Merge pull request #172 from Sparks29032/diffpy.morph

Refactor PDFmorph to diffpy.morph

Author: sbillinge

Diff for: .github/workflows/build-wheel-release-upload.yml

@@ -10,7 +10,7 @@ jobs:
   release:
     uses: Billingegroup/release-scripts/.github/workflows/_build-wheel-release-upload.yml@v0
     with:
-      project: diffpy.pdfmorph
+      project: diffpy.morph
     secrets:
       PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
       PAT_TOKEN: ${{ secrets.PAT_TOKEN }}

Diff for: .github/workflows/check-news-item.yml

@@ -9,4 +9,4 @@ jobs:
   check-news-item:
     uses: Billingegroup/release-scripts/.github/workflows/_check-news-item.yml@v0
     with:
-      project: diffpy.pdfmorph
+      project: diffpy.morph

Diff for: .github/workflows/matrix-and-codecov-on-merge-to-main.yml

@@ -14,7 +14,7 @@ jobs:
   matrix-coverage:
     uses: Billingegroup/release-scripts/.github/workflows/_matrix-and-codecov-on-merge-to-main.yml@v0
     with:
-      project: diffpy.pdfmorph
+      project: diffpy.morph
       c_extension: false
       headless: false
     secrets:

Diff for: .github/workflows/tests-on-pr.yml

@@ -11,7 +11,7 @@ jobs:
   tests-on-pr:
     uses: Billingegroup/release-scripts/.github/workflows/_tests-on-pr.yml@v0
     with:
-      project: diffpy.pdfmorph
+      project: diffpy.morph
       c_extension: false
       headless: false
     secrets:

Diff for: AUTHORS.rst

@@ -7,4 +7,4 @@ Contributors
 ------------
 
 For a list of contributors, visit
-https://github.com/diffpy/diffpy.pdfmorph/graphs/contributors
+https://github.com/diffpy/diffpy.morph/graphs/contributors

Diff for: README.rst

@@ -1,8 +1,8 @@
-|Icon| `diffpy.pdfmorph <https://diffpy.github.io/diffpy.pdfmorph>`_
-====================================================================
+|Icon| `diffpy.morph <https://diffpy.github.io/diffpy.morph>`_
+==============================================================
 
 .. |Icon| image:: https://avatars.githubusercontent.com/diffpy
-        :target: https://diffpy.github.io/diffpy.pdfmorph
+        :target: https://diffpy.github.io/diffpy.morph
         :height: 100px
 
 |PyPi| |Forge| |PythonVersion| |PR|
@@ -12,29 +12,29 @@
 .. |Black| image:: https://img.shields.io/badge/code_style-black-black
         :target: https://github.com/psf/black
 
-.. |CI| image:: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
-        :target: https://github.com/diffpy/diffpy.pdfmorph/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
+.. |CI| image:: https://github.com/diffpy/diffpy.morph/actions/workflows/matrix-and-codecov-on-merge-to-main.yml/badge.svg
+        :target: https://github.com/diffpy/diffpy.morph/actions/workflows/matrix-and-codecov-on-merge-to-main.yml
 
-.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.pdfmorph/branch/main/graph/badge.svg
-        :target: https://codecov.io/gh/diffpy/diffpy.pdfmorph
+.. |Codecov| image:: https://codecov.io/gh/diffpy/diffpy.morph/branch/main/graph/badge.svg
+        :target: https://codecov.io/gh/diffpy/diffpy.morph
 
-.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.pdfmorph
-        :target: https://anaconda.org/conda-forge/diffpy.pdfmorph
+.. |Forge| image:: https://img.shields.io/conda/vn/conda-forge/diffpy.morph
+        :target: https://anaconda.org/conda-forge/diffpy.morph
 
 .. |PR| image:: https://img.shields.io/badge/PR-Welcome-29ab47ff
 
-.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.pdfmorph
-        :target: https://pypi.org/project/diffpy.pdfmorph/
+.. |PyPi| image:: https://img.shields.io/pypi/v/diffpy.morph
+        :target: https://pypi.org/project/diffpy.morph/
 
-.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.pdfmorph
-        :target: https://pypi.org/project/diffpy.pdfmorph/
+.. |PythonVersion| image:: https://img.shields.io/pypi/pyversions/diffpy.morph
+        :target: https://pypi.org/project/diffpy.morph/
 
