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History of us_agencies

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 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/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 02b181b..5d4d823 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__init__.py
@@ -37,7 +37,7 @@ The networks have the following properties:
 tags = ['Social', 'Political', 'Weighted', 'Metadata']
 url = 'http://govmaps.cid.hks.harvard.edu'
 citation = [('S. Kosack et al., "Functional structures of US state governments." Proc. Natl. Acad. Sci. USA (2018)', 'https://doi.org/10.1073/pnas.1803228115')]
-icon_hash = '5be1bbda3b0034c4456910a0'
+date_added = '2020-08-11'
 upstream_license = None
 upstream_prefix = 'https://gov-structure.kimalbrecht.com/material/data'
 files = [((f"us_state_networks.zip:{s}/nodes.txt",
[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/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index c2558c4..02b181b 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__init__.py
@@ -25,15 +25,15 @@ There is one network for each state (e.g. `alabama`, `newyork`), and the network
 
 The networks have the following properties:
 
-- `vid`: the numerical identifier of the website, unique across states.
-- `url` (state networks): the URL of the website (the seed of the crawl).
-- `name` (state networks): the name of the agency.
-- `year` (state networks): the first year in which the website was indexed by the Internet Archive (a proxy for its creation date), or 0 if it was not indexed.
-- `pages` (state networks): the number of webpages of the website found at the time of the crawl.
-- `traffic` (state networks): an estimate of the web traffic of the website, as provided by the authors (its source and units are not documented in the data).
-- `population` (state networks, graph property): the population of the state.
-- `link_counts`: the number of hyperlinks from the webpages of website $i$ to the webpages of website $j$.
-- `rel_link_counts`: in the state networks, `link_counts` divided by the number of pages of website $i$; in the `aggregate` network, `link_counts` divided by the total number of outgoing hyperlinks of website $i$."""
+- (Node) `vid`: the numerical identifier of the website, unique across states.
+- (Node) `url` (state networks): the URL of the website (the seed of the crawl).
+- (Node) `name` (state networks): the name of the agency.
+- (Node) `year` (state networks): the first year in which the website was indexed by the Internet Archive (a proxy for its creation date), or 0 if it was not indexed.
+- (Node) `pages` (state networks): the number of webpages of the website found at the time of the crawl.
+- (Node) `traffic` (state networks): an estimate of the web traffic of the website, as provided by the authors (its source and units are not documented in the data).
+- (Graph) `population` (state networks): the population of the state.
+- (Edge) `link_counts`: the number of hyperlinks from the webpages of website $i$ to the webpages of website $j$.
+- (Edge) `rel_link_counts`: in the state networks, `link_counts` divided by the number of pages of website $i$; in the `aggregate` network, `link_counts` divided by the total number of outgoing hyperlinks of website $i$."""
 tags = ['Social', 'Political', 'Weighted', 'Metadata']
 url = 'http://govmaps.cid.hks.harvard.edu'
 citation = [('S. Kosack et al., "Functional structures of US state governments." Proc. Natl. Acad. Sci. USA (2018)', 'https://doi.org/10.1073/pnas.1803228115')]
[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/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 9fbc953..c2558c4 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__init__.py
@@ -42,8 +42,8 @@ upstream_license = None
 upstream_prefix = 'https://gov-structure.kimalbrecht.com/material/data'
 files = [((f"us_state_networks.zip:{s}/nodes.txt",
            f"us_state_networks.zip:{s}/edges.txt",
-           f"us_state_networks.zip:node_traffic.csv",
-           f"us_state_networks.zip:state_demographic_data.csv"), s, None)
+           "us_state_networks.zip:node_traffic.csv",
+           "us_state_networks.zip:state_demographic_data.csv"), s, None)
          for s in ["alabama", "alaska", "arizona", "arkansas", "california",
                    "colorado", "connecticut", "delaware", "florida", "georgia", "hawaii",
                    "idaho", "illinois", "indiana", "iowa", "kansas", "kentucky",
@@ -54,7 +54,7 @@ files = [((f"us_state_networks.zip:{s}/nodes.txt",
                    "pennsylvania", "rhodeisland", "southcarolina", "southdakota",
                    "tennessee", "texas", "utah", "vermont", "virginia", "washington",
                    "westvirginia", "wisconsin", "wyoming"]] + \
-        [(f"us_state_networks.zip:web_network_aggregation.txt", "aggregate", None)]
+        [("us_state_networks.zip:web_network_aggregation.txt", "aggregate", None)]
 
 def fetch_upstream(force=False):
     return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
@@ -64,7 +64,6 @@ 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 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/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 5578404..9fbc953 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__init__.py
@@ -19,13 +19,26 @@
 from .. import *
 
