Add readme, doc, project.toml

Author: bobleesj

.pre-commit-config.yaml

@@ -15,8 +15,8 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.pdffit2/actions/workflows/main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.pdffit2/actions/workflows/main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.pdffit2/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.pdffit2/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
 
 .. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.pdffit2/branch/main/graph/badge.svg
         :target: https://codecov.io/gh/diffpy/diffpy.pdffit2
@@ -35,7 +35,7 @@
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
         :target: https://github.com/diffpy/diffpy.pdffit2/issues
 
-Real space structure refinement to atomic pair distribution function.
+PDFfit2 - space structure refinement to atomic pair distribution function
 
 The diffpy.pdffit2 package provides functions for calculation and
 refinement of atomic Pair Distribution Function (PDF) from crystal
@@ -58,6 +58,8 @@ To learn more about diffpy.pdffit2 library, see the examples directory
 included in this distribution or the API documentation at
 http://www.diffpy.org/doc/pdffit2.
 
+For more information about the diffpy.pdffit2 library, please consult our `online documentation <https://diffpy.github.io/diffpy.pdffit2>`_.
+
 Citation
 --------
 
@@ -102,11 +104,7 @@ Then, to fully install ``diffpy.pdffit2`` in our active environment, run ::
 
 Another option is to 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, we will also have to install dependencies ::
-
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdffit2/main/requirements/run.txt
-
-and then install the package ::
+To install using ``pip`` into your ``diffpy.pdffit2_env`` environment, type ::
 
         pip install diffpy.pdffit2
 
@@ -155,9 +153,9 @@ 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 contribuing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdffit2/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------
 
-For more information on diffpy.pdffit2 please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
+For more information on diffpy.pdffit2 please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].

Makefile

@@ -1,36 +1,36 @@
-@ECHO OFF
-
-pushd %~dp0
-
-REM Command file for Sphinx documentation
-
-if "%SPHINXBUILD%" == "" (
-	set SPHINXBUILD=sphinx-build
-)
-set SOURCEDIR=source
-set BUILDDIR=build
-set SPHINXPROJ=PackagingScientificPython
-
-if "%1" == "" goto help
-
-%SPHINXBUILD% >NUL 2>NUL
-if errorlevel 9009 (
-	echo.
-	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
-	echo.installed, then set the SPHINXBUILD environment variable to point
-	echo.to the full path of the 'sphinx-build' executable. Alternatively you
-	echo.may add the Sphinx directory to PATH.
-	echo.
-	echo.If you don't have Sphinx installed, grab it from
-	echo.http://sphinx-doc.org/
-	exit /b 1
-)
-
-%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-goto end
-
-:help
-%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
-
-:end
-popd
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=PackagingScientificPython
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

README.rst

@@ -34,3 +34,4 @@ diffpy.pdffit2.ipy_ext module
     :members:
     :undoc-members:
     :show-inheritance:
+

doc/make.bat

@@ -50,14 +50,14 @@ 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 
+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
 ============

doc/source/api/diffpy.pdffit2.rst

@@ -2,4 +2,55 @@
 
 .. index:: license
 
-.. include:: ../../LICENSE.rst
+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.
+
+If you use this program to do productive 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)
+
+Copyright 2006-2007, Board of Trustees of Michigan State University,
+Copyright 2008-2024, 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 [email protected]
+
+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.

doc/source/index.rst

@@ -2,6 +2,5 @@ name: diffpy.pdffit2
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10
+  - python=3
   - pip
-  - conda

doc/source/license.rst

@@ -45,7 +45,7 @@ dirty_template = "{tag}"
 [tool.setuptools.packages.find]
 where = ["src"]  # list of folders that contain the packages (["."] by default)
 include = ["*"]  # package names should match these glob patterns (["*"] by default)
-exclude = ["diffpy.pdffit2.tests*"]  # exclude packages matching these glob patterns (empty by default)
+exclude = []  # exclude packages matching these glob patterns (empty by default)
 namespaces = false  # to disable scanning PEP 420 namespaces (true by default)
 
 [tool.setuptools.dynamic]