History of macaque_neural

The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.

2026-11-03 [entries] Add the date when each entry was added, and remove icon_hash by Tiago de Paula Peixoto beff7c9

The dates are those of the commits that first added the entries' files
(2020-08-11 for the entries of the initial commit); renamed entries keep
the date of their first name.

Changed: none

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 06c4d44..0432148 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -37,7 +37,7 @@ url = 'https://sites.google.com/site/bctnet/datasets'
 citation = [('M. P. Young, "The organization of neural systems in the primate cerebral cortex", Proc. R. Soc. Lond. B 252, 13-18 (1993)', 'https://doi.org/10.1098/rspb.1993.0040'),
             ('C. J. Honey, R. Kötter, M. Breakspear, O. Sporns, "Network structure of cerebral cortex shapes functional connectivity on multiple time scales", Proc. Natl. Acad. Sci. USA 104, 10240-10245 (2007)', 'https://doi.org/10.1073/pnas.0701519104'),
             ('R. Kötter, "Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database", Neuroinformatics 2, 127-144 (2004)', 'https://doi.org/10.1385/NI:2:2:127')]
-icon_hash = ['56a85c8e26855e083a2f7929', '56a85c8e26855e083a2f7922']
+date_added = '2020-08-11'
 upstream_prefix = 'https://web.archive.org/web/2020id_/https://sites.google.com/site/bctnet/Home/functions'
 files = [('macaque47.mat', 'cocomac47', 'matlab'),
          ('macaque71.mat', 'young71', 'matlab')]

2026-11-03 [entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) by Tiago de Paula Peixoto bc3dbbd

The lists of properties at the end of the descriptions marked edge
properties with "Edge" but left node properties unmarked, or grouped
them in "Nodes: `a`, ...; `b`, ..." items, so the kind of a property
was often unclear. Every item now starts with (Node), (Edge) or (Graph),
followed by the property names, a colon and the explanation, one item
per property or group of properties; qualifications (kinds of nodes,
networks) follow the names in parentheses. Properties that were only
named got a short explanation, and a few items that named the wrong
kind of property were corrected.

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 7989916..06c4d44 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -31,7 +31,7 @@ Both networks are directed and unweighted: an edge $i\to j$ indicates a projecti
 
 The networks have the following properties:
 
-- `name`: the name of the cortical area (with the padding spaces of the source files removed)."""
+- (Node) `name`: the name of the cortical area (with the padding spaces of the source files removed)."""
 tags = ['Biological', 'Connectome', 'Unweighted']
 url = 'https://sites.google.com/site/bctnet/datasets'
 citation = [('M. P. Young, "The organization of neural systems in the primate cerebral cortex", Proc. R. Soc. Lond. B 252, 13-18 (1993)', 'https://doi.org/10.1098/rspb.1993.0040'),

2026-11-02 [entries] Remove unneeded code from the entries by Tiago de Paula Peixoto 2c69f19

Unneeded "global files" statements, unused imports and variables,
f-strings without placeholders, duplicate keys in foodweb_little_rock
(keeping the order and the values used), and the second definition of
get_lines() in twitter_higgs. Nothing changes in the networks or
descriptions.

Changed: none

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index a51faab..7989916 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -59,7 +59,6 @@ def fetch_upstream(force=False):
 @coerce_props()
 @annotate()
 def parse(alts=None):
-    global files
     name = __name__.split(".")[-1]
     for fname, alt, fmt in files:
         if alts is not None and alt not in alts:

2026-10-25 [entries] Merge duplicate entries and add cross-references between related ones by Tiago de Paula Peixoto 9bc6033

