Automated template update from cookiecutter-scverse

.cruft.json

@@ -1,23 +1,23 @@
 {
-    "template": "/~https://github.com/scverse/cookiecutter-scverse",
-    "commit": "7cc5403b05e299d7a4bb169c2bd8c27a2a7676f3",
-    "context": {
-        "cookiecutter": {
-            "project_name": "infercnvpy",
-            "package_name": "infercnvpy",
-            "project_description": "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. ",
-            "author_full_name": "Gregor Sturm",
-            "author_email": "mail@gregor-sturm.de",
-            "github_user": "grst",
-            "project_repo": "/~https://github.com/icbi-lab/infercnvpy",
-            "license": "BSD 3-Clause License",
-            "_copy_without_render": [
-                ".github/workflows/**.yaml",
-                "docs/_templates/autosummary/**.rst"
-            ],
-            "_template": "/~https://github.com/scverse/cookiecutter-scverse"
-        }
-    },
-    "directory": null,
-    "checkout": "v0.1.3"
+  "template": "/~https://github.com/scverse/cookiecutter-scverse",
+  "commit": "57f6267716826dad73baba46dc3c00fe7262c459",
+  "context": {
+    "cookiecutter": {
+      "project_name": "infercnvpy",
+      "package_name": "infercnvpy",
+      "project_description": "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy. ",
+      "author_full_name": "Gregor Sturm",
+      "author_email": "mail@gregor-sturm.de",
+      "github_user": "grst",
+      "project_repo": "/~https://github.com/icbi-lab/infercnvpy",
+      "license": "BSD 3-Clause License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_template": "/~https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null,
+  "checkout": "v0.2.0"
 }

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,8 +8,8 @@ body:
               **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
               detailing how to provide the necessary information for us to reproduce your bug. In brief:
                 * Please provide exact steps how to reproduce the bug in a clean Python environment.
-                * In case it's not clear what's causing this bug, please provide the data or the data generation procecure.
-                * Sometimes it is not possible to share the data but usually it is possible to replicate problems on publicly
+                * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+                * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
                   available datasets or to share a subset of your data.
 
     - type: textarea

.gitignore

@@ -1,9 +1,13 @@
 # Temp files
 .DS_Store
 *~
+buck-out/
 
 # Compiled files
+.venv/
 __pycache__/
+.mypy_cache/
+.ruff_cache/
 
 # Distribution / packaging
 /build/

.pre-commit-config.yaml.rej

@@ -0,0 +1,81 @@
+diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
+@@ -7,32 +7,28 @@ default_stages:
+ minimum_pre_commit_version: 2.16.0
+ repos:
+     - repo: /~https://github.com/psf/black
+-      rev: 23.1.0
++      rev: "23.1.0"
+       hooks:
+           - id: black
+-    - repo: /~https://github.com/pre-commit/mirrors-prettier
+-      rev: v3.0.0-alpha.6
+-      hooks:
+-          - id: prettier
+     - 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/asottile/yesqa
+-      rev: v1.4.0
++    - repo: /~https://github.com/pre-commit/mirrors-prettier
++      rev: v3.0.0-alpha.6
+       hooks:
+-          - id: yesqa
+-            additional_dependencies:
+-                - flake8-tidy-imports
+-                - flake8-docstrings
+-                - flake8-rst-docstrings
+-                - flake8-comprehensions
+-                - flake8-bugbear
+-                - flake8-blind-except
++          - 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: v0.0.255
++      hooks:
++          - id: ruff
++            args: [--fix, --exit-non-zero-on-fix]
+     - repo: /~https://github.com/pre-commit/pre-commit-hooks
+       rev: v4.4.0
+       hooks:
+@@ -43,31 +39,6 @@ repos:
+             args: [--fix=lf]
+           - id: trailing-whitespace
+           - id: check-case-conflict
+-    - repo: /~https://github.com/myint/autoflake
+-      rev: v2.0.2
+-      hooks:
+-          - id: autoflake
+-            args:
+-                - --in-place
+-                - --remove-all-unused-imports
+-                - --remove-unused-variable
+-                - --ignore-init-module-imports
+-    - repo: /~https://github.com/PyCQA/flake8
+-      rev: 6.0.0
+-      hooks:
+-          - id: flake8
+-            additional_dependencies:
+-                - flake8-tidy-imports
+-                - flake8-docstrings
+-                - flake8-rst-docstrings
+-                - flake8-comprehensions
+-                - flake8-bugbear
+-                - flake8-blind-except
+-    - repo: /~https://github.com/asottile/pyupgrade
+-      rev: v3.3.1
+-      hooks:
+-          - id: pyupgrade
+-            args: [--py3-plus, --py38-plus, --keep-runtime-typing]
+     - repo: local
+       hooks:
+           - id: forbid-to-commit

docs/_templates/autosummary/class.rst

@@ -39,9 +39,6 @@ Attributes
 
 {% for item in attributes %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. autoattribute:: {{ [objname, item] | join(".") }}
 {%- endfor %}
 
@@ -56,9 +53,6 @@ Methods
 {% for item in methods %}
 {%- if item != '__init__' %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. automethod:: {{ [objname, item] | join(".") }}
 {%- endif -%}
 {%- endfor %}

docs/conf.py

@@ -65,7 +65,7 @@
 napoleon_include_init_with_doc = False
 napoleon_use_rtype = True  # having a separate entry generally helps readability
 napoleon_use_param = True
-myst_heading_anchors = 3  # create anchors for h1-h3
+myst_heading_anchors = 6  # create anchors for h1-h6
 myst_enable_extensions = [
     "amsmath",
     "colon_fence",
@@ -121,6 +121,7 @@
 html_theme_options = {
     "repository_url": repository_url,
     "use_repository_button": True,
+    "path_to_docs": "docs/",
 }
 
 pygments_style = "default"

docs/conf.py.rej

@@ -0,0 +1,9 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -87,6 +87,7 @@ source_suffix = {
+ }
+
+ intersphinx_mapping = {
++    "python": ("https://docs.python.org/3", None),
+     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
+     "numpy": ("https://numpy.org/doc/stable/", None),
+ }

docs/extensions/typed_returns.py

@@ -1,24 +1,27 @@
 # code from /~https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
 # with some minor adjustment
+from __future__ import annotations
+
 import re
+from collections.abc import Generator, Iterable
 
 from sphinx.application import Sphinx
 from sphinx.ext.napoleon import NumpyDocstring
 
 
-def _process_return(lines):
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
     for line in lines:
-        m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
-        if m:
-            # Once this is in scanpydoc, we can use the fancy hover stuff
+        if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
             yield f'-{m["param"]} (:class:`~{m["type"]}`)'
         else:
             yield line
 
 
-def _parse_returns_section(self, section):
-    lines_raw = list(_process_return(self._dedent(self._consume_to_next_section())))
-    lines = self._format_block(":returns: ", lines_raw)
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+    lines_raw = self._dedent(self._consume_to_next_section())
+    if lines_raw[0] == ":":
+        del lines_raw[0]
+    lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
     if lines and lines[-1]:
         lines.append("")
     return lines