Merge branch 'main' into silence-deprecated-warning

Author: hakonanes

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ ci:
   submodules: false
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
@@ -21,31 +21,31 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.5.1
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 9.0.0a3
     hooks:
       - id: isort
         args: ["--profile", "black"]
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.7.1
+    rev: 0.9.1
     hooks:
       - id: nbstripout
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: no-commit-to-branch
         name: Prevent Commit to Main Branch
         args: ["--branch", "main"]
         stages: [pre-commit]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.2
     hooks:
       - id: codespell
         additional_dependencies:
@@ -58,8 +58,8 @@ repos:
         additional_dependencies:
           - "prettier@^3.2.4"
   # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  - repo: https://github.com/PyCQA/docformatter
+    rev: v1.7.8
     hooks:
       - id: docformatter
         additional_dependencies: [tomli]

devutils/sgtbx_extra_groups.py

@@ -10,7 +10,6 @@
 Not to be included with code distributions.
 """
 
-
 import math
 import re
 

news/CI-badge-fix.rst

@@ -2,6 +2,7 @@
 
 * No News Added: fix CI badge and target in README.rst
 
+
 **Changed:**
 
 * <news item>

news/fix-internal-deps.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: fix internal use of deprecated functions.
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

news/pre-commit_edits.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news needed: updating docformatter not user facing
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/structure/__init__.py

@@ -33,7 +33,6 @@
     * SymmetryError
 """
 
-
 import os
 import sys
 
@@ -102,10 +101,10 @@ def load_structure(filename, fmt="auto", **kw):
         Path to the file to be loaded.
     fmt : str, Optional
         Format of the structure file such as 'cif' or 'xyz'. Must be
-        one of the formats listed by the `parsers.inputFormats` function.
+        one of the formats listed by the `parsers.input_formats` function.
         When 'auto', all supported formats are tried in a sequence.
     kw : Optional
-        Extra keyword arguments that are passed to `parsers.getParser`
+        Extra keyword arguments that are passed to `parsers.get_parser`
         function. These configure the dedicated Parser object that
         is used to read content in filename.
 

src/diffpy/structure/_legacy_importer.py

@@ -27,7 +27,6 @@
 This module is deprecated and will be removed in the future.
 """
 
-
 import importlib.abc
 import sys
 from warnings import warn

src/diffpy/structure/apps/anyeye.py

@@ -187,7 +187,7 @@ def convert_structure_file(pd):
     fmt = pd.get("format", "auto")
     stru = None
     if fmt == "auto":
-        stru, fmt = loadStructureFile(strufile)
+        stru, fmt = load_structure_file(strufile)
         pd["fmt"] = fmt
     # if fmt is recognized by the viewer, use as is
     if fmt in pd["formats"] and pd["formula"] is None:

src/diffpy/structure/apps/vesta_viewer.py

@@ -72,12 +72,13 @@
 
 
 def usage(style=None):
-    """Show usage info. for ``style=="brief"`` show only first 2 lines.
+    """Show usage info.
 
-    Parameters
-    ----------
-    style : str, optional
-        The usage display style.
+    for ``style=="brief"`` show only first 2 lines.
+        Parameters
+        ----------
+        style : str, optional
+            The usage display style.
     """
     myname = Path(sys.argv[0]).name
     msg = __doc__.replace("vestaview", myname)