- Removed duplicates, merged into the entries holding the same data:
  dblp_coauthor_snap (soc_net_comms), cattle and bison (dom; bison's
  breeding data move there, as do the wolves' age and sex),
  football_tsevans (football, with both conference assignments),
  eu_procurements_alt (eu_procurements), foursquare_friendships
  (foursquare_global).
- software_dependencies: colt and scolt are one network; ambassador: the
  duplicate 2001 network is dropped and the three same-edge networks
  combined; dom: the dataset count corrected (436).
- macaque_neural: Young's 71-area network added (young71; the 47-area one
  is now cocomac47), both from archived copies.
- collins_yeast, celegans_interactomes: from archived copies of the dead
  CCSB site (byte-identical files).
- Cross-references between entries holding versions of the same data
  (food webs, Wikipedia, Slashdot, physicians, SNAP/Mislove, CCSB).
- ICON ids of duplicate records added; macaque_neural's corrected.
- prosper, dbpedia_all: string properties given in edge-index order (needs
  graph-tool with the fixed vals ordering).

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 9308264..a51faab 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -19,25 +19,41 @@
 from .. import *
 from scipy.io import loadmat
 
-title = "Macaque cortical connectivity (CoCoMac, 47 areas)"
-description = r"""Network of anatomical connections among 47 areas of the visual, somatosensory and motor cortex of the macaque monkey. Nodes are cortical areas, defined according to the parcellation of Felleman and Van Essen (as in "V1", "MT", "FEF" or "46"), and edges are axonal pathways between them, as identified by anatomical tract-tracing studies. The 47-area matrix (not to be confused with Young's 71-area data set) was obtained from the Brain Connectivity Toolbox; it was contributed by R. Kötter and used by C. J. Honey, R. Kötter, M. Breakspear and O. Sporns (PNAS 104, 10240-10245, 2007). There, the results of published tracing studies were manually collated in the CoCoMac database, mapped onto the Felleman–Van Essen parcellation, and redundant and inconsistent reports were resolved to obtain a binary connection matrix with 505 connections.
+title = "Macaque cortical connectivity (Young 1993; CoCoMac 2007)"
+description = r"""Two networks of anatomical connections among areas of the cerebral cortex of the macaque monkey, compiled from published axonal tract-tracing studies, and distributed with the Brain Connectivity Toolbox (BCT). In both, nodes are cortical areas and edges are axonal pathways (projections) between them.
 
-The network is directed: an edge $i\to j$ indicates a projection from area $i$ to area $j$ (an entry $a_{ij}=1$ of the source matrix, following the Brain Connectivity Toolbox convention); 192 pairs of areas are reciprocally connected.
+- `young71`: the 71-area network of M. P. Young (Proc. R. Soc. B 252, 13-18, 1993), who collated the tract-tracing literature into a connection matrix covering visual, somatosensory, auditory, motor, prefrontal and limbic (cingulate, insular, parahippocampal) areas. The BCT matrix contains 746 connections, with 308 reciprocally connected pairs of areas. Area names follow the source file, with numbered (Brodmann-type) areas prefixed by "A" (e.g. "A46" is area 46, "A7a" is area 7a), together with visual areas such as "V1", "MT" or "PITd" and auditory and temporal areas such as "KA", "PAAR" or "TS1".
+- `cocomac47`: 47 areas of the visual, somatosensory and motor cortex, defined according to the parcellation of Felleman and Van Essen (as in "V1", "MT", "FEF" or "46"). This matrix was contributed by R. Kötter and used by C. J. Honey, R. Kötter, M. Breakspear and O. Sporns (PNAS 104, 10240-10245, 2007). There, the results of published tracing studies were manually collated in the CoCoMac database, mapped onto the Felleman–Van Essen parcellation, and redundant and inconsistent reports were resolved to obtain a binary connection matrix with 505 connections; 192 pairs of areas are reciprocally connected.
 
-The network has the following properties:
+The two networks are independent compilations of the tracing literature using different parcellations, so the 47-area network is not a subnetwork of the 71-area one (several areas, such as "MDP", "MIP" or "36", appear only in the former, while the auditory, prefrontal and limbic areas appear only in the latter); nodes with the same name in both refer to the same anatomical area only approximately.
 
