History of arxiv_collab

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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index d7e4c49..9611499 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__init__.py
@@ -30,7 +30,7 @@ The networks have the following properties:
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
 url = 'http://www-personal.umich.edu/~mejn/netdata/'
 citation = [('M. E. J. Newman, "The structure of scientific collaboration networks." Proc. Natl. Acad. Sci. USA 98(2), 404-409 (2001). arxiv:cond-mat/0007214', 'https://doi.org/10.1073/pnas.98.2.404')]
-icon_hash = '56a85c8e26855e083a2f78a8'
+date_added = '2020-08-11'
 upstream_license = None
 upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata/'
 files = [("cond-mat.zip:cond-mat.gml", "cond-mat-1999", "gml"),

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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index 6713772..d7e4c49 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__init__.py
@@ -25,8 +25,8 @@ Edge weights account for the fact that authors of papers with many co-authors kn
 
 The networks have the following properties:
 
-- Nodes: `label`, the author's name ("SURNAME, INITIALS").
-- Edges: `value`, the collaboration weight $w_{ij}$ described above."""
+- (Node) `label`: the author's name ("SURNAME, INITIALS").
+- (Edge) `value`: the collaboration weight $w_{ij}$ described above."""
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
 url = 'http://www-personal.umich.edu/~mejn/netdata/'
 citation = [('M. E. J. Newman, "The structure of scientific collaboration networks." Proc. Natl. Acad. Sci. USA 98(2), 404-409 (2001). arxiv:cond-mat/0007214', 'https://doi.org/10.1073/pnas.98.2.404')]

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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index a649a81..6713772 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__init__.py
@@ -47,7 +47,6 @@ 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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index b567d57..a649a81 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__init__.py
@@ -19,13 +19,19 @@
 from .. import *
 
 title = "Scientific collaborations in physics (1995-2005)"
-description = """Collaboration graphs for scientists, extracted from the Los Alamos e-Print arXiv (physics), for 1995-1999 for three categories, and additionally for 1995-2003 and 1995-2005 for one category. For copyright reasons, the MEDLINE (biomedical research) and NCSTRL (computer science) collaboration graphs from this paper are not publicly available.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = r"""Weighted co-authorship networks of scientists who posted preprints on the arXiv e-print repository, compiled by M. E. J. Newman. Nodes are authors, identified by their surname and initials, and an undirected edge connects two authors if they co-authored at least one preprint. There is one network for each of three arXiv archives over the period 1995–1999 (`astro-ph-1999`: astrophysics; `cond-mat-1999`: condensed matter physics; `hep-th-1999`: high energy physics, theory), and two updated versions of the condensed matter network, covering preprints posted between January 1, 1995 and June 30, 2003 (`cond-mat-2003`) and between January 1, 1995 and March 31, 2005 (`cond-mat-2005`).
+
+Edge weights account for the fact that authors of papers with many co-authors know each other less well on average: each paper $k$ with $n_k$ authors contributes $1/(n_k-1)$ to the weight of the edge between each pair of its authors, so that $w_{ij} = \sum_k \delta_i^k\delta_j^k/(n_k-1)$, where $\delta_i^k=1$ if $i$ is an author of paper $k$ and $0$ otherwise. Papers with a single author do not contribute. Since authors are identified by surname and initials, different people with the same surname and initials may be merged into a single node, and the same person may appear under different names.
+
+The networks have the following properties:
+
+- Nodes: `label`, the author's name ("SURNAME, INITIALS").
+- Edges: `value`, the collaboration weight $w_{ij}$ described above."""
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
 url = 'http://www-personal.umich.edu/~mejn/netdata/'
 citation = [('M. E. J. Newman, "The structure of scientific collaboration networks." Proc. Natl. Acad. Sci. USA 98(2), 404-409 (2001). arxiv:cond-mat/0007214', 'https://doi.org/10.1073/pnas.98.2.404')]
 icon_hash = '56a85c8e26855e083a2f78a8'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata/'
 files = [("cond-mat.zip:cond-mat.gml", "cond-mat-1999", "gml"),
          ("cond-mat-2003.zip:cond-mat-2003.gml", "cond-mat-2003", "gml"),

