Ruff config

Signed-off-by: zethson <lukas.heumos@posteo.net>

.pre-commit-config.yaml

@@ -1,65 +1,56 @@
+fail_fast: false
+default_language_version:
+  python: python3
+default_stages:
+  - commit
+  - push
+minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.2.0
-    hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
-        exclude: |
-          (?x)(
-              .github/workflows/latest-changes.jinja2
-          )
-      - id: check-yaml
-      - id: check-added-large-files
-  - repo: https://github.com/psf/black
-    rev: 22.6.0
-    hooks:
-      - id: black-jupyter
-  - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.4
     hooks:
-      - id: flake8
-        additional_dependencies:
-          - flake8-black==0.3.3
-          - flake8-typing-imports==1.10.0
-        language_version: python3
-        args:
-          - --max-line-length=88
-          - --ignore=E203,W503,BLK100,TYP001
+      - id: prettier
         exclude: |
           (?x)(
-              __init__.py
+            docs/changelog.md
           )
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.6.2
-    hooks:
-      - id: prettier
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.3.9
+    rev: 0.6.1
     hooks:
       - id: nbstripout
         exclude: |
           (?x)(
               docs/examples/|
               docs/notes/
           )
-  - repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.1.9
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.5
     hooks:
-      - id: forbid-crlf
-      - id: remove-crlf
-  - repo: https://github.com/pycqa/isort
-    rev: 5.12.0
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix, --unsafe-fixes]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
     hooks:
-      - id: isort
-        name: isort (python)
-        args: ["--profile", "black"]
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)(
+              .github/workflows/latest-changes.jinja2
+            )
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.940
+    rev: v1.7.1
     hooks:
       - id: mypy
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: 6.1.1
-    hooks:
-      - id: pydocstyle
-        args: # google style + __init__, see http://www.pydocstyle.org/en/stable/error_codes.html
-          - --ignore=D100,D101,D102,D103,D104,D106,D107,D203,D204,D213,D215,D400,D401,D403,D404,D406,D407,D408,D409,D412,D413
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies:
+          ["types-pkg-resources", "types-requests", "types-attrs"]
+        exclude: |
+          (?x)(
+              test_notebooks.py
+          )

lamin_utils/__init__.py

@@ -2,6 +2,6 @@
 
 __version__ = "0.13.2"
 
-from ._core import colors  # noqa
+from ._core import colors
 from ._logger import logger
-from ._python_version import py_version_warning  # noqa
+from ._python_version import py_version_warning

lamin_utils/_base62.py

@@ -119,13 +119,11 @@ def _value(ch, charset):
     try:
         return charset.index(ch)
     except ValueError:
-        raise ValueError("base62: Invalid character (%s)" % ch)
+        raise ValueError(f"base62: Invalid character ({ch})") from None
 
 
 def _check_type(value, expected_type):
     """Checks if the input is in an appropriate type."""
     if not isinstance(value, expected_type):
-        msg = "Expected {} object, not {}".format(
-            expected_type, value.__class__.__name__
-        )
+        msg = f"Expected {expected_type} object, not {value.__class__.__name__}"
         raise TypeError(msg)

lamin_utils/_core.py

@@ -1,18 +1,18 @@
 # ANSI color code: https://gist.github.com/iansan5653/c4a0b9f5c30d74258c5f132084b78db9
-ANSI_COLORS = dict(
-    bold="\x1b[1m",
-    italic="\x1b[3m",
-    underline="\x1b[4m",
-    black="\x1b[1;90m",
-    red="\x1b[1;91m",
-    green="\x1b[1;92m",
-    yellow="\x1b[1;93m",
-    blue="\x1b[1;94m",
-    purple="\x1b[1;95m",
-    cyan="\x1b[1;96m",
-    white="\x1b[1;97m",
-    reset="\x1b[0m",
-)
+ANSI_COLORS = {
+    "bold": "\x1b[1m",
+    "italic": "\x1b[3m",
+    "underline": "\x1b[4m",
+    "black": "\x1b[1;90m",
+    "red": "\x1b[1;91m",
+    "green": "\x1b[1;92m",
+    "yellow": "\x1b[1;93m",
+    "blue": "\x1b[1;94m",
+    "purple": "\x1b[1;95m",
+    "cyan": "\x1b[1;96m",
+    "white": "\x1b[1;97m",
+    "reset": "\x1b[0m",
+}
 
 
 class colors:

