Change docformatter, update all other hooks (diffpy#302)

* Change docformatter, update all other hooks

* News

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

* Fix black/docformatter conflict

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
# Conflicts:
#	src/diffpy/morph/morph_io.py

Author: Sparks29032

.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
@@ -21,45 +21,45 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 26.3.1
     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:
           - tomli
   # prettier - multi formatter for .json, .yml, and .md files
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: f12edd9c7be1c20cfa42420fd0e6df71e42b51ea # frozen: v4.0.0-alpha.8
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         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]

news/docformatter.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Now use `PyCQA/docformatter` to format Python docstrings.
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/diffpy/morph/morph_helpers/transformpdftordf.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class TransformXtalPDFtoRDF -- Transform crystal PDFs to RDFs."""
 
-
 from diffpy.morph.morphs.morph import LABEL_GR, LABEL_RA, LABEL_RR, Morph
 
 

src/diffpy/morph/morph_helpers/transformrdftopdf.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Class TransformXtalRDFtoPDF -- Transform crystal RDFs to PDFs."""
 
-
 import numpy
 
 from diffpy.morph.morphs.morph import LABEL_GR, LABEL_RA, LABEL_RR, Morph

src/diffpy/morph/morph_io.py

@@ -124,61 +124,9 @@ def build_morph_inputs_container(
     return morph_inputs
 
 
-def get_terminal_morph_output(mr_copy, uncertainties):
-    morphs_out = "# Optimized morphing parameters:\n"
-    # Handle special inputs (numerical)
-    if "squeeze" in mr_copy:
-        sq_dict = mr_copy.pop("squeeze")
-        rw_pos = list(mr_copy.keys()).index("Rw")
-        morph_results_list = list(mr_copy.items())
-        for idx, _ in enumerate(sq_dict):
-            morph_results_list.insert(
-                rw_pos + idx, (f"squeeze a{idx}", sq_dict[f"a{idx}"])
-            )
-        mr_copy = dict(morph_results_list)
-
-    # Handle special inputs (functional remove)
-    func_dicts = {
-        "funcxy": [None, None],
-        "funcx": [None, None],
-        "funcy": [None, None],
-    }
-    for func in func_dicts.keys():
-        if f"{func}_function" in mr_copy:
-            func_dicts[func][0] = mr_copy.pop(f"{func}_function")
-        if func in mr_copy:
-            func_dicts[func][1] = mr_copy.pop(func)
-            rw_pos = list(mr_copy.keys()).index("Rw")
-            morph_results_list = list(mr_copy.items())
-            for idx, key in enumerate(func_dicts[func][1]):
-                morph_results_list.insert(
-                    rw_pos + idx, (f"{func} {key}", func_dicts[func][1][key])
-                )
-            mr_copy = dict(morph_results_list)
-
-    # Get uncertainties
-    if uncertainties is None:
-        morphs_out += "\n".join(
-            f"# {key} = {mr_copy[key]:.6f}" for key in mr_copy.keys()
-        )
-    else:
-        morphs_out += "\n".join(
-            f"# {key} = {mr_copy[key]:.6f}"
-            + (
-                f" +/- {uncertainties[key]:.6f}"
-                if key in uncertainties
-                else ""
-            )
-            for key in mr_copy
-        )
-
-    return morphs_out, func_dicts
-
-
 def single_morph_output(
     morph_inputs,
     morph_results,
-    uncertainties=None,
     save_file=None,
     morph_file=None,
     xy_out=None,
@@ -194,8 +142,6 @@ def single_morph_output(
         Parameters given by the user.
     morph_results: dict
         Resulting data after morphing.
-    uncertainties: dict
-        Uncertainties of all morphed parameters.
     save_file
         Name of file to print to. If None (default) print to terminal.
     morph_file
@@ -220,7 +166,41 @@ def single_morph_output(
     )
 
     mr_copy = morph_results.copy()
-    morphs_out, func_dicts = get_terminal_morph_output(mr_copy, uncertainties)
+    morphs_out = "# Optimized morphing parameters:\n"
+    # Handle special inputs (numerical)
+    if "squeeze" in mr_copy:
+        sq_dict = mr_copy.pop("squeeze")
+        rw_pos = list(mr_copy.keys()).index("Rw")
+        morph_results_list = list(mr_copy.items())
+        for idx, _ in enumerate(sq_dict):
+            morph_results_list.insert(
+                rw_pos + idx, (f"squeeze a{idx}", sq_dict[f"a{idx}"])
+            )
+        mr_copy = dict(morph_results_list)
+
+    # Handle special inputs (functional remove)
+    func_dicts = {
+        "funcxy": [None, None],
+        "funcx": [None, None],
+        "funcy": [None, None],
+    }
+    for func in func_dicts.keys():
+        if f"{func}_function" in mr_copy:
+            func_dicts[func][0] = mr_copy.pop(f"{func}_function")
+        if func in mr_copy:
+            func_dicts[func][1] = mr_copy.pop(func)
+            rw_pos = list(mr_copy.keys()).index("Rw")
+            morph_results_list = list(mr_copy.items())
+            for idx, key in enumerate(func_dicts[func][1]):
+                morph_results_list.insert(
+                    rw_pos + idx, (f"{func} {key}", func_dicts[func][1][key])
+                )
+            mr_copy = dict(morph_results_list)
+
+    # Normal inputs
+    morphs_out += "\n".join(
+        f"# {key} = {mr_copy[key]:.6f}" for key in mr_copy.keys()
+    )
 