 .. |Tracking| image:: https://img.shields.io/badge/issue_tracking-github-blue
-        :target: https://github.com/diffpy/diffpy.pdfmorph/issues
+        :target: https://github.com/diffpy/diffpy.morph/issues
 
 Tools for manipulating and comparing PDF profiles
 
-PDFmorph is a Python software package designed to increase the insight
+``diffpy.morph`` is a Python software package designed to increase the insight
 researchers can obtain from measured atomic pair distribution functions
 (PDFs) in a model-independent way. The program was designed to help a
 researcher answer the question: "Has my material undergone a phase
@@ -44,42 +44,42 @@ One approach is to compare the two PDFs in a plot and view the difference
 curve underneath. However, significant signal can be seen in the
 difference curve from benign effects such as thermal expansion (peak
 shifts) and increased thermal motion (peak broadening) or a change in
-scale due to differences in incident flux, for example. PDFmorph will
+scale due to differences in incident flux, for example. ``diffpy.morph`` will
 do its best to correct for these benign effects before computing and
 plotting the difference curve. One measured PDF (typically that collected
 at higher temperature) is identified as the target PDF and the second
 PDF is then morphed by "stretching" (changing the r-axis to simulate a
 uniform lattice expansion), "smearing" (broadening peaks through a
 uniform convolution to simulate increased thermal motion), and "scaling"
-(self-explanatory). PDFmorph will vary the amplitude of the morphing
+(self-explanatory). ``diffpy.morph`` will vary the amplitude of the morphing
 transformations to obtain the best fit between the morphed and the target
 PDFs, then plot them on top of each other with the difference plotted
 below.
 
 There are also a few other morphing transformations in the program.
 
-Finally, we note that PDFmorph should work on other spectra that are not
+Finally, we note that ``diffpy.morph`` should work on other spectra that are not
 PDFs, though it has not been extensively tested beyond the PDF.
 
 
-For more information about the diffpy.pdfmorph library, please consult our `online documentation <https://diffpy.github.io/diffpy.pdfmorph>`_.
+For more information about the diffpy.morph library, please consult our `online documentation <https://diffpy.github.io/diffpy.morph>`_.
 
 Citation
 --------
 
-If you use diffpy.pdfmorph in a scientific publication, we would like you to cite this package as
+If you use diffpy.morph in a scientific publication, we would like you to cite this package as
 
-        diffpy.pdfmorph Package, https://github.com/diffpy/diffpy.pdfmorph
+        diffpy.morph Package, https://github.com/diffpy/diffpy.morph
 
 REQUIREMENTS
 ------------------------------------------------------------------------
 
-PDFmorph is currently run from the command line, which requires opening
+``diffpy.morph`` is currently run from the command line, which requires opening
 and typing into a terminal window or Windows command prompt. It is
 recommended that you consult online resources and become somewhat
-familiar before using PDFmorph.
+familiar before using ``diffpy.morph``.
 
-PDFmorph can be run with Python 3.10 or higher. It makes use of several third party
+``diffpy.morph`` can be run with Python 3.10 or higher. It makes use of several third party
 libraries that you'll need to run the app and its components.
 
 * `NumPy`              - library for scientific computing with Python
@@ -102,79 +102,79 @@ To add "conda-forge" to the conda channels, run the following in a terminal. ::
         conda config --add channels conda-forge
 
 We want to install our packages in a suitable conda environment.
-The following creates and activates a new environment named ``diffpy.pdfmorph_env`` ::
+The following creates and activates a new environment named ``diffpy.morph_env`` ::
 
-        conda create -n diffpy.pdfmorph_env diffpy.pdfmorph
-        conda activate diffpy.pdfmorph_env
+        conda create -n diffpy.morph_env diffpy.morph
+        conda activate diffpy.morph_env
 
 To confirm that the installation was successful, type::
 
-        python -c "import diffpy.pdfmorph; print(diffpy.pdfmorph.__version__)"
+        python -c "import diffpy.morph; print(diffpy.morph.__version__)"
 
         The output should print the latest version displayed on the badges above.
 