lamin_utils/_inspect.py

@@ -95,7 +95,7 @@ def _validate_logging(result: "InspectResult", field: Optional[str] = None):
     success_msg = ""
     if len(result.validated) > 0:
         success_msg = (
-            f"{colors.green(f'{len(result.validated)} term{s}')} ({result.frac_validated:.2f}%)"  # noqa
+            f"{colors.green(f'{len(result.validated)} term{s}')} ({result.frac_validated:.2f}%)"
             f" {are} validated{field_msg}"
         )
     if result.frac_validated < 100:
@@ -105,7 +105,7 @@ def _validate_logging(result: "InspectResult", field: Optional[str] = None):
         if len(result.non_validated) > 20:
             print_values += ", ..."
         warn_msg = (
-            f"{colors.yellow(f'{len(result.non_validated)} term{s}')} ({(100-result.frac_validated):.2f}%)"  # noqa
+            f"{colors.yellow(f'{len(result.non_validated)} term{s}')} ({(100-result.frac_validated):.2f}%)"
             f" {are} not validated{field_msg}: {colors.yellow(print_values)}"
         )
         if len(empty_warn_msg) > 0:
@@ -147,7 +147,8 @@ def inspect(
     # empty DataFrame or input
     if df.shape[0] == 0 or len(uniq_identifiers) == 0:
         result = _validate_stats(
-            identifiers=identifiers, matches=[False] * len(identifiers)  # type:ignore
+            identifiers=identifiers,
+            matches=[False] * len(identifiers),  # type:ignore
         )
         if not mute:
             _validate_logging(result=result, field=field)
@@ -194,7 +195,7 @@ def inspect(
                 info_msg = f"detected {labels}: {colors.yellow(print_values)}"
                 result._synonyms_mapper = synonyms_mapper
 
-        except Exception:
+        except Exception:  # noqa: S110
             pass
     if not mute:
         _validate_logging(result=result, field=field)
@@ -231,7 +232,7 @@ def __init__(
 
     @property
     def df(self) -> "pd.DataFrame":
-        """A DataFrame indexed by values with a boolean `__validated__` column."""  # noqa
+        """A DataFrame indexed by values with a boolean `__validated__` column."""
         return self._df
 
     @property

lamin_utils/_logger.py

@@ -30,6 +30,7 @@
 # OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 """Logging and Profiling."""
+
 import logging
 
 # import platform
@@ -122,38 +123,38 @@ def log(  # type: ignore
         super().log(level, msg, extra=extra)
         return now
 
-    def critical(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def critical(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(CRITICAL, msg, time=time, deep=deep, extra=extra)
 
-    def error(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def error(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(ERROR, msg, time=time, deep=deep, extra=extra)
 
-    def warning(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def warning(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(WARNING, msg, time=time, deep=deep, extra=extra)
 
-    def important(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def important(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(IMPORTANT, msg, time=time, deep=deep, extra=extra)
 
-    def success(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def success(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(SUCCESS, msg, time=time, deep=deep, extra=extra)
 
-    def info(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def info(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(INFO, msg, time=time, deep=deep, extra=extra)
 
-    def save(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def save(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(SAVE, msg, time=time, deep=deep, extra=extra)
 
-    def hint(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def hint(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(HINT, msg, time=time, deep=deep, extra=extra)
 
-    def debug(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def debug(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(DEBUG, msg, time=time, deep=deep, extra=extra)
 
-    def print(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def print(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(PRINT, msg, time=time, deep=deep, extra=extra)
 
     # backward compat
-    def download(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore  # noqa
+    def download(self, msg, *, time=None, deep=None, extra=None) -> datetime:  # type: ignore
         return self.log(SAVE, msg, time=time, deep=deep, extra=extra)
 
 
@@ -178,7 +179,8 @@ def format(self, record: logging.LogRecord):
         if record.time_passed:  # type: ignore
             if "{time_passed}" in record.msg:
                 record.msg = record.msg.replace(
-                    "{time_passed}", record.time_passed  # type: ignore
+                    "{time_passed}",
+                    record.time_passed,  # type: ignore
                 )
             else:
                 self._style._fmt += " ({time_passed})"

lamin_utils/_standardize.py

@@ -135,7 +135,7 @@ def standardize(
                 for k, v in mapper.items()
                 if k
                 not in set(
-                    chain(*[v if isinstance(v, list) else [v] for v in result.values()])  # type: ignore # noqa
+                    chain(*[v if isinstance(v, list) else [v] for v in result.values()])  # type: ignore
                 )
             }
         )