 title = "U.S. government agency websites (2018)"
-description = """50 networks, one for each U.S. state, representing the web-based links between their associated government agencies websites. A node is an entire agency website and a directed edge (i,j) represents the existence of a hyperlink from any webpage in website i to some webpage in website j. Data was collected with a crawler. Nodes are annotated with the number of webpages per website, website name (related to its government function) and URL, and year the website was indexed by the Internet Archive (proxy for birthday). Edges are weighted by the number of hyperlinks between a pair of websites.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = r"""Networks of hyperlinks among the websites of the government agencies of the 50 U.S. states, collected by S. Kosack, M. Coscia and collaborators (Harvard Center for International Development) by crawling the websites in 2017. A node is the entire website of an agency, and a directed edge $i \to j$ indicates that at least one webpage of website $i$ contains a hyperlink to a webpage of website $j$.
+
+There is one network for each state (e.g. `alabama`, `newyork`), and the network `aggregate` combines the websites of all 50 states. The node identifiers are consistent across the networks.
+
+The networks have the following properties:
+
+- `vid`: the numerical identifier of the website, unique across states.
+- `url` (state networks): the URL of the website (the seed of the crawl).
+- `name` (state networks): the name of the agency.
+- `year` (state networks): the first year in which the website was indexed by the Internet Archive (a proxy for its creation date), or 0 if it was not indexed.
+- `pages` (state networks): the number of webpages of the website found at the time of the crawl.
+- `traffic` (state networks): an estimate of the web traffic of the website, as provided by the authors (its source and units are not documented in the data).
+- `population` (state networks, graph property): the population of the state.
+- `link_counts`: the number of hyperlinks from the webpages of website $i$ to the webpages of website $j$.
+- `rel_link_counts`: in the state networks, `link_counts` divided by the number of pages of website $i$; in the `aggregate` network, `link_counts` divided by the total number of outgoing hyperlinks of website $i$."""
 tags = ['Social', 'Political', 'Weighted', 'Metadata']
 url = 'http://govmaps.cid.hks.harvard.edu'
 citation = [('S. Kosack et al., "Functional structures of US state governments." Proc. Natl. Acad. Sci. USA (2018)', 'https://doi.org/10.1073/pnas.1803228115')]
 icon_hash = '5be1bbda3b0034c4456910a0'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'https://gov-structure.kimalbrecht.com/material/data'
 files = [((f"us_state_networks.zip:{s}/nodes.txt",
            f"us_state_networks.zip:{s}/edges.txt",
Update copyright information by Tiago de Paula Peixoto 73a4f0d
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 9c83134..5578404 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__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 by Tiago de Paula Peixoto 3d288ea
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index c141096..9c83134 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__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 by Tiago de Paula Peixoto 8d005ae
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 5142a23..c141096 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__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 by Tiago de Paula Peixoto db2efcc
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 2ab1b7e..5142a23 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__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 by Tiago de Paula Peixoto e878874
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 39e6927..2ab1b7e 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__init__.py
@@ -23,7 +23,7 @@ description = """50 networks, one for each U.S. state, representing the web-base
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Political', 'Weighted', 'Metadata']
 url = 'http://govmaps.cid.hks.harvard.edu'
-citation = [('S. Kosack et al., "Functional structures of US state governments." Proc. Natl. Acad. Sci. USA (2018)', 'http://www.pnas.org/content/early/2018/10/24/1803228115')]
+citation = [('S. Kosack et al., "Functional structures of US state governments." Proc. Natl. Acad. Sci. USA (2018)', 'https://doi.org/10.1073/pnas.1803228115')]
 icon_hash = '5be1bbda3b0034c4456910a0'
 ustream_license = None
 upstream_prefix = 'https://gov-structure.kimalbrecht.com/material/data'
Change license from GPLv3 to AGPLv3 by Tiago de Paula Peixoto d754be5
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 33082c3..39e6927 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__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 by Tiago de Paula Peixoto 1645314
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
index 1075a5c..33082c3 100644
--- a/entries/us_agencies/__init__.py
+++ b/entries/us_agencies/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "U.S. government agency websites (2018)"
-description = "50 networks, one for each U.S. state, representing the web-based links between their associated government agencies websites. A node is an entire agency website and a directed edge (i,j) represents the existence of a hyperlink from any webpage in website i to some webpage in website j. Data was collected with a crawler. Nodes are annotated with the number of webpages per website, website name (related to its government function) and URL, and year the website was indexed by the Internet Archive (proxy for birthday). Edges are weighted by the number of hyperlinks between a pair of websites."
