Merge branch 'master' into main_documentation_pages

6 files changed, 42 insertions, 70 deletions

diff --git a/src/common/doc/MathJax.js b/src/common/doc/MathJax.js
deleted file mode 100644
index 35e1994e..00000000
--- a/src/common/doc/MathJax.js
+++ /dev/null
@@ -1,53 +0,0 @@
-(function () {
-  var newMathJax = 'https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js';
-  var oldMathJax = 'cdn.mathjax.org/mathjax/latest/MathJax.js';
-
-  var replaceScript = function (script, src) {
-    //
-    //  Make redirected script
-    //
-    var newScript = document.createElement('script');
-    newScript.src = newMathJax + src.replace(/.*?(\?|$)/, '$1');
-    //
-    //  Move onload and onerror handlers to new script
-    //
-    newScript.onload = script.onload; 
-    newScript.onerror = script.onerror;
-    script.onload = script.onerror = null;
-    //
-    //  Move any content (old-style configuration scripts)
-    //
-    while (script.firstChild) newScript.appendChild(script.firstChild);
-    //
-    //  Copy script id
-    //
-    if (script.id != null) newScript.id = script.id;
-    //
-    //  Replace original script with new one
-    //
-    script.parentNode.replaceChild(newScript, script);
-    //
-    //  Issue a console warning
-    //
-    console.warn('WARNING: cdn.mathjax.org has been retired. Check https://www.mathjax.org/cdn-shutting-down/ for migration tips.')
-  }
-
-  if (document.currentScript) {
-    var script = document.currentScript;
-    replaceScript(script, script.src);
-  } else {
-    //
-    // Look for current script by searching for one with the right source
-    //
-    var n = oldMathJax.length;
-    var scripts = document.getElementsByTagName('script');
-    for (var i = 0; i < scripts.length; i++) {
-      var script = scripts[i];
-      var src = (script.src || '').replace(/.*?:\/\//,'');
-      if (src.substr(0, n) === oldMathJax) {
-        replaceScript(script, src);
-        break;
-      }
-    }
-  }
-})();
\ No newline at end of file
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 23214e25..235296d3 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -29,6 +29,32 @@ namespace Gudhi {
 
  \tableofcontents
 
+ \section FileFormatsOFF OFF file format
+
+ OFF files must be conform to format described here: http://www.geomview.org/docs/html/OFF.html
+
+ OFF files are mainly used as point cloud inputs. Here is an example of 7 points in a 3-dimensional space. As edges and
+ faces are not used for point set, there is no need to specify them (just set their numbers to 0):
+
+ \include points/alphacomplexdoc.off
+
+ For dimensions bigger than 3, the dimension can be set like here:
+ \verbatim
+  # Dimension is no more 3
+  nOFF
+  # dimension 4 - 7 vertices - 0 face - 0 edge
+  4 7 0 0
+  # Point set:
+  1.0 1.0  0.0 0.0
+  7.0 0.0  0.0 0.0
+  4.0 6.0  0.0 0.0
+  9.0 6.0  0.0 0.0
+  0.0 14.0 0.0 0.0
+  2.0 19.0 0.0 0.0
+  9.0 17.0 0.0 0.0
+ \endverbatim
+
+
  \section FileFormatsPers Persistence Diagram
 
  Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index 8fb8b330..5d581b08 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -44,7 +44,7 @@ make doxygen
 \endverbatim
  *
  * \subsection helloworld Hello world !
- * The <a target="_blank" href="https://gitlab.inria.fr/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
+ * The <a target="_blank" href="https://github.com/GUDHI/hello-gudhi-world">Hello world for GUDHI</a>
  * project is an example to help developers to make their own C++ project on top of the GUDHI library.
  *
  * \section optionallibrary Optional third-party library
diff --git a/src/common/example/vectordoubleoffreader_result.txt b/src/common/example/vectordoubleoffreader_result.txt
index 1deb8dbd..b399425a 100644
--- a/src/common/example/vectordoubleoffreader_result.txt
+++ b/src/common/example/vectordoubleoffreader_result.txt
@@ -1,7 +1,7 @@
-Point[0] = 1 1 
-Point[1] = 7 0 
-Point[2] = 4 6 
-Point[3] = 9 6 
-Point[4] = 0 14 
-Point[5] = 2 19 
-Point[6] = 9 17 
+Point[0] = 1 1 0 
+Point[1] = 7 0 0 
+Point[2] = 4 6 0 
+Point[3] = 9 6 0 
+Point[4] = 0 14 0 
+Point[5] = 2 19 0 
+Point[6] = 9 17 0 
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 05a1e145..fc951fe7 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -37,8 +37,7 @@ namespace Gudhi {
 
 /** \brief OFF file reader top class visitor. 
  * 
- * OFF file must be conform to format described here : 
- * http://www.geomview.org/docs/html/OFF.html
+ * OFF file must be conform to \ref FileFormatsOFF
  */
 class Off_reader {
  public:
diff --git a/src/common/test/test_points_off_reader.cpp b/src/common/test/test_points_off_reader.cpp
index ba3bab71..e4b76ed7 100644
--- a/src/common/test/test_points_off_reader.cpp
+++ b/src/common/test/test_points_off_reader.cpp
@@ -44,19 +44,19 @@ BOOST_AUTO_TEST_CASE( points_doc_test )
   BOOST_CHECK(point_cloud.size() == 7);
 
   std::vector<Point_d> expected_points;
-  std::vector<double> point = {1.0, 1.0};
+  std::vector<double> point = {1.0, 1.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {7.0, 0.0};
+  point = {7.0, 0.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {4.0, 6.0};
+  point = {4.0, 6.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {9.0, 6.0};
+  point = {9.0, 6.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {0.0, 14.0};
+  point = {0.0, 14.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {2.0, 19.0};
+  point = {2.0, 19.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
-  point = {9.0, 17.0};
+  point = {9.0, 17.0, 0.0};
   expected_points.push_back(Point_d(point.begin(), point.end()));
 
   BOOST_CHECK(point_cloud == expected_points);