Update pyproject

.editorconfig

@@ -1,6 +1,3 @@
-# EditorConfig is awesome: https://EditorConfig.org
-
-# top-most EditorConfig file
 root = true
 
 [*]
@@ -11,10 +8,8 @@ charset = utf-8
 trim_trailing_whitespace = true
 insert_final_newline = true
 
-[makefile]
-end_of_line = lf
-charset = utf-8
-trim_trailing_whitespace = true
-insert_final_newline = true
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
+[Makefile]
 indent_style = tab
-indent_size = 4

.pre-commit-config.yaml

@@ -1,54 +1,46 @@
 fail_fast: false
 default_language_version:
-    python: python3
+  python: python3
 default_stages:
-    - commit
-    - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-    - repo: https://github.com/psf/black
-      rev: "23.1.0"
-      hooks:
-          - id: black-jupyter
-    - repo: https://github.com/asottile/blacken-docs
-      rev: 1.13.0
-      hooks:
-          - id: blacken-docs
-    - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.4
-      hooks:
-          - id: prettier
-            # Newer versions of node don't work on systems that have an older version of GLIBC
-            # (in particular Ubuntu 18.04 and Centos 7)
-            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
-            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
-            # https://github.com/jupyterlab/jupyterlab/issues/12675
-            language_version: "17.9.1"
-    - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.253
-      hooks:
-          - id: ruff
-            args: [--fix, --exit-non-zero-on-fix]
-    - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.4.0
-      hooks:
-          - id: detect-private-key
-          - id: check-ast
-          - id: end-of-file-fixer
-          - id: mixed-line-ending
-            args: [--fix=lf]
-          - id: trailing-whitespace
-          - id: check-case-conflict
-    - repo: local
-      hooks:
-          - id: forbid-to-commit
-            name: Don't commit rej files
-            entry: |
-                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-                Fix the merge conflicts manually and remove the .rej files.
-            language: fail
-            files: '.*\.rej$'
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v4.0.0-alpha.8
+    hooks:
+      - id: prettier
+  - repo: https://github.com/tox-dev/pyproject-fmt
+    rev: "2.3.1"
+    hooks:
+      - id: pyproject-fmt
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff
+        types_or: [python, pyi, jupyter]
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+        types_or: [python, pyi, jupyter]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: detect-private-key
+      - id: check-ast
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: trailing-whitespace
+      - id: check-case-conflict
+      # Check that there are no merge conflicts (could be generated by template sync)
+      - id: check-merge-conflict
+        args: [--assume-in-merge]
+  - repo: local
+    hooks:
+      - id: forbid-to-commit
+        name: Don't commit rej files
+        entry: |
+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
+          Fix the merge conflicts manually and remove the .rej files.
+        language: fail
+        files: '.*\.rej$'

.prettierrc.yaml

@@ -0,0 +1,7 @@
+overrides:
+  # JSON with comments and trailing commas
+  - files: .vscode/*.json
+    options:
+      parser: json5
+      quoteProps: preserve
+      singleQuote: false

pyproject.toml

@@ -1,114 +1,95 @@
 [build-system]
-requires = ['setuptools', 'setuptools_scm']
-build-backend = 'setuptools.build_meta'
+build-backend = "hatchling.build"
+requires = [ "hatchling" ]
 
 [project]
 name = "fancypackage"
-version = "0.0.0"
+version = "0.0.1"
 description = "Fancy Package"
 readme = "README.md"
-requires-python = ">=3.10"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
+maintainers = [
+  { name = "Jane Doe", email = "[email protected]" },
+]
 authors = [
-    {name = "Jane Doe"},
+  { name = "Jane Doe" },
 ]
-maintainers = [
-    {name = "Jane Doe", email = "[email protected]"},
+requires-python = ">=3.10"
+classifiers = [
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
 ]
-urls.Source = "https://github.com/url/to/repo.git"
-urls.Home-page = "https://github.com/url/to/repo.git"
 dependencies = [
-    "anndata",
-    "scanpy",
+  "anndata",
+  # for debug logging (referenced from the issue template)
+  "session-info",
+]
+optional-dependencies.dev = [
+  "pre-commit",
+  "twine>=4.0.2",
 ]
 
-[project.optional-dependencies]
-dev = [
-    "pre-commit",
+optional-dependencies.test = [
+  "coverage",
+  "pytest",
 ]
+# https://docs.pypi.org/project_metadata/#project-urls
+urls.Homepage = "https://github.com/url/to/repo.git"
+urls.Source = "https://github.com/url/to/repo.git"
 
