Automated template update from cookiecutter-scverse (#70)

* Automated template update from cookiecutter-scverse * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix merge conflicts * update pre-commit * Update pre-commit and fix complaints --------- Co-authored-by: grst <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Gregor Sturm <[email protected]>
icbi-lab · Apr 5, 2023 · 133cefc · 133cefc
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diff --git a/.cruft.json b/.cruft.json
@@ -1,6 +1,6 @@
 {
     "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "7cc5403b05e299d7a4bb169c2bd8c27a2a7676f3",
+    "commit": "57f6267716826dad73baba46dc3c00fe7262c459",
     "context": {
         "cookiecutter": {
             "project_name": "infercnvpy",
@@ -19,5 +19,5 @@
         }
     },
     "directory": null,
-    "checkout": "v0.1.3"
+    "checkout": "v0.2.0"
 }
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.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

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

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
     - repo: https://github.com/psf/black
-      rev: 23.1.0
+      rev: "23.3.0"
       hooks:
           - id: black
     - repo: https://github.com/pre-commit/mirrors-prettier
@@ -16,6 +16,17 @@ repos:
           - id: prettier
             # doesn't work in combination with jupytext hook yet. See https://github.com/mwouts/jupytext/issues/580
             exclude: "docs/notebooks/.*\\.md"
+            # 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: v0.0.260
+      hooks:
+          - id: ruff
+            args: [--fix, --exit-non-zero-on-fix]
     - repo: https://github.com/asottile/blacken-docs
       rev: 1.13.0
       hooks:
@@ -24,21 +35,6 @@ repos:
             exclude: "docs/notebooks/.*"
             additional_dependencies:
                 - black==22.6.0 # Matches hook
-    - repo: https://github.com/PyCQA/isort
-      rev: 5.12.0
-      hooks:
-          - id: isort
-    - 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
     - repo: https://github.com/pre-commit/pre-commit-hooks
       rev: v4.4.0
       hooks:
@@ -49,31 +45,6 @@ repos:
             args: [--fix=lf]
           - id: trailing-whitespace
           - id: check-case-conflict
-    - repo: https://github.com/PyCQA/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

diff --git a/docs/_templates/autosummary/class.rst b/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 %}

diff --git a/docs/conf.py b/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",
@@ -87,6 +87,7 @@
 }
 
 intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
     "scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "h5py": ("https://docs.h5py.org/en/stable/", None),
@@ -96,7 +97,6 @@
     "matplotlib": ("https://matplotlib.org/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
     "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
-    "python": ("https://docs.python.org/3", None),
     "scipy": ("https://docs.scipy.org/doc/scipy/reference/", None),
     "seaborn": ("https://seaborn.pydata.org/", None),
     "sklearn": ("https://scikit-learn.org/stable/", None),
@@ -121,6 +121,7 @@
 html_theme_options = {
     "repository_url": repository_url,
     "use_repository_button": True,
+    "path_to_docs": "docs/",
 }
 
 pygments_style = "default"

diff --git a/docs/extensions/typed_returns.py b/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

diff --git a/docs/template_usage.md b/docs/template_usage.md
@@ -131,6 +131,10 @@ If your project is private, there are ways to enable docs rendering on [readthed
 check code for errors, inconsistencies and code styles, before the code
 is committed.
 
+This template uses a number of pre-commit checks. In this section we'll detail what is used, where they're defined, and how to modify these checks.
+
+#### Pre-commit CI
+
 We recommend setting up [pre-commit.ci][] to enforce consistency checks on every commit
 and pull-request.
 
@@ -142,78 +146,116 @@ Once authorized, pre-commit.ci should automatically be activated.
 
