Ignore md files for Doxygen

Fix relative path issue


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3179 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c8f88a757fdf681327f1cef9feadf7bf8d12da83

5 files changed, 7 insertions, 6 deletions

diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index 56bce602..0e500e53 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -106,7 +106,8 @@ Refer to the [CGAL's 3D Periodic Triangulations User Manual](https://doc.cgal.or
 where

 

 * `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

-* `<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid).

+* `<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described

+[here](../doc/latest/fileformats.html#FileFormatsIsoCuboid).

 

 **Allowed options**

 

@@ -124,7 +125,7 @@ periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off
 

 N.B.:

 

-* Cuboid file must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid).

+* Cuboid file must be in the format described [here](../doc/latest/fileformats.html#FileFormatsIsoCuboid).

 * Filtration values are alpha square values.

 

 

diff --git a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
index 393b2654..3a9e6aac 100644
--- a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
+++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
@@ -15,7 +15,7 @@ Must be in conformity with _data/navigation.yml
 

 ## cubical_complex_persistence ##

 This program computes persistent homology, by using the Bitmap_cubical_complex class, of cubical complexes provided in text files in Perseus style.

-See [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format.

+See [here](../doc/latest/fileformats.html#FileFormatsPerseus) for a description of the file format.

 

 **Example**

 

diff --git a/src/Bottleneck_distance/utilities/bottleneckdistance.md b/src/Bottleneck_distance/utilities/bottleneckdistance.md
index 04e1c4bd..e9079058 100644
--- a/src/Bottleneck_distance/utilities/bottleneckdistance.md
+++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md
@@ -26,5 +26,5 @@ This program computes the Bottleneck distance between two persistence diagram fi
 

 where

 

-* `<file_1.pers>` and `<file_2.pers>` must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsPers).

+* `<file_1.pers>` and `<file_2.pers>` must be in the format described [here](../doc/latest/fileformats.html#FileFormatsPers).

 * `<tolerance>` is an error bound on the bottleneck distance (set by default to the smallest positive double value).

diff --git a/src/Doxyfile b/src/Doxyfile
index 2d5adea1..763c240e 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -801,7 +801,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       =
+EXCLUDE_PATTERNS       = */utilities/*/*.md
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md
index 5cdb1f88..40864871 100644
--- a/src/Witness_complex/utilities/witnesscomplex.md
+++ b/src/Witness_complex/utilities/witnesscomplex.md
@@ -13,7 +13,7 @@ Must be in conformity with _data/navigation.yml
 {:/comment}

 

 

-For more details about the witness complex, please read the [user manual of the package](http://gudhi.gforge.inria.fr/doc/latest/group__witness__complex.html).

+For more details about the witness complex, please read the [user manual of the package](../doc/latest/group__witness__complex.html).

 

 ## weak_witness_persistence ##

 This program computes the persistent homology with coefficient field *Z/pZ* of a Weak witness complex defined on a set of input points.