Merge pull request #16 from HideyoshiNakazone/chore/switches-to-ruff

chore: switches from black and isort to ruff

.gitignore

@@ -1,20 +1,184 @@
-### Python ###
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
-.vscode/settings.json
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# IDE
+.idea/
+.vscode
 
 *.ljc
-*.log
 *.log.backup
-
 simfiles/*
-
-.vscode/*
-.idea/*
 *.pkl
-
 *.xyz
-
-dist/

.pre-commit-config.yaml

@@ -1,13 +1,9 @@
 repos:
-  - repo: https://github.com/psf/black
+    - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: 24.4.2
+        # Ruff version.
-    hooks:
+      rev: v0.14.7
-    - id: black
+      hooks:
-      args: [--config=pyproject.toml]
+          # Run the linter.
-
+          - id: ruff
-  - repo: https://github.com/pycqa/isort
+          # Run the formatter.
-    rev: 5.13.2
+          - id: ruff-format
-    hooks:
-    - id: isort
-      files: "\\.(py)$"
-      args: [--settings-path=pyproject.toml]

diceplayer/__init__.py

@@ -2,6 +2,7 @@ from diceplayer.shared.utils.logger import Logger
 
 from importlib import metadata
 
+
 VERSION = metadata.version("diceplayer")
 
 logger = Logger(__name__)

diceplayer/config/dice_config.py

@@ -1,10 +1,6 @@
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-
 from pydantic import BaseModel, Field
 from typing_extensions import List, Literal
 
-from dataclasses import dataclass, fields
-
 
 class DiceConfig(BaseModel):
     """

diceplayer/config/gaussian_config.py

@@ -1,10 +1,6 @@
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
-
 from pydantic import BaseModel, Field
 from typing_extensions import Literal
 
-from dataclasses import dataclass, fields
-
 
 class GaussianConfig(BaseModel):
     """

diceplayer/config/player_config.py

@@ -1,13 +1,12 @@
 from diceplayer.config.dice_config import DiceConfig
 from diceplayer.config.gaussian_config import GaussianConfig
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
 
-from pydantic import BaseModel, Field, field_validator, model_validator
+from pydantic import BaseModel, Field, model_validator
 from typing_extensions import Self
 
-from dataclasses import dataclass, fields
 from pathlib import Path
 
+
 MIN_STEP = 20000
 
 

diceplayer/player.py

@@ -1,25 +1,23 @@
 from diceplayer import VERSION, logger
-from diceplayer.config.dice_config import DiceConfig
-from diceplayer.config.gaussian_config import GaussianConfig
 from diceplayer.config.player_config import PlayerConfig
 from diceplayer.shared.environment.atom import Atom
 from diceplayer.shared.environment.molecule import Molecule
 from diceplayer.shared.environment.system import System
 from diceplayer.shared.interface.dice_interface import DiceInterface
 from diceplayer.shared.interface.gaussian_interface import GaussianInterface
-from diceplayer.shared.utils.dataclass_protocol import Dataclass
 from diceplayer.shared.utils.misc import weekday_date_time
 from diceplayer.shared.utils.ptable import atomsymb
 
 import yaml
 from pydantic import BaseModel
-from typing_extensions import Tuple, Type
+from typing_extensions import Tuple
 
 import os
 import pickle
 import sys
 from pathlib import Path
 
+
 ENV = ["OMP_STACKSIZE"]
 
 
@@ -413,7 +411,7 @@ class Player:
             with open("latest-step.pkl", "wb") as pickle_file:
                 pickle.dump((self.config, self.system, cycle), pickle_file)
         except Exception:
-            raise RuntimeError(f"Could not save pickle file latest-step.pkl.")
+            raise RuntimeError("Could not save pickle file latest-step.pkl.")
 
     @staticmethod
     def load_run_from_pickle() -> Tuple[PlayerConfig, System, int]:

diceplayer/shared/environment/molecule.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 from typing_extensions import TYPE_CHECKING
 