 #### Overview of pre-commit hooks used by the template
 
-The following pre-commit checks are for code style and format:
-
--   [black](https://black.readthedocs.io/en/stable/): standard code
-    formatter in Python.
--   [isort](https://pycqa.github.io/isort/): sort module imports into
-    sections and types.
--   [prettier](https://prettier.io/docs/en/index.html): standard code
-    formatter for non-Python files (e.g. YAML).
--   [blacken-docs](https://github.com/asottile/blacken-docs): black on
-    python code in docs.
-
-The following pre-commit checks are for errors and inconsistencies:
-
--   [flake8](https://flake8.pycqa.org/en/latest/): standard check for errors in Python files.
-    -   [flake8-tidy-imports](https://github.com/adamchainz/flake8-tidy-imports):
-        tidy module imports.
-    -   [flake8-docstrings](https://github.com/PyCQA/flake8-docstrings):
+The following pre-commit hooks are for code style and format:
+
+-   [black](https://black.readthedocs.io/en/stable/):
+    standard code formatter in Python.
+-   [blacken-docs](https://github.com/asottile/blacken-docs):
+    black on Python code in docs.
+-   [prettier](https://prettier.io/docs/en/index.html):
+    standard code formatter for non-Python files (e.g. YAML).
+-   [ruff][] based checks:
+    -   [isort](https://beta.ruff.rs/docs/rules/#isort-i) (rule category: `I`):
+        sort module imports into sections and types.
+    -   [pydocstyle](https://beta.ruff.rs/docs/rules/#pydocstyle-d) (rule category: `D`):
         pydocstyle extension of flake8.
-    -   [flake8-rst-docstrings](https://github.com/peterjc/e8-rst-docstrings):
-        extension of `flake8-docstrings` for `rst` docs.
-    -   [flake8-comprehensions](https://github.com/adamchainz/e8-comprehensions):
+    -   [flake8-tidy-imports](https://beta.ruff.rs/docs/rules/#flake8-tidy-imports-tid) (rule category: `TID`):
+        tidy module imports.
+    -   [flake8-comprehensions](https://beta.ruff.rs/docs/rules/#flake8-comprehensions-c4) (rule category: `C4`):
         write better list/set/dict comprehensions.
-    -   [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear):
-        find possible bugs and design issues in program.
-    -   [flake8-blind-except](https://github.com/elijahandrews/flake8-blind-except):
-        checks for blind, catch-all `except` statements.
--   [yesqa](https://github.com/asottile/yesqa):
-    remove unneccesary `# noqa` comments, follows additional dependencies listed above.
--   [autoflake](https://github.com/PyCQA/autoflake):
-    remove unused imports and variables.
--   [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks.
+    -   [pyupgrade](https://beta.ruff.rs/docs/rules/#pyupgrade-up) (rule category: `UP`):
+        upgrade syntax for newer versions of the language.
+
+The following pre-commit hooks are for errors and inconsistencies:
+
+-   [pre-commit-hooks](https://github.com/pre-commit/pre-commit-hooks): generic pre-commit hooks for text files.
     -   **detect-private-key**: checks for the existence of private keys.
     -   **check-ast**: check whether files parse as valid python.
-    -   **end-of-file-fixer**:check files end in a newline and only a newline.
+    -   **end-of-file-fixer**: check files end in a newline and only a newline.
     -   **mixed-line-ending**: checks mixed line ending.
     -   **trailing-whitespace**: trims trailing whitespace.
     -   **check-case-conflict**: check files that would conflict with case-insensitive file systems.
--   [pyupgrade](https://github.com/asottile/pyupgrade):
-    upgrade syntax for newer versions of the language.
--   **forbid-to-commit**: Make sure that `*.rej` files cannot be commited. These files are created by the
-    [automated template sync](#automated-template-sync) if there's a merge conflict and need to be addressed manually.
+    -   **forbid-to-commit**: Make sure that `*.rej` files cannot be commited.
+        These files are created by the [automated template sync](#automated-template-sync)
+        if there's a merge conflict and need to be addressed manually.
+-   [ruff][] based checks:
+    -   [pyflakes](https://beta.ruff.rs/docs/rules/#pyflakes-f) (rule category: `F`):
+        various checks for errors.
+    -   [pycodestyle](https://beta.ruff.rs/docs/rules/#pycodestyle-e-w) (rule category: `E`, `W`):
+        various checks for errors.
+    -   [flake8-bugbear](https://beta.ruff.rs/docs/rules/#flake8-bugbear-b) (rule category: `B`):
+        find possible bugs and design issues in program.
+    -   [flake8-blind-except](https://beta.ruff.rs/docs/rules/#flake8-blind-except-ble) (rule category: `BLE`):
+        checks for blind, catch-all `except` statements.
+    -   [Ruff-specific rules](https://beta.ruff.rs/docs/rules/#ruff-specific-rules-ruf) (rule category: `RUF`):
+        -   `RUF100`: remove unneccesary `# noqa` comments ()
 
