update pre-commits and unpin numba and numpy (#643)

.github/.codecov.yml

@@ -1,18 +1,17 @@
+# Based on pydata/xarray
 codecov:
-    require_ci_to_pass: no
-    strict_yaml_branch: main
+    require_ci_to_pass: false
 
 coverage:
-    range: 80..100
     status:
         project:
             default:
+                # Require 1% coverage, i.e., always succeed
                 target: 1
-        patch: off
+        patch: false
+        changes: false
 
 comment:
-    layout: reach, diff, files
-    behavior: default
-    require_changes: true
-    branches:
-        - main
+    layout: "diff, flags, files"
+    behavior: once
+    require_base: false

.github/workflows/test.yml

@@ -90,11 +90,11 @@ jobs:
               run: |
                   tox -vv
 
-            - name: Upload coverage
-              env:
-                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
-              run: |
-                  codecov --no-color --required --flags unittests
+            - name: Upload coverage to Codecov
+              uses: codecov/codecov-action@v3.1.1
+              with:
+                  name: coverage
+                  verbose: true
 
     regenerate-notebooks:
         needs: test

.mypy.ini

@@ -28,8 +28,7 @@ show_error_codes = True
 show_column_numbers = True
 error_summary = True
 
-[mypy-tests.*]
-ignore_errors = True
+no_namespace_packages = True
 
-[mypy-docs.*]
+[mypy-tests.*]
 ignore_errors = True

.pre-commit-config.yaml

@@ -7,45 +7,23 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v0.982
+      rev: v1.0.0
       hooks:
           - id: mypy
             additional_dependencies:
                 [numpy==1.21.0, scipy, pandas, types-requests]
             exclude: .scripts/ci/download_data.py|squidpy/datasets/_(dataset|image).py # See https://github.com/pre-commit/mirrors-mypy/issues/33
     - repo: https://github.com/psf/black
-      rev: 22.10.0
+      rev: 23.1.0
       hooks:
           - id: black
             additional_dependencies: [toml]
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.2
+      rev: v3.0.0-alpha.4
       hooks:
           - id: prettier
-    - repo: https://github.com/timothycrosley/isort
-      rev: 5.10.1
-      hooks:
-          - id: isort
-            additional_dependencies: [toml]
-            args: [--order-by-type]
-    - repo: https://github.com/asottile/yesqa
-      rev: v1.4.0
-      hooks:
-          - id: yesqa
-            additional_dependencies:
-                [
-                    flake8-tidy-imports,
-                    flake8-docstrings,
-                    flake8-rst-docstrings,
-                    flake8-comprehensions,
-                    flake8-bugbear,
-                    flake8-blind-except,
-                    flake8-builtins,
-                    flake8-pytest-style,
-                    flake8-string-format,
-                ]
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.3.0
+      rev: v4.4.0
       hooks:
           - id: detect-private-key
           - id: check-merge-conflict
@@ -67,51 +45,24 @@ repos:
           - id: check-yaml
           - id: check-toml
           - id: requirements-txt-fixer
-    - repo: https://github.com/myint/autoflake
-      rev: v1.7.6
-      hooks:
-          - id: autoflake
-            args:
-                [
-                    --in-place,
-                    --remove-all-unused-imports,
-                    --remove-unused-variable,
-                    --ignore-init-module-imports,
-                ]
-    - repo: https://github.com/pycqa/flake8.git
-      rev: 5.0.4
-      hooks:
-          - id: flake8
-            additional_dependencies:
-                [
-                    flake8-tidy-imports,
-                    flake8-docstrings,
-                    flake8-rst-docstrings,
-                    flake8-comprehensions,
-                    flake8-bugbear,
-                    flake8-blind-except,
-                    flake8-builtins,
-                    flake8-pytest-style,
-                    flake8-string-format,
-                ]
     - repo: https://github.com/jumanjihouse/pre-commit-hooks
       rev: 3.0.0
       hooks:
           - id: script-must-have-extension
             name: Check executable files use .sh extension
             types: [shell, executable]
     - repo: https://github.com/asottile/blacken-docs
-      rev: v1.12.1
+      rev: 1.13.0
       hooks:
           - id: blacken-docs
-            additional_dependencies: [black==20.8b1]
-    - repo: https://github.com/asottile/pyupgrade
-      rev: v3.1.0
+    - repo: https://github.com/charliermarsh/ruff-pre-commit
+      # Ruff version.
+      rev: v0.0.246
       hooks:
-          - id: pyupgrade
-            args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
     - repo: https://github.com/pre-commit/pygrep-hooks
-      rev: v1.9.0
+      rev: v1.10.0
       hooks:
           - id: python-no-eval
           - id: python-use-type-annotations
@@ -120,6 +71,6 @@ repos:
           - id: rst-directive-colons
           - id: rst-inline-touching-normal
     - repo: https://github.com/PyCQA/doc8
-      rev: v1.0.0
+      rev: v1.1.1
       hooks:
           - id: doc8