-- `name`: the name of the cortical area (padded with trailing spaces in the source file)."""
+Both networks are directed and unweighted: an edge $i\to j$ indicates a projection from area $i$ to area $j$ (an entry $a_{ij}=1$ of the binary source matrix, following the BCT convention); absent entries mean that no connection was reported. There are no self-loops.
+
+The networks have the following properties:
+
+- `name`: the name of the cortical area (with the padding spaces of the source files removed)."""
 tags = ['Biological', 'Connectome', 'Unweighted']
 url = 'https://sites.google.com/site/bctnet/datasets'
-citation = [('C. J. Honey, R. Kötter, M. Breakspear, O. Sporns, "Network structure of cerebral cortex shapes functional connectivity on multiple time scales", Proc. Natl. Acad. Sci. USA 104, 10240-10245 (2007)', 'https://doi.org/10.1073/pnas.0701519104'),
+citation = [('M. P. Young, "The organization of neural systems in the primate cerebral cortex", Proc. R. Soc. Lond. B 252, 13-18 (1993)', 'https://doi.org/10.1098/rspb.1993.0040'),
+            ('C. J. Honey, R. Kötter, M. Breakspear, O. Sporns, "Network structure of cerebral cortex shapes functional connectivity on multiple time scales", Proc. Natl. Acad. Sci. USA 104, 10240-10245 (2007)', 'https://doi.org/10.1073/pnas.0701519104'),
             ('R. Kötter, "Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database", Neuroinformatics 2, 127-144 (2004)', 'https://doi.org/10.1385/NI:2:2:127')]
-icon_hash = '56a85c8e26855e083a2f7922'
-upstream_prefix = 'https://sites.google.com/site/bctnet/Home/functions'
-files = [('macaque47.mat', None, 'matlab')]
+icon_hash = ['56a85c8e26855e083a2f7929', '56a85c8e26855e083a2f7922']
+upstream_prefix = 'https://web.archive.org/web/2020id_/https://sites.google.com/site/bctnet/Home/functions'
+files = [('macaque47.mat', 'cocomac47', 'matlab'),
+         ('macaque71.mat', 'young71', 'matlab')]
+# The files are no longer available from the Brain Connectivity Toolbox site
+# (its file attachments were lost when the site was migrated); they are
+# obtained from the Internet Archive.
+archived_urls = {
+    'macaque47.mat':
+    'https://web.archive.org/web/20201022115225id_/https://sites.google.com/site/bctnet/Home/functions/macaque47.mat?attredirects=0&d=1',
+    'macaque71.mat':
+    'https://web.archive.org/web/20201022115225id_/https://sites.google.com/site/bctnet/Home/functions/macaque71.mat?attredirects=0&d=1'}
 
 def fetch_upstream(force=False):
-    return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
-                                force)
+    # The Internet Archive URLs carry a query string, so the files are
+    # fetched from them directly.
+    return fetch_archived_files(__name__.split(".")[-1], archived_urls, force)
 
 @cache_network()
 @coerce_props()
@@ -58,5 +74,5 @@ def parse(alts=None):
                         g.add_edge(i, j)
             g.vp.name = g.new_vp("string")
             for i, n in enumerate(m["Names"]):
-                g.vp.name[i] = n
+                g.vp.name[i] = n.strip()
         yield alt, g

2026-10-25 [pipeline] Fix KONECT entity files, seekable upstream files and archive formats by Tiago de Paula Peixoto 2f6e19f

- konect.py: each ent.<net>.<entity>.<attr> file becomes a vertex
  property on the side of the entity it describes (per-vertex or per-edge
  files), instead of all of them being written from vertex 0 into `meta`
  (which put e.g. the item names of bibsonomy and reuters on the wrong
  nodes); only leading "%" lines are comments.
- open_upstream_file(..., seekable=True) returns a seekable file (via a
  temporary file) for readers that need one (openpyxl, scipy.io.loadmat,
  zipfile), replacing the per-entry BytesIO copies.
- .xz files can be read again; .xz, .rar and .7z downloads are stored as
  they are, and "x.tar.xz:", "x.rar:" and "x.7z:" member access works
  (with py7zr or the 7z command); caches in the previous layouts are still
  read.
- parsers.py: vprops_from_txt matches rows by name for graphs keyed by
  name; the Wikimedia dump readers (stub histories, SQL tables) are shared
  helpers; new read_doc (tables of Word documents via LibreOffice) and
  read_epanet (EPANET water network files) readers.
- The entries' workarounds are removed (all parse identically).

