Fix doc

BGL/doc/BGL/PackageDescription.txt

@@ -731,6 +731,8 @@ user might encounter.
 - `CGAL::read_GOCAD()`
 - `CGAL::write_GOCAD()`
 
+- `CGAL::read_polygon_mesh()`
+- `CGAL::write_polygon_mesh()`
 */
 
 /*!

Point_set_processing_3/doc/Point_set_processing_3/PackageDescription.txt

@@ -7,11 +7,14 @@
 Collection of algorithms of point set processing (smoothing,
 simplification, etc.).
 
-\defgroup PkgPointSetProcessing3IO IO (XYZ/OFF Formats)
+\defgroup PkgPointSetProcessing3IO IO (I/O Functions)
 \ingroup PkgPointSetProcessing3Ref
 
-Read and write points (with or without normal vectors) in XYZ and OFF
+\defgroup PkgPointSetProcessing3IOOff IO (OFF Formats)
-formats.
+\ingroup PkgPointSetProcessing3Ref
+
+\defgroup PkgPointSetProcessing3IOXyz IO (XYZ Formats)
+\ingroup PkgPointSetProcessing3Ref
 
 \defgroup PkgPointSetProcessing3IOPly IO (PLY Format)
 \ingroup PkgPointSetProcessing3Ref
@@ -73,10 +76,8 @@ format.
 
 \cgalCRPSection{IO (XYZ/OFF Formats)}
 
-- `CGAL::read_off_points()`
+- \link PkgPointSetProcessing3IOOff OFF I/O Functions (`read_OFF()` and `write_OFF()`)\endlink
-- `CGAL::read_xyz_points()`
+- \link PkgPointSetProcessing3IOXyz XYZ I/O Functions (`read_XYZ()` and `write_XYZ()`)\endlink
-- `CGAL::write_off_points()`
-- `CGAL::write_xyz_points()`
 
 \cgalCRPSection{IO (PLY Format)}
 
@@ -99,5 +100,9 @@ format.
 - `CGAL::make_las_point_reader()`
 - `CGAL::make_las_point_writer()`
 
+\cgalCRPSection{IO (All Formats)}
+
+- `CGAL::read_points()`
+- `CGAL::write_points()`
 */
 

Point_set_processing_3/include/CGAL/IO/read_off_points.h

@@ -37,7 +37,7 @@ namespace CGAL {
 
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOOff
    Reads points (positions + normals, if available) from a .off ASCII stream.
    The function expects for each point a line with the x y z position,
    optionally followed by the nx ny nz normal.
@@ -187,7 +187,7 @@ read_OFF(
 
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOOff
    Reads points (positions + normals, if available) from a .off ASCII file.
    The function expects for each point a line with the x y z position,
    optionally followed by the nx ny nz normal.
@@ -525,35 +525,40 @@ read_off_points(
 
 
 #ifndef CGAL_NO_DEPRECATED_CODE
+#ifdef DOXYGEN_RUNNING
 /*!
-/**
+   \ingroup PkgPointSetProcessing3IOOff
-   \ingroup PkgPointSetProcessing3IO
    @todo update version
    \deprecated This function is deprecated since \cgal 5.1, `CGAL::read_OFF()` should be used instead.
 */
 template <typename OutputIteratorValueType,
           typename OutputIterator,
-#ifdef DOXYGEN_RUNNING
           typename NamedParameters
-#else
-          typename CGAL_BGL_NP_TEMPLATE_PARAMETERS
-#endif
 >
-
-/// \cond SKIP_IN_MANUAL
 CGAL_DEPRECATED bool
 read_off_points(
     std::istream& stream,
     OutputIterator output,
-#ifdef DOXYGEN_RUNNING
     const NamedParameters& np)
-#else
-    const CGAL_BGL_NP_CLASS& np)
-#endif
 {
   return read_OFF(stream, output, np);
 }
 
