Update template to v0.2.22 (#449)

* Update template to v0.2.22

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix merge conflicts

* update pre-commit

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: scverse-bot <None>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "6a4338030e0c83a9034d607ed66abeff83e18840",
-  "checkout": null,
+  "commit": "605f95714130c960bce12eab98a4e023e8932249",
+  "checkout": "v0.2.22",
   "context": {
     "cookiecutter": {
       "project_name": "scirpy",

.github/workflows/test.yaml

@@ -5,6 +5,8 @@ on:
     branches: [main]
   pull_request:
     branches: [main]
+  schedule:
+    - cron: "0 5 1,15 * *"
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.0
+    rev: v3.0.1
     hooks:
       - id: prettier
         # Newer versions of node don't work on systems that have an older version of GLIBC
@@ -26,7 +26,7 @@ repos:
         language_version: "17.9.1"
         exclude: '^\.conda'
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.0.281
+    rev: v0.0.284
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
@@ -40,6 +40,9 @@ repos:
         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

docs/conf.py

@@ -60,6 +60,7 @@
     "sphinx_autodoc_typehints",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
+    "sphinxext.opengraph",
     *[p.stem for p in (HERE / "extensions").glob("*.py")],
 ]
 

pyproject.toml

@@ -48,6 +48,7 @@ dev = [
     "pre-commit"
 ]
 doc = [
+    "docutils>=0.8,!=0.18.*,!=0.19.*",
     'sphinx>=4',
     "sphinx-book-theme>=1.0.0",
     "myst-nb",
@@ -57,6 +58,7 @@ doc = [
     'ipykernel',
     'ipython',
     "sphinx-copybutton",
+    "sphinxext-opengraph",
     'leidenalg',
     'myst_nb',
     'jupytext',
@@ -109,12 +111,10 @@ norecursedirs = [ '.*', 'build', 'dist', '*.egg', 'data', '__pycache__']
 
 [tool.black]
 line-length = 120
-target-version = ["py39"]
 
 [tool.ruff]
 src = ["src"]
 line-length = 120
-target-version = "py39"
 select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle

src/scirpy/io/_tracerlib/core.py

@@ -368,26 +368,17 @@ def get_summary(self):
         if not self.has_D_segment:
             V_segment = self.summary[0]
             J_segment = self.summary[1]
-            segments_string = "V segment:\t{V_segment}\n" "J segment:\t{J_segment}\n".format(
-                V_segment=V_segment, J_segment=J_segment
-            )
+            segments_string = f"V segment:\t{V_segment}\n" f"J segment:\t{J_segment}\n"
         else:
             V_segment = self.summary[0]
             D_segment = self.summary[1]
             J_segment = self.summary[2]
-            segments_string = "V segment:\t{V_segment}\nD segment:\t{D_segment}\n" "J segment:\t{J_segment}\n".format(
-                V_segment=V_segment, D_segment=D_segment, J_segment=J_segment
-            )
+            segments_string = f"V segment:\t{V_segment}\nD segment:\t{D_segment}\n" f"J segment:\t{J_segment}\n"
         summary_string += segments_string
         summary_string += f"ID:\t{self.identifier}\n"
         summary_string += (
-            "TPM:\t{TPM}\nProductive:\t{productive}\nStop codon:"
-            "\t{stop_codon}\nIn frame:\t{in_frame}\n".format(
-                TPM=self.TPM,
-                productive=self.productive,
-                stop_codon=self.stop_codon,
-                in_frame=self.in_frame,
-            )
+            f"TPM:\t{self.TPM}\nProductive:\t{self.productive}\nStop codon:"
+            f"\t{self.stop_codon}\nIn frame:\t{self.in_frame}\n"
         )
 
         # lowercase CDR3 sequences if non-productive

src/scirpy/util/__init__.py

@@ -463,8 +463,8 @@ def deprecated(message):
     def deprecated_decorator(func):
         def deprecated_func(*args, **kwargs):
             warnings.warn(
-                "{} is a deprecated function and will be removed in a "
-                "future version of scirpy. {}".format(func.__name__, message),
+                f"{func.__name__} is a deprecated function and will be removed in a "
+                f"future version of scirpy. {message}",
                 category=FutureWarning,
                 stacklevel=2,
             )