History of arxiv_citation

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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index a01f342..4c236ef 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__init__.py
@@ -30,7 +30,7 @@ url = ['https://snap.stanford.edu/data/cit-HepPh.html',
        'https://snap.stanford.edu/data/cit-HepTh.html',
        'https://www.cs.cornell.edu/projects/kddcup/datasets.html']
 citation = [('J. Gehrke, P. Ginsparg, J. M. Kleinberg. "Overview of the 2003 KDD Cup." SIGKDD Explorations 5(2), 149-151 (2003)', 'https://doi.org/10.1145/980972.980992')]
-icon_hash = '571512be6afce8e9253875e8'
+date_added = '2020-08-11'
 upstream_license = None
 upstream_prefix = 'https://snap.stanford.edu/data'
 # SNAP's cit-HepTh-dates.txt.gz is a copy of cit-HepPh-dates.txt.gz (the

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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index 1cd8545..a01f342 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__init__.py
@@ -23,7 +23,8 @@ description = r"""Citation networks among papers posted on the arXiv e-print rep
 
 The networks have the following properties:
 
-- Nodes: `name`, the arXiv identifier of the paper within its category, as an integer, i.e. without the leading zeros (e.g. `9301253` is hep-ph/9301253, and `1001` is hep-th/0001001); `date`, the date the paper was first submitted to arXiv (YYYY-MM-DD). In `HepPh`, the dates are those published by SNAP, and are empty for the 3,988 papers without a date there; in `HepTh`, they are SLAC's submission dates from the original KDD Cup 2003 data, available for all papers (SNAP's file of `HepTh` dates is a copy of the `HepPh` one)."""
+- (Node) `name`: the arXiv identifier of the paper within its category, as an integer, i.e. without the leading zeros (e.g. `9301253` is hep-ph/9301253, and `1001` is hep-th/0001001).
+- (Node) `date`: the date the paper was first submitted to arXiv (YYYY-MM-DD). In `HepPh`, the dates are those published by SNAP, and are empty for the 3,988 papers without a date there; in `HepTh`, they are SLAC's submission dates from the original KDD Cup 2003 data, available for all papers (SNAP's file of `HepTh` dates is a copy of the `HepPh` one)."""
 tags = ['Informational', 'Citation', 'Unweighted']
 url = ['https://snap.stanford.edu/data/cit-HepPh.html',
        'https://snap.stanford.edu/data/cit-HepTh.html',

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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index d183263..1cd8545 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__init__.py
@@ -52,7 +52,6 @@ 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 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/arxiv_citation/__init__.py b/entries/arxiv_citation/__init__.py
index 2330b58..d183263 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__init__.py
@@ -19,19 +19,33 @@
 from .. import *
 
 title = "arXiv citation networks (1993-2003)"
-description = """Citations among papers posted on arxiv.org under the hep-ph and hep-th categories, between 1993 and 2003. This time begins a few months after axiv was launched. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) These data were originally released as part of the 2003 KDD Cup.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = r"""Citation networks among papers posted on the arXiv e-print repository in two categories of high energy physics, phenomenology (`HepPh`) and theory (`HepTh`). The data cover papers posted from January 1993 to April 2003 (124 months), beginning a few months after the inception of arXiv, and were originally released as part of the 2003 KDD Cup (with data provided by P. Ginsparg and arXiv). A directed edge $i \to j$ means that paper $i$ cites paper $j$. Only citations among papers in the data set are included: citations to or from papers outside of it are not recorded.
+
+The networks have the following properties:
+
+- Nodes: `name`, the arXiv identifier of the paper within its category, as an integer, i.e. without the leading zeros (e.g. `9301253` is hep-ph/9301253, and `1001` is hep-th/0001001); `date`, the date the paper was first submitted to arXiv (YYYY-MM-DD). In `HepPh`, the dates are those published by SNAP, and are empty for the 3,988 papers without a date there; in `HepTh`, they are SLAC's submission dates from the original KDD Cup 2003 data, available for all papers (SNAP's file of `HepTh` dates is a copy of the `HepPh` one)."""
 tags = ['Informational', 'Citation', 'Unweighted']
-url = 'http://snap.stanford.edu/data/cit-HepPh.html'
+url = ['https://snap.stanford.edu/data/cit-HepPh.html',
+       'https://snap.stanford.edu/data/cit-HepTh.html',
+       'https://www.cs.cornell.edu/projects/kddcup/datasets.html']
 citation = [('J. Gehrke, P. Ginsparg, J. M. Kleinberg. "Overview of the 2003 KDD Cup." SIGKDD Explorations 5(2), 149-151 (2003)', 'https://doi.org/10.1145/980972.980992')]
 icon_hash = '571512be6afce8e9253875e8'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'https://snap.stanford.edu/data'
+# SNAP's cit-HepTh-dates.txt.gz is a copy of cit-HepPh-dates.txt.gz (the
+# dates of hep-ph papers), so the dates of the hep-th papers are taken from
+# the original KDD Cup 2003 data (SLAC's submission dates)
+kdd_prefix = 'https://www.cs.cornell.edu/projects/kddcup/download'
+kdd_dates = "hep-th-slacdates.tar.gz:hep-th-slacdates"
 files = [(("cit-HepPh.txt.gz", "cit-HepPh-dates.txt.gz"), "HepPh", "snap"),
-         (("cit-HepTh.txt.gz", "cit-HepTh-dates.txt.gz"), "HepTh", "snap")]
+         (("cit-HepTh.txt.gz", kdd_dates), "HepTh", "snap")]
 
 def fetch_upstream(force=False):
-    return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+    name = __name__.split(".")[-1]
+    snap = [([f for f in fnames if f != kdd_dates], alt, fmt)
+            for fnames, alt, fmt in files]
+    fetch_upstream_files(name, upstream_prefix, snap, force)
+    return fetch_upstream_files(name, kdd_prefix, [(kdd_dates, "HepTh", None)],
                                 force)
 
