History of yeast_transcription

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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index bb6a4ad..486b420 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__init__.py
@@ -28,7 +28,7 @@ The network has the following properties:
 tags = ['Biological', 'Gene regulation', 'Unweighted']
 url = 'http://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
 citation = [('R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002).', 'https://doi.org/10.1126/science.298.5594.824')]
-icon_hash = '56a85c8e26855e083a2f78f0'
+date_added = '2020-08-11'
 upstream_prefix = 'https://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks'
 files = [('yeastdata.mat', None, 'matlab_yeast')]

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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index 0e05040..bb6a4ad 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__init__.py
@@ -23,8 +23,8 @@ description = r"""Transcriptional regulation network of the yeast *Saccharomyces
 
 The network has the following properties:
 
-- `name`: the name of the gene.
-- `regulation`: the type of regulation, coded as 1, 2 or 3. In the networks of this collection these codes denote activation, repression, and dual (both) regulation, respectively, but the codes are not documented in the upstream file."""
+- (Node) `name`: the name of the gene.
+- (Edge) `regulation`: the type of regulation, coded as 1, 2 or 3. In the networks of this collection these codes denote activation, repression, and dual (both) regulation, respectively, but the codes are not documented in the upstream file."""
 tags = ['Biological', 'Gene regulation', 'Unweighted']
 url = 'http://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
 citation = [('R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002).', 'https://doi.org/10.1126/science.298.5594.824')]

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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index da4b882..0e05040 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__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:

2026-10-25 [pipeline] Fix KONECT entity files, seekable upstream files and archive formats by Tiago de Paula Peixoto 2f6e19f

- konect.py: each ent.<net>.<entity>.<attr> file becomes a vertex
  property on the side of the entity it describes (per-vertex or per-edge
  files), instead of all of them being written from vertex 0 into `meta`
  (which put e.g. the item names of bibsonomy and reuters on the wrong
  nodes); only leading "%" lines are comments.
- open_upstream_file(..., seekable=True) returns a seekable file (via a
  temporary file) for readers that need one (openpyxl, scipy.io.loadmat,
  zipfile), replacing the per-entry BytesIO copies.
- .xz files can be read again; .xz, .rar and .7z downloads are stored as
  they are, and "x.tar.xz:", "x.rar:" and "x.7z:" member access works
  (with py7zr or the 7z command); caches in the previous layouts are still
  read.
- parsers.py: vprops_from_txt matches rows by name for graphs keyed by
  name; the Wikimedia dump readers (stub histories, SQL tables) are shared
  helpers; new read_doc (tables of Word documents via LibreOffice) and
  read_epanet (EPANET water network files) readers.
- The entries' workarounds are removed (all parse identically).

diff --git a/entries/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index 1d18781..da4b882 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__init__.py
@@ -19,8 +19,12 @@
 from .. import *
 
 title = "Yeast transcription network (2002)"
-description = """Network of operons and their pairwise interactions, via transcription factor-based regulation, within the yeast Saccharomyces cerevisiae[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = r"""Transcriptional regulation network of the yeast *Saccharomyces cerevisiae*, from the collection of networks of U. Alon's lab used by R. Milo et al. to identify network motifs, compiled from the Yeast Proteome Database (Costanzo et al., 2001). Nodes are genes (including the genes of transcription factors) and a directed edge $i \to j$ indicates that the transcription factor encoded by gene $i$ regulates the transcription of gene $j$. The upstream adjacency matrix also includes 226 genes without any regulatory interaction, which appear as isolated nodes.
+
+The network has the following properties:
+
+- `name`: the name of the gene.
+- `regulation`: the type of regulation, coded as 1, 2 or 3. In the networks of this collection these codes denote activation, repression, and dual (both) regulation, respectively, but the codes are not documented in the upstream file."""
 tags = ['Biological', 'Gene regulation', 'Unweighted']
 url = 'http://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
 citation = [('R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002).', 'https://doi.org/10.1126/science.298.5594.824')]
@@ -44,6 +48,7 @@ def parse(alts=None):
         if isinstance(fnames, str):
             fnames = [fnames]
         with ExitStack() as stack:
-            fs = [stack.enter_context(open_upstream_file(name, fn, "rb")) for fn in fnames]
+            fs = [stack.enter_context(open_upstream_file(name, fn, "rb", seekable=True))
+                  for fn in fnames]
             g = parse_graph(fs, fmt, directed=True)
         yield alt, g

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

diff --git a/entries/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index f7d0e60..1d18781 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index 38b0927..f7d0e60 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index 9fadac2..38b0927 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index d649687..9fadac2 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index df689c9..d649687 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__init__.py
@@ -23,7 +23,7 @@ description = """Network of operons and their pairwise interactions, via transcr
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Gene regulation', 'Unweighted']
 url = 'http://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
-citation = [('R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002).', 'http://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks/networkmotifs.pdf')]
+citation = [('R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002).', 'https://doi.org/10.1126/science.298.5594.824')]
 icon_hash = '56a85c8e26855e083a2f78f0'
 upstream_prefix = 'https://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks'
 files = [('yeastdata.mat', None, 'matlab_yeast')]

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

diff --git a/entries/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index db53b51..df689c9 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__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/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
index 85bb0ec..db53b51 100644
--- a/entries/yeast_transcription/__init__.py
+++ b/entries/yeast_transcription/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "Yeast transcription network (2002)"
-description = "Network of operons and their pairwise interactions, via transcription factor-based regulation, within the yeast Saccharomyces cerevisiae"
+description = """Network of operons and their pairwise interactions, via transcription factor-based regulation, within the yeast Saccharomyces cerevisiae[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Biological', 'Gene regulation', 'Unweighted']
 url = 'http://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
 citation = [('R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002).', 'http://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks/networkmotifs.pdf')]

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

diff --git a/entries/yeast_transcription/__init__.py b/entries/yeast_transcription/__init__.py
new file mode 100644
index 0000000..85bb0ec
--- /dev/null
+++ b/entries/yeast_transcription/__init__.py
@@ -0,0 +1,48 @@
+#! /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 = "Yeast transcription network (2002)"
+description = "Network of operons and their pairwise interactions, via transcription factor-based regulation, within the yeast Saccharomyces cerevisiae"
+tags = ['Biological', 'Gene regulation', 'Unweighted']
+url = 'http://www.weizmann.ac.il/mcb/UriAlon/download/collection-complex-networks'
+citation = [('R. Milo et al., "Network Motifs: Simple Building Blocks of Complex Networks." Science 298, 824-827 (2002).', 'http://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks/networkmotifs.pdf')]
+icon_hash = '56a85c8e26855e083a2f78f0'
+upstream_prefix = 'https://www.weizmann.ac.il/mcb/UriAlon/sites/mcb.UriAlon/files/uploads/CollectionsOfComplexNetwroks'
+files = [('yeastdata.mat', None, 'matlab_yeast')]
+
+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)
+        yield alt, g