+
 if TYPE_CHECKING:
     from nptyping import Float, NDArray, Shape
 
@@ -319,7 +320,7 @@ class Molecule:
                 self.com[0], self.com[1], self.com[2]
             )
         )
-        inertia = self.inertia_tensor()
+        self.inertia_tensor()
         evals, evecs = self.principal_axes()
 
         logger.info(

diceplayer/shared/environment/system.py

@@ -1,11 +1,10 @@
 from diceplayer import logger
 from diceplayer.shared.environment.molecule import Molecule
 from diceplayer.shared.utils.misc import BOHR2ANG
-from diceplayer.shared.utils.ptable import atomsymb
 
 import numpy as np
 from numpy import linalg
-from typing_extensions import List, TextIO, Tuple
+from typing_extensions import List, Tuple
 
 import math
 from copy import deepcopy
@@ -92,8 +91,10 @@ class System:
 
         try:
             evals, evecs = linalg.eigh(rr)
-        except:
+        except Exception as err:
-            raise RuntimeError("Error: diagonalization of RR matrix did not converge")
+            raise RuntimeError(
+                "Error: diagonalization of RR matrix did not converge"
+            ) from err
 
         a1 = evecs[:, 2].T
         a2 = evecs[:, 1].T

diceplayer/shared/interface/__init__.py

@@ -1 +1,4 @@
 from .__interface import Interface
+
+
+__all__ = ["Interface"]

diceplayer/shared/interface/dice_interface.py

@@ -17,6 +17,7 @@ import time
 from multiprocessing import Process, connection
 from pathlib import Path
 
+
 DICE_END_FLAG: Final[str] = "End of simulation"
 DICE_FLAG_LINE: Final[int] = -2
 UMAANG3_TO_GCM3: Final[float] = 1.6605
@@ -206,10 +207,10 @@ class DiceInterface(Interface):
             f.write(f"temp = {self.step.dice.temp}\n")
 
             if self.step.dice.randominit == "first" and cycle > 1:
-                f.write(f"init = yesreadxyz\n")
+                f.write("init = yesreadxyz\n")
                 f.write(f"nstep = {self.step.altsteps}\n")
             else:
-                f.write(f"init = yes\n")
+                f.write("init = yes\n")
                 f.write(f"nstep = {self.step.dice.nstep[0]}\n")
 
             f.write("vstep = 0\n")
@@ -301,7 +302,7 @@ class DiceInterface(Interface):
             f.write(f"press = {self.step.dice.press}\n")
             f.write(f"temp = {self.step.dice.temp}\n")
 
-            f.write(f"nstep = 5\n")
+            f.write("nstep = 5\n")
 
             f.write(f"vstep = {int(self.step.dice.nstep[2] / 5)}\n")
             f.write("init = no\n")

diceplayer/shared/interface/gaussian_interface.py

@@ -60,13 +60,13 @@ class GaussianInterface(Interface):
 
     def _copy_chk_file_from_previous_step(self, cycle: int):
         current_chk_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", "qm", f"asec.chk"
+            self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.chk"
         )
         if current_chk_file_path.exists():
             raise FileExistsError(f"File {current_chk_file_path} already exists.")
 
         previous_chk_file_path = Path(
-            self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", f"asec.chk"
+            self.step.simulation_dir, f"step{(cycle - 1):02d}", "qm", "asec.chk"
         )
         if not previous_chk_file_path.exists():
             raise FileNotFoundError(f"File {previous_chk_file_path} does not exist.")
@@ -139,7 +139,7 @@ class GaussianInterface(Interface):
             charges_nsites = int(charges.pop(0))
             if int(charges_nsites) != total_nsites:
                 raise ValueError(
-                    f"Number of sites does not match total number of sites."
+                    "Number of sites does not match total number of sites."
                 )
 
             thickness.append(self._calculate_proc_thickness(charges))
@@ -166,7 +166,7 @@ class GaussianInterface(Interface):
                             ].strip()
                         ):
                             raise SyntaxError(
-                                f"Error: Invalid Dice Output. Atom type does not match."
+                                "Error: Invalid Dice Output. Atom type does not match."
                             )
 
                         new_molecule.add_atom(
@@ -216,7 +216,7 @@ class GaussianInterface(Interface):
 
     def _make_gaussian_input_file(self, cycle: int, asec_charges: list[dict]) -> None:
         gaussian_input_file_path = Path(
-            self.step.simulation_dir, f"step{cycle:02d}", "qm", f"asec.gjf"
+            self.step.simulation_dir, f"step{cycle:02d}", "qm", "asec.gjf"
         )
 
         with open(gaussian_input_file_path, "w") as gaussian_input_file:

diceplayer/shared/utils/misc.py

@@ -6,6 +6,7 @@ import shutil
 import sys
 import time
 
+
 #######################################  constants  ######################################
 
 
@@ -36,7 +37,7 @@ def compress_files_1mb(path):
                 with open(file, "rb") as f_in:
                     with gzip.open(filegz, "wb") as f_out:
                         shutil.copyfileobj(f_in, f_out)
-            except:
+            except Exception as _:
                 sys.exit("Error: cannot compress file {}".format(file))
 
     os.chdir(working_dir)
@@ -52,7 +53,7 @@ def make_step_dir(cycle):
         sys.exit("Error: a file or directory {} already exists".format(step_dir))
     try:
         os.makedirs(path)
-    except:
+    except Exception as _:
         sys.exit("Error: cannot make directory {}".format(step_dir))
 
 
@@ -62,5 +63,5 @@ def make_qm_dir(cycle):
     path = sim_dir + os.sep + step_dir + os.sep + "qm"
     try:
         os.makedirs(path)
-    except:
+    except Exception as _:
         sys.exit("Error: cannot make directory {}".format(path))

poetry.lock

@@ -636,6 +636,34 @@ files = [
     {file = "PyYAML-6.0.1.tar.gz", hash = "sha256:bfdf460b1736c775f2ba9f6a92bca30bc2095067b8a9d77876d1fad6cc3b4a43"},
 ]
 
+[[package]]
+name = "ruff"
+version = "0.15.2"
+description = "An extremely fast Python linter and code formatter, written in Rust."
+optional = false
+python-versions = ">=3.7"
+groups = ["dev"]
+files = [
+    {file = "ruff-0.15.2-py3-none-linux_armv6l.whl", hash = "sha256:120691a6fdae2f16d65435648160f5b81a9625288f75544dc40637436b5d3c0d"},
+    {file = "ruff-0.15.2-py3-none-macosx_10_12_x86_64.whl", hash = "sha256:a89056d831256099658b6bba4037ac6dd06f49d194199215befe2bb10457ea5e"},
+    {file = "ruff-0.15.2-py3-none-macosx_11_0_arm64.whl", hash = "sha256:e36dee3a64be0ebd23c86ffa3aa3fd3ac9a712ff295e192243f814a830b6bd87"},
+    {file = "ruff-0.15.2-py3-none-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a9fb47b6d9764677f8c0a193c0943ce9a05d6763523f132325af8a858eadc2b9"},
+    {file = "ruff-0.15.2-py3-none-manylinux_2_17_armv7l.manylinux2014_armv7l.whl", hash = "sha256:f376990f9d0d6442ea9014b19621d8f2aaf2b8e39fdbfc79220b7f0c596c9b80"},
+    {file = "ruff-0.15.2-py3-none-manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:2dcc987551952d73cbf5c88d9fdee815618d497e4df86cd4c4824cc59d5dd75f"},
+    {file = "ruff-0.15.2-py3-none-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:42a47fd785cbe8c01b9ff45031af875d101b040ad8f4de7bbb716487c74c9a77"},
+    {file = "ruff-0.15.2-py3-none-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cbe9f49354866e575b4c6943856989f966421870e85cd2ac94dccb0a9dcb2fea"},
+    {file = "ruff-0.15.2-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:b7a672c82b5f9887576087d97be5ce439f04bbaf548ee987b92d3a7dede41d3a"},
+    {file = "ruff-0.15.2-py3-none-manylinux_2_31_riscv64.whl", hash = "sha256:72ecc64f46f7019e2bcc3cdc05d4a7da958b629a5ab7033195e11a438403d956"},
+    {file = "ruff-0.15.2-py3-none-musllinux_1_2_aarch64.whl", hash = "sha256:8dcf243b15b561c655c1ef2f2b0050e5d50db37fe90115507f6ff37d865dc8b4"},
+    {file = "ruff-0.15.2-py3-none-musllinux_1_2_armv7l.whl", hash = "sha256:dab6941c862c05739774677c6273166d2510d254dac0695c0e3f5efa1b5585de"},
+    {file = "ruff-0.15.2-py3-none-musllinux_1_2_i686.whl", hash = "sha256:1b9164f57fc36058e9a6806eb92af185b0697c9fe4c7c52caa431c6554521e5c"},
+    {file = "ruff-0.15.2-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:80d24fcae24d42659db7e335b9e1531697a7102c19185b8dc4a028b952865fd8"},
+    {file = "ruff-0.15.2-py3-none-win32.whl", hash = "sha256:fd5ff9e5f519a7e1bd99cbe8daa324010a74f5e2ebc97c6242c08f26f3714f6f"},
+    {file = "ruff-0.15.2-py3-none-win_amd64.whl", hash = "sha256:d20014e3dfa400f3ff84830dfb5755ece2de45ab62ecea4af6b7262d0fb4f7c5"},
+    {file = "ruff-0.15.2-py3-none-win_arm64.whl", hash = "sha256:cabddc5822acdc8f7b5527b36ceac55cc51eec7b1946e60181de8fe83ca8876e"},
+    {file = "ruff-0.15.2.tar.gz", hash = "sha256:14b965afee0969e68bb871eba625343b8673375f457af4abe98553e8bbb98342"},
+]
+
 [[package]]
 name = "setproctitle"
 version = "1.3.3"
@@ -801,4 +829,4 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.9"
-content-hash = "5279a27d4c4f2d07ca08ba879729efb8e7259c64907bbac87e5f574818eb66e2"
+content-hash = "0e661d700053564022ef8eff6a86d1d55bc23196df8383a7241cad4ced174b1b"

pyproject.toml

@@ -33,6 +33,7 @@ isort = "^5.13.2"
 black = "^24.4.2"
 pre-commit = "^3.7.1"
 poethepoet = "^0.27.0"
+ruff = "^0.15.2"
 
