Fix after web review

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@3189 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: fd42bab9b27a3c086adeaf75068c83a911ede000

7 files changed, 62 insertions, 140 deletions

diff --git a/src/Alpha_complex/utilities/alphacomplex.md b/src/Alpha_complex/utilities/alphacomplex.md
index 0e500e53..aace85d3 100644
--- a/src/Alpha_complex/utilities/alphacomplex.md
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -1,18 +1,47 @@
----

-layout: page

-title: "Alpha complex"

-meta_title: "alphacomplex"

-subheadline: ""

-teaser: ""

-permalink: "/alphacomplex/"

----

-{::comment}

-These flags above are here for web site generation, please let them.

-cf. https://gitlab.inria.fr/GUDHI/website

-Must be in conformity with _data/navigation.yml

-{:/comment}

 

 

+# Alpha complex #

+

+

+## alpha_complex_persistence ##

+

+This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud.

+The output diagram contains one bar per line, written with the convention:

+

+```

+   p dim birth death

+```

+

+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,

+and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).

+

+**Usage**

+

+```

+   alpha_complex_persistence [options] <input OFF file>

+```

+

+where

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

+

+**Allowed options**

+

+* `-h [ --help ]` Produce help message

+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.

+* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction.

+* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.

+* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

+

+**Example**

+

+```

+   alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off

+```

+

+N.B.:

+

+* Filtration values are alpha square values.

+

 

 ## alpha_complex_3d_persistence ##

 This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention:

@@ -107,7 +136,7 @@ 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](../doc/latest/fileformats.html#FileFormatsIsoCuboid).

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

 

 **Allowed options**

 

@@ -125,46 +154,5 @@ 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](../doc/latest/fileformats.html#FileFormatsIsoCuboid).

-* Filtration values are alpha square values.

-

-

-

-## alpha_complex_persistence ##

-

-This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud.

-The output diagram contains one bar per line, written with the convention:

-

-```

-   p dim birth death

-```

-

-where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature,

-and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).

-

-**Usage**

-

-```

-   alpha_complex_persistence [options] <input OFF file>

-```

-

-where

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

-

-**Allowed options**

-

-* `-h [ --help ]` Produce help message

-* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.

-* `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction.

-* `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.

-* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.

-

-**Example**

-

-```

-   alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off

-```

-

-N.B.:

-

+* 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 3a9e6aac..6e1b2578 100644
--- a/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
+++ b/src/Bitmap_cubical_complex/utilities/cubicalcomplex.md
@@ -1,21 +1,10 @@
----

-layout: page

-title: "Bitmap cubical complex"

-meta_title: "cubicalcomplex"

-subheadline: ""

-teaser: ""

-permalink: "/cubicalcomplex/"

----

-{::comment}

-These flags above are here for web site generation, please let them.

-cf. https://gitlab.inria.fr/GUDHI/website

-Must be in conformity with _data/navigation.yml

-{:/comment}

 

 

+# Cubical complex#

+

 ## 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](../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 e9079058..526f5822 100644
--- a/src/Bottleneck_distance/utilities/bottleneckdistance.md
+++ b/src/Bottleneck_distance/utilities/bottleneckdistance.md
@@ -1,18 +1,6 @@
----

-layout: page

-title: "Bottleneck distance"

-meta_title: "bottleneckdistance"

-subheadline: ""

-teaser: ""

-permalink: "/bottleneckdistance/"

----

-{::comment}

-These flags above are here for web site generation, please let them.

-cf. https://gitlab.inria.fr/GUDHI/website

-Must be in conformity with _data/navigation.yml

-{:/comment}

 

 

+# Bottleneck distance #

 

 ## bottleneck_read_file_example ##

 

@@ -26,5 +14,5 @@ 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](../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/Nerve_GIC/utilities/covercomplex.md b/src/Nerve_GIC/utilities/covercomplex.md
index 41489b66..f33cb2e0 100644
--- a/src/Nerve_GIC/utilities/covercomplex.md
+++ b/src/Nerve_GIC/utilities/covercomplex.md
@@ -1,18 +1,7 @@
----
-layout: page
-title: "Cover complex"
-meta_title: "covercomplex"
-subheadline: ""
-teaser: ""
-permalink: "/covercomplex/"
----
-{::comment}
-These flags above are here for web site generation, please let them.
-cf. https://gitlab.inria.fr/GUDHI/website
-Must be in conformity with _data/navigation.yml
-{:/comment}
 
 
+# Cover complex #
+
 
 ## Nerve ##
 This program builds the Nerve of a point cloud sampled on an OFF file.
diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md
index 44a37543..4291fae7 100644
--- a/src/Rips_complex/utilities/ripscomplex.md
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -1,21 +1,9 @@
----
-layout: page
-title: "Rips complex"
-meta_title: "ripscomplex"
-subheadline: ""
-teaser: ""
-permalink: "/ripscomplex/"
----
-{::comment}
-These flags above are here for web site generation, please let them.
-cf. https://gitlab.inria.fr/GUDHI/website
-Must be in conformity with _data/navigation.yml
-{:/comment}
 
 
+# Rips complex #
 
 ## rips_persistence ##
-This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points. The output diagram contains one bar per line, written with the convention:
+This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points, using Euclidean distance. The output diagram contains one bar per line, written with the convention:
 
 `p dim birth death`
 
diff --git a/src/Witness_complex/utilities/witnesscomplex.md b/src/Witness_complex/utilities/witnesscomplex.md
index 40864871..2341759b 100644
--- a/src/Witness_complex/utilities/witnesscomplex.md
+++ b/src/Witness_complex/utilities/witnesscomplex.md
@@ -1,19 +1,9 @@
----

-layout: page

-title: "Witness complex"

-meta_title: "witnesscomplex"

-subheadline: ""

-teaser: ""

-permalink: "/witnesscomplex/"

----

-{::comment}

-These flags above are here for web site generation, please let them.

-cf. https://gitlab.inria.fr/GUDHI/website

-Must be in conformity with _data/navigation.yml

-{:/comment}

-

-

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

+

+

+# Witness complex #

+

+

+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.

diff --git a/src/common/utilities/pointsetgenerator.md b/src/common/utilities/pointsetgenerator.md
index f39c63b8..284715d4 100644
--- a/src/common/utilities/pointsetgenerator.md
+++ b/src/common/utilities/pointsetgenerator.md
@@ -1,16 +1,6 @@
----
-layout: page
-title: "Pointset generator"
-meta_title: "pointsetgenerator"
-subheadline: ""
-teaser: ""
-permalink: "/pointsetgenerator/"
----
-{::comment}
-These flags above are here for web site generation, please let them.
-cf. https://gitlab.inria.fr/GUDHI/website
-Must be in conformity with _data/navigation.yml
-{:/comment}
+
+
+# common #
 
 ## off_file_from_shape_generator ##