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-rw-r--r--debian/README.Debian18
-rw-r--r--debian/README.source51
-rw-r--r--debian/changelog5
-rw-r--r--debian/compat1
-rw-r--r--debian/control49
-rw-r--r--debian/copyright46
-rw-r--r--debian/netbunch-docs.docs2
-rw-r--r--debian/patches/readme30
-rw-r--r--debian/patches/series1
-rwxr-xr-xdebian/rules25
-rw-r--r--debian/source/format1
-rw-r--r--doc/ba.1.html2
-rw-r--r--doc/bb_fitness.1.html2
-rw-r--r--doc/bbv.1.html2
-rw-r--r--doc/bet_dependency.1.html2
-rw-r--r--doc/betweenness.1.html2
-rw-r--r--doc/clust.1.html2
-rw-r--r--doc/clust_w.1.html2
-rw-r--r--doc/cnm.1.html2
-rw-r--r--doc/components.1.html2
-rw-r--r--doc/conf_model_deg.12
-rw-r--r--doc/conf_model_deg.1.html4
-rw-r--r--doc/conf_model_deg_nocheck.1.html2
-rw-r--r--doc/deg_seq.1.html2
-rw-r--r--doc/deg_seq_w.1.html2
-rw-r--r--doc/dijkstra.1.html2
-rw-r--r--doc/dms.1.html4
-rw-r--r--doc/er_A.1.html2
-rw-r--r--doc/er_B.1.html2
-rw-r--r--doc/f3m.1.html2
-rw-r--r--doc/fitmle.1.html2
-rw-r--r--doc/gn.1.html2
-rw-r--r--doc/graph_info.1.html2
-rw-r--r--doc/hv_net.1.html2
-rw-r--r--doc/johnson_cycles.1.html2
-rw-r--r--doc/knn.1.html2
-rw-r--r--doc/knn_w.1.html2
-rw-r--r--doc/kruskal.1.html2
-rw-r--r--doc/label_prop.1.html2
-rw-r--r--doc/largest_component.1.html2
-rw-r--r--doc/node_components.1.html2
-rw-r--r--doc/power_law.1.html2
-rw-r--r--doc/shortest.1.html2
-rw-r--r--doc/shortest_avg_max_hist.12
-rw-r--r--doc/shortest_avg_max_hist.1.html4
-rw-r--r--doc/strong_conn.1.html2
-rw-r--r--doc/ws.1.html2
47 files changed, 268 insertions, 39 deletions
diff --git a/debian/README.Debian b/debian/README.Debian
new file mode 100644
index 0000000..47131eb
--- /dev/null
+++ b/debian/README.Debian
@@ -0,0 +1,18 @@
+netbunch for Debian/Devuan/Ubuntu
+------------------
+
+This is NetBunch, the collection of software for network analysis
+accompanying the book:
+
+ "Complex Networks: Principles, Methods and Application"
+ V. Latora, V. Nicosia, G. Russo, Cambridge University
+ Press (2017), ISBN: 9781107103184
+ https://www.cambridge.org/9781107103184
+
+NetBunch includes all the programs implementing the algorithms
+described in the Appendices of the book, and several more. If you use
+a program included in NetBunch, please add a citation to the textbook
+above and to the relevant References indicated in the corresponding
+source files.
+
+ -- Vincenzo (KatolaZ) Nicosia <katolaz@freaknet.org> Thu, 28 Sep 2017 06:46:47 +0100
diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..60c282a
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,51 @@
+===== NetBunch-1.0 =====
+
+This is NetBunch, the collection of software for network analysis
+accompanying the book:
+
+ "Complex Networks: Principles, Methods and Application"
+ V. Latora, V. Nicosia, G. Russo, Cambridge University
+ Press (2017), ISBN: 9781107103184
+ http://www.cambridge.org/gb/academic/subjects/physics/statistical-physics/complex-networks-principles-methods-and-applications?format=HB
+
+NetBunch includes all the programs implementing the algorithms
+described in the Appendices of the book, and several more. If you use
+a program included in NetBunch, please add a citation to the textbook
+above and to the relevant References indicated in the corresponding
+source files.
+
+See 'INSTALL' for information about downloading and installing
+NetBunch.
+
+NetBunch is written and maintained by Vincenzo 'KatolaZ' Nicosia
+(v.nicosia@qmul.ac.uk) (c) 2009-2017.
+
+The programs included in NetBunch can be used, modified, and redistributed
+under the terms of the GNU General Public License, either version 3 of the
+License or, at your option, any later version.
+
+NetBunch is distributed in the hope that it will be useful, but WITHOUT ANY
+WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+details.