+#else
+          typename CGAL_BGL_NP_TEMPLATE_PARAMETERS
+template <typename OutputIteratorValueType,
+          typename OutputIterator,
+          typename CGAL_BGL_NP_TEMPLATE_PARAMETERS>
+CGAL_DEPRECATED bool
+read_off_points(
+    std::istream& stream,
+    OutputIterator output,
+    const CGAL_BGL_NP_CLASS& np)
+{
+  return read_OFF(stream, output, np);
+}
+#endif
+/// \cond SKIP_IN_MANUAL
 template <typename OutputIteratorValueType,
           typename OutputIterator>
 CGAL_DEPRECATED bool

Point_set_processing_3/include/CGAL/IO/read_xyz_points.h

@@ -32,7 +32,7 @@
 namespace CGAL {
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOXyz
    Reads points (positions + normals, if available) from a .xyz ASCII stream.
    The function expects for each point a line with the x y z position,
    optionally followed by the nx ny nz normal.
@@ -175,7 +175,7 @@ read_XYZ(
 }
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOXyz
    Reads points (positions + normals, if available) from a .xyz ASCII file.
    The function expects for each point a line with the x y z position,
    optionally followed by the nx ny nz normal.
@@ -516,7 +516,7 @@ read_xyz_points(
 ///
 ///
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOXyz
    @todo update version
    \deprecated This function is deprecated since \cgal 5.1, `CGAL::read_XYZ()` should be used instead.
 

Point_set_processing_3/include/CGAL/IO/write_las_points.h

@@ -372,7 +372,7 @@ write_las_points(
 /// \endcond
 #ifndef CGAL_NO_DEPRECATED_CODE
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOLas
   @todo update version
   \deprecated This function is deprecated since \cgal 5.1, `CGAL::write_LAS_with_properties()` should be used instead.
 */
@@ -392,7 +392,7 @@ write_las_points_with_properties (std::ostream& stream,
 }
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOLas
   @todo update version
   \deprecated This function is deprecated since \cgal 5.1, `CGAL::write_LAS()` should be used instead.
 */

Point_set_processing_3/include/CGAL/IO/write_off_points.h

@@ -31,7 +31,7 @@ namespace CGAL {
 
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOOff
    Saves the range of `points` (positions + normals, if available) to a .off ASCII stream.
    The function writes for each point a line with the x y z position
    followed by the nx ny nz normal (if available).
@@ -321,7 +321,7 @@ write_off_points(
 /// \endcond
 #ifndef CGAL_NO_DEPRECATED_CODE
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOOff
   @todo update version
   \deprecated This function is deprecated since \cgal 5.1, `CGAL::write_OFF()` should be used instead.
 */

Point_set_processing_3/include/CGAL/IO/write_xyz_points.h

@@ -30,7 +30,7 @@ namespace CGAL {
 
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOXyz
    Saves the range of `points` (positions + normals, if available) to a .xyz ASCII stream.
    The function writes for each point a line with the x y z position
    followed by the nx ny nz normal (if available).
@@ -272,7 +272,7 @@ write_xyz_points(
 #ifndef CGAL_NO_DEPRECATED_CODE
 
 /**
-   \ingroup PkgPointSetProcessing3IO
+   \ingroup PkgPointSetProcessing3IOXyz
   @todo update version
   \deprecated This function is deprecated since \cgal 5.1, `CGAL::write_XYZ()` should be used instead.
 */

Stream_support/doc/Stream_support/PackageDescription.txt

@@ -67,7 +67,8 @@ the printing mode.
 - \link OffIoFuncs I/O on OFF files (`CGAL::write_OFF()`and `CGAL::read_OFF()`)\endlink
 - \link GocadIoFuncs I/O on GOCAD files (`CGAL::write_GOCAD()`and `CGAL::read_GOCAD()`)\endlink
 - \link VtpIoFuncs I/O on VTP files (`CGAL::write_VTP()`and `CGAL::read_VTP()`)\endlink
-
+- `GCAL::read_polygon_soup()`
+- `GCAL::write_polygon_soup()`
 - `GCAL::read_WKT()`
 - `CGAL::read_point_WKT()`
 - `GCAL::read_multi_point_WKT()`
@@ -89,6 +90,5 @@ the printing mode.
 - `CGAL::Verbose_ostream`
 - `CGAL::Input_rep<T,F>`
 - `CGAL::Output_rep<T,F>`
-
 */