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 2c2b61f..9308264 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -17,11 +17,10 @@
 # with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 from .. import *
-import io
 from scipy.io import loadmat
 
 title = "Macaque cortical connectivity (CoCoMac, 47 areas)"
-description = """Network of anatomical connections among 47 areas of the visual, somatosensory and motor cortex of the macaque monkey. Nodes are cortical areas, defined according to the parcellation of Felleman and Van Essen (as in "V1", "MT", "FEF" or "46"), and edges are axonal pathways between them, as identified by anatomical tract-tracing studies. The 47-area matrix (not to be confused with Young's 71-area data set) was obtained from the Brain Connectivity Toolbox; it was contributed by R. Kötter and used by C. J. Honey, R. Kötter, M. Breakspear and O. Sporns (PNAS 104, 10240-10245, 2007). There, the results of published tracing studies were manually collated in the CoCoMac database, mapped onto the Felleman–Van Essen parcellation, and redundant and inconsistent reports were resolved to obtain a binary connection matrix with 505 connections.
+description = r"""Network of anatomical connections among 47 areas of the visual, somatosensory and motor cortex of the macaque monkey. Nodes are cortical areas, defined according to the parcellation of Felleman and Van Essen (as in "V1", "MT", "FEF" or "46"), and edges are axonal pathways between them, as identified by anatomical tract-tracing studies. The 47-area matrix (not to be confused with Young's 71-area data set) was obtained from the Brain Connectivity Toolbox; it was contributed by R. Kötter and used by C. J. Honey, R. Kötter, M. Breakspear and O. Sporns (PNAS 104, 10240-10245, 2007). There, the results of published tracing studies were manually collated in the CoCoMac database, mapped onto the Felleman–Van Essen parcellation, and redundant and inconsistent reports were resolved to obtain a binary connection matrix with 505 connections.
 
 The network is directed: an edge $i\to j$ indicates a projection from area $i$ to area $j$ (an entry $a_{ij}=1$ of the source matrix, following the Brain Connectivity Toolbox convention); 192 pairs of areas are reciprocally connected.
 
@@ -49,8 +48,8 @@ def parse(alts=None):
     for fname, alt, fmt in files:
         if alts is not None and alt not in alts:
             continue
-        with open_upstream_file(name, fname, "rb") as f:
-            m = loadmat(io.BytesIO(f.read()))
+        with open_upstream_file(name, fname, "rb", seekable=True) as f:
+            m = loadmat(f)
             g = Graph(directed=True)
             a = m["CIJ"]
             for i in range(a.shape[0]):

2026-10-25 [entries] Fix parse bugs and improve the metadata of existing entries by Tiago de Paula Peixoto c996a0e

From a review of the dataset descriptions against the upstream sources
and papers, and from user reports:

- parse fixes (wrong edge direction or directedness, shifted or
  misnamed properties, merged node identities, duplicated or missing
  edges and nodes, wrong types), e.g. arxiv_citation (the HepTh dates
  were a copy of the HepPh ones; now from the KDD Cup 2003 data),
  eu_procurements, foursquare_global, hiv_transmission, genetic_multiplex,
  gnutella (adds the 05 snapshot), roadnet, macaque_neural, python_dependency
- descriptions rewritten from the upstream sources, documenting every
  property
- corrected titles, citations and DOIs, licences (ustream_license typo,
  the data's own terms), tags and ICON ids
- url lists for entries with several sources or dataset pages
- SocioPatterns entries moved to the site's new data location, with the
  daily networks of sp_infectious and sp_primary_school
- the Michael Fire entries marked as orphans (served from the mirror)
- redundant type forcings removed after the graph-tool coercion fixes

