From fb156029a68c583598e346861b565b866a0a74de Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Tue, 10 Jun 2025 18:10:48 -0400
Subject: [PATCH 1/7] skpkg: migrate src folder

---
 .pre-commit-config.yaml       | 14 ++++++++++++++
 src/diffpy/__init__.py        | 14 ++------------
 src/diffpy/morph/__init__.py  | 12 ++++--------
 src/diffpy/morph/functions.py | 31 +++++++++++++++++++++++++++++++
 src/diffpy/morph/version.py   |  6 +++---
 5 files changed, 54 insertions(+), 23 deletions(-)
 create mode 100644 src/diffpy/morph/functions.py

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 194374f9..0e4a84d1 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -50,3 +50,17 @@ repos:
       - 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
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - "prettier@^3.2.4"
+  # docformatter - PEP 257 compliant docstring formatter
+  - repo: https://github.com/s-weigand/docformatter
+    rev: 5757c5190d95e5449f102ace83df92e7d3b06c6c
+    hooks:
+      - id: docformatter
+        additional_dependencies: [tomli]
+        args: [--in-place, --config, ./pyproject.toml]
diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
index a14a0c96..d8e13db0 100644
--- a/src/diffpy/__init__.py
+++ b/src/diffpy/__init__.py
@@ -1,24 +1,14 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.pdfmorph/graphs/contributors
+# https://github.com/diffpy/diffpy.morph/graphs/contributors
 #
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""morph - tools for manipulating and comparing PDF data.
-
-"""
-
-
-from pkgutil import extend_path
-
-__path__ = extend_path(__path__, __name__)
-
-# End of file
diff --git a/src/diffpy/morph/__init__.py b/src/diffpy/morph/__init__.py
index c87d5b6c..52d9ee8e 100644
--- a/src/diffpy/morph/__init__.py
+++ b/src/diffpy/morph/__init__.py
@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
-# File coded by: Billinge Group members and community contributors.
+# File coded by: Sangjoon Lee, Simon Billinge, Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
 # https://github.com/diffpy/diffpy.morph/graphs/contributors
@@ -12,16 +12,12 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""Tools for manipulating and comparing PDF profiles."""
-
-# key used when saving multiple morphs
-__save_morph_as__ = "save_morph_as"
+"""Python package for manipulating and comparing PDF profiles."""
 
 # package version
-from diffpy.morph.version import __version__
+from diffpy.morph.version import __version__  # noqa
 
 # silence the pyflakes syntax checker
 assert __version__ or True
 
-
 # End of file
diff --git a/src/diffpy/morph/functions.py b/src/diffpy/morph/functions.py
new file mode 100644
index 00000000..e7e2c8e4
--- /dev/null
+++ b/src/diffpy/morph/functions.py
@@ -0,0 +1,31 @@
+import numpy as np
+
+
+def dot_product(a, b):
+    """Compute the dot product of two vectors of any size.
+
+    Ensure that the inputs, a and b, are of the same size.
+    The supported types are "array_like" objects, which can
+    be converted to a NumPy array. Examples include lists and tuples.
+
+    Parameters
+    ----------
+    a : array_like
+        The first input vector.
+    b : array_like
+        The second input vector.
+
+    Returns
+    -------
+    float
+        The dot product of the two vectors.
+
+    Examples
+    --------
+    Compute the dot product of two lists:
+    >>> a = [1, 2, 3]
+    >>> b = [4, 5, 6]
+    >>> dot_product(a, b)
+    32.0
+    """
+    return float(np.dot(a, b))
diff --git a/src/diffpy/morph/version.py b/src/diffpy/morph/version.py
index effe3cd5..f40af37f 100644
--- a/src/diffpy/morph/version.py
+++ b/src/diffpy/morph/version.py
@@ -1,13 +1,13 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2024 The Trustees of Columbia University in the City of New York.
+# (c) 2025 The Trustees of Columbia University in the City of New York.
 # All rights reserved.
 #
-# File coded by: Billinge Group members and community contributors.
+# File coded by: Sangjoon Lee, Simon Billinge, Billinge Group members.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.pdfmorph/graphs/contributors
+# https://github.com/diffpy/diffpy.morph/graphs/contributors  # noqa: E501
 #
 # See LICENSE.rst for license information.
 #

