Merge pull request #153 from diffpy/migration

sbillinge · web-flow · commit 477371530e41 · 2025-11-23T07:52:18.000-05:00
Migration
diff --git a/.flake8 b/.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
diff --git a/.github/ISSUE_TEMPLATE/release_checklist.md b/.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.
 
diff --git a/.github/workflows/build-wheel-release-upload.yml b/.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
diff --git a/.isort.cfg b/.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
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -10,4 +10,4 @@ python:
     - requirements: requirements/docs.txt
 
 sphinx:
-  configuration: doc/source/conf.py
+  configuration: docs/source/conf.py
diff --git a/CODE-OF-CONDUCT.rst b/CODE-OF-CONDUCT.rst
diff --git a/LICENSE.rst b/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.
diff --git a/README.rst b/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/
@@ -116,16 +117,18 @@ Install pdffit2 using ``pip`` to download and install the latest version from `P
 
         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 .
 
+
+You can type the following command to verify the installation is successful. ::
+
+        python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"
+
+
 Getting Started
 ---------------
 
@@ -170,7 +173,7 @@ 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
 -------
diff --git a/cookiecutter.json b/cookiecutter.json
@@ -0,0 +1,18 @@
+{
+  "maintainer_name": "Simon Billinge",
+  "maintainer_email": "sb2896@columbia.edu",
+  "maintainer_github_username": "sbillinge",
+  "contributors": "Pavol Juhas, Chris Farrow, 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": "Yes",
+  "project_has_gui_tests": "No"
+}
diff --git a/docs/source/conf.py b/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
@@ -22,17 +22,19 @@
 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()))
 
 # abbreviations
-ab_authors = "Billinge group and community members."
+ab_authors = (
+    "Pavol Juhas, Chris Farrow, Simon Billinge, Billinge Group members"
+)
 
 # -- General configuration ------------------------------------------------
 
@@ -56,7 +58,6 @@
 autodoc_mock_imports = [
     "diffpy.pdffit2.pdffit2",
 ]
-
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -144,7 +145,7 @@
     "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
diff --git a/docs/source/license.rst b/docs/source/license.rst
@@ -25,32 +25,26 @@ 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.
diff --git a/pyproject.toml b/pyproject.toml
@@ -48,6 +48,9 @@ include = ["*"]  # package names should match these glob patterns (["*"] by defa
 exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
+[project.scripts]
+diffpy-pdffit2 = "diffpy.pdffit2_app:main"
+
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}
 
diff --git a/src/diffpy/__init__.py b/src/diffpy/__init__.py
@@ -14,13 +14,3 @@
 # See LICENSE.rst for license information.
 #
 ##############################################################################
-"""diffpy - tools for structure analysis by diffraction.
-
-Blank namespace package for module diffpy."""
-
-
-from pkgutil import extend_path
-
-__path__ = extend_path(__path__, __name__)
-
-# End of file
diff --git a/src/diffpy/pdffit2/pdffit2_app.py b/src/diffpy/pdffit2/pdffit2_app.py
@@ -0,0 +1,33 @@
+import argparse
+
+from diffpy.pdffit2.version import __version__  # noqa
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="diffpy.pdffit2",
+        description=(
+            "PDFfit2 - real space structure refinement program.\n\n"
+            "For more information, visit: "
+            "https://github.com/diffpy/diffpy.pdffit2/"
+        ),
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    parser.add_argument(
+        "--version",
+        action="store_true",
+        help="Show the program's version number and exit",
+    )
+
+    args = parser.parse_args()
+
+    if args.version:
+        print(f"diffpy.pdffit2 {__version__}")
+    else:
+        # Default behavior when no arguments are given
+        parser.print_help()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/src/diffpy/pdffit2/version.py b/src/diffpy/pdffit2/version.py
@@ -7,17 +7,22 @@
 # File coded by: Billinge Group members and community contributors.
 #
 # See GitHub contributions for a more detailed list of contributors.
-# https://github.com/diffpy/diffpy.pdffit2/graphs/contributors
+# https://github.com/diffpy/diffpy.pdffit2/graphs/contributors  # noqa: E501
 #
 # See LICENSE.rst for license information.
 #
 ##############################################################################
 """Definition of __version__."""
 
+#  We do not use the other three variables, but can be added back if needed.
+#  __all__ = ["__date__", "__git_commit__", "__timestamp__", "__version__"]
+
 import datetime
 import json
 import urllib.request
-from importlib.metadata import version
+
+# obtain version information
+from importlib.metadata import PackageNotFoundError, version
 from pathlib import Path
 
 
@@ -57,9 +62,9 @@ def get_pypi_release_date(package_name, timeout=5):
     return str(release_date)
 
 
-__version__ = version("diffpy.pdffit2")
 __date__ = get_pypi_release_date("diffpy.pdffit2")
 
-# End of file
-
-# Release date: 2025-02-07
+try:
+    __version__ = version("diffpy.pdffit2")
+except PackageNotFoundError:
+    __version__ = "unknown"
diff --git a/tests/test_exceptions.py b/tests/test_exceptions.py
@@ -18,7 +18,8 @@
 
 import pytest
 
-from diffpy.pdffit2 import PdfFit, pdffit2
+from diffpy.pdffit2 import pdffit2
+from diffpy.pdffit2.pdffit import PdfFit
 
 
 class read_structExceptions(unittest.TestCase):
diff --git a/tests/test_pdffit.py b/tests/test_pdffit.py
@@ -6,7 +6,8 @@
 
 import pytest
 
-from diffpy.pdffit2 import PdfFit, pdffit2
+from diffpy.pdffit2 import pdffit2
+from diffpy.pdffit2.pdffit import PdfFit
 from diffpy.structure import loadStructure
 
 # ----------------------------------------------------------------------------
diff --git a/tests/test_phase_fractions.py b/tests/test_phase_fractions.py
@@ -6,7 +6,7 @@
 
 import pytest
 
-from diffpy.pdffit2 import PdfFit
+from diffpy.pdffit2.pdffit import PdfFit
 
 
 ##############################################################################
diff --git a/tests/test_shape_factors.py b/tests/test_shape_factors.py
@@ -8,7 +8,8 @@
 import numpy
 import pytest
 
-from diffpy.pdffit2 import PdfFit, pdffit2
+from diffpy.pdffit2 import pdffit2
+from diffpy.pdffit2.pdffit import PdfFit
 
 
 def spherefactor(r, d):
diff --git a/tests/test_version.py b/tests/test_version.py
