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Merged
sawenzel merged 5 commits into from
Dec 20, 2019
Merged

Fixes in Doxygen documentation: #2725

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6db6277
Fixes in Doxygen documentation:
ihrivnac Dec 18, 2019
0b866e2
Reverting changes in .travis.yml
ihrivnac Dec 18, 2019
627f340
Disabled filtering in doxygen generation in .tarvis.yml
ihrivnac Dec 18, 2019
216a322
More fixes in Doxygen documentation:
ihrivnac Dec 19, 2019
2fec4be
- Removed commented lines in .travis.yml
ihrivnac Dec 20, 2019
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5 changes: 0 additions & 5 deletions .travis.yml
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Expand Up @@ -68,11 +68,6 @@ matrix:
cat > CMakeLists.txt <<\EOF
add_subdirectory(doc)
EOF
# This is required because of differences between doxygen and github
# markdown syntax for code blocks. The committed code should use
# the github flavour and we generate the doxygen one on the fly.
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'
find . -name "*.old" -delete
cmake .
make doc
deploy:
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4 changes: 4 additions & 0 deletions Algorithm/README.md
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<!-- doxy
\page refAlgorithm Module 'Algorithm'
/doxy -->

# Algorithm

A description of this module is not yet available.
2 changes: 2 additions & 0 deletions CCDB/README.md
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<!-- doxy
\page refCCDB Module 'CCDB'
/doxy -->

# CCDB

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4 changes: 4 additions & 0 deletions Common/Field/macro/README.md
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<!-- doxy
\page refCommonFieldMacros Field Macros
/doxy -->