From 88d6b233f8598618e6f4508a03201c1fbe3bb484 Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Tue, 10 Jun 2025 18:12:01 -0400
Subject: [PATCH 2/7] skpkg: migrate tests folder

---
 tests/test_functions.py | 40 ++++++++++++++++++++++++++++++++++++++++
 tests/test_version.py   |  2 +-
 2 files changed, 41 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_functions.py

diff --git a/tests/test_functions.py b/tests/test_functions.py
new file mode 100644
index 00000000..e7ee91b1
--- /dev/null
+++ b/tests/test_functions.py
@@ -0,0 +1,40 @@
+import numpy as np
+import pytest
+
+from diffpy.morph import functions  # noqa
+
+
+def test_dot_product_2D_list():
+    a = [1, 2]
+    b = [3, 4]
+    expected = 11.0
+    actual = functions.dot_product(a, b)
+    assert actual == expected
+
+
+def test_dot_product_3D_list():
+    a = [1, 2, 3]
+    b = [4, 5, 6]
+    expected = 32.0
+    actual = functions.dot_product(a, b)
+    assert actual == expected
+
+
+@pytest.mark.parametrize(
+    "a, b, expected",
+    [
+        # Test whether the dot product function works with 2D and 3D vectors
+        # C1: lists, expect correct float output
+        ([1, 2], [3, 4], 11.0),
+        ([1, 2, 3], [4, 5, 6], 32.0),
+        # C2: tuples, expect correct float output
+        ((1, 2), (3, 4), 11.0),
+        ((1, 2, 3), (4, 5, 6), 32.0),
+        # C3: numpy arrays, expect correct float output
+        (np.array([1, 2]), np.array([3, 4]), 11.0),
+        (np.array([1, 2, 3]), np.array([4, 5, 6]), 32.0),
+    ],
+)
+def test_dot_product(a, b, expected):
+    actual = functions.dot_product(a, b)
+    assert actual == expected
diff --git a/tests/test_version.py b/tests/test_version.py
index 38aa5669..68915adc 100644
--- a/tests/test_version.py
+++ b/tests/test_version.py
@@ -1,6 +1,6 @@
 """Unit tests for __version__.py."""
 
-import diffpy.morph
+import diffpy.morph  # noqa
 
 
 def test_package_version():

From 52a9c0a37516c9fc0c084b8455b3ac8d2dec3a19 Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Tue, 10 Jun 2025 18:14:10 -0400
Subject: [PATCH 3/7] skpkg: list dependencies in requirements folder

---
 requirements/build.txt | 2 --
 requirements/conda.txt | 4 ----
 requirements/docs.txt  | 1 +
 requirements/pip.txt   | 4 ----
 requirements/test.txt  | 2 +-
 5 files changed, 2 insertions(+), 11 deletions(-)
 delete mode 100644 requirements/build.txt

diff --git a/requirements/build.txt b/requirements/build.txt
deleted file mode 100644
index f72d870d..00000000
--- a/requirements/build.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-python
-setuptools
diff --git a/requirements/conda.txt b/requirements/conda.txt
index e67cf6e2..24ce15ab 100644
--- a/requirements/conda.txt
+++ b/requirements/conda.txt
@@ -1,5 +1 @@
 numpy
-scipy
-diffpy.utils
-matplotlib-base
-bg-mpl-stylesheets
diff --git a/requirements/docs.txt b/requirements/docs.txt
index ab17b1c8..5f34c6ed 100644
--- a/requirements/docs.txt
+++ b/requirements/docs.txt
@@ -1,4 +1,5 @@
 sphinx
 sphinx_rtd_theme
+sphinx-copybutton
 doctr
 m2r
diff --git a/requirements/pip.txt b/requirements/pip.txt
index a8bb45b4..24ce15ab 100644
--- a/requirements/pip.txt
+++ b/requirements/pip.txt
@@ -1,5 +1 @@
 numpy
-scipy
-diffpy.utils
-matplotlib
-bg-mpl-stylesheets
diff --git a/requirements/test.txt b/requirements/test.txt
index f33bd0e3..a7277865 100644
--- a/requirements/test.txt
+++ b/requirements/test.txt
@@ -2,5 +2,5 @@ flake8
 pytest
 codecov
 coverage
-pytest-env
 pytest-cov
+pytest-env

