chore: change email and instruction (#182)

* chore: change email and instruction

* build: replace docformatter with ruff and make auto-fix

Author: stevenhua0320

.pre-commit-config.yaml

@@ -57,10 +57,9 @@ repos:
       - id: prettier
         additional_dependencies:
           - "prettier@^3.2.4"
-  # docformatter - PEP 257 compliant docstring formatter
-  - repo: https://github.com/s-weigand/docformatter
-    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+  # ruff - An extremely fast Python linter and code formatter, written in Rust.
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.12
     hooks:
-      - id: docformatter
-        additional_dependencies: [tomli]
-        args: [--in-place, --config, ./pyproject.toml]
+      - id: ruff-check
+        args: [--fix]

CODE-OF-CONDUCT.rst

@@ -67,7 +67,7 @@ Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
 reported to the community leaders responsible for enforcement at
-sb2896@columbia.edu. All complaints will be reviewed and investigated promptly and fairly.
+sbillinge@ucsb.edu. All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the
 reporter of any incident.

LICENSE-PDFgui.rst

@@ -24,7 +24,7 @@ program by citing the following paper in your publication:
 For more information please visit the diffpy web-page at
     http://www.diffpy.org
 or email Luke Granlund at luke.r.granlund@gmail.com, or Prof. Simon
-Billinge at sb2896@columbia.edu.
+Billinge at sbillinge@ucsb.edu.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

LICENSE.rst

@@ -17,7 +17,7 @@ program by citing the following paper in your publication:
 For more information please visit the diffpy web-page at
     http://www.diffpy.org
 or email Luke Granlund at luke.r.granlund@gmail.com, or Prof. Simon
-Billinge at sb2896@columbia.edu.
+Billinge at sbillinge@ucsb.edu.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

README.rst

@@ -102,7 +102,9 @@ The following creates and activates a new environment named ``diffpy.srmise_env`
         conda create -n diffpy.srmise_env diffpy.srmise
         conda activate diffpy.srmise_env
 
-The output should print the latest version displayed on the badges above.
+You can also install diffpy.srmise in another activated environment with ::
+
+        conda install -c conda-forge diffpy.srmise
 
 If the above does not work, you can use ``pip`` to download and install the latest release from
 `Python Package Index <https://pypi.python.org>`_.
@@ -120,6 +122,7 @@ This package also provides command-line utilities. To check the software has bee
 
         diffpy.srmise --version
 
+The output should print the latest version displayed on the badges above.
 You can also type the following command to verify the installation. ::
 
         python -c "import diffpy.srmise; print(diffpy.srmise.__version__)"

docs/examples/multimodel-unknown-dG2.py

@@ -140,7 +140,7 @@ def run(plot=True):
         dG = ms.dgs[np.argmax(cls_probs)]
         best_dGs.append(dG)
 
-    print("\n--------- Best models for at least one dG ---------" % dG)
+    print(f"\n--------- Best models for at least one dG: {dG} ---------")
     print("   Best dG  Model  Class  Free       AIC     Prob  File")
     for dG in best_dGs:
 

docs/source/license.rst

@@ -29,7 +29,7 @@ program by citing the following paper in your publication:
 For more information please visit the diffpy web-page at
     http://www.diffpy.org
 or email Luke Granlund at luke.r.granlund@gmail.com, or Prof. Simon
-Billinge at sb2896@columbia.edu.
+Billinge at sbillinge@ucsb.edu.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

news/email.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No News Added: change email to the right one and add instruction to install in existing env
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -60,10 +60,11 @@ exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
 skip = "*.cif,*.dat"
 
-[tool.docformatter]
-recursive = true
-wrap-summaries = 72
-wrap-descriptions = 72
+[tool.ruff]
+line-length = 115
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
 
 [tool.black]
 line-length = 115

src/diffpy/srmise/__init__.py

@@ -13,7 +13,8 @@
 #
 ##############################################################################
 """Peak extraction and peak fitting tool for atomic pair distribution
-functions."""
+functions.
+"""
 
 # package version
 from diffpy.srmise.version import __version__  # noqa