+
+See the file 'COPYING' for additional details.
+
+
+===== DOCUMENTATION =====
+
+The documentation of all the programs included in NetBunch is
+available at the URL:
+
+ http://www.complex-networks.net
+
+Moreover, all the manpages are available in HTML format in the folder
+'netbunch-doc' of the binary distributions.
+
+If you compile NetBunch from sources, the HTML files will be put under
+$(prefix)/netbunch-doc (default to /usr/local/netbunch-doc), while the
+manpages will be installed under $(prefix)/share/man/man1 (default to
+/usr/local/share/man/man1).
+
+All the documentation in NetBunch can be used and distributed
+according to the terms the GNU Free Documentation License, version 1.3. \ No newline at end of file
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..5ec9a50
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+netbunch (1.0-1) unstable; urgency=medium
+
+ * Initial release
+
+ -- Vincenzo (KatolaZ) Nicosia <katolaz@freaknet.org> Thu, 28 Sep 2017 06:46:47 +0100
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..3fe75a8
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,49 @@
+Source: netbunch
+Section: science
+Priority: optional
+Maintainer: Vincenzo (KatolaZ) Nicosia <katolaz@freaknet.org>
+Build-Depends: debhelper (>= 9), autotools-dev
+Standards-Version: 3.9.8
+Homepage: http://www.complex-networks.net
+Vcs-Git: https://github.com/KatolaZ/NetBunch/
+#Vcs-Browser: https://anonscm.debian.org/cgit/collab-maint/netbunch.git
+
+Package: netbunch
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: A collection of programs for complex networks analysis
+ NetBunch is a collection of command-line programs for complex
+ networks analysis, accompanying the textbook "Complex Networks:
+ Principles, Methods and Applications" by V. Latora, V. Nicosia,
+ G. Russo, Cambridge University Press (2017).
+ .
+ The suite includes programs to compute simple node and graph
+ properties, such as:
+ .
+ - connected components
+ - degrees and degree correlations
+ - node centrality
+ - paths and distances
+ - node and edge betweenness
+ - centrality
+ - clustering
+ - cycles
+ - motifs
+ - communities
+ - spanning trees
+ - ...
+ .
+ Moreover, NetBunch includes utilities to create synthetic
+ networks using different models, such as:
+ .
+ - Erdos-Renyi random graphs
+ - Configuration model
+ - Small-world model (Watts-Strogatz)
+ - Linear preferential attachment (Barabasi-Albert)
+ - Linear preferential attachment with tunable exponent
+ (Dorogovtsev-Mendes-Samukin)
+ - Fitness model (Bianconi-Barabasi)
+ - Hidden-variable model (Boguna and Pastor-Satorras)
+ - ....
+
+
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..847cc23
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,46 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: netbunch
+Source: https://github.com/KatolaZ/NetBunch
+
+Files: *
+Copyright: 2009-2017 Vincenzo 'KatolaZ' Nicosia <katolaz@freaknet.org>
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or (at
+ your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+
+# If you want to use GPL v2 or later for the /debian/* files use
+# the following clauses, or change it to suit. Delete these two lines
+Files: debian/*
+Copyright: 2017 Vincenzo (KatolaZ) Nicosia <katolaz@freaknet.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+# Please also look if there are files or directories which have a
+# different copyright/license attached and list them here.
+# Please avoid picking licenses with terms that are more restrictive than the
+# packaged work, as it may make Debian's contributions unacceptable upstream.
diff --git a/debian/netbunch-docs.docs b/debian/netbunch-docs.docs
new file mode 100644
index 0000000..efea0a6
--- /dev/null
+++ b/debian/netbunch-docs.docs
@@ -0,0 +1,2 @@
+README.Debian
+README.source
diff --git a/debian/patches/readme b/debian/patches/readme
new file mode 100644
index 0000000..31c126f
--- /dev/null
+++ b/debian/patches/readme
@@ -0,0 +1,30 @@
+Description: readme changed
+ netbunch (1.0-1) unstable; urgency=medium
+ .
