leidenbase 0.1.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: leidenbase
 Type: Package
 Title: R and C wrappers to run the Leiden find_partition function
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: person( 'Brent', 'Ewing', role = c( 'aut', 'cre' ), email = '[email protected]' )
 Description: An R to C interface that runs the Leiden community
     detection algorithm to find a basic partition. It runs the
@@ -27,6 +27,6 @@ LazyData: true
 RoxygenNote: 7.1.1
 Suggests: testthat
 NeedsCompilation: yes
-Packaged: 2020-10-02 18:40:44 UTC; brent
+Packaged: 2021-04-09 17:15:46 UTC; brent
 Author: Brent Ewing [aut, cre]
 Maintainer: Brent Ewing <[email protected]>

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for leidenbase 0.1.2.
+# Generated by GNU Autoconf 2.69 for leidenbase 0.1.3.
 #
 #
 # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
@@ -577,8 +577,8 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='leidenbase'
 PACKAGE_TARNAME='leidenbase'
-PACKAGE_VERSION='0.1.2'
-PACKAGE_STRING='leidenbase 0.1.2'
+PACKAGE_VERSION='0.1.3'
+PACKAGE_STRING='leidenbase 0.1.3'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
@@ -1253,7 +1253,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures leidenbase 0.1.2 to adapt to many kinds of systems.
+\`configure' configures leidenbase 0.1.3 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1315,7 +1315,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of leidenbase 0.1.2:";;
+     short | recursive ) echo "Configuration of leidenbase 0.1.3:";;
    esac
   cat <<\_ACEOF
 
@@ -1405,7 +1405,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-leidenbase configure 0.1.2
+leidenbase configure 0.1.3
 generated by GNU Autoconf 2.69
 
 Copyright (C) 2012 Free Software Foundation, Inc.
@@ -2081,7 +2081,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by leidenbase $as_me 0.1.2, which was
+It was created by leidenbase $as_me 0.1.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   $ $0 $@
@@ -4935,7 +4935,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by leidenbase $as_me 0.1.2, which was
+This file was extended by leidenbase $as_me 0.1.3, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -4988,7 +4988,7 @@ _ACEOF
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
 ac_cs_version="\\
-leidenbase config.status 0.1.2
+leidenbase config.status 0.1.3
 configured by $0, generated by GNU Autoconf 2.69,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -6,7 +6,7 @@ dnl We acknowledge Gabor Csardi's work on the R/C igraph
 dnl distributions and for making the source code publicly 
 dnl and freely available.
 dnl
-AC_INIT([leidenbase], 0.1.2)
+AC_INIT([leidenbase], 0.1.3)
 AC_CONFIG_SRCDIR(src/leidenFindPartition.cpp)
 
 : ${R_HOME=`R RHOME`}

src/cigraph/include/igraph_blas.h

@@ -60,6 +60,9 @@ DECLDIR void igraph_blas_dgemv_array(igraph_bool_t transpose, igraph_real_t alph
 
 DECLDIR igraph_real_t igraph_blas_dnrm2(const igraph_vector_t *v);
 
+DECLDIR int igraph_blas_ddot(const igraph_vector_t *v1, const igraph_vector_t *v2,
+                               igraph_real_t *res);
+
 __END_DECLS
 
 #endif

src/cigraph/include/igraph_cliques.h

@@ -83,7 +83,7 @@ DECLDIR int igraph_independence_number(const igraph_t *graph, igraph_integer_t *
 
