History of mag_geology_coauthor

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/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index ada5659..237215d 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__init__.py
@@ -34,7 +34,7 @@ The networks have the following properties:
 tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Weighted', 'Projection', 'Multigraph']
 url = 'http://www.cs.cornell.edu/~arb/data/coauth-MAG-Geology/index.html'
 citation = [('A. R. Benson et al., "Simplicial Closure and Higher-order Link Prediction." Preprint, arXiv:1802.06916 (2018)', 'https://arxiv.org/abs/1802.06916')]
-icon_hash = '5b7ed190dfd5c2fc3b0978d5'
+date_added = '2020-08-11'
 upstream_license = None
 upstream_prefix = 'gdrive://'
 files = [(('14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-nverts.txt',

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/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index 1e823e1..ada5659 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__init__.py
@@ -28,9 +28,9 @@ There are four versions of the data:
 
 The networks have the following properties:
 
-- `label`: the name of the author (empty for publication nodes).
-- `is_simplex`: whether the node is a publication (otherwise it is an author; bipartite versions only).
-- `time`: the year of publication of the corresponding paper."""
+- (Node) `label`: the name of the author (empty for publication nodes).
+- (Node) `is_simplex`: whether the node is a publication (otherwise it is an author; bipartite versions only).
+- (Edge) `time`: the year of publication of the corresponding paper."""
 tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Weighted', 'Projection', 'Multigraph']
 url = 'http://www.cs.cornell.edu/~arb/data/coauth-MAG-Geology/index.html'
 citation = [('A. R. Benson et al., "Simplicial Closure and Higher-order Link Prediction." Preprint, arXiv:1802.06916 (2018)', 'https://arxiv.org/abs/1802.06916')]

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/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index 582c15d..1e823e1 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__init__.py
@@ -62,7 +62,6 @@ def fetch_upstream(force=False):
 @coerce_props()
 @annotate()
 def parse(alts=None):
-    global files
     name = __name__.split(".")[-1]
     for fnames, alt, fmt in files:
         if alts is not None and alt not in alts:

2026-10-25 [entries] Fix parse bugs and improve descriptions and metadata by Tiago de Paula Peixoto 6bb6851

- parse fixes from the review of the descriptions, e.g. us_patents
  (directed), celegans_2019 (synapse direction), ecoli_transcription and
  yeast_transcription (regulator to target), bitcoin (direction, phantom
  node), ego_social (Google+ features and circles), scotus_majority,
  arxiv_authors and social_location (as in SNAP), caida_as, dnc, dom,
  mist, reuters and bibsonomy (names on the right nodes), uci_zoo
- every description now states explicitly what the nodes and edges
  represent; corrected titles, years, tags, citations and licences
- the "Hypergraph" tag is removed; very large entries are marked
  `huge = True` (see --skip-huge)
- ICON ids of partial duplicates added (hiv_transmission, congress_bills,
  openflights, dutch_school)

diff --git a/entries/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index 3f874c7..582c15d 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__init__.py
@@ -31,7 +31,7 @@ The networks have the following properties:
 - `label`: the name of the author (empty for publication nodes).
 - `is_simplex`: whether the node is a publication (otherwise it is an author; bipartite versions only).
 - `time`: the year of publication of the corresponding paper."""
-tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Hypergraph', 'Weighted', 'Projection', 'Multigraph']
+tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Weighted', 'Projection', 'Multigraph']
 url = 'http://www.cs.cornell.edu/~arb/data/coauth-MAG-Geology/index.html'
 citation = [('A. R. Benson et al., "Simplicial Closure and Higher-order Link Prediction." Preprint, arXiv:1802.06916 (2018)', 'https://arxiv.org/abs/1802.06916')]
 icon_hash = '5b7ed190dfd5c2fc3b0978d5'

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/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index f18e20c..3f874c7 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__init__.py
@@ -19,13 +19,23 @@
 from .. import *
 
 title = "MAG Geology coauthor simplices (2017)"
-description = """A hypergraph representing collaborations among authors listed in the Microsoft Academic Graph (MAG), derived from papers with the \"Geology\" tag as of 3 Sept. 2017. Each node represents an author, and each publication is represented by a simplex (a set of nodes, i.e., a hyperedge), timestamped by the year of publication. Simplices are restricted to at most 25 authors. In addition to the hypergraph, a weighted projection of the same network is available.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
-tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Hypergraph', 'Weighted', 'Projection']
+description = """Coauthorship networks of publications in the field of Geology, assembled by A. R. Benson and collaborators from the Microsoft Academic Graph (MAG), as distributed in the Open Academic Graph. Each publication whose fields of study include the tag "Geology" is a set of authors (a simplex, or hyperedge), timestamped by its year of publication (from 1800 to 2018).
+
+There are four versions of the data:
+
+- `max-25-bip`, `full-bip`: bipartite networks where each publication is a node connected to its authors. The `max-25` versions include only publications with at most 25 authors, while the `full` versions include all publications.
+- `max-25-proj`, `full-proj`: one-mode projections onto the authors, where every pair of coauthors of a publication is connected by an edge. Each publication contributes its own edges, so a pair of authors who wrote $k$ publications together is connected by $k$ parallel edges, each with the year of its publication.
+
+The networks have the following properties:
+
+- `label`: the name of the author (empty for publication nodes).
+- `is_simplex`: whether the node is a publication (otherwise it is an author; bipartite versions only).
+- `time`: the year of publication of the corresponding paper."""
+tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Hypergraph', 'Weighted', 'Projection', 'Multigraph']
 url = 'http://www.cs.cornell.edu/~arb/data/coauth-MAG-Geology/index.html'
 citation = [('A. R. Benson et al., "Simplicial Closure and Higher-order Link Prediction." Preprint, arXiv:1802.06916 (2018)', 'https://arxiv.org/abs/1802.06916')]
 icon_hash = '5b7ed190dfd5c2fc3b0978d5'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'gdrive://'
 files = [(('14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-nverts.txt',
            '14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-times.txt',