## Macros for magnetic field manipulations

```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``)
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24 changes: 16 additions & 8 deletions Common/README.md
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<!-- doxy
\page refCommon Module 'Common'
/doxy -->

# Common

There is no module description yet.

<!-- doxy
This module contains the following submodules:

- \subpage refCommonConstants
- \subpage refCommonField
- \subpage refCommonMathUtils
- \subpage refCommonSimConfig
- \subpage refCommonTopologies
- \subpage refCommonTypes
- \subpage refCommonUtils
- \subpage refCommonmaps
* \subpage refCommonConstants
* \subpage refCommonFieldMacros
* \subpage refCommonMathUtils
* \subpage refCommonSimConfig
* \subpage refCommonTopologies
* \subpage refCommonTypes
* \subpage refCommonUtils
* \subpage refCommonmaps
/doxy -->
2 changes: 2 additions & 0 deletions Common/SimConfig/doc/ConfigurableParam.md
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<!-- doxy
\page refCommonSimConfig SimConfig
/doxy -->

# Configurable Parameters

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26 changes: 17 additions & 9 deletions DataFormats/README.md
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<!-- doxy
\page refDataFormats Module 'DataFormats'
/doxy -->

# Data Formats

There is no module description yet.

<!-- doxy
This module contains the following submodules:

- \subpage refDataFormatsDetectors
- \subpage refDataFormatsHeaders
- \subpage refDataFormatsLegacy
- \subpage refDataFormatsMemoryResources
- \subpage refDataFormatsParameters
- \subpage refDataFormatsReconstruction
- \subpage refDataFormatsTimeFrame
- \subpage refDataFormatscommon
- \subpage refDataFormatssimulation
* \subpage refDataFormatsDetectors
* \subpage refDataFormatsHeaders
* \subpage refDataFormatsLegacy
* \subpage refDataFormatsMemoryResources
* \subpage refDataFormatsParameters
* \subpage refDataFormatsReconstruction
* \subpage refDataFormatsTimeFrame
* \subpage refDataFormatscommon
* \subpage refDataFormatssimulation
/doxy -->
4 changes: 4 additions & 0 deletions Detectors/Base/test/README.md
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<!-- doxy
\page refDetectorsBasetest Detectors Base test
/doxy -->

# WORK IN PROGRESS: Mat.Budget LUT classes


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5 changes: 3 additions & 2 deletions Detectors/ITSMFT/MFT/README.md
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<!-- doxy
\page refMFT MFT
/doxy -->

The Muon Forward Tracker
========================
# The Muon Forward Tracker

#### When?
* After the second LHC Long Shutdown.
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2 changes: 2 additions & 0 deletions Detectors/ITSMFT/MFT/base/README.md
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<!-- doxy
\page refMFTbase MFT base
/doxy -->

# MFT base classes

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5 changes: 3 additions & 2 deletions Detectors/ITSMFT/MFT/reconstruction/README.md
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<!-- doxy
\page refMFTreconstruction MFT reconstruction
/doxy -->

MFT track reconstruction
========================
# MFT track reconstruction

(for the moment see macros/README)

12 changes: 9 additions & 3 deletions Detectors/ITSMFT/README.md
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<!-- doxy
\page refDetectorsITSMFT ITSMFT
/doxy -->

# ITSMFT

This is a top page for the ITSMFT detector documentation.

- \subpage refMFT
- \subpage refMFTbase
- \subpage refMFTreconstruction
<!-- doxy
* \subpage refMFT
* \subpage refMFTbase
* \subpage refMFTreconstruction
/doxy -->
2 changes: 2 additions & 0 deletions Detectors/MUON/MCH/Contour/README.md
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<!-- doxy
\page refMUONMCHContour MCH Contour
/doxy -->

# MCH Contour library

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2 changes: 2 additions & 0 deletions Detectors/MUON/MCH/Mapping/Impl3/README.md
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<!-- doxy
\page refMUONMCHMappingImpl3 MCH Mapping Impl3
/doxy -->

# MCH Mapping Implementation

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2 changes: 2 additions & 0 deletions Detectors/MUON/MCH/Mapping/README.md
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<!-- doxy
\page refMUONMCHMapping MCH Mapping
/doxy -->

# MCH Mapping

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2 changes: 2 additions & 0 deletions Detectors/MUON/MCH/Mapping/SegContour/README.md
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<!-- doxy
\page refMUONMCHMappingSegContour MCH Mapping SegContour
/doxy -->

# Segmentation contours

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4 changes: 3 additions & 1 deletion Detectors/MUON/MCH/Mapping/test/src/README.md
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\page refMUONMCHMappingtest MCH Mapping test
<!-- doxy
\page refMUONMCHMappingtest MCH Mapping test
/doxy -->

By default the tests are running without any input.

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2 changes: 2 additions & 0 deletions Detectors/MUON/MID/Clustering/README.md
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<!-- doxy
\page refMUONMIDClustering MID Clustering
/doxy -->

# Running MID clustering

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2 changes: 2 additions & 0 deletions Detectors/MUON/MID/Tracking/README.md
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<!-- doxy
