Automated template update from cookiecutter-scverse

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "c96cadaa981a71113cc97ada8e5085188ed22ed7",
-  "checkout": "v0.1.1",
+  "commit": "57f6267716826dad73baba46dc3c00fe7262c459",
+  "checkout": "v0.2.0",
   "context": {
     "cookiecutter": {
       "project_name": "multi-view-atlas",

.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.rej

@@ -0,0 +1,15 @@
+diff a/.gitignore b/.gitignore	(rejected hunks)
+@@ -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: v0.0.259
++      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

README.md

@@ -3,7 +3,7 @@
 [![Tests][badge-tests]][link-tests]
 [![Documentation][badge-docs]][link-docs]
 
-[badge-tests]: https://img.shields.io/github/workflow/status/emdann/multi-view-atlas/Test/main
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/emdann/multi-view-atlas/test.yaml?branch=main
 [link-tests]: https://github.com/emdann/multi-view-atlas/actions/workflows/test.yml
 [badge-docs]: https://img.shields.io/readthedocs/multi-view-atlas
 

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",
@@ -87,11 +87,11 @@
 }
 
 intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
 }
 
-
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
@@ -110,6 +110,7 @@
 html_theme_options = {
     "repository_url": repository_url,
     "use_repository_button": True,
+    "path_to_docs": "docs/",
 }
 
 pygments_style = "default"