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

diff --git a/entries/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index 153379c..f18e20c 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__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/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index 985705a..153379c 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__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/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index dc8799d..985705a 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__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/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index acc692b..dc8799d 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__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

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

diff --git a/entries/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index 63471a0..acc692b 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__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 *

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

diff --git a/entries/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
index d9c3e1e..63471a0 100644
--- a/entries/mag_geology_coauthor/__init__.py
+++ b/entries/mag_geology_coauthor/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "MAG Geology coauthor simplices (2017)"
-description = "A hypergraph representing collaborations among authors listed in the Microsoft Academic Graph (MAG), derived from papers with the \"Geology\" tag as of 3 Sept. 2017. Each node represents an author, and each publication is represented by a simplex (a set of nodes, i.e., a hyperedge), timestamped by the year of publication. Simplices are restricted to at most 25 authors. In addition to the hypergraph, a weighted projection of the same network is available."
+description = """A hypergraph representing collaborations among authors listed in the Microsoft Academic Graph (MAG), derived from papers with the \"Geology\" tag as of 3 Sept. 2017. Each node represents an author, and each publication is represented by a simplex (a set of nodes, i.e., a hyperedge), timestamped by the year of publication. Simplices are restricted to at most 25 authors. In addition to the hypergraph, a weighted projection of the same network is available.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Hypergraph', 'Weighted', 'Projection']
 url = 'http://www.cs.cornell.edu/~arb/data/coauth-MAG-Geology/index.html'
 citation = [('A. R. Benson et al., "Simplicial Closure and Higher-order Link Prediction." Preprint, arXiv:1802.06916 (2018)', 'https://arxiv.org/abs/1802.06916')]

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

diff --git a/entries/mag_geology_coauthor/__init__.py b/entries/mag_geology_coauthor/__init__.py
new file mode 100644
index 0000000..d9c3e1e
--- /dev/null
+++ b/entries/mag_geology_coauthor/__init__.py
@@ -0,0 +1,98 @@
+#! /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 *
+
+title = "MAG Geology coauthor simplices (2017)"
+description = "A hypergraph representing collaborations among authors listed in the Microsoft Academic Graph (MAG), derived from papers with the \"Geology\" tag as of 3 Sept. 2017. Each node represents an author, and each publication is represented by a simplex (a set of nodes, i.e., a hyperedge), timestamped by the year of publication. Simplices are restricted to at most 25 authors. In addition to the hypergraph, a weighted projection of the same network is available."
+tags = ['Social', 'Collaboration', 'Unweighted', 'Timestamps', 'Hypergraph', 'Weighted', 'Projection']
+url = 'http://www.cs.cornell.edu/~arb/data/coauth-MAG-Geology/index.html'
+citation = [('A. R. Benson et al., "Simplicial Closure and Higher-order Link Prediction." Preprint, arXiv:1802.06916 (2018)', 'https://arxiv.org/abs/1802.06916')]
+icon_hash = '5b7ed190dfd5c2fc3b0978d5'
+ustream_license = None
+upstream_prefix = 'gdrive://'
+files = [(('14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-nverts.txt',
+           '14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-times.txt',
+           '14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-simplices.txt',
+           '14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-node-labels.txt'), 'max-25-bip', None),
+         (('14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-nverts.txt',
+           '14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-times.txt',
+           '14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-simplices.txt',
+           '14MOWsEJyNGiFKumvmgMcU1CqekDBayYV:tar.gz:coauth-MAG-Geology/coauth-MAG-Geology-node-labels.txt'), 'max-25-proj', None),
+         (('1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-nverts.txt',
+           '1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-times.txt',
+           '1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-simplices.txt',
+           '1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-node-labels.txt'), 'full-bip', None),
+         (('1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-nverts.txt',
+           '1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-times.txt',
+           '1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-simplices.txt',
+           '1bk5uTnuijgHEAOi5sA-sM8Cxyg3Ejr43:tar.gz:coauth-MAG-Geology-full/coauth-MAG-Geology-full-node-labels.txt'), 'full-proj', None)]
+
+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 fnames, alt, fmt in files:
+        if alts is not None and alt not in alts:
+            continue
+        if isinstance(fnames, str):
+            fnames = [fnames]
+        with ExitStack() as stack:
+            fs = [stack.enter_context(open_upstream_file(name, fn, "r")) for fn in fnames]
+            g = Graph(directed=False)
+
+            g.vp.label = label = g.new_vp("string")
+            g.ep.time = time = g.new_ep("int64_t")
+            names = [" ".join(s.split()[1:]) for s in fs[3]]
+
+            bip = "bip" in alt
+            if bip:
+                g.vp.is_simplex = is_simplex = g.new_vp("bool")
+                n_simplex = 0
+
+            for n_simplex, line in enumerate(fs[0]):
+                pass
+            n_simplex += 1
+            fs[0].seek(0)
+            for s, (n, t) in enumerate(zip(fs[0], fs[1])):
+                n = int(n)
+                t = int(t)
+                vs = []
+                for i in range(n):
+                    vs.append(int(next(fs[2]))-1)
+                if bip:
+                    for v in vs:
+                        e = g.add_edge(s, v + n_simplex, add_missing=True)
+                        time[e] = t
+                        label[v + n_simplex] = names[v]
+                    is_simplex[s] = True
+                else:
+                    for u in vs:
+                        for v in vs:
+                            if v <= u:
+                                continue
+                            e = g.add_edge(u, v, add_missing=True)
+                            time[e] = t
+                        label[u] = names[u]
+        yield alt, g