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Fixes in Doxygen documentation: (AliceO2Group#2725)
* Fixes in Doxygen documentation: - Restored the main page and fixed links to internal pages - Fixed links to sub pages - Updated DoxygenInstructions.md - Updated instructions in .travis.yaml and moved the filtering instructions (now obsolete) in commented lines in doc/scripts/filter_for_doxygen.sh * Reverting changes in .travis.yml * Disabled filtering in doxygen generation in .tarvis.yml * More fixes in Doxygen documentation: - Disabled Doxygen keywords rendering on GitHub - Use Markdown syntax in the lists - Fixes in Doxygen pages tag names * - Removed commented lines in .travis.yml - Updated doxygen filter for code higlighting
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‎.travis.yml‎

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cat > CMakeLists.txt <<\EOF
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add_subdirectory(doc)
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EOF
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# This is required because of differences between doxygen and github
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# markdown syntax for code blocks. The committed code should use
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# the github flavour and we generate the doxygen one on the fly.
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git grep -l '^```[a-zA-Z]' | xargs sed -i .old -e 's|```\([a-zA-Z][a-zA-Z]*\)|\n```{.\1}\n|g;s|[.]bash|.sh|g;s|```|~~~~~~~|g'
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find . -name "*.old" -delete
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cmake .
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make doc
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deploy:

‎Algorithm/README.md‎

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<!-- doxy
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\page refAlgorithm Module 'Algorithm'
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/doxy -->
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# Algorithm
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A description of this module is not yet available.

‎CCDB/README.md‎

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\page refCCDB Module 'CCDB'
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/doxy -->
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# CCDB
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‎Common/Field/macro/README.md‎

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<!-- doxy
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\page refCommonFieldMacros Field Macros
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/doxy -->
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## Macros for magnetic field manipulations
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```o2::field::MagneticWrapperChebyshev``` class allows to dump the field data to text file and recreate it back as a ROOT object from this file. This is useful if one needs to change the name or the namespace of this class or persistent classes it usese internally (e.g. ``MathUtils/Chebyshev3D.h``, ``MathUtils/Chebyshev3DCalc.h``)

‎Common/README.md‎

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<!-- doxy
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\page refCommon Module 'Common'
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/doxy -->
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# Common
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There is no module description yet.
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<!-- doxy
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This module contains the following submodules:
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- \subpage refCommonConstants
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- \subpage refCommonField
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- \subpage refCommonMathUtils
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- \subpage refCommonSimConfig
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- \subpage refCommonTopologies
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- \subpage refCommonTypes
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- \subpage refCommonUtils
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- \subpage refCommonmaps
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* \subpage refCommonConstants
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* \subpage refCommonFieldMacros
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* \subpage refCommonMathUtils
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* \subpage refCommonSimConfig
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* \subpage refCommonTopologies
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* \subpage refCommonTypes
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* \subpage refCommonUtils
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* \subpage refCommonmaps
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/doxy -->

‎Common/SimConfig/doc/ConfigurableParam.md‎

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\page refCommonSimConfig SimConfig
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# Configurable Parameters
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‎DataFormats/README.md‎

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<!-- doxy
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\page refDataFormats Module 'DataFormats'
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/doxy -->
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# Data Formats
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There is no module description yet.
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<!-- doxy
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This module contains the following submodules:
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- \subpage refDataFormatsDetectors
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- \subpage refDataFormatsHeaders
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- \subpage refDataFormatsLegacy
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- \subpage refDataFormatsMemoryResources
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- \subpage refDataFormatsParameters
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- \subpage refDataFormatsReconstruction
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- \subpage refDataFormatsTimeFrame
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- \subpage refDataFormatscommon
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- \subpage refDataFormatssimulation
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* \subpage refDataFormatsDetectors
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* \subpage refDataFormatsHeaders
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* \subpage refDataFormatsLegacy
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* \subpage refDataFormatsMemoryResources
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* \subpage refDataFormatsParameters
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* \subpage refDataFormatsReconstruction
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* \subpage refDataFormatsTimeFrame
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* \subpage refDataFormatscommon
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* \subpage refDataFormatssimulation
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/doxy -->

‎Detectors/Base/test/README.md‎

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<!-- doxy
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\page refDetectorsBasetest Detectors Base test
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/doxy -->
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# WORK IN PROGRESS: Mat.Budget LUT classes
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‎Detectors/ITSMFT/MFT/README.md‎

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<!-- doxy
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\page refMFT MFT
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/doxy -->
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The Muon Forward Tracker
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========================
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# The Muon Forward Tracker
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#### When?
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* After the second LHC Long Shutdown.

‎Detectors/ITSMFT/MFT/base/README.md‎

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<!-- doxy
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\page refMFTbase MFT base
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# MFT base classes
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