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

diff --git a/entries/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index 66492d4..b567d57 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index 80ed068..66492d4 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index 39d2293..80ed068 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index cd3390f..39d2293 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index a5e4080..cd3390f 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__init__.py
@@ -23,7 +23,7 @@ description = """Collaboration graphs for scientists, extracted from the Los Ala
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
 url = 'http://www-personal.umich.edu/~mejn/netdata/'
-citation = [('M. E. J. Newman, "The structure of scientific collaboration networks." Proc. Natl. Acad. Sci. USA 98(2), 404-409 (2001). arxiv:cond-mat/0007214', 'http://www.pnas.org/content/98/2/404.abstract')]
+citation = [('M. E. J. Newman, "The structure of scientific collaboration networks." Proc. Natl. Acad. Sci. USA 98(2), 404-409 (2001). arxiv:cond-mat/0007214', 'https://doi.org/10.1073/pnas.98.2.404')]
 icon_hash = '56a85c8e26855e083a2f78a8'
 ustream_license = None
 upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata/'

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

diff --git a/entries/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index 35d4a1b..a5e4080 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__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/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
index 2a0604c..35d4a1b 100644
--- a/entries/arxiv_collab/__init__.py
+++ b/entries/arxiv_collab/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "Scientific collaborations in physics (1995-2005)"
-description = "Collaboration graphs for scientists, extracted from the Los Alamos e-Print arXiv (physics), for 1995-1999 for three categories, and additionally for 1995-2003 and 1995-2005 for one category. For copyright reasons, the MEDLINE (biomedical research) and NCSTRL (computer science) collaboration graphs from this paper are not publicly available."
+description = """Collaboration graphs for scientists, extracted from the Los Alamos e-Print arXiv (physics), for 1995-1999 for three categories, and additionally for 1995-2003 and 1995-2005 for one category. For copyright reasons, the MEDLINE (biomedical research) and NCSTRL (computer science) collaboration graphs from this paper are not publicly available.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
 url = 'http://www-personal.umich.edu/~mejn/netdata/'
 citation = [('M. E. J. Newman, "The structure of scientific collaboration networks." Proc. Natl. Acad. Sci. USA 98(2), 404-409 (2001). arxiv:cond-mat/0007214', 'http://www.pnas.org/content/98/2/404.abstract')]

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

diff --git a/entries/arxiv_collab/__init__.py b/entries/arxiv_collab/__init__.py
new file mode 100644
index 0000000..2a0604c
--- /dev/null
+++ b/entries/arxiv_collab/__init__.py
@@ -0,0 +1,53 @@
+#! /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 = "Scientific collaborations in physics (1995-2005)"
+description = "Collaboration graphs for scientists, extracted from the Los Alamos e-Print arXiv (physics), for 1995-1999 for three categories, and additionally for 1995-2003 and 1995-2005 for one category. For copyright reasons, the MEDLINE (biomedical research) and NCSTRL (computer science) collaboration graphs from this paper are not publicly available."
+tags = ['Social', 'Collaboration', 'Weighted', 'Projection']
+url = 'http://www-personal.umich.edu/~mejn/netdata/'
+citation = [('M. E. J. Newman, "The structure of scientific collaboration networks." Proc. Natl. Acad. Sci. USA 98(2), 404-409 (2001). arxiv:cond-mat/0007214', 'http://www.pnas.org/content/98/2/404.abstract')]
+icon_hash = '56a85c8e26855e083a2f78a8'
+ustream_license = None
+upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata/'
+files = [("cond-mat.zip:cond-mat.gml", "cond-mat-1999", "gml"),
+         ("cond-mat-2003.zip:cond-mat-2003.gml", "cond-mat-2003", "gml"),
+         ("cond-mat-2005.zip:cond-mat-2005.gml", "cond-mat-2005", "gml"),
+         ("astro-ph.zip:astro-ph.gml", "astro-ph-1999", "gml"),
+         ("hep-th.zip:hep-th.gml", "hep-th-1999", "gml")]
+
+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, "rb")) for fn in fnames]
+            g = parse_graph(fs, fmt, directed=False)
+        yield alt, g