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Merge pull request #22 from zmx27/fix-issues
skpkg: add cookiecutter.json, fix rendering issues in readme, add index.rst, add conftest.py, update requirements folder, update manifest.in
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‎LICENSENOTICE.txt‎ renamed to ‎LICENSENOTICE.rst‎

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‎MANIFEST.in‎

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

‎README.rst‎

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

‎cookiecutter.json‎

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{
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"maintainer_name": "Simon Billinge",
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"maintainer_email": "sb2896@columbia.edu",
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"maintainer_github_username": "sbillinge",
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"contributors": "Xiaohao Yang and Billinge Group members",
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"license_holders": "The Trustees of Columbia University in the City of New York",
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"project_name": "diffpy.distanceprinter",
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"github_username_or_orgname": "diffpy",
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"github_repo_name": "diffpy.distanceprinter",
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"conda_pypi_package_dist_name": "diffpy.distanceprinter",
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"package_dir_name": "diffpy.distanceprinter",
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"project_short_description": "Distance Printer, calculate the inter atomic distances. Part of xPDFsuite.",
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"project_keywords": "diffpy, pdf, data-interpretation",
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"minimum_supported_python_version": "3.11",
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"maximum_supported_python_version": "3.13",
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"project_needs_c_code_compiled": "No",
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"project_has_gui_tests": "No"
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}

‎docs/source/index.rst‎

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

‎news/fix-issues.rst‎

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**Added:**
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* No news added: Fix documentation errors
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**Changed:**
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* <news item>
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**Deprecated:**
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* <news item>
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**Removed:**
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* <news item>
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**Fixed:**
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* <news item>
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**Security:**
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* <news item>

‎pyproject.toml‎

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namespaces = false # to disable scanning PEP 420 namespaces (true by default)
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[project.scripts]
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diffpy-distanceprinter = "diffpy.distanceprinter:main"
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diffpy-distanceprinter = "diffpy.distanceprinter.distanceprinter_app:main"
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[tool.setuptools.dynamic]
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dependencies = {file = ["requirements/pip.txt"]}

‎requirements/pip.txt‎

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numpy
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diffpy.pdffit2
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diffpy.structure

‎src/diffpy/distanceprinter/distanceprinter_app.py‎

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import argparse
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from diffpy.distanceprinter.version import __version__ # noqa
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def main():
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parser = argparse.ArgumentParser(
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prog="diffpy.distanceprinter",
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description=(
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"Distance Printer, calculate the inter atomic distances. Part of xPDFsuite.\n\n"
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"For more information, visit: "
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"https://github.com/diffpy/diffpy.distanceprinter/"
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),
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formatter_class=argparse.RawDescriptionHelpFormatter,
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)
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parser.add_argument(
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"--version",
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action="store_true",
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help="Show the program's version number and exit",
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)
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args = parser.parse_args()
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if args.version:
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print(f"diffpy.distanceprinter {__version__}")
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else:
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# Default behavior when no arguments are given
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parser.print_help()
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if __name__ == "__main__":
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main()

‎tests/conftest.py‎

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

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