+ * Initial release
+Author: Vincenzo (KatolaZ) Nicosia <katolaz@freaknet.org>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout http://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: <vendor|upstream|other>, <url of original patch>
+Bug: <url in upstream bugtracker>
+Bug-Debian: https://bugs.debian.org/<bugnumber>
+Bug-Ubuntu: https://launchpad.net/bugs/<bugnumber>
+Forwarded: <no|not-needed|url proving that it has been forwarded>
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: 2017-09-28
+
+--- netbunch-1.0.orig/README
++++ netbunch-1.0/README
+@@ -6,7 +6,7 @@ accompanying the book:
+ "Complex Networks: Principles, Methods and Application"
+ V. Latora, V. Nicosia, G. Russo, Cambridge University
+ Press (2017), ISBN: 9781107103184
+- http://www.cambridge.org/gb/academic/subjects/physics/statistical-physics/complex-networks-principles-methods-and-applications?format=HB
++ https://www.cambridge.org/9781107103184
+
+ NetBunch includes all the programs implementing the algorithms
+ described in the Appendices of the book, and several more. If you use
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..8178c76
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+readme
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..1b9aee5
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,25 @@
+#!/usr/bin/make -f
+# See debhelper(7) (uncomment to enable)
+# output every command that modifies files on the build system.
+export DH_VERBOSE = 1
+
+
+# see FEATURE AREAS in dpkg-buildflags(1)
+#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+
+# see ENVIRONMENT in dpkg-buildflags(1)
+# package maintainers to append CFLAGS
+#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
+# package maintainers to append LDFLAGS
+#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
+
+
+%:
+ dh $@ --with autotools_dev
+
+
+# dh_make generated override targets
+# This is example for Cmake (See https://bugs.debian.org/641051 )
+#override_dh_auto_configure:
+# dh_auto_configure -- # -DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH)
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/doc/ba.1.html b/doc/ba.1.html
index 37f6e97..3cb9b8c 100644
--- a/doc/ba.1.html
+++ b/doc/ba.1.html
@@ -121,7 +121,7 @@ file <code>ba_10000_3_5.txt</code> (thanks to the redirection operator <code>&gt
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="bb_fitness.1.html">bb_fitness<span class="s">(1)</span></a>, <a class="man-ref" href="dms.1.html">dms<span class="s">(1)</span></a>, <a class="man-ref" href="bbv.1.html">bbv<span class="s">(1)</span></a></p>
+<p><span class="man-ref">bb_fitness<span class="s">(1)</span></span>, <span class="man-ref">dms<span class="s">(1)</span></span>, <span class="man-ref">bbv<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/bb_fitness.1.html b/doc/bb_fitness.1.html
index dbac594..ed7b162 100644
--- a/doc/bb_fitness.1.html
+++ b/doc/bb_fitness.1.html
@@ -137,7 +137,7 @@ specified file).</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="ba.1.html">ba<span class="s">(1)</span></a>, <a class="man-ref" href="dms.1.html">dms<span class="s">(1)</span></a></p>
+<p><span class="man-ref">ba<span class="s">(1)</span></span>, <span class="man-ref">dms<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/bbv.1.html b/doc/bbv.1.html
index 9fe7016..793ca0b 100644
--- a/doc/bbv.1.html
+++ b/doc/bbv.1.html
@@ -134,7 +134,7 @@ The final graph is saved in the file <code>bbv_10000_3_5_1.0_0.5.txt</code>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="ba.1.html">ba<span class="s">(1)</span></a>, <a class="man-ref" href="bb_fitness.1.html">bb_fitness<span class="s">(1)</span></a>, <a class="man-ref" href="dms.1.html">dms<span class="s">(1)</span></a></p>
+<p><span class="man-ref">ba<span class="s">(1)</span></span>, <span class="man-ref">bb_fitness<span class="s">(1)</span></span>, <span class="man-ref">dms<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/bet_dependency.1.html b/doc/bet_dependency.1.html
index e23f9d6..3e4322a 100644
--- a/doc/bet_dependency.1.html
+++ b/doc/bet_dependency.1.html
