From 11fb1656fa6e196e04abc5eaa854d1be5b88c49d Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 13:49:00 -0400 Subject: [PATCH 01/10] skpkg: gitignore update --- .gitignore | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/.gitignore b/.gitignore index a25212ea..099e2948 100644 --- a/.gitignore +++ b/.gitignore @@ -10,6 +10,7 @@ __pycache__/ .Python env/ build/ +_build/ develop-eggs/ dist/ downloads/ @@ -90,10 +91,3 @@ target/ # Ipython Notebook .ipynb_checkpoints - -# version information -setup.cfg -/src/diffpy/*/version.cfg - -# Rever -rever/ From cbd7c0dfff9c5b5d237f63c4ee59d20694c1b332 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 13:53:04 -0400 Subject: [PATCH 02/10] skpkg: changelog and license files --- CHANGELOG.rst | 2 +- LICENSE.rst | 58 ++++++++++++++++++++++----------------------------- 2 files changed, 26 insertions(+), 34 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 40492b28..322ef065 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,5 +1,5 @@ ============= -Release Notes +Release notes ============= .. current developments diff --git a/LICENSE.rst b/LICENSE.rst index 5862f0d6..a148f3bd 100644 --- a/LICENSE.rst +++ b/LICENSE.rst @@ -1,6 +1,4 @@ -License -####### - +BSD 3-Clause License This program is part of the DiffPy and DANSE open-source projects and is available subject to the conditions and terms laid out below. @@ -13,7 +11,7 @@ the following paper in your publication: in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007) Copyright 2006-2007, Board of Trustees of Michigan State University, -Copyright 2008-2024, Board of Trustees of Columbia University in the +Copyright 2008-2025, Board of Trustees of Columbia University in the city of New York. (Copyright holder indicated in each source file). For more information please visit the project web-page: @@ -21,32 +19,26 @@ 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. From 117de3c20a7da20cd4dc1046c28c8db849adcd8c Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 13:56:42 -0400 Subject: [PATCH 03/10] skpkg: readme file --- README.rst | 42 ++++++++++++++++++++---------------------- 1 file changed, 20 insertions(+), 22 deletions(-) diff --git a/README.rst b/README.rst index dbc10c66..4c90e849 100644 --- a/README.rst +++ b/README.rst @@ -8,7 +8,7 @@ :target: https://diffpy.github.io/diffpy.pdffit2 :height: 100px -|PyPi| |Forge| |PythonVersion| |PR| +|PyPI| |Forge| |PythonVersion| |PR| |CI| |Codecov| |Black| |Tracking| @@ -26,7 +26,7 @@ .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff -.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.pdffit2 +.. |PyPI| image:: https://img.shields.io/pypi/v/diffpy.pdffit2 :target: https://pypi.org/project/diffpy.pdffit2/ .. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.pdffit2 @@ -87,19 +87,17 @@ The preferred method is to use `Miniconda Python `_ and install from the "conda-forge" channel of Conda packages. -Add the "conda-forge" channel by running the following command in a terminal: :: +To add "conda-forge" to the conda channels, run the following in a terminal. :: conda config --add channels conda-forge -Create a new environment named ``diffpy.pdffit2_env`` and install ``diffpy.pdffit2``: :: +We want to install our packages in a suitable conda environment. +The following creates and activates a new environment named ``diffpy.pdffit2_env`` :: conda create -n diffpy.pdffit2_env diffpy.pdffit2 - -Activate the environment: :: - conda activate diffpy.pdffit2_env -Confirm that the installation was successful: :: +To confirm that the installation was successful, type :: python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)" @@ -118,25 +116,20 @@ Install pdffit2 using ``pip`` to download and install the latest version from `P pip install diffpy.pdffit2 -Confirm that the installation was successful: :: +To confirm that the installation was successful, type :: python -c "import diffpy.pdffit2; print(diffpy.pdffit2.