Use BibTeX citations in Doxygen #3304
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Move docstrings above the corresponding functions, remove duplicate docstrings, transform regular comments into docstrings if relevant, fix typos, remove outdated text, typeset math formula.
The bibliographic styles available to Doxygen do not process the DOI field of BibTeX files. The DOI field is now used to create the URL field programmatically.
The citations were obtained from icp.bib.
Doxygen now requires a BibTeX installation.
Codecov Report
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## python #3304 +/- ##
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- Coverage 86% 85% -1%
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Files 536 536
Lines 25564 25513 -51
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- Hits 21995 21923 -72
- Misses 3569 3590 +21
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pkreissl
suggested changes
Nov 14, 2019
They do not provide any useful information and pollute the documentation with irrelevant global variables and mocked structs/classes that have the same name as the corresponding real structs/classes, making it harder to find the relevant documentation page.
pkreissl
reviewed
Nov 14, 2019
| @@ -163,7 +161,7 @@ void dp3m_deactivate(); | |||
| * These parameters are stored in the @ref dp3m object. | |||
| * | |||
| * The function utilizes the analytic expression of the error estimate | |||
| * for the dipolar P3M method in the paper of J. J. Cerda et al., JCP 2008 in | |||
| * for the dipolar P3M method in the paper of @cite cerda08d in | |||
| * order to obtain the rms error in the force for a system of N randomly | |||
| * distributed particles in a cubic box. | |||
| * For the real space error the estimate of Kolafa/Perram is used. | |||
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Just wondering, is there a citation for that one?
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I love references with the author name but no year and no journal...
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@pkreissl I think I got all of them this time. I couldn't deduce the reference for the following 4 citations that have no year information: Krueger and Fedosov, Yeh and Klapp, Schiller, Moshier. |
pkreissl
approved these changes
Nov 15, 2019
Remove outdated information, fix typos, remove double whitespaces, fix broken links, fix doxygen style.
fweik
approved these changes
Nov 15, 2019
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bors r=fweik |
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Nov 15, 2019
3304: Use BibTeX citations in Doxygen r=fweik a=jngrad Follow-up to the Summer School developers meeting Description of changes: - replace all hardcoded literature references in the core by BibTeX references (817e59b) - backport improvements from 4.1.1: grammar and spell check, copyright years - remove unit tests from the doxygen documentation (too much clutter) - cleanup doxygen documentation Co-authored-by: Jean-Noël Grad <jgrad@icp.uni-stuttgart.de>
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Nov 15, 2019
3314: Modernize core r=fweik a=jngrad Follow-up to #3304 Description of changes: - cherry-pick #3312 - add a `BoxGeometry::volume` method - use `bool` for true/false flags - reduce scope of local variables - remove obsolete comments Co-authored-by: Christoph Junghans <junghans@lanl.gov> Co-authored-by: Jean-Noël Grad <jgrad@icp.uni-stuttgart.de>
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Follow-up to the Summer School developers meeting
Description of changes: