- repo: https://github.com/asottile/pyupgrade
-  rev: v3.15.0
-  hooks:
-    - id: pyupgrade
-      args: ["--py37-plus"]
-
-# sort imports
-- repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      args: ["--settings-path=pyproject.toml"]
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
+      - id: python-no-log-warn
+      - id: python-no-eval
+      - id: python-use-type-annotations
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+      - id: text-unicode-replacement-char
 
-# find unused imports
-- repo: https://github.com/hadialqattan/pycln
-  rev: v2.4.0
-  hooks:
-    - id: pycln
-      args: ["--config=pyproject.toml"]
-      stages: ["manual"]
+  # update syntax
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+      - id: pyupgrade
+        args: ["--py37-plus"]
 
-# format code
-- repo: https://github.com/psf/black
-  rev: 23.11.0
-  hooks:
-    - id: black
-      language_version: python3.11
-      args: ["--config=pyproject.toml"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.2.2
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format
 
-# lint code
-- repo: https://github.com/pycqa/flake8
-  rev: 6.1.0
-  hooks:
-    - id: flake8
-      additional_dependencies: ["flake8-black", "flake8-docstrings", "flake8-pyproject"]
+  # find unused imports
+  - repo: https://github.com/hadialqattan/pycln
+    rev: v2.4.0
+    hooks:
+      - id: pycln
+        args: ["--config=pyproject.toml"]
+        stages: ["manual"]
 
-# check types
--   repo: https://github.com/pre-commit/mirrors-mypy
+  # check types
+  - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.7.0
     hooks:
-    -   id: mypy
+      - id: mypy
         additional_dependencies: ["types-PyYAML"]
 
-# find typos
-- repo: https://github.com/codespell-project/codespell
-  rev: v2.2.6
-  hooks:
-    - id: codespell
-      additional_dependencies: ["tomli"]
+  # find typos
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies: ["tomli"]
 
-# security lint
-- repo: https://github.com/PyCQA/bandit
-  rev: 1.7.5
-  hooks:
-  - id: bandit
-    args: ["-c", "pyproject.toml"]
-    additional_dependencies: ["bandit[toml]"]
+  # security lint
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.5
+    hooks:
+      - id: bandit
+        args: ["-c", "pyproject.toml"]
+        additional_dependencies: ["bandit[toml]"]

.vscode/launch.json

@@ -4,9 +4,26 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
+        {
+            "name": "Python: Debug Tests",
+            "type": "debugpy",
+            "request": "launch",
+            "program": "${file}",
+            "purpose": [
+                "debug-test"
+            ],
+            "console": "integratedTerminal",
+            "presentation": {
+                "hidden": true
+            },
+            "justMyCode": false,
+            "env": {
+                "PYTEST_ADDOPTS": "--no-cov"
+            }
+        },
         {
             "name": "bust conditioned on protein and ligand",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -22,7 +39,7 @@
         },
         {
             "name": "bust conditioned on protein and ligand -- long",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -40,7 +57,7 @@
         },
         {
             "name": "bust conditioned on protein",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -54,7 +71,7 @@
         },
         {
             "name": "bust unconditioned",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -66,7 +83,7 @@
         },
         {
             "name": "bust unconditioned - yael test case",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -78,7 +95,7 @@
         },
         {
             "name": "bust table input",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -91,7 +108,7 @@
         },
         {
             "name": "bust table -- long",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -106,7 +123,7 @@
         },
         {
             "name": "bust table -- csv",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -119,25 +136,9 @@
                 "csv",
             ]
         },
-        {
-            "name": "Python: Debug Tests",
-            "type": "python",
-            "request": "launch",
-            "program": "${file}",
-            "cwd": "${workspaceFolder}",
-            "purpose": [
-                "debug-test"
-            ],
-            "stopOnEntry": false,
-            "console": "integratedTerminal",
-            "justMyCode": true,
-            "env": {
-                "PYTEST_ADDOPTS": "--no-cov"
-            }
-        },
         {
             "name": "bust conditioned on protein and ligand -- 1ia1",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -156,7 +157,7 @@
         },
         {
             "name": "bust conditioned on protein -- 1ia1",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -170,7 +171,7 @@
         },
         {
             "name": "bust conditioned on protein -- 1w1p crystal",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -189,7 +190,7 @@
         },
         {
             "name": "bust conditioned on protein -- 1g9v gold",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -210,7 +211,7 @@
         },
         {
             "name": "bust conditioned on protein -- 1gkc",
-            "type": "python",
+            "type": "debugpy",
             "request": "launch",
             "cwd": "${workspaceFolder}",
             "module": "posebusters",
@@ -228,6 +229,6 @@
                 "--outfmt",
                 "long",
             ]
-        }
+        },
     ]
 }

.vscode/settings.json

@@ -8,27 +8,19 @@
         "editor.defaultFormatter": "vscode.json-language-features"
     },
     "[python]": {
-        "editor.defaultFormatter": "ms-python.black-formatter",
+        "editor.defaultFormatter": "charliermarsh.ruff",
         "editor.formatOnSave": true,
         "editor.codeActionsOnSave": {
-            "source.organizeImports": true
+            "source.fixAll": "explicit",
+            "source.organizeImports": "explicit"
         },
     },
     "python.analysis.typeCheckingMode": "basic",
     "python.defaultInterpreterPath": "/usr/local/bin/python",
     "python.testing.pytestEnabled": true,
     "python.testing.unittestEnabled": false,
-    "black-formatter.args": [
-        "--config=pyproject.toml"
-    ],
-    "flake8.args": [
-        "--toml-config=pyproject.toml"
-    ],
-    "isort.args": [
-        "--settings-path=pyproject.toml"
-    ],
-    "pylint.args": [
-        "--rcfile=pyproject.toml"
+    "python.testing.pytestArgs": [
+        "--no-cov"
     ],
     "autoDocstring.docstringFormat": "google-notypes",
     "autoDocstring.generateDocstringOnEnter": true,

posebusters/cli.py

@@ -27,7 +27,7 @@ def main():
         logger.error(e)
 
 
-def bust(
+def bust(  # noqa: PLR0913
     mol_pred: list[Path | Mol] = [],
     mol_true: Path | Mol | None = None,
     mol_cond: Path | Mol | None = None,

posebusters/modules/distance_geometry.py

@@ -64,7 +64,7 @@
 }
 
 
-def check_geometry(
+def check_geometry(  # noqa: PLR0913, PLR0915
     mol_pred: Mol,
     threshold_bad_bond_length: float = 0.2,
     threshold_clash: float = 0.2,
@@ -234,8 +234,8 @@ def _two_bonds_to_angle(bond1: tuple[int, int], bond2: tuple[int, int]) -> None
     set1 = set(bond1)
     set2 = set(bond2)
     all_atoms = set1 | set2
-    # angle requires two bonds to share exactly one atom
-    if len(all_atoms) != 3:
+    # angle requires two bonds to share exactly one atom, that is we must have 3 atoms
+    if len(all_atoms) != 3:  # noqa: PLR2004
         return None
     # find shared atom
     shared_atom = set1 & set2