skpkg: add cookiecutter.json, fix rendering issues in readme, add index.rst, add conftest.py, update requirements folder, update manifest.in

MANIFEST.in

@@ -1,3 +1,12 @@
-recursive-include DistancePrinter *
-prune doc
-exclude MANIFEST.in
+graft src
+graft tests
+graft requirements
+
+include AUTHORS.rst LICENSE*.rst README.rst
+
+# Exclude all bytecode files and __pycache__ directories
+global-exclude *.py[cod]  # Exclude all .pyc, .pyo, and .pyd files.
+global-exclude .DS_Store  # Exclude Mac filesystem artifacts.
+global-exclude __pycache__  # Exclude Python cache directories.
+global-exclude .git*  # Exclude git files and directories.
+global-exclude .idea  # Exclude PyCharm project settings.

README.rst

@@ -44,28 +44,28 @@ Independent Installation
 ------------------------
 You can also install ``diffpy.distanceprinter`` independently for yourself.
 
-Assuming you have a wheel file in the current working directory, in an active conda environment please type
+Assuming you have a wheel file in the current working directory, in an active conda environment please type ::
 
     pip install ./diffpy.distanceprinter-VERSION.whl
 
 where you replace VERSION with the actual version you have so the command matches the filename of the
 wheel file you have.
 
-The commands to create and activate the conda environment with name "distanceprinter-env" is
+The commands to create and activate the conda environment with name "distanceprinter-env" is ::
 
     conda create -n distanceprinter-env python=3.13
     conda activate distanceprinter-env
 
 If you don't have conda installed, we recomment you install `miniconda
 <https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
-To install this software from a Python wheel distribution format execute
+To install this software from a Python wheel distribution format execute ::
 
     pip install ./diffpy.distanceprinter-VERSION.whl
 
 If you are a developer, you can also install this package from sources. First, obtain the source archive
 from `GitHub <https://github.com/diffpy/diffpy.distanceprinter/>`_.
 Install the packages in ``./requirements/conda.txt`` and ``./requirements/tests.txt``
-using the `--file`` command:
+using the ``--file`` command ::
 
     conda activate distanceprinter-env
     conda install --file ./requirements/conda.txt

cookiecutter.json

@@ -0,0 +1,18 @@
+{
+  "maintainer_name": "Simon Billinge",
+  "maintainer_email": "sb2896@columbia.edu",
+  "maintainer_github_username": "sbillinge",
+  "contributors": "Xiaohao Yang and Billinge Group members",
+  "license_holders": "The Trustees of Columbia University in the City of New York",
+  "project_name": "diffpy.distanceprinter",
+  "github_username_or_orgname": "diffpy",
+  "github_repo_name": "diffpy.distanceprinter",
+  "conda_pypi_package_dist_name": "diffpy.distanceprinter",
+  "package_dir_name": "diffpy.distanceprinter",
+  "project_short_description": "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite.",
+  "project_keywords": "diffpy, pdf, data-interpretation",
+  "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/index.rst

@@ -0,0 +1,57 @@
+#######
+|title|
+#######
+
+.. |title| replace:: diffpy.distanceprinter documentation
+
+``diffpy.distanceprinter`` - Distance Printer, calculate the inter atomic distances. Part of xPDFsuite.
+
+| Software version |release|
+| Last updated |today|.
+
+===============
+Getting started
+===============
+
+Welcome to the ``diffpy.distanceprinter`` documentation!
+
+This package is not designed to be installed independently. To get started, please visit
+https://www.diffpy.org/products/xPDFsuite.html for more information about the xpdfsuite package and 
+download the package together with ``diffpy.xpdfsuite``.
+
+=======
+Authors
+=======
+
+``diffpy.distanceprinter`` is developed by Xiaohao Yang and Billinge Group members. The maintainer for this project is Simon Billinge. For a detailed list of contributors see
+https://github.com/diffpy/diffpy.distanceprinter/graphs/contributors.
+
+============
+Installation
+============
+
+See the `README <https://github.com/diffpy/diffpy.distanceprinter#installation>`_
+file included with the distribution.
+
+================
+Acknowledgements
+================
+
+``diffpy.distanceprinter`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
+
+=================
+Table of contents
+=================
+.. toctree::
+   :maxdepth: 2
+
+   Package API <api/diffpy.distanceprinter>
+   release
+   license
+
+=======
+Indices
+=======
+
+* :ref:`genindex`
+* :ref:`search`

news/fix-issues.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Fix documentation errors
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -49,7 +49,7 @@ exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [project.scripts]
-diffpy-distanceprinter = "diffpy.distanceprinter:main"
+diffpy-distanceprinter = "diffpy.distanceprinter.distanceprinter_app:main"
 
 [tool.setuptools.dynamic]
 dependencies = {file = ["requirements/pip.txt"]}

requirements/pip.txt

@@ -0,0 +1,3 @@
+numpy
+diffpy.pdffit2
+diffpy.structure

src/diffpy/distanceprinter/distanceprinter_app.py

@@ -0,0 +1,33 @@
+import argparse
+
+from diffpy.distanceprinter.version import __version__  # noqa
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog="diffpy.distanceprinter",
+        description=(
+            "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite.\n\n"
+            "For more information, visit: "
+            "https://github.com/diffpy/diffpy.distanceprinter/"
+        ),
+        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.distanceprinter {__version__}")
+    else:
+        # Default behavior when no arguments are given
+        parser.print_help()
+
+
+if __name__ == "__main__":
+    main()

tests/conftest.py

@@ -0,0 +1,19 @@
+import json
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def user_filesystem(tmp_path):
+    base_dir = Path(tmp_path)
+    home_dir = base_dir / "home_dir"
+    home_dir.mkdir(parents=True, exist_ok=True)
+    cwd_dir = base_dir / "cwd_dir"
+    cwd_dir.mkdir(parents=True, exist_ok=True)
+
+    home_config_data = {"username": "home_username", "email": "home@email.com"}
+    with open(home_dir / "diffpyconfig.json", "w") as f:
+        json.dump(home_config_data, f)
+
+    yield tmp_path