History of word_adjacency
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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 8f8674a..a5e5b79 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__init__.py
@@ -30,7 +30,7 @@ The networks have the following properties:
tags = ['Informational', 'Language', 'Unweighted']
url = 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
citation = [('R. Milo. et al., "Superfamilies of Evolved and Designed Networks." Science (2004)', 'https://doi.org/10.1126/science.1089167')]
-icon_hash = '5723b74b461efe0c7a675bcd'
+date_added = '2020-08-11'
upstream_license = None
upstream_prefix = 'https://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks'
files = [('darwinbookinter_st.txt', 'darwin', 'loadtxt'),
[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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 527f0dd..8f8674a 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__init__.py
@@ -26,7 +26,7 @@ description = r"""Word adjacency networks of texts in four languages, from the c
The networks have the following properties:
-- `name`: the numerical identifier of the word in the upstream file. The words themselves are not included."""
+- (Node) `name`: the numerical identifier of the word in the upstream file. The words themselves are not included."""
tags = ['Informational', 'Language', 'Unweighted']
url = 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
citation = [('R. Milo. et al., "Superfamilies of Evolved and Designed Networks." Science (2004)', 'https://doi.org/10.1126/science.1089167')]
[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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index ed8581a..527f0dd 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__init__.py
@@ -46,7 +46,6 @@ 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 descriptions and metadata 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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index e08f85f..ed8581a 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__init__.py
@@ -19,13 +19,19 @@
from .. import *
title = "Word Adjacency Networks"
-description = """Directed Networks of word adjacency in texts of several languages including English, French, Spanish and Japanese[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = r"""Word adjacency networks of texts in four languages, from the collection of networks of U. Alon's lab used by R. Milo et al. to study the local structure (network motifs) of networks from different domains. Nodes are words, and a directed edge $i \to j$ indicates that word $j$ directly follows word $i$ at least once in the text.
+
+- `darwin`: an English text by C. Darwin.
+- `french`, `spanish`, `japanese`: texts in French, Spanish and Japanese.
+
+The networks have the following properties:
+
+- `name`: the numerical identifier of the word in the upstream file. The words themselves are not included."""
tags = ['Informational', 'Language', 'Unweighted']
-url = 'https://doi.org/10.1126/science.1089167'
+url = 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
citation = [('R. Milo. et al., "Superfamilies of Evolved and Designed Networks." Science (2004)', 'https://doi.org/10.1126/science.1089167')]
icon_hash = '5723b74b461efe0c7a675bcd'
-ustream_license = None
+upstream_license = None
upstream_prefix = 'https://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks'
files = [('darwinbookinter_st.txt', 'darwin', 'loadtxt'),
('frenchbookinter_st.txt', 'french', 'loadtxt'),
Update copyright information 73a4f0d
diff --git a/entries/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index e7c7b43..e08f85f 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 38fab21..e7c7b43 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 8aa74d6..38fab21 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 1306a70..8aa74d6 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 1135f28..1306a70 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__init__.py
@@ -22,8 +22,8 @@ title = "Word Adjacency Networks"
description = """Directed Networks of word adjacency in texts of several languages including English, French, Spanish and Japanese[^icon]
[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Informational', 'Language', 'Unweighted']
-url = 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
-citation = [('R. Milo. et al., "Superfamilies of Evolved and Designed Networks." Science (2004)', 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks')]
+url = 'https://doi.org/10.1126/science.1089167'
+citation = [('R. Milo. et al., "Superfamilies of Evolved and Designed Networks." Science (2004)', 'https://doi.org/10.1126/science.1089167')]
icon_hash = '5723b74b461efe0c7a675bcd'
ustream_license = None
upstream_prefix = 'https://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks'
Change license from GPLv3 to AGPLv3 d754be5
diff --git a/entries/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 62de463..1135f28 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__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/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
index 7bde03c..62de463 100644
--- a/entries/word_adjacency/__init__.py
+++ b/entries/word_adjacency/__init__.py
@@ -19,7 +19,8 @@
from .. import *
title = "Word Adjacency Networks"
-description = "Directed Networks of word adjacency in texts of several languages including English, French, Spanish and Japanese"
+description = """Directed Networks of word adjacency in texts of several languages including English, French, Spanish and Japanese[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
tags = ['Informational', 'Language', 'Unweighted']
url = 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
citation = [('R. Milo. et al., "Superfamilies of Evolved and Designed Networks." Science (2004)', 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks')]
Initial commit cc85872
diff --git a/entries/word_adjacency/__init__.py b/entries/word_adjacency/__init__.py
new file mode 100644
index 0000000..7bde03c
--- /dev/null
+++ b/entries/word_adjacency/__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 = "Word Adjacency Networks"
+description = "Directed Networks of word adjacency in texts of several languages including English, French, Spanish and Japanese"
+tags = ['Informational', 'Language', 'Unweighted']
+url = 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
+citation = [('R. Milo. et al., "Superfamilies of Evolved and Designed Networks." Science (2004)', 'https://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks')]
+icon_hash = '5723b74b461efe0c7a675bcd'
+ustream_license = None
+upstream_prefix = 'https://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks'
+files = [('darwinbookinter_st.txt', 'darwin', 'loadtxt'),
+ ('frenchbookinter_st.txt', 'french', 'loadtxt'),
+ ('spanishbookinter_st.txt', 'spanish', 'loadtxt'),
+ ('japanesebookinter_st.txt', 'japanese', 'loadtxt')]
+
+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=True)
+ del g.ep["p0"]
+ yield alt, g