-### How to disable or add pre-commit checks
+#### How to add or remove pre-commit checks
 
--   To ignore lint warnigs from **flake8**, see [Ignore certain lint warnings](#how-to-ignore-certain-lint-warnings).
--   You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file.
-    Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` or tool-specific
-    config files, such as `.prettierrc.yml` for **prettier** and `.flake8` for **flake8**.
+The [pre-commit checks](#pre-commit-checks) check for both correctness and stylistic errors.
+In some cases it might overshoot and you may have good reasons to ignore certain warnings.
+This section shows you where these checks are defined, and how to enable/ disable them.
 
-### How to ignore certain lint warnings
+##### pre-commit
 
-The [pre-commit checks](#pre-commit-checks) include [flake8](https://flake8.pycqa.org/en/latest/) which checks
-for errors in Python files, including stylistic errors.
+You can add or remove pre-commit checks by simply deleting relevant lines in the `.pre-commit-config.yaml` file under the repository root.
+Some pre-commit checks have additional options that can be specified either in the `pyproject.toml` (for `ruff` and `black`) or tool-specific
+config files, such as `.prettierrc.yml` for **prettier**.
 
-In some cases it might overshoot and you may have good reasons to ignore certain warnings.
+##### Ruff
 
-To ignore an specific error on a per-case basis, you can add a comment `# noqa` to the offending line. You can also
-specify the error ID to ignore, with e.g. `# noqa: E731`. Check the [flake8 guide][] for reference.
+This template configures `ruff` through the `[tool.ruff]` entry in the `pyproject.toml`.
+For further information `ruff` configuration, see [the docs](https://beta.ruff.rs/docs/configuration/).
 
-Alternatively, you can disable certain error messages for the entire project. To do so, edit the `.flake8`
-file in the root of the repository. Add one line per linting code you wish to ignore and don't forget to add a comment.
+Ruff assigns code to the rules it checks (e.g. `E401`) and groups them under a rule category (e.g. `E`).
+Rule categories are selectively enabled by including them under the `select` key:
 
 ```toml
+[tool.ruff]
 ...
-# line break before a binary operator -> black does not adhere to PEP8
-W503
-# line break occured after a binary operator -> black does not adhere to PEP8
-W504
-...
+
+select = [
+    "F",  # Errors detected by Pyflakes
+    "E",  # Error detected by Pycodestyle
+    "W",  # Warning detected by Pycodestyle
+    "I",  # isort
+    ...
+]
+```
+
+The `ignore` entry is used to disable specific rules for the entire project.
+Add the rule code(s) you want to ignore and don't forget to add a comment explaining why.
+You can find a long list of checks that this template disables by default sitting there already.
+
+```toml
+ignore = [
+    ...
+    # __magic__ methods are are often self-explanatory, allow missing docstrings
+    "D105",
+    ...
+]
+```
+
+Checks can be ignored per-file (or glob pattern) with `[tool.ruff.per-file-ignores]`.
+
+```toml
+[tool.ruff.per-file-ignores]
+"docs/*" = ["I"]
+"tests/*" = ["D"]
+"*/__init__.py" = ["F401"]
+```
+
+To ignore a specific rule on a per-case basis, you can add a `# noqa: <rule>[, <rule>, …]` comment to the offending line.
+Specify the rule code(s) to ignore, with e.g. `# noqa: E731`. Check the [Ruff guide][] for reference.
+
+```{note}
+The `RUF100` check will remove rule codes that are no longer necessary from `noqa` comments.
+If you want to add a code that comes from a tool other than Ruff,
+add it to Ruff’s [`external = [...]`](https://beta.ruff.rs/docs/settings/#external) setting to prevent `RUF100` from removing it.
 ```
 
-[flake8 guide]: https://flake8.pycqa.org/en/3.1.1/user/ignoring-errors.html
+[ruff]: https://beta.ruff.rs/docs/
+[ruff guide]: https://beta.ruff.rs/docs/configuration/#suppressing-errors
 
 ### API design