Ruff and 3.11 (#276)

Zethson · web-flow · commit e71039a89e55 · 2023-12-26T23:26:45.000+01:00
* Ruff and 3.11

Signed-off-by: zethson &lt;lukas.heumos@posteo.net&gt;

* Also support 3.8

Signed-off-by: zethson &lt;lukas.heumos@posteo.net&gt;

---------

Signed-off-by: zethson &lt;lukas.heumos@posteo.net&gt;
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.11"]
 
     steps:
       - name: Checkout main
@@ -26,26 +26,31 @@ jobs:
           ssh-key: ${{ secrets.READ_LNDOCS }}
           path: lndocs
           ref: main
+
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
           cache-dependency-path: ".github/workflows/build.yml" # See dependencies below
+
       - name: Cache nox
         uses: actions/cache@v3
         with:
           path: .nox
           key: nox-${{ runner.os }}
+
       - name: Cache pre-commit
         uses: actions/cache@v3
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
+
       - name: Install Python dependencies
         run: |
           python -m pip install -U pip
           pip install -U laminci
+
       - name: Configure AWS
         uses: aws-actions/configure-aws-credentials@v2
         with:
@@ -54,13 +59,15 @@ jobs:
           aws-region: eu-central-1
       # - run: nox -s lint
       - run: nox -s build
+
       - name: Codecov
-        if: matrix.python-version == '3.9'
+        if: matrix.python-version == '3.11'
         uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Deploy docs
-        if: matrix.python-version == '3.9'
+        if: matrix.python-version == '3.11'
         id: netlify
         uses: nwtgck/actions-netlify@v1.2
         with:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,59 +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
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.4
     hooks:
-      - id: trailing-whitespace
-      - id: end-of-file-fixer
+      - id: prettier
         exclude: |
           (?x)(
-              .github/workflows/latest-changes.jinja2
+            docs/changelog.md
           )
-      - 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/kynan/nbstripout
+    rev: 0.6.1
     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
+      - id: nbstripout
         exclude: |
           (?x)(
-              __init__.py
+              docs/examples/|
+              docs/notes/
           )
-  - 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
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.7
     hooks:
-      - id: nbstripout
-  - repo: https://github.com/Lucas-C/pre-commit-hooks
-    rev: v1.1.9
-    hooks:
-      - id: forbid-crlf
-      - id: remove-crlf
-  - repo: https://github.com/pre-commit/mirrors-isort
-    rev: v5.8.0
+      - 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
-        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,D105,D107,D203,D204,D213,D215,D400,D401,D404,D406,D407,D408,D409,D413
+        args: [--no-strict-optional, --ignore-missing-imports]
+        additional_dependencies:
+          ["types-pkg-resources", "types-requests", "types-attrs"]
+        exclude: |
+          (?x)(
+              test_notebooks.py
+          )
diff --git a/CITATION.cff b/CITATION.cff
@@ -1,26 +1,26 @@
 cff-version: 1.2.0
 title: "nbproject: Manage Jupyter notebooks"
 authors:
-- family-names: Rybakov
-  given-names: Sergei
-  orcid: https://orcid.org/0000-0002-4944-6586
-- family-names: Wolf
-  given-names: Alex
-  orcid: https://orcid.org/0000-0002-8760-7838
-url: https://github.com/laminlabs/nbproject
-preferred-citation:
-  type: article
-  title: "nbproject: Manage Jupyter notebooks"
-  authors:
   - family-names: Rybakov
     given-names: Sergei
     orcid: https://orcid.org/0000-0002-4944-6586
-  - family-names: Heumos
-    given-names: Lukas
-    orcid: https://orcid.org/0000-0002-8937-3457
   - family-names: Wolf
     given-names: Alex
     orcid: https://orcid.org/0000-0002-8760-7838
+url: https://github.com/laminlabs/nbproject
+preferred-citation:
+  type: article
+  title: "nbproject: Manage Jupyter notebooks"
+  authors:
+    - family-names: Rybakov
+      given-names: Sergei
+      orcid: https://orcid.org/0000-0002-4944-6586
+    - family-names: Heumos
+      given-names: Lukas
+      orcid: https://orcid.org/0000-0002-8937-3457
+    - family-names: Wolf
+      given-names: Alex
+      orcid: https://orcid.org/0000-0002-8760-7838
   doi: 10.56528/nbp
   journal: Lamin Reports
   year: 2022
diff --git a/nbproject/__init__.py b/nbproject/__init__.py
@@ -32,7 +32,7 @@
 # trying to init ipylab JupyterFrontEnd can lead to errors on jupyter notebook
 try:
     _init_frontend()
-except:
+except:  # noqa: E722
     pass
 