-[tool.black]
-line-length = 120
-include = '\.pyi?$|\.ipynb?$'
-exclude = '''
-(
-  /(
-      \.eggs
-    | \.git
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-)
-'''
+[tool.hatch.envs.default]
+installer = "uv"
+features = [ "dev" ]
 
-[tool.isort]
-profile = "black"
-use_parentheses = true
-known_num = "networkx,numpy,pandas,scipy,sklearn,statmodels"
-known_plot = "matplotlib,mplscience,mpl_toolkits,seaborn"
-known_bio = "anndata,scanpy"
-sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,BIO,FIRSTPARTY,LOCALFOLDER"
-no_lines_before = "LOCALFOLDER"
-balanced_wrapping = true
-length_sort = "0"
-indent = "    "
-float_to_top = true
-order_by_type = false
+[tool.hatch.envs.hatch-test]
+features = [ "test" ]
 
 [tool.ruff]
-src = ["."]
-line-length = 119
-target-version = "py38"
-select = [
-    "F",  # Errors detected by Pyflakes
-    "E",  # Error detected by Pycodestyle
-    "W",  # Warning detected by Pycodestyle
-    "D",  # pydocstyle
-    "B",  # flake8-bugbear
-    "TID",  # flake8-tidy-imports
-    "C4",  # flake8-comprehensions
-    "BLE",  # flake8-blind-except
-    "UP",  # pyupgrade
-    "RUF100",  # Report unused noqa directives
+line-length = 120
+src = [ "src" ]
+extend-include = [ "*.ipynb" ]
+
+format.docstring-code-format = true
+
+lint.select = [
+  "B",      # flake8-bugbear
+  "BLE",    # flake8-blind-except
+  "C4",     # flake8-comprehensions
+  "D",      # pydocstyle
+  "E",      # Error detected by Pycodestyle
+  "F",      # Errors detected by Pyflakes
+  "I",      # isort
+  "RUF100", # Report unused noqa directives
+  "TID",    # flake8-tidy-imports
+  "UP",     # pyupgrade
+  "W",      # Warning detected by Pycodestyle
+]
+lint.ignore = [
+  "B008", # Errors from function calls in argument defaults. These are fine when the result is immutable.
+  "D100", # Missing docstring in public module
+  "D104", # Missing docstring in public package
+  "D105", # __magic__ methods are often self-explanatory, allow missing docstrings
+  "D107", # Missing docstring in __init__
+  # Disable one in each pair of mutually incompatible rules
+  "D203", # We don’t want a blank line before a class docstring
+  "D213", # <> We want docstrings to start immediately after the opening triple quote
+  "D400", # first line should end with a period [Bug: doesn’t work with single-line docstrings]
+  "D401", # First line should be in imperative mood; try rephrasing
+  "E501", # line too long -> we accept long comment lines; formatter gets rid of long code lines
+  "E731", # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
+  "E741", # allow I, O, l as variable names -> I is the identity matrix
 ]
-ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
-    "E501",
-    # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
-    "E731",
-    # allow I, O, l as variable names -> I is the identity matrix
-    "E741",
-    # Missing docstring in public package
-    "D104",
-    # Missing docstring in public module
-    "D100",
-    # Missing docstring in __init__
-    "D107",
-    # Errors from function calls in argument defaults. These are fine when the result is immutable.
-    "B008",
-    # __magic__ methods are are often self-explanatory, allow missing docstrings
-    "D105",
-    # first line should end with a period [Bug: doesn't work with single-line docstrings]
-    "D400",
-    # First line should be in imperative mood; try rephrasing
-    "D401",
-    ## Disable one in each pair of mutually incompatible rules
-    # We don’t want a blank line before a class docstring
-    "D203",
-    # We want docstrings to start immediately after the opening triple quote
-    "D213",
-    # Missing argument description in the docstring TODO: enable
-    "D417",
-    # Unable to detect undefined names
-    "F403",
-    # Underfined, or defined from star imports: module
-    "F405",
-    # Within an except clause, raise exceptions with `raise ... from err`
-    "B904",
+lint.per-file-ignores."*/__init__.py" = [ "F401" ]
+lint.per-file-ignores."docs/*" = [ "I" ]
+lint.per-file-ignores."tests/*" = [ "D" ]
+lint.pydocstyle.convention = "numpy"
+
+[tool.pytest.ini_options]
+testpaths = [ "tests" ]
+xfail_strict = true
+addopts = [
+  "--import-mode=importlib", # allow using test files with same name
 ]