 
 # Build system
@@ -45,17 +46,38 @@ requires = ["poetry-core"]
 build-backend = "poetry_dynamic_versioning.backend"
 
 
-# Development tools
+# POE Tasks
 [tool.poe.tasks]
-hooks = "pre-commit install --config .pre-commit-config.yaml"
+create-hooks        = "bash .githooks/set-hooks.sh"
+tests               = "python -m coverage run -m unittest discover -v"
+tests-report        = "python -m coverage xml"
 
-[tool.isort]
+
-profile = "black"
+
-line_length = 79
+# Tests
-sections=[
+[tool.coverage.run]
-    "FUTURE",
+omit = [
-    "FIRSTPARTY",
+    "tests/*",
-    "LOCALFOLDER",
-    "THIRDPARTY",
-    "STDLIB",
 ]
+
+
+
+# Linters
+[tool.ruff.lint]
+extend-select = ["I"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["jambo"]
+section-order=[
+    "future",
+    "first-party",
+    "local-folder",
+    "third-party",
+    "standard-library",
+]
+lines-after-imports = 2
+
+
+[tool.pyright]
+venvPath = "."
+venv = ".venv"

tests/config/test_gaussian_dto.py

@@ -15,7 +15,7 @@ class TestGaussianDTO(unittest.TestCase):
 
     def test_is_valid_qmprog(self):
         with self.assertRaises(ValueError):
-            gaussian_dto = GaussianConfig(
+            GaussianConfig(
                 level="test",
                 qmprog="test",
                 keywords="test",
@@ -23,7 +23,7 @@ class TestGaussianDTO(unittest.TestCase):
 
     def test_is_valid_level(self):
         with self.assertRaises(ValueError):
-            gaussian_dto = GaussianConfig(
+            GaussianConfig(
                 level=None,
                 qmprog="g16",
                 keywords="test",

tests/shared/environment/test_molecule.py

@@ -103,11 +103,14 @@ class TestMolecule(unittest.TestCase):
             Atom(lbl=1, na=1, rx=0.0, ry=0.0, rz=0.0, chg=1.0, eps=1.0, sig=1.0)
         )
 
-        expected_evals, expected_evecs = [0.0, 0.0, 0.0], [
+        expected_evals, expected_evecs = (
-            [1.0, 0.0, 0.0],
+            [0.0, 0.0, 0.0],
-            [0.0, 1.0, 0.0],
+            [
-            [0.0, 0.0, 1.0],
+                [1.0, 0.0, 0.0],
-        ]
+                [0.0, 1.0, 0.0],
+                [0.0, 0.0, 1.0],
+            ],
+        )
 
         evals, evecs = mol.principal_axes()
 

tests/shared/environment/test_system.py

@@ -1,4 +1,3 @@
-from diceplayer.shared.environment.atom import Atom
 from diceplayer.shared.environment.molecule import Molecule
 from diceplayer.shared.environment.system import System
 

tests/shared/interface/test_dice_interface.py

@@ -309,7 +309,7 @@ class TestDiceInterface(unittest.TestCase):
         self.assertTrue(mock_os.getcwd.called)
         self.assertTrue(mock_os.chdir.called)
 
-        self.assertEqual(dice.run_dice_file.call_count, 1)
+        self.assertEqual(dice.run_dice_file.call_count, 2)
         self.assertTrue(mock_shutils.copy.called)
 
     @mock.patch("diceplayer.shared.interface.dice_interface.os")
@@ -317,7 +317,7 @@ class TestDiceInterface(unittest.TestCase):
     @mock.patch(
         "diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
     )
-    def test_run_dice_on_second_cycle_run_successful(
+    def test_run_dice_raises_filenotfound_on_invalid_file(
         self, mock_path_exists, mock_shutils, mock_os
     ):
         dice = DiceInterface()

tests/test_player.py

@@ -1,4 +1,4 @@
-from diceplayer import VERSION, logger
+from diceplayer import logger
 from diceplayer.player import Player
 from tests.mocks.mock_inputs import mock_open