 from . import dev
diff --git a/nbproject/_cli.py b/nbproject/_cli.py
@@ -81,7 +81,7 @@ def sync(
     else:
         logger.info(f"Yaml of the project is: {yaml_file.as_posix()}.")
 
-    with open(yaml_file, "r") as stream:
+    with open(yaml_file) as stream:
         yaml_proj = yaml.load(stream, Loader=yaml.FullLoader)
 
     nbs = notebooks_from_files_dirs(files_dirs)
diff --git a/nbproject/_header.py b/nbproject/_header.py
@@ -105,7 +105,9 @@ def header(
     try:
         nb = read_notebook(filepath)  # type: ignore
     except FileNotFoundError:
-        raise RuntimeError("Try passing the filepath manually to nbproject.Header().")
+        raise RuntimeError(
+            "Try passing the filepath manually to nbproject.Header()."
+        ) from None
 
     # make time_run available through API
     time_run = datetime.now(timezone.utc)
diff --git a/nbproject/_is_run_from_ipython.py b/nbproject/_is_run_from_ipython.py
@@ -1,4 +1,4 @@
-# From https://github.com/scverse/scanpy/blob/d7e13025b931ad4afd03b4344ef5ff4a46f78b2b/scanpy/_settings.py  # noqa
+# From https://github.com/scverse/scanpy/blob/d7e13025b931ad4afd03b4344ef5ff4a46f78b2b/scanpy/_settings.py
 # Under BSD 3-Clause License
 # Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab
 import builtins
diff --git a/nbproject/_logger.py b/nbproject/_logger.py
@@ -1 +1 @@
-from lamin_utils import colors, logger  # noqa
+from lamin_utils import colors, logger
diff --git a/nbproject/_meta.py b/nbproject/_meta.py
@@ -8,7 +8,7 @@
 
 
 # https://stackoverflow.com/questions/128573/using-property-on-classmethods/64738850#64738850
-class classproperty(object):
+class classproperty:
     def __init__(self, fget):
         self.fget = fget
 
diff --git a/nbproject/_publish.py b/nbproject/_publish.py
@@ -95,6 +95,7 @@ def publish(
             sets the version to the passed version. Consider semantic versioning.
         i_confirm_i_saved: Only relevant outside Jupyter Lab as a safeguard against
             losing the editor buffer content because of accidentally publishing.
+        kwargs: Additional arguments for publishing.
     """
     if "calling_statement" in kwargs:
         calling_statement = kwargs.pop("calling_statement")
diff --git a/nbproject/dev/_classic_nb_commands.py b/nbproject/dev/_classic_nb_commands.py
@@ -1,6 +1,6 @@
 from time import sleep
 
-from .._logger import logger
+from nbproject._logger import logger
 
 
 def _save_notebook():
diff --git a/nbproject/dev/_consecutiveness.py b/nbproject/dev/_consecutiveness.py
@@ -1,4 +1,5 @@
-from .._logger import logger
+from nbproject._logger import logger
+
 from ._notebook import Notebook
 
 
diff --git a/nbproject/dev/_initialize.py b/nbproject/dev/_initialize.py
@@ -3,7 +3,8 @@
 from datetime import datetime, timezone
 from typing import List, Optional, Union
 
-from .._logger import logger
+from nbproject._logger import logger
+
 from ._lamin_communicate import lamin_user_settings
 from ._meta_store import MetaContainer
 from ._notebook import Notebook
diff --git a/nbproject/dev/_jupyter_communicate.py b/nbproject/dev/_jupyter_communicate.py
@@ -5,7 +5,8 @@
 
 import orjson
 
-from .._logger import logger
+from nbproject._logger import logger
+
 from ._jupyter_lab_commands import _lab_notebook_path
 