     # Handle special inputs (functional add)
     for func in func_dicts.keys():
@@ -360,7 +340,6 @@ def multiple_morph_output(
     morph_inputs,
     morph_results,
     target_files,
-    uncertainties_dict=None,
     field=None,
     field_list=None,
     save_directory=None,
@@ -381,8 +360,6 @@ def multiple_morph_output(
         Resulting data after morphing.
     target_files: list
         Files that acted as targets to morphs.
-    uncertainties_dict: dict
-        Dictionary of uncertainties for each morph.
     save_directory
         Name of directory to save morphs in.
     field
@@ -422,11 +399,11 @@ def multiple_morph_output(
                 output = f"\n# Target: {target}\n"
             else:
                 output = f"\n# Morph: {target}\n"
-
-            mr_copy = morph_results[target].copy()
-            uncertainties = uncertainties_dict[target]
-            output_body, _ = get_terminal_morph_output(mr_copy, uncertainties)
-            output += output_body
+            output += "# Optimized morphing parameters:\n"
+            output += "\n".join(
+                f"# {param} = {morph_results[target][param]:.6f}"
+                for param in morph_results[target]
+            )
             verbose_outputs += f"{output}\n"
 
     # Get items we want to put in table

src/diffpy/morph/morphapp.py

@@ -258,7 +258,7 @@ def morph_error(self, msg, error):
         help=(
             "Slope of the baseline. "
             "For a bulk material with scale factor 1, "
-            "this will have value -4\u03C0 times the atomic density. "
+            "this will have value -4\u03c0 times the atomic density. "
             "Otherwise, you can estimate it by dividing the y "
             "position from the x position "
             "of the base of the first peak. "
@@ -350,7 +350,7 @@ def morph_error(self, msg, error):
         "--noplot",
         action="store_false",
         dest="plot",
-        help="""Do not show a plot.""",
+        help="Do not show a plot.",
     )
     group.add_option(
         "--mlabel",
@@ -462,7 +462,7 @@ def morph_error(self, msg, error):
         "--reverse",
         dest="reverse",
         action="store_true",
-        help="""Sort from highest to lowest instead.""",
+        help="Sort from highest to lowest instead.",
     )
     group.add_option(
         "--serial-file",
@@ -1320,7 +1320,7 @@ def getPDFFromFile(fn):
 
 def main():
     parser = create_option_parser()
-    (opts, pargs) = parser.parse_args()
+    opts, pargs = parser.parse_args()
     if opts.multiple_targets:
         multiple_targets(parser, opts, pargs, stdout_flag=True)
     elif opts.multiple_morphs:

src/diffpy/morph/morphpy.py

@@ -22,7 +22,7 @@ def get_args(parser, params, kwargs):
             else:
                 inputs.append(f"--{key}")
                 inputs.append(f"{value}")
-    (opts, pargs) = parser.parse_args(inputs)
+    opts, pargs = parser.parse_args(inputs)
     return opts, pargs
 
 

src/diffpy/morph/morphs/__init__.py

@@ -14,7 +14,6 @@
 ##############################################################################
 """Definition of morphs."""
 
-
 from diffpy.morph.morphs.morph import Morph  # noqa: F401
 from diffpy.morph.morphs.morphchain import MorphChain  # noqa: F401
 from diffpy.morph.morphs.morphfuncx import MorphFuncx

src/diffpy/morph/morphs/morph.py

@@ -13,6 +13,7 @@
 #
 ##############################################################################
 """Morph -- base class for defining a morph."""
+
 import numpy
 
 LABEL_RA = "r (A)"  # r-grid
@@ -189,9 +190,10 @@ def applyConfig(self, config):
         return
 
     def checkConfig(self):
-        """Verify data in self.config. No action by default.
+        """Verify data in self.config.
 
-        To be overridden in a derived class.
+        No action by default.         To be overridden in a derived
+        class.
         """
         return
 
@@ -257,7 +259,6 @@ def set_extrapolation_info(self, x_true, x_extrapolate):
         x_extrapolate : array
             x values after a morphing process
         """
-
         cutoff_low = min(x_true)
         extrap_low_x = numpy.where(x_extrapolate < cutoff_low)[0]
         is_extrap_low = False if len(extrap_low_x) == 0 else True

src/diffpy/morph/morphs/morphchain.py

@@ -12,8 +12,9 @@
 # See LICENSE.txt for license information.
 #
 ##############################################################################
-"""MorphChain -- Chain of morphs executed in order.
-"""
+"""MorphChain -- Chain of morphs executed in order."""
+
+# Comment required to resolve black/docformatter conflict
 
 
 class MorphChain(list):