 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.pdfmorph_env`` environment, we will also have to install dependencies ::
+To install using ``pip`` into your ``diffpy.morph_env`` environment, we will also have to install dependencies ::
 
-        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.pdfmorph/main/requirements/pip.txt
+        pip install -r https://raw.githubusercontent.com/diffpy/diffpy.morph/main/requirements/pip.txt
 
 and then install the package ::
 
-        pip install diffpy.pdfmorph
+        pip install diffpy.morph
 
 If you prefer to install from sources, after installing the dependencies, obtain the source archive from
-`GitHub <https://github.com/diffpy/diffpy.pdfmorph/>`_. Once installed, ``cd`` into your ``diffpy.pdfmorph`` directory
+`GitHub <https://github.com/diffpy/diffpy.morph/>`_. Once installed, ``cd`` into your ``diffpy.morph`` directory
 and run the following ::
 
         pip install .
 
 Getting Started
 ---------------
 
-You may consult our `online documentation <https://diffpy.github.io/diffpy.pdfmorph>`_ for tutorials and API references.
+You may consult our `online documentation <https://diffpy.github.io/diffpy.morph>`_ for tutorials and API references.
 
-USING PDFmorph
-------------------------------------------------------------------------
+USING diffpy.morph
+------------------
 
 For detailed instructions and full tutorial, consult the user manual
-on our `website <www.diffpy.org/diffpy.pdfmorph/>`.
+on our `website <www.diffpy.org/diffpy.morph/>`.
 
-Once the required software, including PDFmorph is all installed, open
+Once the required software, including ``diffpy.morph`` is all installed, open
 up a terminal and check installation has worked properly by running ::
 
-	source activate pdfmorph_env      #if the environment isn't already active
-	pdfmorph -h			  #get some helpful information
-	pdfmorph --version
+	source activate diffpy.morph_env      #if the environment isn't already active
+	diffpy.morph -h			  #get some helpful information
+	diffpy.morph --version
 
 If installed correctly, this last command should return the version
-of PDFmorph that you have installed on your system. To begin using
-PDFmorph, run a command like ::
+of ``diffpy.morph`` that you have installed on your system. To begin using
+``diffpy.morph``, run a command like ::
 
-	pdfmorph <target PDF file> <morphed PDF file>
+	diffpy.morph <target PDF file> <morphed PDF file>
 
 where both PDFs file are text files which contain PDF data, such as ``.gr``
 or ``.cgr`` files that are produced by ``PDFgetX2``, ``PDFgetX3``,
 or ``PDFgui``. Though some file extensions other than ``.gr`` or ``.cgr``,
 but with the same content structure, have been shown to work with
-PDFmorph, it is recommended to stick with ``.gr`` files.
+``diffpy.morph``, it is recommended to stick with ``.gr`` files.
 
 Enjoy!
 
 
 Support and Contribute
 ----------------------
 
-`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.pdfmorph. Please join the diffpy.pdfmorph users community by joining the Google group. The diffpy.pdfmorph project welcomes your expertise and enthusiasm!
+`Diffpy user group <https://groups.google.com/g/diffpy-users>`_ is the discussion forum for general questions and discussions about the use of diffpy.morph. Please join the diffpy.morph users community by joining the Google group. The diffpy.morph project welcomes your expertise and enthusiasm!
 
-If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.pdfmorph/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.pdfmorph/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
+If you see a bug or want to request a feature, please `report it as an issue <https://github.com/diffpy/diffpy.morph/issues>`_ and/or `submit a fix as a PR <https://github.com/diffpy/diffpy.morph/pulls>`_. You can also post it to the `Diffpy user group <https://groups.google.com/g/diffpy-users>`_.
 
-Feel free to fork the project and contribute. To install diffpy.pdfmorph
+Feel free to fork the project and contribute. To install diffpy.morph
 in a development mode, with its sources being directly used by Python
 rather than copied to a package directory, use the following in the root
 directory ::
 
-        pip install -e .
+	pip install -e .
 
 To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
 hooks.
@@ -190,9 +190,9 @@ trying to commit again.
 
 Improvements and fixes are always appreciated.
 
-Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.pdfmorph/blob/main/CODE_OF_CONDUCT.rst>`_.
+Before contributing, please read our `Code of Conduct <https://github.com/diffpy/diffpy.morph/blob/main/CODE_OF_CONDUCT.rst>`_.
 
 Contact
 -------
 
-For more information on diffpy.pdfmorph please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].
+For more information on diffpy.morph please visit the project `web-page <https://diffpy.github.io/>`_ or email Prof. Simon Billinge at [email protected].