move to ruff formatter (#565)

See https://astral.sh/blog/the-ruff-formatter.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: njzjz

.pre-commit-config.yaml

@@ -17,16 +17,15 @@ repos:
     -   id: check-symlinks
     -   id: check-toml
 # Python
--   repo: https://github.com/psf/black
-    rev: 23.10.1
-    hooks:
-    -   id: black-jupyter
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.1.3
     hooks:
     - id: ruff
       args: ["--fix"]
+      types_or: [python, pyi, jupyter]
+    - id: ruff-format
+      types_or: [python, pyi, jupyter]
 # numpydoc
 -   repo: https://github.com/Carreau/velin
     rev: 0.0.12

docs/make_format.py

@@ -224,8 +224,9 @@ def generate_sub_format_pages(formats: dict):
                     buff.append("""   :noindex:""")
                 buff.append("")
                 if docstring is None or method not in format.__dict__:
-                    docstring = """   Convert this format to :class:`%s`.""" % (
-                        method_classes[method]
+                    docstring = (
+                        """   Convert this format to :class:`%s`."""
+                        % (method_classes[method])
                     )
                 doc_obj = SphinxDocString(docstring)
                 if len(doc_obj["Parameters"]) > 0:
@@ -293,8 +294,8 @@ def generate_sub_format_pages(formats: dict):
                         and "to_system" in format.__dict__
                     )
                 ):
-                    docstring = "Convert :class:`%s` to this format." % (
-                        method_classes[method]
+                    docstring = (
+                        "Convert :class:`%s` to this format." % (method_classes[method])
                     )
                 doc_obj = SphinxDocString(docstring)
                 if len(doc_obj["Parameters"]) > 0:

dpdata/lammps/dump.py

@@ -121,8 +121,8 @@ def safe_get_posi(lines, cell, orig=np.zeros(3), unwrap=False):
                 category=UnwrapWarning,
             )
         return (
-            posis % 1
-        ) @ cell  # Convert scaled coordinates back to Cartesien coordinates with wraping at periodic boundary conditions
+            (posis % 1) @ cell
+        )  # Convert scaled coordinates back to Cartesien coordinates with wraping at periodic boundary conditions
 
 
 def get_dumpbox(lines):

pyproject.toml

@@ -72,7 +72,6 @@ write_to = "dpdata/_version.py"
 profile = "black"
 
 [tool.ruff]
-target-version = "py37"
 select = [
     "E", # errors
     "F", # pyflakes
@@ -101,3 +100,6 @@ ignore = [
     "D404", # TODO: first word of the docstring should not be This
 ]
 ignore-init-module-imports = true
+
+[tool.ruff.pydocstyle]
+convention = "numpy"