From a36ba7a79905848e02e3ee176afce68163c35933 Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Tue, 10 Jun 2025 18:16:29 -0400
Subject: [PATCH 4/7] skpkg: add CI and issue/PR templates

---
 .github/workflows/tests-on-pr.yml | 5 +----
 .gitignore                        | 8 +-------
 2 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/tests-on-pr.yml b/.github/workflows/tests-on-pr.yml
index 8d0a909f..9d7879ea 100644
--- a/.github/workflows/tests-on-pr.yml
+++ b/.github/workflows/tests-on-pr.yml
@@ -1,15 +1,12 @@
 name: Tests on PR
 
 on:
-  push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 
 jobs:
   tests-on-pr:
-    uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
+    uses: scikit-package/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
       project: diffpy.morph
       c_extension: false
diff --git a/.gitignore b/.gitignore
index a25212ea..099e2948 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,7 @@ __pycache__/
 .Python
 env/
 build/
+_build/
 develop-eggs/
 dist/
 downloads/
@@ -90,10 +91,3 @@ target/
 
 # Ipython Notebook
 .ipynb_checkpoints
-
-# version information
-setup.cfg
-/src/diffpy/*/version.cfg
-
-# Rever
-rever/

From 4ab91128ad914192f0193f9036825fd30939deee Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Tue, 10 Jun 2025 18:17:42 -0400
Subject: [PATCH 5/7] skpkg: add pyproject.toml

---
 pyproject.toml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f007f315..48c643f9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,9 +32,6 @@ classifiers = [
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
 
-[project.scripts]
-"diffpy.morph" = "diffpy.morph.morphapp:main"
-
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.morph/"
 Issues = "https://github.com/diffpy/diffpy.morph/issues/"
@@ -57,7 +54,7 @@ dependencies = {file = ["requirements/pip.txt"]}
 [tool.codespell]
 exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
-skip = "*.cif,*.dat,*agr"
+skip = "*.cif,*.dat"
 
 [tool.black]
 line-length = 79

From dfc7e555a60126430a3cd963e6a5aade8415d80a Mon Sep 17 00:00:00 2001
From: Zhi Ming Xu <zhimingx27@gmail.com>
Date: Tue, 10 Jun 2025 18:33:50 -0400
Subject: [PATCH 6/7] fix: revert necessary files that were modified

---
 pyproject.toml                |  5 ++++-
 requirements/conda.txt        |  4 ++++
 requirements/pip.txt          |  4 ++++
 src/diffpy/__init__.py        | 10 +++++++++
 src/diffpy/morph/__init__.py  |  3 +++
 src/diffpy/morph/functions.py | 31 ---------------------------
 tests/test_functions.py       | 40 -----------------------------------
 7 files changed, 25 insertions(+), 72 deletions(-)
 delete mode 100644 src/diffpy/morph/functions.py
 delete mode 100644 tests/test_functions.py

diff --git a/pyproject.toml b/pyproject.toml
index 48c643f9..f007f315 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -32,6 +32,9 @@ classifiers = [
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
 
+[project.scripts]
+"diffpy.morph" = "diffpy.morph.morphapp:main"
+
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.morph/"
 Issues = "https://github.com/diffpy/diffpy.morph/issues/"
@@ -54,7 +57,7 @@ dependencies = {file = ["requirements/pip.txt"]}
 [tool.codespell]
 exclude-file = ".codespell/ignore_lines.txt"
 ignore-words = ".codespell/ignore_words.txt"
-skip = "*.cif,*.dat"
+skip = "*.cif,*.dat,*agr"
 
