History of psi

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/psi/__init__.py b/entries/psi/__init__.py
index 40f4dec..0dfef86 100644
--- a/entries/psi/__init__.py
+++ b/entries/psi/__init__.py
@@ -23,7 +23,7 @@ description = """Weighted directed network of the light-harvesting Photosystem 
 tags = ['Biological', 'Weighted']
 url = 'https://networks.skewed.de/net/psi'
 citation = [('Montepietra D., Bellingeri M., Ross A.M., Scotognella F. and Cassi D., "Modelling photosystem I as a complex interacting network", J. R. Soc. Interface (2020)', 'https://doi.org/10.1098/rsif.2020.0813')]
-icon_hash = None
+date_added = '2023-02-19'
 upstream_license = None
 upstream_prefix = 'https://downloads.skewed.de/data'
 files = [('PSI_graph.csv', None, None)]

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/psi/__init__.py b/entries/psi/__init__.py
index e46fcfd..40f4dec 100644
--- a/entries/psi/__init__.py
+++ b/entries/psi/__init__.py
@@ -36,7 +36,6 @@ 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/psi/__init__.py b/entries/psi/__init__.py
index a8d132a..e46fcfd 100644
--- a/entries/psi/__init__.py
+++ b/entries/psi/__init__.py
@@ -19,7 +19,7 @@
 from .. import *
 
 title = "Plant Photosystem I excitation energy transfer network (2020)"
-description = """Weighted directed network of the light-harvesting Photosystem Ι (PSI) of the plant Pisum sativum. The nodes represent chromophores with different identities (i.e. chlorophyll a, chlorophyll b, β-carotene and derivates, lutein, violaxanthin), while edges represent FRET transfer between chromophores. The link directionality connecting nodes in the PSI network depends on the energy levels of the connected chromophores. The weights correspond to the FRET Efficiency between connected chromophores."""
+description = """Weighted directed network of the light-harvesting Photosystem Ι (PSI) of the plant Pisum sativum. The nodes represent chromophores with different identities (i.e. chlorophyll a, chlorophyll b, β-carotene and derivates, lutein, violaxanthin), while edges represent FRET transfer between chromophores. The link directionality connecting nodes in the PSI network depends on the energy levels of the connected chromophores. The weights correspond to the FRET Efficiency between connected chromophores. Hence a directed edge $(i,j)$ represents the transfer of excitation energy from chromophore $i$ to chromophore $j$, presumably from donor to acceptor (the direction convention of the data file is not documented), weighted by the efficiency of this transfer; most pairs of chromophores (about 80% of the edges) are connected in both directions, with different efficiencies."""
 tags = ['Biological', 'Weighted']
 url = 'https://networks.skewed.de/net/psi'
 citation = [('Montepietra D., Bellingeri M., Ross A.M., Scotognella F. and Cassi D., "Modelling photosystem I as a complex interacting network", J. R. Soc. Interface (2020)', 'https://doi.org/10.1098/rsif.2020.0813')]

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/psi/__init__.py b/entries/psi/__init__.py
index 556104e..a8d132a 100644
--- a/entries/psi/__init__.py
+++ b/entries/psi/__init__.py
@@ -24,7 +24,7 @@ tags = ['Biological', 'Weighted']
 url = 'https://networks.skewed.de/net/psi'
 citation = [('Montepietra D., Bellingeri M., Ross A.M., Scotognella F. and Cassi D., "Modelling photosystem I as a complex interacting network", J. R. Soc. Interface (2020)', 'https://doi.org/10.1098/rsif.2020.0813')]
 icon_hash = None
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'https://downloads.skewed.de/data'
 files = [('PSI_graph.csv', None, None)]

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

diff --git a/entries/psi/__init__.py b/entries/psi/__init__.py
index e4735e8..556104e 100644
--- a/entries/psi/__init__.py
+++ b/entries/psi/__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/psi/__init__.py b/entries/psi/__init__.py
index 50dd895..e4735e8 100644
--- a/entries/psi/__init__.py
+++ b/entries/psi/__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 Add 'psi' entry by Tiago de Paula Peixoto 73a333e

This fixes #7.

diff --git a/entries/psi/__init__.py b/entries/psi/__init__.py
new file mode 100644
index 0000000..50dd895
--- /dev/null
+++ b/entries/psi/__init__.py
@@ -0,0 +1,57 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# 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
+# 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 Affero General Public License for more
+# details.
+#
+# 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 *
+
+title = "Plant Photosystem I excitation energy transfer network (2020)"
+description = """Weighted directed network of the light-harvesting Photosystem Ι (PSI) of the plant Pisum sativum. The nodes represent chromophores with different identities (i.e. chlorophyll a, chlorophyll b, β-carotene and derivates, lutein, violaxanthin), while edges represent FRET transfer between chromophores. The link directionality connecting nodes in the PSI network depends on the energy levels of the connected chromophores. The weights correspond to the FRET Efficiency between connected chromophores."""
+tags = ['Biological', 'Weighted']
+url = 'https://networks.skewed.de/net/psi'
+citation = [('Montepietra D., Bellingeri M., Ross A.M., Scotognella F. and Cassi D., "Modelling photosystem I as a complex interacting network", J. R. Soc. Interface (2020)', 'https://doi.org/10.1098/rsif.2020.0813')]
+icon_hash = None
+ustream_license = None
+upstream_prefix = 'https://downloads.skewed.de/data'
+files = [('PSI_graph.csv', None, 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]
+            g = Graph(directed=True)
+            g.ep.weight = g.new_ep("double")
+            next(fs[0])
+            for line in fs[0]:
+                u, v, w = line.split(",")
+                u = int(u)
+                v = int(v)
+                e = g.add_edge(u - 1, v - 1)
+                g.ep.weight[e] = float(w)
+        yield alt, g