__version__)" -Build from source -~~~~~~~~~~~~~~~~~ +If you prefer to install from sources, after installing the dependencies, obtain the source archive from +`GitHub `_. Once installed, ``cd`` into your ``diffpy.pdffit2`` directory +and run the following :: -For advanced users, obtain the source archive, and in the ``diffpy.pdffit2`` directory, run :: + pip install . - conda create -n diffpy.pdffit2_env python=3.13 \ - --file requirements/test.txt \ - --file requirements/conda.txt \ - --file requirements/build.txt +Getting Started +--------------- -Activate the environment, build the package, and run unit tests by following commands sequentially: :: - - conda activate diffpy.pdffit2_env - pip install . --no-deps - pytest +You may consult our `online documentation `_ for tutorials and API references. Support and Contribute ---------------------- @@ -182,4 +175,9 @@ Before contributing, please read our `Code of Conduct `_ or email Prof. Simon Billinge at sb2896@columbia.edu. +For more information on diffpy.pdffit2 please visit the project `web-page `_ or email Simon Billinge at sb2896@columbia.edu. + +Acknowledgements +---------------- + +``diffpy.pdffit2`` is built and maintained with `scikit-package `_. From dc5027af91926b69c0951336a24556b5e7dd0d2f Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 13:58:03 -0400 Subject: [PATCH 04/10] skpkg: index.rst --- doc/source/index.rst | 83 +++++++++++--------------------------------- 1 file changed, 21 insertions(+), 62 deletions(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index a7eff2a9..962c7dd0 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -4,90 +4,49 @@ .. |title| replace:: diffpy.pdffit2 documentation -diffpy.pdffit2 - PDFfit2 - real space structure refinement program. +``diffpy.pdffit2`` - PDFfit2 - real space structure refinement program. -| Software version |release|. +| Software version |release| | Last updated |today|. -The diffpy.pdffit2 package provides functions for the calculation and -refinement of atomic Pair Distribution Functions (PDF) from crystal -structure models. It is used as a computational engine by PDFgui. All -refinements possible in PDFgui can be done by writing python scripts -directly with diffpy.pdffit2, -although less conveniently and with a fair knowledge of Python. -However, we recommend using `diffpy-cmi -`_ for carrying -out more advanced, python-scripted refinements of nanostructure. - -The PDFfit2 package includes an extension for the interactive `IPython -`_ shell, these days commonly used within -Jupyter notebooks, which tries to mimic the old PDFFIT -program. To start IPython with this extension and also with plotting -functions enabled, use :: - - ipython --ext=diffpy.pdffit2.ipy_ext --pylab - -The IPython extension is suitable for interactive use, however -refinement scripts should be preferably written as a standard -Python code. This is more reliable and needs only a few extra -statements. +=============== +Getting started +=============== + +Welcome to the ``diffpy.pdffit2`` documentation! + +To get started, please visit the :ref:`Getting started ` page. ======= Authors ======= -This code was derived from the first `PDFFIT -`_ program written by Thomas Proffen -and Simon Billinge, which was a FORTRAN implementation of the original -"Real-space Rietveld" code -written by Simon Billinge (Billinge, S. J. L. “Real-space Rietveld: full profile structure refinement of the atomic pair distribution -function”. In: Local Structure from Diffraction. Ed. by S. J. L. Billinge and M. F. Thorpe. New York: -Plenum, 1998, p. 137). -The sources were converted to C++ by Jacques Bloch and then extensively hacked, -extended and purged from most glaring bugs by Chris Farrow and Pavol Juhas. -This code is currently maintained as part of the DiffPy project to create -python modules for structure investigations from diffraction data. - -The DiffPy team is located in the Billinge-group at the Applied Physics -and Applied Mathematics Department of the Columbia University in New York. -Previous significant contributors to this code were made by - - Pavol Juhas, Chris Farrow, Jacques Bloch, Wenduo Zhou - -with more recent contributions from Billinge-group members. -For a more detailed list of contributors see +``diffpy.pdffit2`` is developed by Billinge group and community members.. The maintainer for this project is Simon Billinge. For a detailed list of contributors see https://github.com/diffpy/diffpy.pdffit2/graphs/contributors. - -========= -Reference -========= - -If you use this program for a scientific research that leads to publication, -we ask that you acknowledge use of the program by citing the following paper -in your publication: - - C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen - and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure - in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007) - ============ Installation ============ -Please see the `README `_ +See the `README `_ file included with the distribution. +================ +Acknowledgements +================ + +``diffpy.pdffit2`` is built and maintained with `scikit-package `_. + ================= Table of contents ================= .. toctree:: - :titlesonly: + :maxdepth: 2 - license - release - examples + getting-started Package API + release + license ======= Indices From ce0287c20ff59325fdf5f60588829ac93f1c1526 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 13:59:38 -0400 Subject: [PATCH 05/10] skpkg: lincense.rst in docs --- doc/source/license.rst | 57 ++++++++++++++++++++---------------------- 1 file changed, 27 insertions(+), 30 deletions(-) diff --git a/doc/source/license.rst b/doc/source/license.rst index e8729103..ac33d481 100644 --- a/doc/source/license.rst +++ b/doc/source/license.rst @@ -5,6 +5,9 @@ License ####### +OPEN SOURCE LICENSE AGREEMENT +============================= +BSD 3-Clause License This program is part of the DiffPy and DANSE open-source projects and is available subject to the conditions and terms laid out below. @@ -17,7 +20,7 @@ the following paper in your publication: in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007) Copyright 2006-2007, Board of Trustees of Michigan State University, -Copyright 2008-|year|, Board of Trustees of Columbia University in the +Copyright 2008-2025, Board of Trustees of Columbia University in the city of New York. (Copyright holder indicated in each source file). For more information please visit the project web-page: @@ -25,32 +28,26 @@ 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. From 7e23d38733d0796990fbe2ad8be55ce2bc2bd1f9 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 14:01:26 -0400 Subject: [PATCH 06/10] skpkg: index.rst pt2 --- doc/source/index.rst | 69 +++++++++++++++++++++++++++++++++++++------- 1 file changed, 59 insertions(+), 10 deletions(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index 962c7dd0..10d2ace1 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -9,21 +9,68 @@ | Software version |release| | Last updated |today|. -=============== -Getting started -=============== - -Welcome to the ``diffpy.pdffit2`` documentation! - -To get started, please visit the :ref:`Getting started ` page. +The diffpy.pdffit2 package provides functions for the calculation and +refinement of atomic Pair Distribution Functions (PDF) from crystal +structure models. It is used as a computational engine by PDFgui. All +refinements possible in PDFgui can be done by writing python scripts +directly with diffpy.pdffit2, +although less conveniently and with a fair knowledge of Python. +However, we recommend using `diffpy-cmi +`_ for carrying +out more advanced, python-scripted refinements of nanostructure. + +The PDFfit2 package includes an extension for the interactive `IPython +`_ shell, these days commonly used within +Jupyter notebooks, which tries to mimic the old PDFFIT +program. To start IPython with this extension and also with plotting +functions enabled, use :: + + ipython --ext=diffpy.pdffit2.ipy_ext --pylab + +The IPython extension is suitable for interactive use, however +refinement scripts should be preferably written as a standard +Python code. This is more reliable and needs only a few extra +statements. ======= Authors ======= -``diffpy.pdffit2`` is developed by Billinge group and community members.. The maintainer for this project is Simon Billinge. For a detailed list of contributors see +This code was derived from the first `PDFFIT +`_ program written by Thomas Proffen +and Simon Billinge, which was a FORTRAN implementation of the original +"Real-space Rietveld" code +written by Simon Billinge (Billinge, S. J. L. “Real-space Rietveld: full profile structure refinement of the atomic pair distribution +function”. In: Local Structure from Diffraction. Ed. by S. J. L. Billinge and M. F. Thorpe. New York: +Plenum, 1998, p. 137). +The sources were converted to C++ by Jacques Bloch and then extensively hacked, +extended and purged from most glaring bugs by Chris Farrow and Pavol Juhas. +This code is currently maintained as part of the DiffPy project to create +python modules for structure investigations from diffraction data. + +The DiffPy team is located in the Billinge-group at the Applied Physics +and Applied Mathematics Department of the Columbia University in New York. +Previous significant contributors to this code were made by + + Pavol Juhas, Chris