@@ -135,7 +135,7 @@ saved in the file <code>node_bet_dep</code>.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="betweenness.1.html">betweenness<span class="s">(1)</span></a>, <a class="man-ref" href="shortest.1.html">shortest<span class="s">(1)</span></a></p>
+<p><span class="man-ref">betweenness<span class="s">(1)</span></span>, <span class="man-ref">shortest<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/betweenness.1.html b/doc/betweenness.1.html
index ab25a91..58afae2 100644
--- a/doc/betweenness.1.html
+++ b/doc/betweenness.1.html
@@ -158,7 +158,7 @@ while the values of edge betweenness are printed on STDOUT.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="bet_dependency.1.html">bet_dependency<span class="s">(1)</span></a>, <a class="man-ref" href="shortest.1.html">shortest<span class="s">(1)</span></a></p>
+<p><span class="man-ref">bet_dependency<span class="s">(1)</span></span>, <span class="man-ref">shortest<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/clust.1.html b/doc/clust.1.html
index 63fd5e7..5a1af14 100644
--- a/doc/clust.1.html
+++ b/doc/clust.1.html
@@ -175,7 +175,7 @@ er_1000_5000.txt_node_clust</code>, which redirects the STDERR to the file
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="clust_w.1.html">clust_w<span class="s">(1)</span></a></p>
+<p><span class="man-ref">clust_w<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/clust_w.1.html b/doc/clust_w.1.html
index 49eceb6..5a33cda 100644
--- a/doc/clust_w.1.html
+++ b/doc/clust_w.1.html
@@ -170,7 +170,7 @@ coefficients are saved on the file <code>node_clust_w</code> (notice the syntax
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="clust.1.html">clust<span class="s">(1)</span></a></p>
+<p><span class="man-ref">clust<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/cnm.1.html b/doc/cnm.1.html
index f8aab58..61bb7e1 100644
--- a/doc/cnm.1.html
+++ b/doc/cnm.1.html
@@ -164,7 +164,7 @@ modularity at each step in the file <code>karate_cnm_trace</code>.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="modularity.1.html">modularity<span class="s">(1)</span></a>, <a class="man-ref" href="gn.1.html">gn<span class="s">(1)</span></a>, <a class="man-ref" href="label_prop.1.html">label_prop<span class="s">(1)</span></a></p>
+<p><span class="man-ref">modularity<span class="s">(1)</span></span>, <span class="man-ref">gn<span class="s">(1)</span></span>, <span class="man-ref">label_prop<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/components.1.html b/doc/components.1.html
index 72db2f8..85b46b4 100644
--- a/doc/components.1.html
+++ b/doc/components.1.html
@@ -196,7 +196,7 @@ each connected component, we run:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="strong_conn.1.html">strong_conn<span class="s">(1)</span></a>, <a class="man-ref" href="node_components.1.html">node_components<span class="s">(1)</span></a>, <a class="man-ref" href="largest_component.1.html">largest_component<span class="s">(1)</span></a></p>
+<p><span class="man-ref">strong_conn<span class="s">(1)</span></span>, <span class="man-ref">node_components<span class="s">(1)</span></span>, <span class="man-ref">largest_component<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/conf_model_deg.1 b/doc/conf_model_deg.1
index 3a07489..a51d3d8 100644
--- a/doc/conf_model_deg.1
+++ b/doc/conf_model_deg.1
@@ -28,7 +28,7 @@ Optional number of edge stubs that are allowed to remain unmatched\. This is use
\fBconf_model_deg\fR prints on output the edge list of the sampled graph, and reports on STDERR whether it has been able to find a graph\.
.
.SH "EXAMPLES"
-Let us assume that the file \fBpl_\-3\.0_3_500_10000\fR contains a power\-law degree sequence (\'gamma=\-3\.0\', \'k_min=3\', \'k_max=500\', \'N=10000\'), for instance created using power_law(1) \fIpower_law\.1\.html\fR\. We can sample a simple configuration model graph having that degree sequence using:
+Let us assume that the file \fBpl_\-3\.0_3_500_10000\fR contains a power\-law degree sequence (\'gamma=\-3\.0\', \'k_min=3\', \'k_max=500\', \'N=10000\'), for instance created using [power_law(1)][power_law(1)]\. We can sample a simple configuration model graph having that degree sequence using:
.
.IP "" 4
.