 [tool.black]
 line-length = 79
diff --git a/requirements/conda.txt b/requirements/conda.txt
index 24ce15ab..e67cf6e2 100644
--- a/requirements/conda.txt
+++ b/requirements/conda.txt
@@ -1 +1,5 @@
 numpy
+scipy
+diffpy.utils
+matplotlib-base
+bg-mpl-stylesheets
diff --git a/requirements/pip.txt b/requirements/pip.txt
index 24ce15ab..a8bb45b4 100644
--- a/requirements/pip.txt
+++ b/requirements/pip.txt
@@ -1 +1,5 @@
 numpy
+scipy
+diffpy.utils
+matplotlib
+bg-mpl-stylesheets
diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
index d8e13db0..20e647e9 100644
--- a/src/diffpy/__init__.py
+++ b/src/diffpy/__init__.py
@@ -12,3 +12,13 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
+
+"""morph - tools for manipulating and comparing PDF data.
+"""
+
+
+from pkgutil import extend_path
+
+__path__ = extend_path(__path__, __name__)
+
+# End of file
diff --git a/src/diffpy/morph/__init__.py b/src/diffpy/morph/__init__.py
index 52d9ee8e..48455828 100644
--- a/src/diffpy/morph/__init__.py
+++ b/src/diffpy/morph/__init__.py
@@ -14,6 +14,9 @@
 ##############################################################################
 """Python package for manipulating and comparing PDF profiles."""
 
+# key used when saving multiple morphs
+__save_morph_as__ = "save_morph_as"
+
 # package version
 from diffpy.morph.version import __version__  # noqa
 
diff --git a/src/diffpy/morph/functions.py b/src/diffpy/morph/functions.py
deleted file mode 100644
index e7e2c8e4..00000000
--- a/src/diffpy/morph/functions.py
+++ /dev/null
@@ -1,31 +0,0 @@
-import numpy as np
-
-
-def dot_product(a, b):
-    """Compute the dot product of two vectors of any size.
-
-    Ensure that the inputs, a and b, are of the same size.
-    The supported types are "array_like" objects, which can
-    be converted to a NumPy array. Examples include lists and tuples.
-
-    Parameters
-    ----------
-    a : array_like
-        The first input vector.
-    b : array_like
-        The second input vector.
-
-    Returns
-    -------
-    float
-        The dot product of the two vectors.
-
-    Examples
-    --------
-    Compute the dot product of two lists:
-    >>> a = [1, 2, 3]
-    >>> b = [4, 5, 6]
-    >>> dot_product(a, b)
-    32.0
-    """
-    return float(np.dot(a, b))
diff --git a/tests/test_functions.py b/tests/test_functions.py
deleted file mode 100644
index e7ee91b1..00000000
--- a/tests/test_functions.py
+++ /dev/null
@@ -1,40 +0,0 @@
-import numpy as np
-import pytest
-
-from diffpy.morph import functions  # noqa
-
-
-def test_dot_product_2D_list():
-    a = [1, 2]
-    b = [3, 4]
-    expected = 11.0
-    actual = functions.dot_product(a, b)
-    assert actual == expected
-
-
-def test_dot_product_3D_list():
-    a = [1, 2, 3]
-    b = [4, 5, 6]
-    expected = 32.0
-    actual = functions.dot_product(a, b)
-    assert actual == expected
-
-
-@pytest.mark.parametrize(
-    "a, b, expected",
-    [
-        # Test whether the dot product function works with 2D and 3D vectors
-        # C1: lists, expect correct float output
-        ([1, 2], [3, 4], 11.0),
-        ([1, 2, 3], [4, 5, 6], 32.0),
-        # C2: tuples, expect correct float output
-        ((1, 2), (3, 4), 11.0),
-        ((1, 2, 3), (4, 5, 6), 32.0),
-        # C3: numpy arrays, expect correct float output
-        (np.array([1, 2]), np.array([3, 4]), 11.0),
-        (np.array([1, 2, 3]), np.array([4, 5, 6]), 32.0),
-    ],
-)
-def test_dot_product(a, b, expected):
-    actual = functions.dot_product(a, b)
-    assert actual == expected

From b3b186682e885f1c524a9b8b024f07eb865ae4ed Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 10 Jun 2025 22:35:38 +0000
Subject: [PATCH 7/7] [pre-commit.ci] auto fixes from pre-commit hooks

---
 src/diffpy/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
index 20e647e9..a1bb822e 100644
--- a/src/diffpy/__init__.py
+++ b/src/diffpy/__init__.py
@@ -12,7 +12,6 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-
 """morph - tools for manipulating and comparing PDF data.
 """