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 160b99c..2c2b61f 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -17,14 +17,21 @@
 # with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 from .. import *
+import io
 from scipy.io import loadmat
 
-title = "Macaque cortical connectivity (Young)"
-description = """A network of cortical regions in the Macaque cortex[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+title = "Macaque cortical connectivity (CoCoMac, 47 areas)"
+description = """Network of anatomical connections among 47 areas of the visual, somatosensory and motor cortex of the macaque monkey. Nodes are cortical areas, defined according to the parcellation of Felleman and Van Essen (as in "V1", "MT", "FEF" or "46"), and edges are axonal pathways between them, as identified by anatomical tract-tracing studies. The 47-area matrix (not to be confused with Young's 71-area data set) was obtained from the Brain Connectivity Toolbox; it was contributed by R. Kötter and used by C. J. Honey, R. Kötter, M. Breakspear and O. Sporns (PNAS 104, 10240-10245, 2007). There, the results of published tracing studies were manually collated in the CoCoMac database, mapped onto the Felleman–Van Essen parcellation, and redundant and inconsistent reports were resolved to obtain a binary connection matrix with 505 connections.
+
+The network is directed: an edge $i\to j$ indicates a projection from area $i$ to area $j$ (an entry $a_{ij}=1$ of the source matrix, following the Brain Connectivity Toolbox convention); 192 pairs of areas are reciprocally connected.
+
+The network has the following properties:
+
+- `name`: the name of the cortical area (padded with trailing spaces in the source file)."""
 tags = ['Biological', 'Connectome', 'Unweighted']
 url = 'https://sites.google.com/site/bctnet/datasets'
-citation = [('M.P. Young, "The organization of neural systems in the primate cerebral cortex." Proc. R. Soc. London B 252,13-18 (1993)', 'https://doi.org/10.1098/rspb.1993.0040')]
+citation = [('C. J. Honey, R. Kötter, M. Breakspear, O. Sporns, "Network structure of cerebral cortex shapes functional connectivity on multiple time scales", Proc. Natl. Acad. Sci. USA 104, 10240-10245 (2007)', 'https://doi.org/10.1073/pnas.0701519104'),
+            ('R. Kötter, "Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database", Neuroinformatics 2, 127-144 (2004)', 'https://doi.org/10.1385/NI:2:2:127')]
 icon_hash = '56a85c8e26855e083a2f7922'
 upstream_prefix = 'https://sites.google.com/site/bctnet/Home/functions'
 files = [('macaque47.mat', None, 'matlab')]
@@ -43,8 +50,8 @@ def parse(alts=None):
         if alts is not None and alt not in alts:
             continue
         with open_upstream_file(name, fname, "rb") as f:
-            m = loadmat(f)
-            g = Graph(directed=False)
+            m = loadmat(io.BytesIO(f.read()))
+            g = Graph(directed=True)
             a = m["CIJ"]
             for i in range(a.shape[0]):
                 for j in range(a.shape[1]):

2026-10-24 Update copyright information by Tiago de Paula Peixoto 73a4f0d

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 8f14bee..160b99c 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2026 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2024-05-27 Update copyright information by Tiago de Paula Peixoto 3d288ea

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 89fa2ed..8f14bee 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2024 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2023-02-19 Update copyright information by Tiago de Paula Peixoto 8d005ae

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 4884b54..89fa2ed 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2020-2023 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2021-06-22 Update copyright info by Tiago de Paula Peixoto db2efcc

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index ecbb138..4884b54 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -1,7 +1,7 @@
 #! /usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+# Copyright (C) 2021 Tiago de Paula Peixoto <tiago@skewed.de>
 #
 # This program is free software: you can redistribute it and/or modify it under
 # the terms of the GNU Affero General Public License as published by the Free