diff --git a/doc/conf_model_deg.1.html b/doc/conf_model_deg.1.html
index c70ebdf..54365a9 100644
--- a/doc/conf_model_deg.1.html
+++ b/doc/conf_model_deg.1.html
@@ -115,7 +115,7 @@ and reports on STDERR whether it has been able to find a graph.</p>
<p>Let us assume that the file <code>pl_-3.0_3_500_10000</code> contains a power-law
degree sequence ('gamma=-3.0', 'k_min=3', 'k_max=500', 'N=10000'), for
-instance created using <a href="power_law.1.html">power_law(1)</a>. We can sample a
+instance created using [<span class="man-ref">power_law<span class="s">(1)</span></span>][<span class="man-ref">power_law<span class="s">(1)</span></span>]. We can sample a
simple configuration model graph having that degree sequence using:</p>
<pre><code> $ conf_model_deg pl_-3.0_3_500_10000 &gt; conf_model_-3.0_3_500_10000.net
@@ -160,7 +160,7 @@ stubs will remain unmatched, meaning that the resulting graph has
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="deg_seq.1.html">deg_seq<span class="s">(1)</span></a>, <a class="man-ref" href="conf_model_deg_nocheck.1.html">conf_model_deg_nocheck<span class="s">(1)</span></a>, <a class="man-ref" href="power_law.1.html">power_law<span class="s">(1)</span></a>, <a class="man-ref" href="hv_net.1.html">hv_net<span class="s">(1)</span></a></p>
+<p><span class="man-ref">deg_seq<span class="s">(1)</span></span>, <span class="man-ref">conf_model_deg_nocheck<span class="s">(1)</span></span>, <span class="man-ref">power_law<span class="s">(1)</span></span>, <span class="man-ref">hv_net<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/conf_model_deg_nocheck.1.html b/doc/conf_model_deg_nocheck.1.html
index 5768cdb..3b3001f 100644
--- a/doc/conf_model_deg_nocheck.1.html
+++ b/doc/conf_model_deg_nocheck.1.html
@@ -122,7 +122,7 @@ always finds a multigraph:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="conf_model_deg.1.html">conf_model_deg<span class="s">(1)</span></a>, <a class="man-ref" href="power_law.1.html">power_law<span class="s">(1)</span></a>, <a class="man-ref" href="hv_net.1.html">hv_net<span class="s">(1)</span></a></p>
+<p><span class="man-ref">conf_model_deg<span class="s">(1)</span></span>, <span class="man-ref">power_law<span class="s">(1)</span></span>, <span class="man-ref">hv_net<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/deg_seq.1.html b/doc/deg_seq.1.html
index a38cd4e..5726029 100644
--- a/doc/deg_seq.1.html
+++ b/doc/deg_seq.1.html
@@ -111,7 +111,7 @@ format:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="deg_seq_w.1.html">deg_seq_w<span class="s">(1)</span></a>, <a class="man-ref" href="conf_model_deg.1.html">conf_model_deg<span class="s">(1)</span></a>, <a class="man-ref" href="fitmle.1.html">fitmle<span class="s">(1)</span></a>, <a class="man-ref" href="power_law.1.html">power_law<span class="s">(1)</span></a></p>
+<p><span class="man-ref">deg_seq_w<span class="s">(1)</span></span>, <span class="man-ref">conf_model_deg<span class="s">(1)</span></span>, <span class="man-ref">fitmle<span class="s">(1)</span></span>, <span class="man-ref">power_law<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/deg_seq_w.1.html b/doc/deg_seq_w.1.html
index fed3819..46eb69a 100644
--- a/doc/deg_seq_w.1.html
+++ b/doc/deg_seq_w.1.html
@@ -111,7 +111,7 @@
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="deg_seq.1.html">deg_seq<span class="s">(1)</span></a>, <a class="man-ref" href="conf_model_deg.1.html">conf_model_deg<span class="s">(1)</span></a>, <a class="man-ref" href="fitmle.1.html">fitmle<span class="s">(1)</span></a>, <a class="man-ref" href="power_law.1.html">power_law<span class="s">(1)</span></a></p>
+<p><span class="man-ref">deg_seq<span class="s">(1)</span></span>, <span class="man-ref">conf_model_deg<span class="s">(1)</span></span>, <span class="man-ref">fitmle<span class="s">(1)</span></span>, <span class="man-ref">power_law<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/dijkstra.1.html b/doc/dijkstra.1.html
index 966a443..f1601c9 100644
--- a/doc/dijkstra.1.html
+++ b/doc/dijkstra.1.html
@@ -126,7 +126,7 @@ network).</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="shortest.1.html">shortest<span class="s">(1)</span></a></p>
+<p><span class="man-ref">shortest<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/dms.1.html b/doc/dms.1.html
index e51aa79..2831685 100644
--- a/doc/dms.1.html
+++ b/doc/dms.1.html
@@ -144,13 +144,13 @@ graph will be:</p>
creates <var>m=3</var> new edges and the initial seed network is a ring of
<var>n0=5</var> nodes. The degree distribution of the final graph will have
exponent equal to <code>gamma = 3.0 + a/m = 3.0</code>. In this case, <code>dms</code>
-produces a Barabasi-Albert graph (see <a class="man-ref" href="ba.1.html">ba<span class="s">(1)</span></a> for details). The edge
+produces a Barabasi-Albert graph (see <span class="man-ref">ba<span class="s">(1)</span></span> for details). The edge
list of the graph is saved in the file <code>dms_10000_3_5_0.txt</code> (thanks
