switch to ruff

setup.cfg

@@ -4,7 +4,7 @@
 [metadata]
 name = chemlift
 version = 0.0.1-dev
-description = Chemical language interfaced fine-tuning of large-language models
+description = Chemical language interfaced predictions using large-language models
 long_description = file: README.md
 long_description_content_type = text/markdown
 
@@ -42,15 +42,19 @@ classifiers =
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
     Programming Language :: Python :: 3 :: Only
-keywords =
+keywords = 
+    llm 
+    chemistry
+    lift
+
 
 
 [options]
 install_requires =
     more_itertools
     tqdm
     transformers
-    peft 
+    peft
     gptchem
     datasets
     accelerate
@@ -114,51 +118,35 @@ show_missing = True
 exclude_lines =
     pragma: no cover
     raise NotImplementedError
-    if __name__ == "__main__":
-    if TYPE_CHECKING:
-    def __str__
-    def __repr__
+
 
 ##########################
 # Darglint Configuration #
 ##########################
 [darglint]
-docstring_style = sphinx
+docstring_style = google
 strictness = short
 
-#########################
-# Flake8 Configuration  #
-# (.flake8)             #
-#########################
-[flake8]
-ignore =
-    S301 # pickle
-    S403 # pickle
-    S404
-    S603
-    W503 # Line break before binary operator (flake8 is wrong)
-    E203  # whitespace before ':'
-exclude =
-    .tox,
-    .git,
-    __pycache__,
-    docs/source/conf.py,
-    build,
-    dist,
-    tests/fixtures/*,
-    *.pyc,
-    *.egg-info,
-    .cache,
-    .eggs,
-    data
-max-line-length = 120
-max-complexity = 20
-import-order-style = pycharm
-application-import-names =
-    chemlift
-    tests
-
-
-[tool:pytest]
-env_files =
-    .env
+[tool.ruff]
+exclude = 
+    ".tox"
+    ".git"
+    "__pycache__"
+    "docs/source/conf.py"
+    "build"
+    "dist"
+    "tests/fixtures/*"
+    "*.pyc"
+    "*.egg-info"
+    ".cache"
+    ".eggs"
+    "data"
+line-length = 120
+select = 
+    "C9"
+    "E"
+    "F"
+    "W"
+
+[tool.ruff.mccabe]
+max-complexity = 20

src/chemlift/icl/fewshotclassifier.py

@@ -1,8 +1,6 @@
 from loguru import logger
 from numpy.typing import ArrayLike
-from typing import Union
 from chemlift.icl.fewshotpredictor import FewShotPredictor
-from chemlift.icl.utils import LangChainChatModelWrapper
 
 
 class FewShotClassifier(FewShotPredictor):

src/chemlift/icl/fewshotpredictor.py

@@ -6,7 +6,6 @@
 from numpy.typing import ArrayLike
 import enum
 from typing import Union
-from chemlift.icl.fewshotpredictor import FewShotPredictor
 from chemlift.icl.utils import LangChainChatModelWrapper
 
 

src/chemlift/icl/utils.py

@@ -1,5 +1,13 @@
 class LangChainChatModelWrapper:
-    """Wrapper for chat model to make it accept plain text prompts."""
+    """Wrapper for chat model to make it accept plain text prompts.
+
+    Examples:
+        >>> from chemlift.icl.utils import LangChainChatModelWrapper
+        >>> from langchain.chat_models import ChatOpenAI
+        >>> model = ChatOpenAI(model="gpt-4")
+        >>> model = LangChainChatModelWrapper(model)
+        >>> model.generate(["Hello, how are you?"])
+    """
 
     def __init__(self, model):
         self.model = model

src/chemlift/utils.py

@@ -14,7 +14,7 @@ def array_of_ints_without_nan(arr):
 def try_exccept_nan(f, x):
     try:
         return f(x)
-    except:
+    except Exception:
         return np.nan
 
 

tox.ini

@@ -16,7 +16,7 @@ envlist =
     lint
     manifest
     pyroma
-    flake8
+    rufff
     mypy
     # documentation linters/checkers
     doc8
@@ -39,20 +39,12 @@ extras =
     tests
 
 [testenv:doctests]
-description = Test that documentation examples run properly
 commands =
     xdoctest -m src
 deps =
     xdoctest
     pygments
 
-[testenv:treon]
-description = Test that notebooks can run to completion
-commants =
-    treon notebooks/
-deps =
-    treon
-
 [testenv:coverage-clean]
 deps = coverage
 skip_install = true
@@ -84,23 +76,13 @@ skip_install = true
 commands = check-manifest
 description = Check that the MANIFEST.in is written properly and give feedback on how to fix it.
 
-[testenv:flake8]
-skip_install = true
+[testenv:ruff]
+skip_install = false
 deps =
-    darglint
-    flake8<5.0.0
-    flake8-black
-    flake8-bandit
-    flake8-bugbear
-    flake8-colors
-    flake8-docstrings
-    flake8-isort
-    flake8-print
-    pep8-naming
-    pydocstyle
+    ruff
 commands =
-    flake8 src/ tests/
-description = Run the flake8 tool with several plugins (bandit, docstrings, import order, pep8 naming). See https://cthoyt.com/2020/04/25/how-to-code-with-me-flake8.html for more information.
+    ruff src/ tests/
+description = Run the ruff tool with several plugins (bandit, docstrings, import order, pep8 naming). 
 
 [testenv:pyroma]
 deps =
@@ -221,4 +203,4 @@ commands =
     bump2version patch
     git push
 allowlist_externals =
-    git
+    git