 /**
  * \typedef igraph_clique_handler_t
- * \brief Type of clique handler functions
+ * \brief Type of clique handler functions.
  *
  * Callback type, called when a clique was found.
  *

src/cigraph/include/igraph_coloring.h

@@ -27,7 +27,9 @@ __BEGIN_DECLS
 
 /**
  * \typedef igraph_coloring_greedy_t
- * Ordering heuristics for igraph_vertex_coloring_greedy
+ * \brief Ordering heuristics for greedy graph coloring.
+ *
+ * Ordering heuristics for \ref igraph_vertex_coloring_greedy().
  *
  * \enumval IGRAPH_COLORING_GREEDY_COLORED_NEIGHBORS  Choose vertex with largest number of already colored neighbors.
  *

src/cigraph/include/igraph_datatype.h

@@ -57,11 +57,14 @@ __BEGIN_DECLS
  * - <b>is</b> This is basically the same as <b>os</b>, but this time
  *   for the incoming edges.
  *
- * For undirected graph, the same edge list is stored, ie. an
- * undirected edge is stored only once, and for checking whether there
- * is an undirected edge from \c v1 to \c v2 one
- * should search for both \c from=v1, \c to=v2 and
- * \c from=v2, \c to=v1.
+ * For undirected graphs, the same edge list is stored, i.e. an
+ * undirected edge is stored only once. Currently, undirected edges
+ * are canonicalized so that the index of the 'from' vertex is not greater
+ * than the index of the 'to' vertex. Thus, if v1 <= v2, only the edge (v1, v2)
+ * needs to be searched for, not (v2, v1), to determine if v1 and v2 are connected.
+ * However, this fact is NOT guaranteed by the documented public API, 
+ * and should not be relied upon by the implementation of any functions, 
+ * except those belonging to the minimal API in type_indexededgelist.c.
  *
  * The storage requirements for a graph with \c |V| vertices
  * and \c |E| edges is \c O(|E|+|V|).

src/cigraph/include/igraph_decls.h

@@ -8,18 +8,15 @@
     #define __END_DECLS /* empty */
 #endif
 
+/* In igraph 0.8, we use DECLDIR only with MSVC, not other compilers on Windows. */
 #undef DECLDIR
-#if defined (_WIN32) || defined (WIN32) || defined (_WIN64) || defined (WIN64)
-    #if defined (__MINGW32__) || defined (__CYGWIN32__)
+#if defined (_MSC_VER)
+    #ifdef IGRAPH_EXPORTS
+        #define DECLDIR __declspec(dllexport)
+    #elif defined(IGRAPH_STATIC)
         #define DECLDIR /**/
     #else
-        #ifdef IGRAPH_EXPORTS
-            #define DECLDIR __declspec(dllexport)
-        #elif defined(IGRAPH_STATIC)
-            #define DECLDIR /**/
-        #else
-            #define DECLDIR __declspec(dllimport)
-        #endif
+        #define DECLDIR __declspec(dllimport)
     #endif
 #else
     #define DECLDIR /**/

src/cigraph/include/igraph_hrg.h

@@ -81,6 +81,7 @@ DECLDIR int igraph_hrg_fit(const igraph_t *graph,
 DECLDIR int igraph_hrg_sample(const igraph_t *graph,
                               igraph_t *sample,
                               igraph_vector_ptr_t *samples,
+                              igraph_integer_t no_samples,
                               igraph_hrg_t *hrg,
                               igraph_bool_t start);
 

src/cigraph/include/igraph_nongraph.h

@@ -72,7 +72,6 @@ typedef struct igraph_plfit_result_t {
 
 DECLDIR int igraph_running_mean(const igraph_vector_t *data, igraph_vector_t *res,
                                 igraph_integer_t binwidth);
-DECLDIR int igraph_fisher_yates_shuffle(igraph_vector_t *seq);
 DECLDIR int igraph_random_sample(igraph_vector_t *res, igraph_real_t l, igraph_real_t h,
                                  igraph_integer_t length);
 DECLDIR int igraph_convex_hull(const igraph_matrix_t *data, igraph_vector_t *resverts,

src/cigraph/include/igraph_version.h

@@ -28,7 +28,7 @@
 
 __BEGIN_DECLS
 
-#define IGRAPH_VERSION "0.8.2"
+#define IGRAPH_VERSION "0.8.5"
 #define IGRAPH_VERSION_MAJOR @PACKAGE_VERSION_MAJOR@
 #define IGRAPH_VERSION_MINOR @PACKAGE_VERSION_MINOR@
 #define IGRAPH_VERSION_PATCH @PACKAGE_VERSION_PATCH@