to the redirection operator <code>&gt;</code>).</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="ba.1.html">ba<span class="s">(1)</span></a>, <a class="man-ref" href="bb_fitness.1.html">bb_fitness<span class="s">(1)</span></a></p>
+<p><span class="man-ref">ba<span class="s">(1)</span></span>, <span class="man-ref">bb_fitness<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/er_A.1.html b/doc/er_A.1.html
index 93c9a11..57c40d9 100644
--- a/doc/er_A.1.html
+++ b/doc/er_A.1.html
@@ -124,7 +124,7 @@ file.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="er_B.1.html">er_B<span class="s">(1)</span></a>, <a class="man-ref" href="ws.1.html">ws<span class="s">(1)</span></a></p>
+<p><span class="man-ref">er_B<span class="s">(1)</span></span>, <span class="man-ref">ws<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/er_B.1.html b/doc/er_B.1.html
index 4b7a963..0917b8f 100644
--- a/doc/er_B.1.html
+++ b/doc/er_B.1.html
@@ -124,7 +124,7 @@ redirect the output of the program to a file.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="er_A.1.html">er_A<span class="s">(1)</span></a>, <a class="man-ref" href="ws.1.html">ws<span class="s">(1)</span></a></p>
+<p><span class="man-ref">er_A<span class="s">(1)</span></span>, <span class="man-ref">ws<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/f3m.1.html b/doc/f3m.1.html
index 3890394..21e6722 100644
--- a/doc/f3m.1.html
+++ b/doc/f3m.1.html
@@ -201,7 +201,7 @@ underrepresented, as made evident by value of the z-score (-3.338).</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="johnson_cycles.1.html">johnson_cycles<span class="s">(1)</span></a></p>
+<p><span class="man-ref">johnson_cycles<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/fitmle.1.html b/doc/fitmle.1.html
index 863099c..b99bc9f 100644
--- a/doc/fitmle.1.html
+++ b/doc/fitmle.1.html
@@ -186,7 +186,7 @@ and a much higher p-value:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="deg_seq.1.html">deg_seq<span class="s">(1)</span></a>, <a class="man-ref" href="power_law.1.html">power_law<span class="s">(1)</span></a></p>
+<p><span class="man-ref">deg_seq<span class="s">(1)</span></span>, <span class="man-ref">power_law<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/gn.1.html b/doc/gn.1.html
index 0b1c476..319bf3c 100644
--- a/doc/gn.1.html
+++ b/doc/gn.1.html
@@ -169,7 +169,7 @@ file <code>karate_gn_trace</code>.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="modularity.1.html">modularity<span class="s">(1)</span></a>, <a class="man-ref" href="cnm.1.html">cnm<span class="s">(1)</span></a>, <a class="man-ref" href="label_prop.1.html">label_prop<span class="s">(1)</span></a></p>
+<p><span class="man-ref">modularity<span class="s">(1)</span></span>, <span class="man-ref">cnm<span class="s">(1)</span></span>, <span class="man-ref">label_prop<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/graph_info.1.html b/doc/graph_info.1.html
index 5f41f36..5d452b4 100644
--- a/doc/graph_info.1.html
+++ b/doc/graph_info.1.html
@@ -109,7 +109,7 @@ is the average degree, and <code>avg_k2</code> is the average squared degree of
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="clust.1.html">clust<span class="s">(1)</span></a></p>
+<p><span class="man-ref">clust<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/hv_net.1.html b/doc/hv_net.1.html
index d01545c..7e6284e 100644
--- a/doc/hv_net.1.html
+++ b/doc/hv_net.1.html
@@ -131,7 +131,7 @@ the node in the sampled graph, in the format:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="conf_model_deg.1.html">conf_model_deg<span class="s">(1)</span></a>, <a class="man-ref" href="conf_model_deg_nocheck.1.html">conf_model_deg_nocheck<span class="s">(1)</span></a></p>
+<p><span class="man-ref">conf_model_deg<span class="s">(1)</span></span>, <span class="man-ref">conf_model_deg_nocheck<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/johnson_cycles.1.html b/doc/johnson_cycles.1.html
index 225f95c..4194676 100644
--- a/doc/johnson_cycles.1.html
+++ b/doc/johnson_cycles.1.html
@@ -236,7 +236,7 @@ require exponentially more time.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="f3m.1.html">f3m<span class="s">(1)</span></a>, <a class="man-ref" href="shortest.1.html">shortest<span class="s">(1)</span></a></p>
+<p><span class="man-ref">f3m<span class="s">(1)</span></span>, <span class="man-ref">shortest<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/knn.1.html b/doc/knn.1.html
index c8ea160..c85f043 100644
--- a/doc/knn.1.html
+++ b/doc/knn.1.html
@@ -212,7 +212,7 @@ knn(k) indicates the presence of assortative correlations.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="knn_w.1.html">knn_w<span class="s">(1)</span></a>, <a class="man-ref" href="deg_seq.1.html">deg_seq<span class="s">(1)</span></a></p>
+<p><span class="man-ref">knn_w<span class="s">(1)</span></span>, <span class="man-ref">deg_seq<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/knn_w.1.html b/doc/knn_w.1.html
index 7f2a11d..af4cf7a 100644
--- a/doc/knn_w.1.html
+++ b/doc/knn_w.1.html