 @cache_network()
@@ -50,8 +64,9 @@ def parse(alts=None):
             g = parse_graph(fs, (fmt, dict(hashed=True)), directed=True)
             vs = {g.vp.name[v] : v for v in g.vertices()}
             g.vp.date = g.new_vp("string")
-            next(fs[1])
             for line in fs[1]:
+                if line.startswith(b"#"):
+                    continue
                 vals = line.split()
                 try:
                     v = vs[int(vals[0])]

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

diff --git a/entries/arxiv_citation/__init__.py b/entries/arxiv_citation/__init__.py
index 19c3767..2330b58 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index c85a667..19c3767 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index 03a6761..c85a667 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index 0258691..03a6761 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index 954207e..0258691 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__init__.py
@@ -23,7 +23,7 @@ description = """Citations among papers posted on arxiv.org under the hep-ph and
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Informational', 'Citation', 'Unweighted']
 url = 'http://snap.stanford.edu/data/cit-HepPh.html'
-citation = [('J. Gehrke, P. Ginsparg, J. M. Kleinberg. "Overview of the 2003 KDD Cup." SIGKDD Explorations 5(2), 149-151 (2003)', 'http://www.cs.cmu.edu/~jure/pubs/powergrowth-kdd05.pdf')]
+citation = [('J. Gehrke, P. Ginsparg, J. M. Kleinberg. "Overview of the 2003 KDD Cup." SIGKDD Explorations 5(2), 149-151 (2003)', 'https://doi.org/10.1145/980972.980992')]
 icon_hash = '571512be6afce8e9253875e8'
 ustream_license = None
 upstream_prefix = 'https://snap.stanford.edu/data'

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

diff --git a/entries/arxiv_citation/__init__.py b/entries/arxiv_citation/__init__.py
index dfd8081..954207e 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__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_citation/__init__.py b/entries/arxiv_citation/__init__.py
index 96eea2f..dfd8081 100644
--- a/entries/arxiv_citation/__init__.py
+++ b/entries/arxiv_citation/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "arXiv citation networks (1993-2003)"
-description = "Citations among papers posted on arxiv.org under the hep-ph and hep-th categories, between 1993 and 2003. This time begins a few months after axiv was launched. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) These data were originally released as part of the 2003 KDD Cup."
+description = """Citations among papers posted on arxiv.org under the hep-ph and hep-th categories, between 1993 and 2003. This time begins a few months after axiv was launched. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) These data were originally released as part of the 2003 KDD Cup.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Informational', 'Citation', 'Unweighted']
 url = 'http://snap.stanford.edu/data/cit-HepPh.html'
 citation = [('J. Gehrke, P. Ginsparg, J. M. Kleinberg. "Overview of the 2003 KDD Cup." SIGKDD Explorations 5(2), 149-151 (2003)', 'http://www.cs.cmu.edu/~jure/pubs/powergrowth-kdd05.pdf')]

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

diff --git a/entries/arxiv_citation/__init__.py b/entries/arxiv_citation/__init__.py
new file mode 100644
index 0000000..96eea2f
--- /dev/null
+++ b/entries/arxiv_citation/__init__.py
@@ -0,0 +1,60 @@
+#! /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 = "arXiv citation networks (1993-2003)"
+description = "Citations among papers posted on arxiv.org under the hep-ph and hep-th categories, between 1993 and 2003. This time begins a few months after axiv was launched. If a paper i cites a paper j also in this data set, then a directed edge connects i to j. (Papers not in the data set are excluded.) These data were originally released as part of the 2003 KDD Cup."
+tags = ['Informational', 'Citation', 'Unweighted']
+url = 'http://snap.stanford.edu/data/cit-HepPh.html'
+citation = [('J. Gehrke, P. Ginsparg, J. M. Kleinberg. "Overview of the 2003 KDD Cup." SIGKDD Explorations 5(2), 149-151 (2003)', 'http://www.cs.cmu.edu/~jure/pubs/powergrowth-kdd05.pdf')]
+icon_hash = '571512be6afce8e9253875e8'
+ustream_license = None
+upstream_prefix = 'https://snap.stanford.edu/data'
+files = [(("cit-HepPh.txt.gz", "cit-HepPh-dates.txt.gz"), "HepPh", "snap"),
+         (("cit-HepTh.txt.gz", "cit-HepTh-dates.txt.gz"), "HepTh", "snap")]
+
+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, dict(hashed=True)), directed=True)
+            vs = {g.vp.name[v] : v for v in g.vertices()}
+            g.vp.date = g.new_vp("string")
+            next(fs[1])
+            for line in fs[1]:
+                vals = line.split()
+                try:
+                    v = vs[int(vals[0])]
+                except KeyError:
+                    continue
+                g.vp.date[v] = vals[1]
+        yield alt, g