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Use BibTeX citations in Doxygen #3304

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merged 15 commits into from
Nov 15, 2019
Merged

Use BibTeX citations in Doxygen #3304

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182bb12
Cleanup doxygen
jngrad Nov 12, 2019
3e1a13e
Enable citations in Doxygen
jngrad Nov 12, 2019
ba181e4
Use DOI as link
jngrad Nov 12, 2019
817e59b
Replace hardcoded literature references by BibTeX
jngrad Nov 13, 2019
c7caece
Run Doxygen on CUDA 10
jngrad Nov 13, 2019
749bb74
Formatting
jngrad Nov 13, 2019
7219b6c
Update copyright year
jngrad Nov 13, 2019
7ef2f5a
Document and improve readability of sed expression
jngrad Nov 14, 2019
05b53ea
Fix typos and capitalization
jngrad Nov 14, 2019
ec03cf6
Exclude unit tests from the documentation
jngrad Nov 14, 2019
b70b9b4
Sort BibTeX records alphabetically
jngrad Nov 14, 2019
de53b2a
Cleanup doxygen
jngrad Nov 14, 2019
2b8d88d
Add more BibTeX records
jngrad Nov 14, 2019
ff74ea7
Cleanup doxygen
jngrad Nov 15, 2019
20938fe
Re-shuffle doxygen blocks
jngrad Nov 15, 2019
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4 changes: 2 additions & 2 deletions .gitlab-ci.yml
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Expand Up @@ -472,9 +472,9 @@ run_tutorials:
run_doxygen:
<<: *global_job_definition
stage: additional_checks
image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-9.0
image: gitlab.icp.uni-stuttgart.de:4567/espressomd/docker/ubuntu-python3:cuda-10.1
needs:
- cuda9-maxset
- cuda10-maxset
when: on_success
only:
- python
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12 changes: 12 additions & 0 deletions doc/doxygen/CMakeLists.txt
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Expand Up @@ -7,6 +7,17 @@ if(DOXYGEN_FOUND)
DEPENDS EspressoConfig
)

# transform BibTeX DOI fields into URL fields (bibliographic
# styles available to Doxygen do not process the DOI field)
add_custom_command(
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/bibliography.bib
COMMAND sed -r
"'s_^ *doi *= *([^0-9]+)(10\\.[0-9]+)_url=\\1https://dx.doi.org/\\2_'"
${CMAKE_CURRENT_SOURCE_DIR}/bibliography.bib >
${CMAKE_CURRENT_BINARY_DIR}/bibliography.bib
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/bibliography.bib
)

set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in)
set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)

Expand All @@ -17,6 +28,7 @@ if(DOXYGEN_FOUND)
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMENT "Generating API documentation with Doxygen"
DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/doxy-features
${CMAKE_CURRENT_BINARY_DIR}/bibliography.bib
VERBATIM
)

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7 changes: 4 additions & 3 deletions doc/doxygen/Doxyfile.in
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Expand Up @@ -585,7 +585,7 @@ LAYOUT_FILE =
# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
# feature you need bibtex and perl available in the search path.

CITE_BIB_FILES =
CITE_BIB_FILES = bibliography.bib

#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
Expand Down Expand Up @@ -700,7 +700,8 @@ EXCLUDE_SYMLINKS = NO
# against the file with absolute path, so to exclude all test directories
# for example use the pattern */test/*

EXCLUDE_PATTERNS =
EXCLUDE_PATTERNS = @CMAKE_SOURCE_DIR@/*/unit_tests/* \
@CMAKE_SOURCE_DIR@/*/tests/*

# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
Expand Down Expand Up @@ -1315,7 +1316,7 @@ LATEX_SOURCE_CODE = NO
# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
# http://en.wikipedia.org/wiki/BibTeX for more info.

LATEX_BIB_STYLE = plain
LATEX_BIB_STYLE = plainnat

#---------------------------------------------------------------------------
# configuration options related to the RTF output
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