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sbillinge merged 3 commits into from
Nov 20, 2025
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skpkg: add CHAGELOG.rst, README.rst, license, update pyproject.toml #150

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skpkg: add CHAGELOG.rst, README.rst, license, update pyproject.toml
stevenhua0320 Nov 20, 2025
a0d4c2c
chore: Add instructions back to README.rst and revert history of CHAN…
stevenhua0320 Nov 20, 2025
f795440
chore: add activate for env to make consistent.
stevenhua0320 Nov 20, 2025
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68 changes: 0 additions & 68 deletions CHANGELOG.rst
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Expand Up @@ -3,71 +3,3 @@ Release notes
=============

.. current developments
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@sbillinge sbillinge Nov 20, 2025

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we need to keep all of this. The changelog is updated at each release, by inserting new things at the top. So we need all of this legacy stuff.

1.5.1
=====

**Fixed:**

* Fixed `SystemError` and `MemoryError` for `redirect_stdout` on Windows with Python 3.13.

**Removed:**

* Removed `restore_stdout` function and wrapper.


1.5.0
=====

**Added:**

* Python 3.11, 3.12 support
* Option to skip printing of introductory information when initializing the `PdfFit` class.
* Added additional runtime linker flags in `CustomBuildExt.run` to embed the `RPATH` flags for the built extensions.
* Support for retrieving GSL configuration from `CONDA_PREFIX`/ `GSL_PATH` on all platforms.
* Separate installation instruction for macOS (Arm64) in READEM
* Added `restore_stdout` function and wrapper.
* Added Python 3.13 support.

**Changed:**

* Changed setup.py to lazy evaluate gsl installation.
* Documentation brought up to date
* Merged the GSL configuration logic in `setup.py`.
* Changed `pytest` `capture_output` fixture. Now automatically restores `sys.stdout`.

**Fixed:**

* remove older conda-recipe files
* moved the tests directory from src to the root using conftest.py.
* fixed a circular import bug during " pip install ." in GitHub CI.
* renamed .py files under tests to snake_case.
* add PyPI packages under pip.txt
* re-cookiecutter to group's package standard
* Fix missing `__date__`, use PyPI release date.
* Fixed `SystemError` when running `pytest` on Windows with Python 3.13.

**Removed:**

* Python <= 3.10 support
* Six dependency and py2 support


1.4.2
=====

**Added:**

* Support for Python 3.11, 3.12

**Changed:**

* No notable functional changes from 1.4.1

1.4.4rc0
========

**Fixed:**

* Code linted to group flake8 standards
* Package structure moved to diffpy standard structure
40 changes: 17 additions & 23 deletions README.rst
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Expand Up @@ -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/
Expand Down Expand Up @@ -78,11 +79,6 @@ If you use diffpy.pdffit2 in a scientific publication, we would like you to cite
Installation
------------

diffpy.pdffit2 supports Python 3.11, 3.12, and 3.13.

Windows, macOS (non-Arm64), Linux
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The preferred method is to use `Miniconda Python
<https://docs.conda.io/projects/miniconda/en/latest/miniconda-install.html>`_
and install from the "conda-forge" channel of Conda packages.
Expand All @@ -97,34 +93,32 @@ The following creates and activates a new environment named ``diffpy.pdffit2_env
conda create -n diffpy.pdffit2_env diffpy.pdffit2
conda activate diffpy.pdffit2_env

To confirm that the installation was successful, type ::

python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)"

macOS (Arm64)
~~~~~~~~~~~~~
The output should print the latest version displayed on the badges above.

Create a new conda environment ``diffpy.pdffit2_env``: ::
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 ::

conda create -n diffpy.pdffit2_env python=3.13
pip install diffpy.pdffit2
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instructions here need to be changed to be the same as the instructions in INSTRUCTIONS.txt I think

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@stevenhua0320 stevenhua0320 Nov 20, 2025

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Should it be maintained as the original form of installation guide as before? I don't think we have a INSTRUCTIONS.txt in this package.

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ah, you are right. I was getting confused. Yes, in that case keep it as it was before. I don't think anything changed.


Activate the environment: ::
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 ::

conda activate diffpy.pdffit2_env
pip install .

Install pdffit2 using ``pip`` to download and install the latest version from `Python Package Index <https://pypi.python.org>`_: ::
This package also provides command-line utilities. To check the software has been installed correctly, type ::
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this also needs to be updated as I don't think we have a cli for this program. If we do it just returns version to make sure the installation was correct, but it is never used this way.


pip install diffpy.pdffit2
diffpy.pdffit2 --version

To confirm that the installation was successful, type ::
You can also type the following command to verify the installation. ::

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 .
To view the basic usage and available commands, type ::

diffpy.pdffit2 -h

Getting Started
---------------
Expand Down Expand Up @@ -170,7 +164,7 @@ 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
-------
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52 changes: 23 additions & 29 deletions docs/source/license.rst
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Expand Up @@ -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.
3 changes: 3 additions & 0 deletions pyproject.toml
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Expand Up @@ -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"]}

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