\page refMUONMIDTracking MID Tracking
/doxy -->

# Running MID Tracking

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2 changes: 2 additions & 0 deletions Detectors/MUON/MID/Workflow/README.md
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<!-- doxy
\page refMUONMIDWorkflow MID Workflow
/doxy -->

# Running MID workflow

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21 changes: 14 additions & 7 deletions Detectors/MUON/README.md
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<!-- doxy
\page refDetectorsMUON MUON
/doxy -->

# MUON

This is a top page for the MUON detector documentation.

- \subpage refMUONMIDClustering
- \subpage refMUONMIDTracking
- \subpage refMUONMCHMappingSegContour
- \subpage refMUONMCHMapping
- \subpage refMUONMCHMappingtest
- \subpage refMUONMCHMappingImpl3
- \subpage refMUONMCHContour
<!-- doxy
* \subpage refMUONMIDClustering
* \subpage refMUONMIDTracking
* \subpage refMUONMIDWorkflow
* \subpage refMUONMCHMappingSegContour
* \subpage refMUONMCHMapping
* \subpage refMUONMCHMappingtest
* \subpage refMUONMCHMappingImpl3
* \subpage refMUONMCHContour
/doxy -->
36 changes: 22 additions & 14 deletions Detectors/README.md
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<!-- doxy
\page refDetectors Module 'Detectors'
/doxy -->

# Detectors

There is no module description yet.

<!-- doxy
This module contains the following submodules:

- \subpage refDetectorsBase
- \subpage refDetectorsEMCAL
- \subpage refDetectorsFIT
- \subpage refDetectorsGeometry
- \subpage refDetectorsGlobalTracking
- \subpage refDetectorsHMPID
- \subpage refDetectorsITSMFT
- \subpage refDetectorsMUON
- \subpage refDetectorsPHOS
- \subpage refDetectorsPassive
- \subpage refDetectorsTOF
- \subpage refDetectorsTPC
- \subpage refDetectorsTRD
- \subpage refDetectorsZDC
* \subpage refDetectorsBasetest
* \subpage refDetectorsEMCAL
* \subpage refDetectorsFIT
* \subpage refDetectorsGeometry
* \subpage refDetectorsGlobalTracking
* \subpage refDetectorsHMPID
* \subpage refDetectorsITSMFT
* \subpage refDetectorsMUON
* \subpage refDetectorsPHOS
* \subpage refDetectorsPassive
* \subpage refDetectorsTOF
* \subpage refDetectorsTPC
* \subpage refDetectorsTRD
* \subpage refDetectorsZDC
/doxy -->
8 changes: 7 additions & 1 deletion Detectors/TPC/README.md
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<!-- doxy
\page refDetectorsTPC TPC
/doxy -->

# TPC

This is a top page for the TPC detector documentation.

- \subpage refTPCworkflow
<!-- doxy
* \subpage refTPCworkflow
/doxy -->
2 changes: 2 additions & 0 deletions Detectors/TPC/workflow/README.md
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<!-- doxy
\page refTPCworkflow TPC workflow
/doxy -->

# DPL workflows for the TPC

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8 changes: 7 additions & 1 deletion Detectors/TRD/README.md
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<!-- doxy
\page refDetectorsTRD TRD
/doxy -->

# TRD

This is a top page for the TRD detector documentation.

- \subpage refTRDbase
<!-- doxy
* \subpage refTRDbase
/doxy -->
4 changes: 4 additions & 0 deletions EventVisualisation/Base/README.md
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<!-- doxy
\page refEventVisualisationBase EventVisualisation Base
/doxy -->

# Event Visualisation Base

A description of this module is not yet available.
10 changes: 9 additions & 1 deletion EventVisualisation/README.md
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<!-- doxy
\page refEventVisualisation Module 'EventVisualisation'
/doxy -->

# Event Visualisation

There is no module description yet.

<!-- doxy
This module contains the following submodules:

- \subpage refEventVisualisationBase
* \subpage refEventVisualisationBase
/doxy -->

6 changes: 5 additions & 1 deletion Examples/Ex1/README.md
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\page refEx1 Ex1 A basic example with one library
<!-- doxy
\page refExamplesEx1 Ex1 A basic example with one library
/doxy -->

## Ex1 A basic example with one library

See [CMakeInstructions](../doc/CMakeInstructions.md) for an explanation about this directory.
6 changes: 5 additions & 1 deletion Examples/Ex2/README.md
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\page refEx2 Ex2 A basic library with a Root dictionary
<!-- doxy
\page refExamplesEx2 Ex2 A basic library with a Root dictionary
/doxy -->

## Ex2 A basic library with a Root dictionary

See [CMakeInstructions](../doc/CMakeInstructions.md) for an explanation about this directory.
6 changes: 5 additions & 1 deletion Examples/Ex3/README.md
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\page refEx3 Ex3 Adding an executable
<!-- doxy
\page refExamplesEx3 Ex3 Adding an executable
/doxy -->

## Ex3 Adding an executable

See [CMakeInstructions](../doc/CMakeInstructions.md) for an explanation about this directory.
6 changes: 5 additions & 1 deletion Examples/Ex4/README.md
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\page refEx4 Ex4 Adding tests
<!-- doxy
\page refExamplesEx4 Ex4 Adding tests
/doxy -->

## Ex4 Adding tests

See [CMakeInstructions](../doc/CMakeInstructions.md) for an explanation about this directory.
6 changes: 5 additions & 1 deletion Examples/Ex5/README.md
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\page refEx5 Ex5 Adding a man page
<!-- doxy
\page refExamplesEx5 Ex5 Adding a man page
/doxy -->

## Ex5 Adding a man page

See [CMakeInstructions](../doc/CMakeInstructions.md) for an explanation about this directory.
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