skpkg: scikit-update the package.

Author: stevenhua0320

.flake8

@@ -1,10 +1,12 @@
+# As of now, flake8 does not natively support configuration via pyproject.toml
+# https://github.com/microsoft/vscode-flake8/issues/135
 [flake8]
 exclude =
     .git,
     __pycache__,
     build,
     dist,
-    doc/source/conf.py
+    docs/source/conf.py
 max-line-length = 115
 # Ignore some style 'errors' produced while formatting by 'black'
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -34,7 +34,7 @@ Please let the maintainer know that all checks are done and the package is ready
 <!-- After the maintainer releases the PyPI package, please check the following when creating a PR for conda-forge release.-->
 
 - [ ] Ensure that the full release has appeared on PyPI successfully.
-- [ ] New package dependencies listed in `conda.txt` and `test.txt` are added to `meta.yaml` in the feedstock.
+- [ ] New package dependencies listed in `conda.txt` and `tests.txt` are added to `meta.yaml` in the feedstock.
 - [ ] Close any open issues on the feedstock. Reach out to the maintainer if you have questions.
 - [ ] Tag the maintainer for conda-forge release.
 

.github/workflows/build-wheel-release-upload.yml

@@ -7,7 +7,7 @@ on:
       - "*" # Trigger on all tags initially, but tag and release privilege are verified in _build-wheel-release-upload.yml
 
 jobs:
-  release:
+  build-release:
     uses: scikit-package/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
       project: diffpy.pdffit2

.isort.cfg

@@ -1,4 +1,5 @@
 [settings]
+# Keep import statement below line_length character limit
 line_length = 115
 multi_line_output = 3
 include_trailing_comma = True

.readthedocs.yaml

@@ -10,4 +10,4 @@ python:
     - requirements: requirements/docs.txt
 
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/source/conf.py

CODE-OF-CONDUCT.rst

@@ -0,0 +1,133 @@
+=====================================
+ Contributor Covenant Code of Conduct
+=====================================
+
+Our Pledge
+----------
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socioeconomic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+Our Standards
+-------------
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+Enforcement Responsibilities
+----------------------------
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+Scope
+-----
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official email address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+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.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+Enforcement Guidelines
+----------------------
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+1. Correction
+****************
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+2. Warning
+*************
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+3. Temporary Ban
+******************
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+4. Permanent Ban
+******************
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+Attribution
+-----------
+
+This Code of Conduct is adapted from the `Contributor Covenant <https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>`_.
+
+Community Impact Guidelines were inspired by `Mozilla's code of conduct enforcement ladder <https://github.com/mozilla/inclusion>`_.
+
+For answers to common questions about this code of conduct, see the `FAQ <https://www.contributor-covenant.org/faq>`_. `Translations are available <https://www.contributor-covenant.org/translations>`_

LICENSE.rst

@@ -21,32 +21,26 @@ For more information please visit the project web-page:
 or email Prof. Simon Billinge at sb2896@columbia.edu
 
 Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions
-are met:
-
-  * Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
-
-  * Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
-
-  * Neither the name of the copyright holder nor the names of its
-    contributors may be used to endorse or promote products derived from
-    this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY COPYRIGHT HOLDER "AS IS".  COPYRIGHT HOLDER
-EXPRESSLY DISCLAIMS ANY AND ALL WARRANTIES AND CONDITIONS, EITHER
-EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY, TITLE, FITNESS, ADEQUACY OR SUITABILITY
-FOR A PARTICULAR PURPOSE, AND ANY WARRANTIES OF FREEDOM FROM
-INFRINGEMENT OF ANY DOMESTIC OR FOREIGN PATENT, COPYRIGHTS, TRADE
-SECRETS OR OTHER PROPRIETARY RIGHTS OF ANY PARTY.  IN NO EVENT SHALL
-COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR ANY DIRECT, INDIRECT,
-INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
-NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
-USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
-ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
-THIS SOFTWARE OR RELATING TO THIS AGREEMENT, EVEN IF ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGE.
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

@@ -25,6 +25,7 @@
         :target: https://anaconda.org/conda-forge/diffpy.pdffit2
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
+        :target: https://github.com/diffpy/diffpy.pdffit2/pulls
 
