[med-svn] [Git][med-team/ragout][master] 9 commits: Sibelia is now available
Andreas Tille
gitlab at salsa.debian.org
Sat Mar 28 21:50:27 GMT 2020
Andreas Tille pushed to branch master at Debian Med / ragout
Commits:
cb20c16a by Andreas Tille at 2020-03-28T18:04:30+01:00
Sibelia is now available
- - - - -
078a6b5d by Andreas Tille at 2020-03-28T18:05:19+01:00
R-U: Trailing whitespace in debian/changelog
- - - - -
d7a5ce0a by Andreas Tille at 2020-03-28T18:05:19+01:00
routine-update: Add salsa-ci file
- - - - -
527677ab by Andreas Tille at 2020-03-28T18:05:19+01:00
routine-update: Rules-Requires-Root: no
- - - - -
bf122aed by Andreas Tille at 2020-03-28T18:05:23+01:00
Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
- - - - -
9d0343f7 by Andreas Tille at 2020-03-28T22:25:33+01:00
Fix "AttributeError: module 'networkx' has no attribute 'connected_component_subgraphs'" which became obvious in test suite
- - - - -
b56286b5 by Andreas Tille at 2020-03-28T22:29:06+01:00
lib/ragout was moved to ragout/ragout
- - - - -
44a117ad by Andreas Tille at 2020-03-28T22:34:39+01:00
networkx code copy is not inluded into upstream source any more
- - - - -
6671d05c by Andreas Tille at 2020-03-28T22:48:36+01:00
Upload to unstable
- - - - -
9 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/connected_component_subgraphs.patch
- debian/patches/series
- + debian/salsa-ci.yml
- debian/tests/control_needs_sibelia → debian/tests/control
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,19 @@
+ragout (2.3-2) unstable; urgency=medium
+
+ * Sibelia is now available
+ Closes: #953904
+ * Remove trailing whitespace in debian/changelog (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+ Repository-Browse.
+ * Fix "AttributeError: module 'networkx' has no attribute
+ 'connected_component_subgraphs'" which became obvious in test suite
+ * d/copyright: lib/ragout was moved to ragout/ragout
+ * networkx code copy is not inluded into upstream source any more
+
+ -- Andreas Tille <tille at debian.org> Sat, 28 Mar 2020 22:34:46 +0100
+
ragout (2.3-1) unstable; urgency=medium
* Test-Depends: sibelia
@@ -22,7 +38,7 @@ ragout (2.2+ds-1) unstable; urgency=medium
d/ragout.install accordingly
* bin/ragout was still about to invoke python2
* maketrans is now a static function of str
- * not allowing bin/ragout to change $PATH
+ * not allowing bin/ragout to change $PATH
* demoted sibelia to recommends runtime dependency as there are
modules that don't use it.
TODO: Find out what happened to
=====================================
debian/control
=====================================
@@ -12,6 +12,7 @@ Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/ragout
Vcs-Git: https://salsa.debian.org/med-team/ragout.git
Homepage: https://github.com/fenderglass/Ragout/
+Rules-Requires-Root: no
Package: ragout
Architecture: any
@@ -19,8 +20,7 @@ Depends: ${shlibs:Depends},
${python3:Depends},
${misc:Depends},
python3-networkx (>= 2.2)
-Recommends:
- sibelia
+Recommends: sibelia
Description: Reference-Assisted Genome Ordering UTility
Ragout (Reference-Assisted Genome Ordering UTility) is a tool for
chromosome-level scaffolding using multiple references. Given initial
=====================================
debian/copyright
=====================================
@@ -1,7 +1,6 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Ragout
Source: https://github.com/fenderglass/Ragout/releases
-Files-Excluded: lib/networkx
Files: *
Copyright: 2013-2018 Mikhail Kolmogorov and Joel Armstrong and
@@ -11,7 +10,7 @@ Copyright: 2013-2018 Mikhail Kolmogorov and Joel Armstrong and
Benedict Paten and Son Pham
License: BSD-3-clause
-Files: lib/newick/*
+Files: ragout/newick/*
Copyright: 2003-2008 Thomas Mailund <mailund at birc.au.dk>
License: GPL-2+
This program is free software; you can redistribute it and/or modify
=====================================
debian/patches/connected_component_subgraphs.patch
=====================================
@@ -0,0 +1,69 @@
+Description: Fix "AttributeError: module 'networkx' has no attribute 'connected_component_subgraphs'" which became obvious in test suite