@@ -193,7 +193,7 @@ width by running:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="knn.1.html">knn<span class="s">(1)</span></a>, <a class="man-ref" href="deg_seq.1.html">deg_seq<span class="s">(1)</span></a></p>
+<p><span class="man-ref">knn<span class="s">(1)</span></span>, <span class="man-ref">deg_seq<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/kruskal.1.html b/doc/kruskal.1.html
index c0aeece..179099c 100644
--- a/doc/kruskal.1.html
+++ b/doc/kruskal.1.html
@@ -149,7 +149,7 @@ second parameter:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="clust_w.1.html">clust_w<span class="s">(1)</span></a>, <a class="man-ref" href="dijkstra.1.html">dijkstra<span class="s">(1)</span></a>, <a class="man-ref" href="largest_component.1.html">largest_component<span class="s">(1)</span></a></p>
+<p><span class="man-ref">clust_w<span class="s">(1)</span></span>, <span class="man-ref">dijkstra<span class="s">(1)</span></span>, <span class="man-ref">largest_component<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/label_prop.1.html b/doc/label_prop.1.html
index 1e0eb28..6b6ce89 100644
--- a/doc/label_prop.1.html
+++ b/doc/label_prop.1.html
@@ -164,7 +164,7 @@ flips at each epoch in the file <code>karate_label-prop_trace</code>.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="modularity.1.html">modularity<span class="s">(1)</span></a>, <a class="man-ref" href="gn.1.html">gn<span class="s">(1)</span></a>, <a class="man-ref" href="cnm.1.html">cnm<span class="s">(1)</span></a></p>
+<p><span class="man-ref">modularity<span class="s">(1)</span></span>, <span class="man-ref">gn<span class="s">(1)</span></span>, <span class="man-ref">cnm<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/largest_component.1.html b/doc/largest_component.1.html
index 1d0af04..a8a7523 100644
--- a/doc/largest_component.1.html
+++ b/doc/largest_component.1.html
@@ -109,7 +109,7 @@ component of <var>graph_in</var>, in the format:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="components.1.html">components<span class="s">(1)</span></a>, <a class="man-ref" href="node_components.1.html">node_components<span class="s">(1)</span></a>, <a class="man-ref" href="strong_conn.1.html">strong_conn<span class="s">(1)</span></a></p>
+<p><span class="man-ref">components<span class="s">(1)</span></span>, <span class="man-ref">node_components<span class="s">(1)</span></span>, <span class="man-ref">strong_conn<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/node_components.1.html b/doc/node_components.1.html
index cdbf09b..d528de7 100644
--- a/doc/node_components.1.html
+++ b/doc/node_components.1.html
@@ -180,7 +180,7 @@ parameter. IN this case, it is better to save the output of
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="components.1.html">components<span class="s">(1)</span></a>, <a class="man-ref" href="strong_conn.1.html">strong_conn<span class="s">(1)</span></a>, <a class="man-ref" href="largest_component.1.html">largest_component<span class="s">(1)</span></a></p>
+<p><span class="man-ref">components<span class="s">(1)</span></span>, <span class="man-ref">strong_conn<span class="s">(1)</span></span>, <span class="man-ref">largest_component<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/power_law.1.html b/doc/power_law.1.html
index 7ebae1c..1fdba1e 100644
--- a/doc/power_law.1.html
+++ b/doc/power_law.1.html
@@ -187,7 +187,7 @@ with an odd sum, which thus cannot correspond to a valid degree sequence.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="deg_seq.1.html">deg_seq<span class="s">(1)</span></a>, <a class="man-ref" href="conf_model_deg.1.html">conf_model_deg<span class="s">(1)</span></a>, <a class="man-ref" href="conf_model_deg_nocheck.1.html">conf_model_deg_nocheck<span class="s">(1)</span></a></p>
+<p><span class="man-ref">deg_seq<span class="s">(1)</span></span>, <span class="man-ref">conf_model_deg<span class="s">(1)</span></span>, <span class="man-ref">conf_model_deg_nocheck<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/shortest.1.html b/doc/shortest.1.html
index df962b0..d9bedd2 100644
--- a/doc/shortest.1.html
+++ b/doc/shortest.1.html
@@ -147,7 +147,7 @@ paths will be written to the file <code>er_1000_5000.net_25_paths</code>.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="dijkstra.1.html">dijkstra<span class="s">(1)</span></a>, <a class="man-ref" href="bet_dependency.1.html">bet_dependency<span class="s">(1)</span></a>, <a class="man-ref" href="betweenness.1.html">betweenness<span class="s">(1)</span></a>, <a class="man-ref" href="shortest_avg_max_hist.1.html">shortest_avg_max_hist<span class="s">(1)</span></a></p>
+<p><span class="man-ref">dijkstra<span class="s">(1)</span></span>, <span class="man-ref">bet_dependency<span class="s">(1)</span></span>, <span class="man-ref">betweenness<span class="s">(1)</span></span>, <span class="man-ref">shortest_avg_max_hist<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/shortest_avg_max_hist.1 b/doc/shortest_avg_max_hist.1
index 8bb8653..34642b0 100644
--- a/doc/shortest_avg_max_hist.1
+++ b/doc/shortest_avg_max_hist.1
@@ -10,7 +10,7 @@
\fBshortest_avg_max_hist\fR \fIgraph_in\fR \fInode\fR
.
