[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v5.0.0
+  rev: v6.0.0
   hooks:
   - id: trailing-whitespace
   - id: check-added-large-files
@@ -19,7 +19,7 @@ repos:
 
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.8.2
+  rev: v0.14.10
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

docs/requirements.txt

@@ -1,9 +1,9 @@
+furo
+myst-nb
 # Requirements file for ReadTheDocs, check .readthedocs.yml.
 # To build the module reference correctly, make sure every external package
 # under `install_requires` in `setup.cfg` is also listed here!
 # sphinx_rtd_theme
 myst-parser[linkify]
 sphinx>=3.2.1
-myst-nb
-furo
 sphinx-autodoc-typehints

lib/src/stringsetpool.cpp

@@ -19,7 +19,7 @@ py::tuple create_dnastringset_pool(py::list py_seqs) {
 
     int32_t* starts_ptr = np_starts.mutable_data();
     int32_t* widths_ptr = np_widths.mutable_data();
-    
+
     std::stringstream pool_stream;
     int32_t current_start = 0;
     const std::string valid_chars = "ACGTRYSWKMBDHVN-";
@@ -38,11 +38,11 @@ py::tuple create_dnastringset_pool(py::list py_seqs) {
                 );
             }
         }
-        
+
         pool_stream.write(s.c_str(), current_width);
         current_start += current_width;
     }
-    
+
     py::bytes pool = py::bytes(pool_stream.str());
     return py::make_tuple(pool, np_starts, np_widths);
 }
@@ -54,4 +54,4 @@ void init_stringsetpool(pybind11::module &m) {
         &create_dnastringset_pool,
         "Efficiently create the pool and ranges for a DnaStringset from a list of strings."
     );
-}
+}

src/biostrings/__init__.py

@@ -17,4 +17,4 @@
 
 
 from .dnastring import DNAString
-from .dnastringset import DNAStringSet
+from .dnastringset import DNAStringSet

tests/conftest.py

@@ -1,10 +1,10 @@
 """
-    Dummy conftest.py for biostrings.
+Dummy conftest.py for biostrings.
 
-    If you don't know what this is for, just leave it empty.
-    Read more about conftest.py under:
-    - https://docs.pytest.org/en/stable/fixture.html
-    - https://docs.pytest.org/en/stable/writing_plugins.html
+If you don't know what this is for, just leave it empty.
+Read more about conftest.py under:
+- https://docs.pytest.org/en/stable/fixture.html
+- https://docs.pytest.org/en/stable/writing_plugins.html
 """
 
 # import pytest