Updating liguros repo

6 files changed, 279 insertions, 0 deletions

diff --git a/dev-python/networkx/Manifest b/dev-python/networkx/Manifest
new file mode 100644
index 000000000000..a5e05b0f2ba5
--- /dev/null
+++ b/dev-python/networkx/Manifest
@@ -0,0 +1 @@
+DIST networkx-2.4.tar.gz 1462338 BLAKE2B 90fd7d249f3b022dd9c861dd023881fd241cba0515e2e9991516c278a40b92ee03663eb2b15bd584f179c066529df0587293f9c9a211e7c526addf77fdaf5cd6 SHA512 38eabef56e3667b7fa85206ae01a0a8f5c71bfa2f324bc2490c433cb973508a03955183a0c58ae40390f86d6a4741135cdb426c4c15e53e2f123072f0cac1b89
diff --git a/dev-python/networkx/files/networkx-2.4-py38.patch b/dev-python/networkx/files/networkx-2.4-py38.patch
new file mode 100644
index 000000000000..9ce3003d1042
--- /dev/null
+++ b/dev-python/networkx/files/networkx-2.4-py38.patch
@@ -0,0 +1,84 @@
+From 488e824439124f4dd52f8230c452a3df681b1bab Mon Sep 17 00:00:00 2001
+From: Steve Kowalik <steven@wedontsleep.org>
+Date: Fri, 15 Nov 2019 13:48:33 +1100
+Subject: [PATCH] Fix test_numpy_type to pass under Python 3.8
+
+readwrite.tests.test_gexf.TestGEXF.test_numpy_type failed under Python
+3.8 due to ordering of XML attributes, handle it as per f75dbe8. Also
+change travis to no longer allow failures under 3.8.
+
+Fixes #3720
+---
+ .travis.yml                           |  2 --
+ networkx/readwrite/tests/test_gexf.py | 51 ++++++++++++++++++++++++++-
+ 2 files changed, 50 insertions(+), 3 deletions(-)
+
+diff --git a/networkx/readwrite/tests/test_gexf.py b/networkx/readwrite/tests/test_gexf.py
+index afc40111ce..f16504c047 100644
+--- a/networkx/readwrite/tests/test_gexf.py
++++ b/networkx/readwrite/tests/test_gexf.py
+@@ -404,7 +404,8 @@ def test_numpy_type(self):
+         nx.set_node_attributes(G, {n: n for n in numpy.arange(4)}, 'number')
+         G[0][1]['edge-number'] = numpy.float64(1.1)
+ 
+-        expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft"\
++        if sys.version_info < (3, 8):
++            expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft"\
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\
+ ="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd">
+   <meta lastmodifieddate="{}">
+@@ -449,6 +450,54 @@ def test_numpy_type(self):
+       <edge id="2" source="2" target="3" />
+     </edges>
+   </graph>
++</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
++        else:
++            expected = """<gexf xmlns="http://www.gexf.net/1.2draft"\
++ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\
++="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd"\
++ version="1.2">
++  <meta lastmodifieddate="{}">
++    <creator>NetworkX {}</creator>
++  </meta>
++  <graph defaultedgetype="undirected" mode="static" name="">
++    <attributes mode="static" class="edge">
++      <attribute id="1" title="edge-number" type="float" />
++    </attributes>
++    <attributes mode="static" class="node">
++      <attribute id="0" title="number" type="int" />
++    </attributes>
++    <nodes>
++      <node id="0" label="0">
++        <attvalues>
++          <attvalue for="0" value="0" />
++        </attvalues>
++      </node>
++      <node id="1" label="1">
++        <attvalues>
++          <attvalue for="0" value="1" />
++        </attvalues>
++      </node>
++      <node id="2" label="2">
++        <attvalues>
++          <attvalue for="0" value="2" />
++        </attvalues>
++      </node>
++      <node id="3" label="3">
++        <attvalues>
++          <attvalue for="0" value="3" />
++        </attvalues>
++      </node>
++    </nodes>
++    <edges>
++      <edge source="0" target="1" id="0">
++        <attvalues>
++          <attvalue for="1" value="1.1" />
++        </attvalues>
++      </edge>
++      <edge source="1" target="2" id="1" />
++      <edge source="2" target="3" id="2" />
++    </edges>
++  </graph>
+ </gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
+         obtained = '\n'.join(nx.generate_gexf(G))
+         assert expected == obtained
diff --git a/dev-python/networkx/files/networkx-2.4-py39.patch b/dev-python/networkx/files/networkx-2.4-py39.patch
new file mode 100644
index 000000000000..7efe8998b35f
--- /dev/null
+++ b/dev-python/networkx/files/networkx-2.4-py39.patch
@@ -0,0 +1,46 @@
+From 0cb12b33df48788c10fa21b326803ae66d74cbe6 Mon Sep 17 00:00:00 2001
+From: Jarrod Millman <jarrod.millman@gmail.com>
+Date: Mon, 21 Oct 2019 00:56:04 -0700
+Subject: [PATCH] Remove unused imports
+
+---
+ .travis.yml                                         |  3 ---
+ networkx/algorithms/assortativity/connectivity.py   |  2 --
+ networkx/algorithms/assortativity/correlation.py    | 13 ++++++-------
+ networkx/algorithms/assortativity/mixing.py         |  1 -
+ .../algorithms/assortativity/neighbor_degree.py     |  1 -
+ networkx/algorithms/assortativity/pairs.py          |  1 -
+ networkx/algorithms/cluster.py                      |  1 -
+ networkx/algorithms/community/modularity_max.py     |  1 -
+ networkx/algorithms/components/biconnected.py       |  1 -
+ networkx/algorithms/isolate.py                      |  1 -
+ networkx/algorithms/isomorphism/isomorphvf2.py      |  1 -
+ networkx/algorithms/traversal/beamsearch.py         |  1 -
+ networkx/classes/graph.py                           |  2 +-
+ networkx/classes/reportviews.py                     |  1 -
+ networkx/conftest.py                                |  8 ++++++--
+ networkx/linalg/attrmatrix.py                       |  1 -
+ networkx/readwrite/gexf.py                          | 11 ++---------
+ networkx/readwrite/gpickle.py                       |  1 -
+ networkx/readwrite/graphml.py                       | 11 ++---------
+ networkx/readwrite/nx_yaml.py                       |  1 -
+ networkx/readwrite/tests/test_graphml.py            |  4 ++--
+ tools/travis/script.sh                              |  2 +-
+ 22 files changed, 20 insertions(+), 49 deletions(-)
+
+diff --git a/networkx/readwrite/tests/test_graphml.py b/networkx/readwrite/tests/test_graphml.py
+index 00b97d77..1946c487 100644
+--- a/networkx/readwrite/tests/test_graphml.py
++++ b/networkx/readwrite/tests/test_graphml.py
+@@ -879,7 +879,7 @@ class TestWriteGraphML(BaseGraphML):
+ 
+         xml = parse(fh)
+         # Children are the key elements, and the graph element
+-        children = xml.getroot().getchildren()
++        children = list(xml.getroot())
+         assert len(children) == 3
+ 
+         keys = [child.items() for child in children[:2]]
+-- 
+2.27.0
+
diff --git a/dev-python/networkx/metadata.xml b/dev-python/networkx/metadata.xml
new file mode 100644
index 000000000000..0d5472957160
--- /dev/null
+++ b/dev-python/networkx/metadata.xml
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>python@gentoo.org</email>
+    <name>Python</name>
+  </maintainer>
+  <longdescription lang="en">
+  NetworkX is a Python-based package for the creation, manipulation, and
+  study of the structure, dynamics, and functions of complex networks.
+  The structure of a graph or network is encoded in the edges (connections,
+  links, ties, arcs, bonds) between nodes (vertices, sites, actors). If
+  unqualified, by graph we mean a simple undirected graph, i.e. no
+  self-loops and no multiple edges are allowed. By a network we usually
+  mean a graph with weights (fields, properties) on nodes and/or edges.
+  The potential audience for NetworkX includes: mathematicians, physicists,
+  biologists, computer scientists, social scientists.
+</longdescription>
+  <upstream>
+    <remote-id type="pypi">networkx</remote-id>
+    <remote-id type="github">networkx/networkx</remote-id>
+  </upstream>
+  <use>
+    <flag name="extras">Provide graph drawing and graph layout algorithms along with shapefile format reading and writing</flag>
+    <flag name="pandas">Provides a DataFrame, which is a tabular data structure with labeled axes</flag>
+    <flag name="scipy">Enables scipy backend</flag>
+    <flag name="yaml">Provides YAML format reading and writing</flag>
+  </use>
+	<origin>gentoo-staging</origin>
+</pkgmetadata>
diff --git a/dev-python/networkx/networkx-2.4-r1.ebuild b/dev-python/networkx/networkx-2.4-r1.ebuild
new file mode 100644
index 000000000000..988703d38773
--- /dev/null
+++ b/dev-python/networkx/networkx-2.4-r1.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+inherit distutils-r1 virtualx
+
+DESCRIPTION="Python tools to manipulate graphs and complex networks"
+HOMEPAGE="https://networkx.github.io/ https://github.com/networkx/networkx"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos"
+IUSE="examples extras pandas scipy test xml yaml"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	>=dev-python/decorator-4.3.0[${PYTHON_USEDEP}]
+	>=dev-python/matplotlib-2.2.2[${PYTHON_USEDEP}]
+	extras? (
+		>=dev-python/pydot-1.2.4[${PYTHON_USEDEP}]
+		$(python_gen_cond_dep '
+			>=dev-python/pygraphviz-1.5[${PYTHON_USEDEP}]
+			>=sci-libs/gdal-1.10.0[python,${PYTHON_USEDEP}]
+		' python3_{6,7,8})
+	)
+	pandas? (
+		>=dev-python/pandas-0.23.3[${PYTHON_USEDEP}]
+	)
+	scipy? ( >=sci-libs/scipy-1.1.0[${PYTHON_USEDEP}] )
+	xml? ( >=dev-python/lxml-4.2.3[${PYTHON_USEDEP}] )
+	yaml? ( >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}] )"
+
+distutils_enable_tests pytest
+
+PATCHES=(
+	"${FILESDIR}"/${P}-py38.patch
+	"${FILESDIR}"/${P}-py39.patch
+)
+
+src_prepare() {
+	# incompatible deps?
+	sed -e 's:test_multigraph_edgelist_tuples:_&:' \
+		-i networkx/drawing/tests/test_pylab.py || die
+
+	distutils-r1_src_prepare
+}
+
+src_test() {
+	virtx distutils-r1_src_test
+}
+
+python_install_all() {
+	use examples && dodoc -r examples
+
+	distutils-r1_python_install_all
+}
diff --git a/dev-python/networkx/networkx-2.4.ebuild b/dev-python/networkx/networkx-2.4.ebuild
new file mode 100644
index 000000000000..07a98d729cc8
--- /dev/null
+++ b/dev-python/networkx/networkx-2.4.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+# networkx-2.4 supports up to python3_8
+PYTHON_COMPAT=( python3_{6,7} )
+inherit distutils-r1 virtualx
+
+DESCRIPTION="Python tools to manipulate graphs and complex networks"
+HOMEPAGE="http://networkx.github.io/ https://github.com/networkx/networkx"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="amd64 ~arm64 x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos"
+IUSE="examples extras pandas scipy test xml yaml"
+RESTRICT="!test? ( test )"
+
+REQUIRED_USE="
+	test? ( extras pandas scipy xml yaml )"
+
+COMMON_DEPEND="
+	>=dev-python/matplotlib-2.2.2[${PYTHON_USEDEP}]
+	extras? (
+		>=dev-python/pydot-1.2.4[${PYTHON_USEDEP}]
+		>=dev-python/pygraphviz-1.5[${PYTHON_USEDEP}]
+		>=sci-libs/gdal-1.10.0[python,${PYTHON_USEDEP}]
+	)
+	pandas? ( >=dev-python/pandas-0.23.3[${PYTHON_USEDEP}] )
+	scipy? ( >=sci-libs/scipy-1.1.0[${PYTHON_USEDEP}] )
+	xml? ( >=dev-python/lxml-4.2.3[${PYTHON_USEDEP}] )
+	yaml? ( >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}] )"
+DEPEND="
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	>=dev-python/decorator-4.3.0[${PYTHON_USEDEP}]
+	${COMMON_DEPEND}
+	test? (
+		dev-python/nose[${PYTHON_USEDEP}]
+	)"
+RDEPEND="
+	>=dev-python/decorator-4.3.0[${PYTHON_USEDEP}]
+	${COMMON_DEPEND}
+	examples? (
+		dev-python/pyparsing[${PYTHON_USEDEP}]
+	)"
+
+PATCHES=(
+)
+
+python_test() {
+	virtx nosetests -vv
+}
+
+python_install_all() {
+	use examples && dodoc -r examples
+
+	distutils-r1_python_install_all
+}