 DIR_KEYS = ("notebook_dir", "root_dir")
@@ -33,7 +34,7 @@ def query_server(server: dict):
             "Unable to access server;\n"
             "querying requires either no security or token based security."
         )
-        raise Exception(CONN_ERROR)
+        raise Exception(CONN_ERROR) from None
 
 
 def running_servers():
diff --git a/nbproject/dev/_jupyter_lab_commands.py b/nbproject/dev/_jupyter_lab_commands.py
@@ -3,7 +3,7 @@
 
 from ipylab import JupyterFrontEnd
 
-from .._is_run_from_ipython import is_run_from_ipython
+from nbproject._is_run_from_ipython import is_run_from_ipython
 
 app = None
 
diff --git a/nbproject/dev/_meta_live.py b/nbproject/dev/_meta_live.py
@@ -2,7 +2,8 @@
 from pathlib import Path
 from typing import Optional, Union
 
-from .._logger import logger
+from nbproject._logger import logger
+
 from ._consecutiveness import check_consecutiveness
 from ._jupyter_lab_commands import _save_notebook
 from ._lamin_communicate import lamin_user_settings
diff --git a/nbproject/dev/_meta_store.py b/nbproject/dev/_meta_store.py
@@ -3,7 +3,8 @@
 
 from pydantic import BaseModel, Extra
 
-from .._logger import logger
+from nbproject._logger import logger
+
 from ._frontend_commands import _reload_notebook, _save_notebook
 from ._metadata_display import table_metadata
 from ._notebook import Notebook, read_notebook, write_notebook
@@ -61,7 +62,7 @@ class MetaContainer(BaseModel):
     user_name: Optional[str] = None
     """User name from lamindb."""
 
-    class Config:  # noqa
+    class Config:
         extra = Extra.allow
 
 
diff --git a/nbproject/dev/_metadata_display.py b/nbproject/dev/_metadata_display.py
@@ -30,8 +30,8 @@ def display_html(html: str):
 
 # display configuration
 class DisplayConf(BaseModel):
-    time_init: Enum("choice", ["date", "datetime"]) = "datetime"  # type: ignore # noqa
-    time_run: Enum("choice", ["date", "datetime"]) = "datetime"  # type: ignore # noqa
+    time_init: Enum("choice", ["date", "datetime"]) = "datetime"  # type: ignore
+    time_run: Enum("choice", ["date", "datetime"]) = "datetime"  # type: ignore
 
 
 def color_id(id: str):
diff --git a/nbproject/dev/_pypackage.py b/nbproject/dev/_pypackage.py
@@ -1,7 +1,7 @@
 import re
 import sys
 from ast import Import, ImportFrom, parse, walk
-from typing import Iterable, List, Optional, Union  # noqa
+from typing import Iterable, List, Optional, Union
 
 from importlib_metadata import PackageNotFoundError, packages_distributions, version
 
@@ -63,7 +63,7 @@ def infer_pypackages(
     see :meth:`~nbproject.dev.MetaLive.pypackage`.
 
     Args:
-        nb: A notebook to infer pypackages from.
+        content: A notebook to infer pypackages from.
         add_pkgs: Additional packages to add.
         pin_versions: If `True`, fixes versions from the current environment.
 
diff --git a/nbproject/dev/_set_version.py b/nbproject/dev/_set_version.py
@@ -1,6 +1,6 @@
 from typing import Union
 
-from .._meta import meta
+from nbproject._meta import meta
 
 
 def set_version(
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/tests/test_cli.py b/tests/test_cli.py
diff --git a/tests/test_jupyter.py b/tests/test_jupyter.py
diff --git a/tests/test_notebooks.py b/tests/test_notebooks.py

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# From https://github.com/scverse/scanpy/blob/d7e13025b931ad4afd03b4344ef5ff4a46f78b2b/scanpy/_settings.py # noqa`
	`1`	`+# From https://github.com/scverse/scanpy/blob/d7e13025b931ad4afd03b4344ef5ff4a46f78b2b/scanpy/_settings.py`
`2`	`2`	`# Under BSD 3-Clause License`
`3`	`3`	`# Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab`
`4`	`4`	`import builtins`
Original file line number	Diff line number	Diff line change
`@@ -1 +1 @@`
`1`		`-from lamin_utils import colors, logger # noqa`
	`1`	`+from lamin_utils import colors, logger`