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Merged
merged 13 commits into from
Jun 16, 2024
Merged

PDFmorph manual PDF and HTML #117

merged 13 commits into from
Jun 16, 2024

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Sparks29032
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@Sparks29032 Sparks29032 commented Jun 7, 2024

When complete, this should close #24, close #26, and close #27. Can also close #30 and close #39 in this PR after the manual is finished.

@sbillinge I have commented changes to our current .rst files (added references to the user manuals).
You do not have to check the changes in the .texinfo files as I have compiled it into a PDF.
If you have time, I would like some feedback on section 4 and what in that section is okay to include in the paper proper.

User manual todo:

  • Acknowledgements
  • Disclaimer and redistribution
  • Introduction
  • Installation
  • Tutorials
  • Theory behind morphs (isotropic expansion, temperature as independent assumption, shape prefactor)
  • Summary of options in reference guide

Website todo (requires merging PR #120 and #121 and doing a pull):

  • Add links to webpage and manual on README.rst
  • Edit webpage landing and quickstart so they refer users to the manual first

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codecov bot commented Jun 8, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.66%. Comparing base (804feaf) to head (59edcab).
Report is 18 commits behind head on main.

Current head 59edcab differs from pull request most recent head 217babf

Please upload reports for the commit 217babf to get more accurate results.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #117   +/-   ##
=======================================
  Coverage   83.65%   83.66%           
=======================================
  Files          38       38           
  Lines        1891     1892    +1     
=======================================
+ Hits         1582     1583    +1     
  Misses        309      309           

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I am happy to merge these fixes without pre-commit passing, but we need to figure out the right configuration of things to get this right. there seems to be a conflict between black and flake8. i left a comment on one of @Caden's prs. here ae some recommendations:
https://github.com/psf/black/blob/06ccb88bf2bd35a4dc5d591bb296b5b299d07323/docs/guides/using_black_with_other_tools.md#flake8

i also thought it is better to go with 88 instead of 115 for the line length which will make abit more work, but good to standardize I think

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Opened PR #118 to fix pre-commit errors.

@Sparks29032 Sparks29032 changed the title Manual installation instructions PDFmorph manual PDF and HTML Jun 11, 2024
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one small tweak? Or maybe just leave it as "diffpy" project and we won't have to update it for all the different packages?

Benjamin Frandsen during his PhD at Columbia Unversity,
and Long Yang from Tonji University.

The PDFmorph development team is the set of all contributors to the PDFgui project.
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pdfmorph project?

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Yep, sorry referenced the PDFgui blurb

@Sparks29032 Sparks29032 marked this pull request as ready for review June 16, 2024 20:39
Comment on lines +110 to +111
For detailed instructions and full tutorial, consult the user manual
on our `website <www.diffpy.org/diffpy.pdfmorph/>`.
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Reference user manual in README.rst.

Comment on lines +7 to +8
and some of what it can do. For a more detailed tutorial, check out
our :download:`user manual <../pdfmorph.pdf>`.
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Reference user manual in quickstart.rst.

Comment on lines +38 to +39
To get started, please download our :download:`user manual <../pdfmorph.pdf>`
or visit the :ref:`quick_start`.
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Reference user manual in index.rst.

Comment on lines +7 to +15
The DiffPy development team is the set of all contributors to DiffPy projects.
Each member of the development team maintains copyright on their individual
contributions to the code base. For a detailed contribution history of
@code{PDFmorph}, see the git logs at @url{https://github.com/diffpy/diffpy.pdfmorph}.

For more information about the application, please visit
@url{https://www.diffpy.org/diffpy.pdfmorph}.
Report any bugs to diffpy-users@@googlegroups.com or submit
an issue to @url{https://github.com/diffpy/diffpy.pdfmorph/issues}.
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Edited per in-line comment.

@sbillinge sbillinge merged commit 83fa5c6 into diffpy:main Jun 16, 2024
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