.scripts/ci/download_data.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
-from typing import Any
-from pathlib import Path
 import argparse
+from pathlib import Path
+from typing import Any
 
 _CNT = 0  # increment this when you want to rebuild the CI cache
 _ROOT = Path.home() / ".cache" / "squidpy"
@@ -20,7 +20,7 @@ def _maybe_download_data(func_name: str, path: Path) -> Any:
 
     try:
         return getattr(sq.datasets, func_name)(path=path)
-    except Exception as e:
+    except Exception as e:  # noqa: BLE001
         print(f"File {str(path):>25} seems to be corrupted: {e}. Removing and retrying")
         path.unlink()
 

docs/source/_ext/typed_returns.py

@@ -1,7 +1,8 @@
-from typing import List, Iterable, Iterator
+import re
+from typing import Iterable, Iterator, List
+
 from sphinx.application import Sphinx
 from sphinx.ext.napoleon import NumpyDocstring
-import re
 
 
 def _process_return(lines: Iterable[str]) -> Iterator[str]:

docs/source/conf.py

@@ -4,25 +4,25 @@
 # list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-from pathlib import Path
-from datetime import datetime
-from sphinx.application import Sphinx
-from sphinx_gallery.gen_gallery import DEFAULT_GALLERY_CONF
-
 # -- Path setup --------------------------------------------------------------
 import os
 import sys
+from datetime import datetime
+from pathlib import Path
+
+from sphinx.application import Sphinx
+from sphinx_gallery.gen_gallery import DEFAULT_GALLERY_CONF
 
 HERE = Path(__file__).parent
 sys.path.insert(0, str(HERE.parent.parent))  # this way, we don't have to install squidpy
 sys.path.insert(0, os.path.abspath("_ext"))
 
+import squidpy  # noqa: E402
 from docs.source.utils import (  # noqa: E402
-    _get_thumbnails,
-    _fetch_notebooks,
     MaybeMiniGallery,
+    _fetch_notebooks,
+    _get_thumbnails,
 )
-import squidpy  # noqa: E402
 
 needs_sphinx = "4.0"
 

docs/source/create_news_fragment.py

@@ -1,10 +1,11 @@
+import argparse
+import logging
+import textwrap
 from enum import Enum
-from typing import Any, List, Mapping, Optional
 from pathlib import Path
-import logging
-import argparse
+from typing import Any, List, Mapping, Optional
+
 import requests
-import textwrap
 
 _root = Path(__file__).parent / "release" / "changelog"
 _valid_types = ("feature", "bugfix", "deprecation", "misc", "doc", "ignore-towncrier")
@@ -92,7 +93,7 @@ def create_news_fragment(issue_number: str, use_title: bool = False, add_author:
             print(add_author, author)
             if add_author and author is not None:
                 print(author, file=fout)
-    except Exception as e:
+    except Exception as e:  # noqa: BLE001
         logging.error(f"Unable to generate news fragment. Reason: `{e}`")
         exit(1)
 

docs/source/references.bib

@@ -46,7 +46,7 @@ @techreport{networkx
      year = {2008},
      place = {United States},
      institution = {Los Alamos National Lab.(LANL), Los Alamos, NM (United States)},
-     URL = {https://www.osti.gov/biblio/960616},
+     URL = {https://conference.scipy.org/proceedings/SciPy2008/paper_2/},
 }
 
 @article{tangram,

docs/source/utils.py

@@ -1,13 +1,14 @@
-from git import Repo
-from shutil import rmtree, copytree
-from typing import Any, Dict, List, Union, ForwardRef
+import os
+import re
 from logging import info, warning
 from pathlib import Path
+from shutil import copytree, rmtree
 from tempfile import TemporaryDirectory
+from typing import Any, Dict, ForwardRef, List, Union
+
 from enchant.tokenize import Filter
+from git import Repo
 from sphinx_gallery.directives import MiniGallery
-import os
-import re
 
 HERE = Path(__file__).parent
 
@@ -42,7 +43,7 @@ def fetch_local(repo_path: Union[str, Path]) -> None:
     )
     try:
         fetch_local(notebooks_local_path)
-    except Exception as e:
+    except Exception as e:  # noqa: BLE001
         warning(f"Unable to fetch notebooks locally from `{notebooks_local_path}`, reason: `{e}`. Trying remote")
         download = int(os.environ.get("SQUIDPY_DOWNLOAD_NOTEBOOKS", 1))
         if not download: