History of python_dependency

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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index b4c9cdb..ac4cb7b 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__init__.py
@@ -32,7 +32,7 @@ The network has the following properties:
 tags = ['Technological', 'Software', 'Unweighted']
 url = 'http://kgullikson88.github.io/blog/pypi-analysis.html'
 citation = [('Kevin Gullikson, "Python Dependency Analysis"', 'http://kgullikson88.github.io/blog/pypi-analysis.html')]
-icon_hash = '56c53507a6d70217090cdb80'
+date_added = '2020-08-11'
 upstream_license = None
 upstream_prefix = 'http://kgullikson88.github.io/blog/Downloads/PypiDependencies'
 files = [('requirements.csv', None, 'csv')]

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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index ea9e6eb..b4c9cdb 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__init__.py
@@ -27,8 +27,8 @@ In the source data, for some rows the package name is missing, and only the comb
 
 The network has the following properties:
 
-- `name`: the name of the package, as given in the source data.
-- `versions`: the versions of the package in the source data (empty for packages that appear only as requirements)."""
+- (Node) `name`: the name of the package, as given in the source data.
+- (Node) `versions`: the versions of the package in the source data (empty for packages that appear only as requirements)."""
 tags = ['Technological', 'Software', 'Unweighted']
 url = 'http://kgullikson88.github.io/blog/pypi-analysis.html'
 citation = [('Kevin Gullikson, "Python Dependency Analysis"', 'http://kgullikson88.github.io/blog/pypi-analysis.html')]

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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index 0ef3581..ea9e6eb 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__init__.py
@@ -45,7 +45,6 @@ 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 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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index 4bcfb7f..0ef3581 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__init__.py
@@ -17,15 +17,23 @@
 # with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 from .. import *
+import csv
+import re
 
 title = "Python Dependency Network"
-description = """Python's package dependency networks. Nodes in the network are Python's packages registered to PyPI and edges are dependencies among packages.[^icon]
-[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+description = """Network of dependencies among Python packages registered in the Python Package Index (PyPI), assembled by K. Gullikson and published in February 2016. The source distributions of the packages on PyPI were downloaded, and their dependencies were extracted with a modified version of the requirements-detector tool, by parsing the `install_requires` argument in `setup.py`, or, failing that, the requirements files of the package; packages whose `setup.py` could not be parsed were left out. Nodes are packages, and a directed edge $(i,j)$ indicates that package $i$ requires package $j$. Parallel edges were removed. Package names are matched as on PyPI, i.e. ignoring case and treating "-", "_" and "." as equivalent (the requirements are often spelled differently from the package names). Some packages appear in the source data with more than one version, which are merged into a single node. Packages without any detected requirement have no outgoing edges, and nodes without a version are packages that appear only as requirements.
+
+In the source data, for some rows the package name is missing, and only the combined package and version string (as in "abook-0.2.1") is given; the name was obtained here by splitting off the version. The network contains 92 self-loops, from packages that list themselves as a requirement in the source data.
+
+The network has the following properties:
+
+- `name`: the name of the package, as given in the source data.
+- `versions`: the versions of the package in the source data (empty for packages that appear only as requirements)."""
 tags = ['Technological', 'Software', 'Unweighted']
 url = 'http://kgullikson88.github.io/blog/pypi-analysis.html'
 citation = [('Kevin Gullikson, "Python Dependency Analysis"', 'http://kgullikson88.github.io/blog/pypi-analysis.html')]
 icon_hash = '56c53507a6d70217090cdb80'
-ustream_license = None
+upstream_license = None
 upstream_prefix = 'http://kgullikson88.github.io/blog/Downloads/PypiDependencies'
 files = [('requirements.csv', None, 'csv')]
 
@@ -46,11 +54,46 @@ def parse(alts=None):
             fnames = [fnames]
         with ExitStack() as stack:
             fs = [stack.enter_context(open_upstream_file(name, fn, "r")) for fn in fnames]
+            rows = list(csv.reader(fs[0]))[1:]
+
+        # PyPI names are case-insensitive, and "-", "_" and "." are
+        # equivalent in them (PEP 503); the requirement names are often
+        # spelled differently from the package names
+        def norm(s):
+            return re.sub(r"[-_.]+", "-", s).lower()
+
+        known = set(norm(r[2]) for r in rows if r[2])
+        def split_package(pkg):
+            # package name missing in the source: split "name-version"
+            for m in re.finditer(r"-(?=[0-9])", pkg):
+                if norm(pkg[:m.start()]) in known:
+                    return pkg[:m.start()], pkg[m.end():]
+            m = (re.match(r"^(.*)-([0-9][^-]*)$", pkg) or
+                 re.match(r"^(.*?)-([0-9].*)$", pkg))
+            if m is None:
+                return pkg, ""
+            return m.group(1), m.group(2)
 
-            fs[0].readline()
+        g = Graph(directed=True)
+        g.vp.name = g.new_vp("string")
+        g.vp.versions = g.new_vp("vector<string>")
+        vs = {}
+        def get_vertex(n):
+            v = vs.get(norm(n))
+            if v is None:
+                v = vs[norm(n)] = g.add_vertex()
+                g.vp.name[v] = n
+            return v
 
-            g = load_graph_from_csv(fs[0], hashed=True, hash_type="string",
-                                    ecols=(2,1), directed=True)
-            remove_parallel_edges(g)
+        for pkg, req, pname, version in rows:
+            if pname == "":
+                pname, version = split_package(pkg)
+            u = get_vertex(pname)
+            g.vp.name[u] = pname  # the package's own spelling
+            if version not in g.vp.versions[u]:
+                g.vp.versions[u].append(version)
+            if req != "":
+                g.add_edge(u, get_vertex(req))
+        remove_parallel_edges(g)
 
         yield alt, g

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

diff --git a/entries/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index fe1f684..4bcfb7f 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index 18198e6..fe1f684 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index 968aa74..18198e6 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index 4458c8e..968aa74 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index c3fcf07..4458c8e 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__init__.py
@@ -23,7 +23,7 @@ description = """Python's package dependency networks. Nodes in the network are
 [^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Technological', 'Software', 'Unweighted']
 url = 'http://kgullikson88.github.io/blog/pypi-analysis.html'
-citation = [('http://kgullikson88.github.io/blog/pypi-analysis.html', 'http://kgullikson88.github.io/blog/pypi-analysis.html')]
+citation = [('Kevin Gullikson, "Python Dependency Analysis"', 'http://kgullikson88.github.io/blog/pypi-analysis.html')]
 icon_hash = '56c53507a6d70217090cdb80'
 ustream_license = None
 upstream_prefix = 'http://kgullikson88.github.io/blog/Downloads/PypiDependencies'

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

diff --git a/entries/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index b918542..c3fcf07 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__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/python_dependency/__init__.py b/entries/python_dependency/__init__.py
index 9b43d6a..b918542 100644
--- a/entries/python_dependency/__init__.py
+++ b/entries/python_dependency/__init__.py
@@ -19,7 +19,8 @@
 from .. import *
 
 title = "Python Dependency Network"
-description = "Python's package dependency networks. Nodes in the network are Python's packages registered to PyPI and edges are dependencies among packages."
+description = """Python's package dependency networks. Nodes in the network are Python's packages registered to PyPI and edges are dependencies among packages.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
 tags = ['Technological', 'Software', 'Unweighted']
 url = 'http://kgullikson88.github.io/blog/pypi-analysis.html'
 citation = [('http://kgullikson88.github.io/blog/pypi-analysis.html', 'http://kgullikson88.github.io/blog/pypi-analysis.html')]

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

diff --git a/entries/python_dependency/__init__.py b/entries/python_dependency/__init__.py
new file mode 100644
index 0000000..9b43d6a
--- /dev/null
+++ b/entries/python_dependency/__init__.py
@@ -0,0 +1,55 @@
+#! /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 = "Python Dependency Network"
+description = "Python's package dependency networks. Nodes in the network are Python's packages registered to PyPI and edges are dependencies among packages."
+tags = ['Technological', 'Software', 'Unweighted']
+url = 'http://kgullikson88.github.io/blog/pypi-analysis.html'
+citation = [('http://kgullikson88.github.io/blog/pypi-analysis.html', 'http://kgullikson88.github.io/blog/pypi-analysis.html')]
+icon_hash = '56c53507a6d70217090cdb80'
+ustream_license = None
+upstream_prefix = 'http://kgullikson88.github.io/blog/Downloads/PypiDependencies'
+files = [('requirements.csv', None, 'csv')]
+
+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]
+
+            fs[0].readline()
+
+            g = load_graph_from_csv(fs[0], hashed=True, hash_type="string",
+                                    ecols=(2,1), directed=True)
+            remove_parallel_edges(g)
+
+        yield alt, g