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 28 Mar 2020 18:03:41 +0100
+
+--- a/ragout/breakpoint_graph/breakpoint_graph.py
++++ b/ragout/breakpoint_graph/breakpoint_graph.py
+@@ -77,7 +77,7 @@ class BreakpointGraph(object):
+ logger.debug("Built breakpoint graph with %d nodes", len(self.bp_graph))
+
+ def connected_components(self):
+- subgraphs = nx.connected_component_subgraphs(self.bp_graph)
++ subgraphs = list(self.bp_graph.subgraph(c) for c in nx.connected_components(self.bp_graph))
+ bp_graphs = []
+ for subgr in subgraphs:
+ bg = BreakpointGraph()
+--- a/ragout/breakpoint_graph/inferer.py
++++ b/ragout/breakpoint_graph/inferer.py
+@@ -81,7 +81,7 @@ class AdjacencyInferer(object):
+ unused_nodes = set(trimmed_graph.nodes)
+
+ chosen_edges = []
+- for trim_subgraph in nx.connected_component_subgraphs(trimmed_graph):
++ for trim_subgraph in list(trimmed_graph.subgraph(c) for c in nx.connected_components(trimmed_graph)):
+ if len(trim_subgraph) < 2:
+ continue
+
+--- a/ragout/scaffolder/merge_iters.py
++++ b/ragout/scaffolder/merge_iters.py
+@@ -179,7 +179,7 @@ class RearrangementProjector:
+ def project(self):
+ #look for valid k-breaks
+ num_kbreaks = 0
+- subgraphs = list(nx.connected_component_subgraphs(self.bp_graph))
++ subgraphs = list(self.bp_graph.subgraph(c) for c in nx.connected_components(self.bp_graph))
+ for subgr in subgraphs:
+ #this is a cycle
+ if any(len(subgr[node]) != 2 for node in subgr.nodes):
+@@ -237,9 +237,9 @@ class RearrangementProjector:
+ new_adj_graph.add_edge(u, v)
+
+ old_sets = [set(g.nodes) for g in
+- nx.connected_component_subgraphs(self.adj_graph)]
++ list(self.adj_graph.subgraph(c) for c in nx.connected_components(self.adj_graph))]
+ new_sets = [set(g.nodes) for g in
+- nx.connected_component_subgraphs(new_adj_graph)]
++ list(new_adj_graph.subgraph(c) for c in nx.connected_components(new_adj_graph))]
+ if len(old_sets) != len(new_sets):
+ return False
+
+--- a/scripts/debug-report.py
++++ b/scripts/debug-report.py
+@@ -130,7 +130,7 @@ def compose_breakpoint_graph(base_dot, p
+
+ def output_graph(graph, output_dir, only_predicted):
+ MAX_SIZE = 100
+- subgraphs = nx.connected_component_subgraphs(graph)
++ subgraphs = graph.subgraph(c) for c in nx.connected_components(graph)
+ for comp_id, subgr in enumerate(subgraphs):
+ if len(subgr) == 2:
+ continue
+@@ -193,7 +193,7 @@ def add_overlap_edges(graph, overlap_dot
+
+ overlap_graph = nx.read_dot(overlap_dot)
+
+- subgraphs = nx.connected_component_subgraphs(graph)
++ subgraphs = graph.subgraph(c) for c in nx.connected_components(graph)
+ for subgr in subgraphs:
+ for v1, v2 in combinations(subgr.nodes, 2):
+ v1, v2 = int(v1), int(v2)
=====================================
debian/patches/series
=====================================
@@ -1 +1,2 @@
# adjustSetupParsingBinaries.patch
+connected_component_subgraphs.patch
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/tests/control_needs_sibelia → debian/tests/control
=====================================
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Bug-Database: https://github.com/fenderglass/Ragout/issues
+Bug-Submit: https://github.com/fenderglass/Ragout/issues/new
Reference:
- Author: >
Mikhail Kolmogorov and Joel Armstrong and Brian J. Raney and Ian Streeter
@@ -31,3 +33,5 @@ Registry:
Entry: ragout
- Name: OMICtools
Entry: OMICS_07883
+Repository: https://github.com/fenderglass/Ragout.git
+Repository-Browse: https://github.com/fenderglass/Ragout
=====================================
debian/watch
=====================================
@@ -1,4 +1,3 @@
version=4
-opts="repacksuffix=+ds,dversionmangle=auto,repack,compression=xz" \
- https://github.com/fenderglass/Ragout/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
+https://github.com/fenderglass/Ragout/releases/latest .*/archive/v?@ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/ragout/-/compare/53c2a2b557240870a13fa089da10b2fb8a3581aa...6671d05ca0915a59aa5d4be195f3b6895e7e6fba
--
View it on GitLab: https://salsa.debian.org/med-team/ragout/-/compare/53c2a2b557240870a13fa089da10b2fb8a3581aa...6671d05ca0915a59aa5d4be195f3b6895e7e6fba
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