 .. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.pdffit2
         :target: https://pypi.org/project/diffpy.pdffit2/
@@ -108,24 +109,31 @@ Create a new conda environment ``diffpy.pdffit2_env``: ::
 
         conda create -n diffpy.pdffit2_env python=3.13
 
-Activate the environment: ::
-
-        conda activate diffpy.pdffit2_env
-
-Install pdffit2 using ``pip`` to download and install the latest version from `Python Package Index <https://pypi.python.org>`_: ::
+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>`_.
+To install using ``pip`` into your ``diffpy.pdffit2_env`` environment, type ::
 
         pip install diffpy.pdffit2
 
-To confirm that the installation was successful, type ::
-
-        python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
-
 If you prefer to install from sources, after installing the dependencies, obtain the source archive from
 `GitHub <https://github.com/diffpy/diffpy.pdffit2/>`_. Once installed, ``cd`` into your ``diffpy.pdffit2`` directory
 and run the following ::
 
         pip install .
 
+This package also provides command-line utilities. To check the software has been installed correctly, type ::
+
+        diffpy.pdffit2 --version
+
+You can also type the following command to verify the installation. ::
+
+        python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
+
+
+To view the basic usage and available commands, type ::
+
+        diffpy.pdffit2 -h
+
 Getting Started
 ---------------
 
@@ -170,7 +178,7 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdffit2/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdffit2/blob/main/CODE-OF-CONDUCT.rst>`_.
 
 Contact
 -------

cookiecutter.json

@@ -0,0 +1,18 @@
+{
+  "maintainer_name": "Simon Billinge",
+  "maintainer_email": "sb2896@columbia.edu",
+  "maintainer_github_username": "sbillinge",
+  "contributors": "Sangjoon Lee, Simon Billinge, Billinge Group members",
+  "license_holders": "The Trustees of Columbia University in the City of New York",
+  "project_name": "diffpy.pdffit2",
+  "github_username_or_orgname": "diffpy",
+  "github_repo_name": "diffpy.pdffit2",
+  "conda_pypi_package_dist_name": "diffpy.pdffit2",
+  "package_dir_name": "diffpy.pdffit2",
+  "project_short_description": "PDFfit2 - real space structure refinement program.",
+  "project_keywords": "PDF, structure refinement",
+  "minimum_supported_python_version": "3.11",
+  "maximum_supported_python_version": "3.13",
+  "project_needs_c_code_compiled": "No",
+  "project_has_gui_tests": "No"
+}

docs/source/conf.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# diffpy.pdffit2 documentation build configuration file, created by
+# diffpy.pdffit2 documentation build configuration file, created by  # noqa: E501
 # sphinx-quickstart on Thu Jan 30 15:49:41 2014.
 #
 # This file is execfile()d with the current directory set to its
@@ -22,11 +22,11 @@
 try:
     fullversion = version("diffpy.pdffit2")
 except Exception:
-    fullversion = "No version found. The correct version will appear in the released version."
+    fullversion = "No version found. The correct version will appear in the released version."  # noqa: E501
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use Path().resolve() to make it absolute, like shown here.
+# documentation root, use Path().resolve() to make it absolute, like shown here.  # noqa: E501
 # sys.path.insert(0, str(Path(".").resolve()))
 sys.path.insert(0, str(Path("../..").resolve()))
 sys.path.insert(0, str(Path("../../src").resolve()))
@@ -53,10 +53,6 @@
     "m2r",
 ]
 
-autodoc_mock_imports = [
-    "diffpy.pdffit2.pdffit2",
-]
-
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -79,7 +75,6 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-fullversion = version(project)
 # The short X.Y version.
 version = "".join(fullversion.split(".post")[:1])
 # The full version, including alpha/beta/rc tags.
@@ -144,7 +139,7 @@
     "github_user": "diffpy",
     "github_repo": "diffpy.pdffit2",
     "github_version": "main",
-    "conf_py_path": "/doc/source/",
+    "conf_py_path": "/docs/source/",
 }
 
 # Theme options are theme-specific and customize the look and feel of a theme