2020-11-28 Update citations to use DOIs by Tiago de Paula Peixoto e878874

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 936e482..ecbb138 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -24,7 +24,7 @@ description = """A network of cortical regions in the Macaque cortex[^icon]
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Connectome', 'Unweighted']
 url = 'https://sites.google.com/site/bctnet/datasets'
-citation = [('M.P. Young, "The organization of neural systems in the primate cerebral cortex." Proc. R. Soc. London B 252,13-18 (1993)', 'http://www.jstor.org/stable/49912')]
+citation = [('M.P. Young, "The organization of neural systems in the primate cerebral cortex." Proc. R. Soc. London B 252,13-18 (1993)', 'https://doi.org/10.1098/rspb.1993.0040')]
 icon_hash = '56a85c8e26855e083a2f7922'
 upstream_prefix = 'https://sites.google.com/site/bctnet/Home/functions'
 files = [('macaque47.mat', None, 'matlab')]

2020-09-15 Change license from GPLv3 to AGPLv3 by Tiago de Paula Peixoto d754be5

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 9e50253..936e482 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -3,18 +3,18 @@
 #
 # Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
 #
-# 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 free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero 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.
+# 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 Affero 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/>.
+# You should have received a copy of the GNU Affero General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 from .. import *
 from scipy.io import loadmat

2020-09-13 Add explicit attribution to descriptions obtained from ICON by Tiago de Paula Peixoto 1645314

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
index 68c315a..9e50253 100644
--- a/entries/macaque_neural/__init__.py
+++ b/entries/macaque_neural/__init__.py
@@ -20,7 +20,8 @@ from .. import *
 from scipy.io import loadmat
 
 title = "Macaque cortical connectivity (Young)"
-description = "A network of cortical regions in the Macaque cortex"
+description = """A network of cortical regions in the Macaque cortex[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Connectome', 'Unweighted']
 url = 'https://sites.google.com/site/bctnet/datasets'
 citation = [('M.P. Young, "The organization of neural systems in the primate cerebral cortex." Proc. R. Soc. London B 252,13-18 (1993)', 'http://www.jstor.org/stable/49912')]

2020-08-11 Initial commit by Tiago de Paula Peixoto cc85872

diff --git a/entries/macaque_neural/__init__.py b/entries/macaque_neural/__init__.py
new file mode 100644
index 0000000..68c315a
--- /dev/null
+++ b/entries/macaque_neural/__init__.py
@@ -0,0 +1,55 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+#
+# 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/>.
+
+from .. import *
+from scipy.io import loadmat
+
+title = "Macaque cortical connectivity (Young)"
+description = "A network of cortical regions in the Macaque cortex"
+tags = ['Biological', 'Connectome', 'Unweighted']
+url = 'https://sites.google.com/site/bctnet/datasets'
+citation = [('M.P. Young, "The organization of neural systems in the primate cerebral cortex." Proc. R. Soc. London B 252,13-18 (1993)', 'http://www.jstor.org/stable/49912')]
+icon_hash = '56a85c8e26855e083a2f7922'
+upstream_prefix = 'https://sites.google.com/site/bctnet/Home/functions'
+files = [('macaque47.mat', None, 'matlab')]
+
+def fetch_upstream(force=False):
+    return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+                                force)
+
+@cache_network()
+@coerce_props()
+@annotate()
+def parse(alts=None):
+    global files
+    name = __name__.split(".")[-1]
+    for fname, alt, fmt in files:
+        if alts is not None and alt not in alts:
+            continue
+        with open_upstream_file(name, fname, "rb") as f:
+            m = loadmat(f)
+            g = Graph(directed=False)
+            a = m["CIJ"]
+            for i in range(a.shape[0]):
+                for j in range(a.shape[1]):
+                    if a[i,j] > 0:
+                        g.add_edge(i, j)
+            g.vp.name = g.new_vp("string")
+            for i, n in enumerate(m["Names"]):
+                g.vp.name[i] = n
+        yield alt, g