+description = """50 networks, one for each U.S. state, representing the web-based links between their associated government agencies websites. A node is an entire agency website and a directed edge (i,j) represents the existence of a hyperlink from any webpage in website i to some webpage in website j. Data was collected with a crawler. Nodes are annotated with the number of webpages per website, website name (related to its government function) and URL, and year the website was indexed by the Internet Archive (proxy for birthday). Edges are weighted by the number of hyperlinks between a pair of websites.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Social', 'Political', 'Weighted', 'Metadata']
 url = 'http://govmaps.cid.hks.harvard.edu'
 citation = [('S. Kosack et al., "Functional structures of US state governments." Proc. Natl. Acad. Sci. USA (2018)', 'http://www.pnas.org/content/early/2018/10/24/1803228115')]
Initial commit by Tiago de Paula Peixoto cc85872
diff --git a/entries/us_agencies/__init__.py b/entries/us_agencies/__init__.py
new file mode 100644
index 0000000..1075a5c
--- /dev/null
+++ b/entries/us_agencies/__init__.py
@@ -0,0 +1,121 @@
+#! /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 = "U.S. government agency websites (2018)"
+description = "50 networks, one for each U.S. state, representing the web-based links between their associated government agencies websites. A node is an entire agency website and a directed edge (i,j) represents the existence of a hyperlink from any webpage in website i to some webpage in website j. Data was collected with a crawler. Nodes are annotated with the number of webpages per website, website name (related to its government function) and URL, and year the website was indexed by the Internet Archive (proxy for birthday). Edges are weighted by the number of hyperlinks between a pair of websites."
+tags = ['Social', 'Political', 'Weighted', 'Metadata']
+url = 'http://govmaps.cid.hks.harvard.edu'
+citation = [('S. Kosack et al., "Functional structures of US state governments." Proc. Natl. Acad. Sci. USA (2018)', 'http://www.pnas.org/content/early/2018/10/24/1803228115')]
+icon_hash = '5be1bbda3b0034c4456910a0'
+ustream_license = None
+upstream_prefix = 'https://gov-structure.kimalbrecht.com/material/data'
+files = [((f"us_state_networks.zip:{s}/nodes.txt",
+           f"us_state_networks.zip:{s}/edges.txt",
+           f"us_state_networks.zip:node_traffic.csv",
+           f"us_state_networks.zip:state_demographic_data.csv"), s, None)
+         for s in ["alabama", "alaska", "arizona", "arkansas", "california",
+                   "colorado", "connecticut", "delaware", "florida", "georgia", "hawaii",
+                   "idaho", "illinois", "indiana", "iowa", "kansas", "kentucky",
+                   "louisiana", "maine", "maryland", "massachusetts", "michigan",
+                   "minnesota", "mississippi", "missouri", "montana", "nebraska",
+                   "nevada", "newhampshire", "newjersey", "newmexico", "newyork",
+                   "northcarolina", "northdakota", "ohio", "oklahoma", "oregon",
+                   "pennsylvania", "rhodeisland", "southcarolina", "southdakota",
+                   "tennessee", "texas", "utah", "vermont", "virginia", "washington",
+                   "westvirginia", "wisconsin", "wyoming"]] + \
+        [(f"us_state_networks.zip:web_network_aggregation.txt", "aggregate", 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]
+
+            if alt == "aggregate":
+                g = Graph()
+                g.ep.link_counts = g.new_ep("int")
+                g.ep.rel_link_counts = g.new_ep("double")
+                next(fs[0])
+                edges = numpy.loadtxt(fs[0])
+                g.vp.vid = g.add_edge_list(edges, hashed=True,
+                                           eprops=[g.ep.link_counts,
+                                                   g.ep.rel_link_counts])
+            else:
+                g = Graph()
+
+                g.gp.population = g.new_gp("int")
+                g.vp.vid = g.new_vp("int")
+                g.vp.url = g.new_vp("string")
+                g.vp.name = g.new_vp("string")
+                g.vp.year = g.new_vp("int")
+                g.vp.pages = g.new_vp("int")
+                g.vp.traffic = g.new_vp("double")
+                g.ep.link_counts = g.new_ep("int")
+                g.ep.rel_link_counts = g.new_ep("double")
+
+                vs = {}
+                next(fs[0])
+                for line in fs[0]:
+                    vals = line.split("\t")
+                    v = g.add_vertex()
+                    g.vp.vid[v] = int(vals[0])
+                    vs[g.vp.vid[v]] = v
+                    g.vp.url[v] = vals[1]
+                    g.vp.name[v] = vals[2]
+                    g.vp.year[v] = float(vals[3])
+                    g.vp.pages[v] = float(vals[4].strip())
+
+                next(fs[1])
+                for line in fs[1]:
+                    vals = line.split("\t")
+                    s = vs[int(vals[0])]
+                    t = vs[int(vals[1])]
+                    e = g.add_edge(s, t)
+                    g.ep.link_counts[e] = vals[2]
+                    g.ep.rel_link_counts[e] = vals[3].strip()
+
+                next(fs[2])
+                for line in fs[2]:
+                    vals = line.split("\t")
+                    try:
+                        v = vs[int(vals[0])]
+                    except KeyError:
+                        continue
+                    g.vp.traffic[v] = vals[1]
+
+                next(fs[3])
+                for line in fs[3]:
+                    vals = line.split("\t")
+                    if vals[0] == alt:
+                        g.gp.population = int(vals[-1].strip())
+                        break
+        yield alt, g