History of dolphins
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.
[entries] Add the date when each entry was added, and remove icon_hash 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/dolphins/__init__.py b/entries/dolphins/__init__.py
index 2d91cb6..8a018a5 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__init__.py
@@ -27,7 +27,7 @@ The network has the following properties:
tags = ['Social', 'Animal', 'Unweighted']
url = 'http://www-personal.umich.edu/~mejn/netdata/'
citation = [('D. Lusseau et al., "The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations." Behavioral Ecology and Sociobiology 54(4), 396-405 (2003).', 'https://doi.org/10.1007/s00265-003-0651-y')]
-icon_hash = '56a85c8e26855e083a2f789f'
+date_added = '2020-08-11'
upstream_license = None
upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
files = [('dolphins.zip:dolphins.gml', None, 'gml')]
[entries] Prefix the properties in the descriptions with (Node), (Edge) or (Graph) 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/dolphins/__init__.py b/entries/dolphins/__init__.py
index af2012d..2d91cb6 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__init__.py
@@ -23,7 +23,7 @@ description = """An undirected social network of frequent associations among 62
The network has the following properties:
-- Nodes: `label`, the name given to the dolphin by the researchers."""
+- (Node) `label`: the name given to the dolphin by the researchers."""
tags = ['Social', 'Animal', 'Unweighted']
url = 'http://www-personal.umich.edu/~mejn/netdata/'
citation = [('D. Lusseau et al., "The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations." Behavioral Ecology and Sociobiology 54(4), 396-405 (2003).', 'https://doi.org/10.1007/s00265-003-0651-y')]
[entries] Remove unneeded code from the entries 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/dolphins/__init__.py b/entries/dolphins/__init__.py
index f5198d3..af2012d 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__init__.py
@@ -40,7 +40,6 @@ 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:
[entries] Fix parse bugs and improve the metadata of existing entries 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/dolphins/__init__.py b/entries/dolphins/__init__.py
index 833cc26..f5198d3 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__init__.py
@@ -19,13 +19,16 @@
from .. import *
title = "Dolphin social network (1994-2001)"
-description = """An undirected social network of frequent associations observed among 62 dolphins (Tursiops) in a community living off Doubtful Sound, New Zealand, from 1994-2001.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """An undirected social network of frequent associations among 62 bottlenose dolphins (*Tursiops* sp.) of a community living in Doubtful Sound, a fjord in New Zealand, compiled by D. Lusseau and collaborators from boat-based observations made between 1994 and 2001. Individual dolphins were identified from photographs of natural markings on their dorsal fins. During surveys, groups of dolphins were followed and photographed, and two dolphins were considered associated when they were observed in the same group. An edge connects two dolphins whose association, measured by the half-weight index, was significantly stronger than expected by chance, i.e. pairs that were observed together more often than random association would predict (preferred companionships).
+
+The network has the following properties:
+
+- Nodes: `label`, the name given to the dolphin by the researchers."""
tags = ['Social', 'Animal', 'Unweighted']
url = 'http://www-personal.umich.edu/~mejn/netdata/'
citation = [('D. Lusseau et al., "The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations." Behavioral Ecology and Sociobiology 54(4), 396-405 (2003).', 'https://doi.org/10.1007/s00265-003-0651-y')]
icon_hash = '56a85c8e26855e083a2f789f'
-ustream_license = None
+upstream_license = None
upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
files = [('dolphins.zip:dolphins.gml', None, 'gml')]
Update copyright information 73a4f0d
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
index 2b95a55..833cc26 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__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
Update copyright information 3d288ea
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
index 49c799c..2b95a55 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__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
Update copyright information 8d005ae
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
index f545f03..49c799c 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__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
Update copyright info db2efcc
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
index 00e8f83..f545f03 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__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
Update citations to use DOIs e878874
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
index b79a997..00e8f83 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__init__.py
@@ -23,7 +23,7 @@ description = """An undirected social network of frequent associations observed
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Social', 'Animal', 'Unweighted']
url = 'http://www-personal.umich.edu/~mejn/netdata/'
-citation = [('D. Lusseau et al., "The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations." Behavioral Ecology and Sociobiology 54(4), 396-405 (2003).', 'http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.174.3721&rep=rep1&type=pdf')]
+citation = [('D. Lusseau et al., "The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations." Behavioral Ecology and Sociobiology 54(4), 396-405 (2003).', 'https://doi.org/10.1007/s00265-003-0651-y')]
icon_hash = '56a85c8e26855e083a2f789f'
ustream_license = None
upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
index 44a1b5d..b79a997 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__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 *
Add explicit attribution to descriptions obtained from ICON 1645314
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
index 7975090..44a1b5d 100644
--- a/entries/dolphins/__init__.py
+++ b/entries/dolphins/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "Dolphin social network (1994-2001)"
-description = "An undirected social network of frequent associations observed among 62 dolphins (Tursiops) in a community living off Doubtful Sound, New Zealand, from 1994-2001."
+description = """An undirected social network of frequent associations observed among 62 dolphins (Tursiops) in a community living off Doubtful Sound, New Zealand, from 1994-2001.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Social', 'Animal', 'Unweighted']
url = 'http://www-personal.umich.edu/~mejn/netdata/'
citation = [('D. Lusseau et al., "The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations." Behavioral Ecology and Sociobiology 54(4), 396-405 (2003).', 'http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.174.3721&rep=rep1&type=pdf')]
Initial commit cc85872
diff --git a/entries/dolphins/__init__.py b/entries/dolphins/__init__.py
new file mode 100644
index 0000000..7975090
--- /dev/null
+++ b/entries/dolphins/__init__.py
@@ -0,0 +1,49 @@
+#! /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 = "Dolphin social network (1994-2001)"
+description = "An undirected social network of frequent associations observed among 62 dolphins (Tursiops) in a community living off Doubtful Sound, New Zealand, from 1994-2001."
+tags = ['Social', 'Animal', 'Unweighted']
+url = 'http://www-personal.umich.edu/~mejn/netdata/'
+citation = [('D. Lusseau et al., "The bottlenose dolphin community of Doubtful Sound features a large proportion of long-lasting associations." Behavioral Ecology and Sociobiology 54(4), 396-405 (2003).', 'http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.174.3721&rep=rep1&type=pdf')]
+icon_hash = '56a85c8e26855e083a2f789f'
+ustream_license = None
+upstream_prefix = 'http://www-personal.umich.edu/~mejn/netdata'
+files = [('dolphins.zip:dolphins.gml', None, '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