Farrow, Jacques Bloch, Wenduo Zhou + +with more recent contributions from Billinge-group members. +For a more detailed list of contributors see https://github.com/diffpy/diffpy.pdffit2/graphs/contributors. + +========= +Reference +========= + +If you use this program for a scientific research that leads to publication, +we ask that you acknowledge use of the program by citing the following paper +in your publication: + + C. L. Farrow, P. Juhás, J. W. Liu, D. Bryndin, E. S. Božin, J. Bloch, Th. Proffen + and S. J. L. Billinge, PDFfit2 and PDFgui: computer programs for studying nanostructure + in crystals (https://stacks.iop.org/0953-8984/19/335219), *J. Phys.: Condens. Matter*, 19, 335219 (2007) + ============ Installation ============ @@ -41,9 +88,11 @@ Acknowledgements Table of contents ================= .. toctree:: - :maxdepth: 2 + :titlesonly: - getting-started + license + release + examples Package API release license From 254c1907874ef42de78a5fc26ae8b5e928bc5ba3 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 14:01:52 -0400 Subject: [PATCH 07/10] diffpy.pdffit2.rst file --- doc/source/api/diffpy.pdffit2.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/doc/source/api/diffpy.pdffit2.rst b/doc/source/api/diffpy.pdffit2.rst index 759fb63c..9bbc4637 100644 --- a/doc/source/api/diffpy.pdffit2.rst +++ b/doc/source/api/diffpy.pdffit2.rst @@ -1,7 +1,9 @@ :tocdepth: -1 -diffpy.pdffit2 package -====================== +|title| +======= + +.. |title| replace:: diffpy.pdffit2 package .. automodule:: diffpy.pdffit2 :members: From 1fd96ae5b3803b6b6c3313e3e67561956a7af7ed Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 14:06:46 -0400 Subject: [PATCH 08/10] skpkg: remove duplicates in index.rst --- doc/source/index.rst | 2 -- src/diffpy/pdffit2/version.py | 2 ++ 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/source/index.rst b/doc/source/index.rst index 10d2ace1..866af1a9 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -90,8 +90,6 @@ Table of contents .. toctree:: :titlesonly: - license - release examples Package API release diff --git a/src/diffpy/pdffit2/version.py b/src/diffpy/pdffit2/version.py index a09785ea..86159280 100644 --- a/src/diffpy/pdffit2/version.py +++ b/src/diffpy/pdffit2/version.py @@ -61,3 +61,5 @@ def get_pypi_release_date(package_name, timeout=5): __date__ = get_pypi_release_date("diffpy.pdffit2") # End of file + +# Release date: 2025-02-07 From 68c86271a90db034c29f82c0d59e397e6e0ef297 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 14:53:25 -0400 Subject: [PATCH 09/10] docs: fix doc rendering issues --- CHANGELOG.rst | 2 +- doc/source/conf.py | 4 ++++ doc/source/license.rst | 4 +--- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 322ef065..1253f933 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -65,7 +65,7 @@ Release notes * No notable functional changes from 1.4.1 1.4.4rc0 -===== +======== **Fixed:** diff --git a/doc/source/conf.py b/doc/source/conf.py index 742d3a53..58fb11f6 100644 --- a/doc/source/conf.py +++ b/doc/source/conf.py @@ -53,6 +53,10 @@ "m2r", ] +autodoc_mock_imports = [ + "diffpy.pdffit2.pdffit2", +] + # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] diff --git a/doc/source/license.rst b/doc/source/license.rst index ac33d481..3b2bbb98 100644 --- a/doc/source/license.rst +++ b/doc/source/license.rst @@ -23,9 +23,7 @@ Copyright 2006-2007, Board of Trustees of Michigan State University, Copyright 2008-2025, Board of Trustees of Columbia University in the city of New York. (Copyright holder indicated in each source file). -For more information please visit the project web-page: - http://www.diffpy.org/ -or email Prof. Simon Billinge at sb2896@columbia.edu +For more information please visit the project web-page: http://www.diffpy.org/ 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: From 6915dc82e7cafa4d49c936abc4a5e82c404fa910 Mon Sep 17 00:00:00 2001 From: Caden Myers Date: Thu, 12 Jun 2025 15:00:52 -0400 Subject: [PATCH 10/10] chore: news --- news/rst-migration.rst | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/rst-migration.rst diff --git a/news/rst-migration.rst b/news/rst-migration.rst new file mode 100644 index 00000000..e010dcad --- /dev/null +++ b/news/rst-migration.rst @@ -0,0 +1,23 @@ +**Added:** + +* + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* Migrate documentation to `scikit-package 0.1.0` standards, including a mock import for API rendering. + +**Security:** + +*