.SH "DESCRIPTION"
-\fBshortest_avg_max_hist\fR computes the distance (and the shortest paths) between a given node and all the other nodes of an undirected graph provided as input\. The program implements the Breadth\-First Search algorithm, and works almost exactly as shortest(1) \fIshortest\.1\.html\fR, except for the output\.
+\fBshortest_avg_max_hist\fR computes the distance (and the shortest paths) between a given node and all the other nodes of an undirected graph provided as input\. The program implements the Breadth\-First Search algorithm, and works almost exactly as [shortest(1)][], except for the output\.
.
.SH "PARAMETERS"
.
diff --git a/doc/shortest_avg_max_hist.1.html b/doc/shortest_avg_max_hist.1.html
index 8169b7c..2b94e33 100644
--- a/doc/shortest_avg_max_hist.1.html
+++ b/doc/shortest_avg_max_hist.1.html
@@ -90,7 +90,7 @@
<p><code>shortest_avg_max_hist</code> computes the distance (and the shortest paths)
between a given node and all the other nodes of an undirected graph
provided as input. The program implements the Breadth-First Search
-algorithm, and works almost exactly as <a href="shortest.1.html">shortest(1)</a>, except for the
+algorithm, and works almost exactly as [<span class="man-ref">shortest<span class="s">(1)</span></span>][], except for the
output.</p>
<h2 id="PARAMETERS">PARAMETERS</h2>
@@ -122,7 +122,7 @@ nodes in the graph (<code>3.2002</code>), the eccentricity of node <code>25</cod
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="shortest.1.html">shortest<span class="s">(1)</span></a>, <a class="man-ref" href="betweenness.1.html">betweenness<span class="s">(1)</span></a>, <a class="man-ref" href="bet_dependency.1.html">bet_dependency<span class="s">(1)</span></a></p>
+<p><span class="man-ref">shortest<span class="s">(1)</span></span>, <span class="man-ref">betweenness<span class="s">(1)</span></span>, <span class="man-ref">bet_dependency<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/strong_conn.1.html b/doc/strong_conn.1.html
index 4b4e0af..f76a467 100644
--- a/doc/strong_conn.1.html
+++ b/doc/strong_conn.1.html
@@ -169,7 +169,7 @@ using:</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="components.1.html">components<span class="s">(1)</span></a>, <a class="man-ref" href="node_components.1.html">node_components<span class="s">(1)</span></a>, <a class="man-ref" href="largest_component.1.html">largest_component<span class="s">(1)</span></a></p>
+<p><span class="man-ref">components<span class="s">(1)</span></span>, <span class="man-ref">node_components<span class="s">(1)</span></span>, <span class="man-ref">largest_component<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>
diff --git a/doc/ws.1.html b/doc/ws.1.html
index c3ff511..3a71d5b 100644
--- a/doc/ws.1.html
+++ b/doc/ws.1.html
@@ -145,7 +145,7 @@ edges, since <code>SHOW</code> was specified as a fourth parameter.</p>
<h2 id="SEE-ALSO">SEE ALSO</h2>
-<p><a class="man-ref" href="er_A.1.html">er_A<span class="s">(1)</span></a>, <a class="man-ref" href="er_B.1.html">er_B<span class="s">(1)</span></a></p>
+<p><span class="man-ref">er_A<span class="s">(1)</span></span>, <span class="man-ref">er_B<span class="s">(1)</span></span></p>
<h2 id="REFERENCES">REFERENCES</h2>